Citrus Sinensis ID: 003038

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850----
Protein Sequence
MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKESNVLVLSQTASATKVSKPRVSLDPIRNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWAEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLITTDSDLQSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWLQQYKNEKKATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHKTHRDWAVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNSTSSSDIMEMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRACSPPTKQKSDGCEEEKGAAMEGTSPSVSLDLNICIDDDSTEDQSIDDIGLLESVDKRIIFKIMEL
Secondary Structure (PSIPRED)
ccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHcccccHHHHHHHHHccccccHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHccccccccccccccccccccccccHHHHHHcccccccccccccccHHHHHHHHHHHHccccccEEEEccccccHHHHHHHHHHccccccccccccccEEEEEcccccccccHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHcccccccccccccccHHHHccHHHHccccccccEEEEEEHHcHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcHHHHHHHHHHHHHHccccccccccccccccHHHHHHcHHHHHHHccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHcccccccccccccccccccEEEEEEccccHHHHHHHHHHHHHHccccccEEEEccccccccccccccccccccccccccccHHHHHHHHHHccccEEEEEcccccccHHHHHHHHHHHHccccccccccEEccccEEEEEccccccHHHHcccccccccccccHHHHHHHHcccccccccccccccccccccccccccEEEEccccHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHccHHHHHcHHHHHHHHHHHHHHHHHccccHHHHHHHccccHHHHHHHHHHHHcccEccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHcccccEEEccccccHHHHHHHHHHHHHcccccccccccEEEEEcHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEccHHEEcccccccccccccccHHHHEEccHHHHHHHHHcccEEEEccccHHHHHHHHHHcHHHHHHHcHcccccccHHHHHHHHHcccccEEEEccccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHcccccccccccccccccccEEEEEcccccccHHHHHHHHHHHHcccHHcEEEEcHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHccccEEEEEHHHHHHcHHHHHHHHHHHHccccccccccEEEcccEEEEEEcccHHHHHHHHccccccccccHHHHHHHHHHHHHHHccHHHHHHcccEEEEcccccEEEEEccccHHHHHHHHcc
Coil and Loop (DISEMBL)
mraggctiqqgLTAEAASVVKQAMTLARRrghaqvtpLHVANTMLAASTGLLRtaclqshshplqcKALELCFNVALnrlpaststpmlgghcqfptISNALVAAFKRAQAhqrrgsienqqQPLLAVKIELEQLIISilddpsvsrvmreagfsstqvKSNVEQAVSLEicsqstpvssnkskesNVLVLSQTasatkvskprvsldpirneDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIdkiekgdvpealrdvkclplsissfrhmnrVEVEQRVEEIKNLVRSCLgrgivlnlgdlewaEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSymrcksghpsletlwslhpltipagslslslittdsdlqsqstskkaeSGVSWLLFegeeenkqltccadCSAKFEAEARslqssscnsdsptsslpAWLQQYKNEKkatlsnndkdsgvRDLCKKWNSicnsihkqpyysertltfssaspssstsgfsydqqypnfhkthrdwavvepkqswrehhflfsheasdkstsepslrlyipehkdlkqplssnrnstpnstsssdiMEMEYVHKFKELNSENLTSLCNALekkvpwqkdtVYDIANTVLKCrsgtmrrkgkfkdhsevkeETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSsfsstradstedsrnkrsrdeQSCSYIERFAEAvsnnphrvfliedveqadycsqkGFKRAIESgrivtssgdevslGDAIVILSCEsfssrsracspptkqksdgceeekgaamegtspsvsldlnicidddstedqsiddiglLESVDKRIIFKIMEL
Flexible Loop (DISEMBL)
mraggctiqqgltaeAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGfsstqvksnvEQAVSLEICsqstpvssnkskesNVLVLsqtasatkvskprvsldpirneDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKiekgdvpealrdvkclplsissfrhmnrvEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWAEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLITTDSDLQSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWLQQYKNEKkatlsnndkdsgVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHKTHRDWAVVEPKQSWREHHFLFsheasdkstsepSLRLYIPEHkdlkqplssnrnstpnstsssdIMEMEYVHKFKELNSENLTSLCNALEkkvpwqkdtvyDIANTvlkcrsgtmrrkgkfkdhsevkeetwLFFQGVDADAKEKIAKELARLVFGSHNNFVSIalssfsstradstedsrnkrsrdeqSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIEsgrivtssgdevslGDAIVILSCEsfssrsracspptkqksdgcEEEKGAamegtspsvsLDLNICIDDDStedqsiddigllesvdkriifkimel
Low Complexity Region (SEG)
MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKESNVLVLSQTASATKVSKPRVSLDPIRNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWAEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGslslslittdsdlqsqstsKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQssscnsdsptssLPAWLQQYKNEKKATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFssaspssstsgfsYDQQYPNFHKTHRDWAVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLssnrnstpnstsssDIMEMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRACSPPTKQKSDGCEEEKGAAMEGTSPSVSLDLNICidddstedqsiddiGLLESVDKRIIFKIMEL
Disordered region (IsUnstruct)
***********LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRA**************PLLAVKIELEQLIISILDDP******************************************************************IRNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWAEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLI******************VSWLLFEGEEENKQLTCCADCSA**********************************************VRDLCKKWNSICNSIHKQPYYSE**********************YPNFHKTHRDWAVVEPKQSWREHHFLF************************************************YVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMR****F****EVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIAL*************************SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCE*************************************DLNICID********IDDIGLLESVDKRIIFKI***
Disordered Region (DISOPRED)
****GCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNR********************NALVAAFKRAQA*************LLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSN**********************************************PIRNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWAEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLITTDSD***************WLLFEGEEENKQLTCCADCSAKFEAEA***********************************************W********************************************************************************************************************FKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGT**************EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS*****************SRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESF**********************************LDLNICIDDDSTEDQSIDDIGLLESVDKRIIFKIMEL
Disordered Region (DISEMBL)
MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKR***********NQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEIC****************LVLSQTASATKVSKPRVSLDPIRNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWAEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLITT***************GVSWLLFEGEEENKQLTCCADCSAKFEA******************LPAWLQQYKNEKKATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTL**************SYDQQYPNFHKTHRDWAVVEPKQSWREHHFLFSH*********PSLRLYIPEHKDLK****************SDIMEMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGT***********EVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF*********************CSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESF*****************************SPSVSLDLNICIDDDSTEDQSIDDIGLLESVDKRIIFKIMEL
Disordered Region (DISPRO)
*****CTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPAST**********FPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLE*CS*******NKSKESNVLVLSQTASATKVSKPRVSLDPIRNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWAEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLITTDSDLQSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWLQQYKNEKKATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHKTHRDWAVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPE******PLSSNRNSTPNSTSSSDIMEMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRR**********KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRACSPPTKQKSDGCEEEKGAAMEGTSPSVSLDLNICIDDDSTEDQSIDDIGLLESVDKRIIFKIMEL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKESNVLVLSQTASATKVSKPRVSLDPIRNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWAEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLITTDSDLQSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWLQQYKNEKKATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHKTHRDWAVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNSTSSSDIMEMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRACSPPTKQKSDGCEEEKGAAMEGTSPSVSLDLNICIDDDSTEDQSIDDIGLLESVDKRIIFKIMEL
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	854	2.2.26 [Sep-21-2011]
P42730	911	Chaperone protein ClpB1 O	no	no	0.303	0.284	0.295	1e-18
Q6F2Y7	912	Chaperone protein ClpB1 O	no	no	0.295	0.276	0.285	4e-14
Q8G4X4	889	Chaperone protein ClpB OS	yes	no	0.380	0.365	0.236	9e-10
P31540	927	Heat shock protein hsp98	N/A	no	0.281	0.258	0.225	2e-09
F4JVJ1	623	Putative chaperone protei	no	no	0.270	0.370	0.238	3e-09
Q6N1H2	879	Chaperone protein ClpB OS	yes	no	0.310	0.301	0.239	4e-09
Q92MK7	868	Chaperone protein ClpB OS	yes	no	0.302	0.297	0.266	7e-09
O83110	878	Chaperone protein ClpB OS	yes	no	0.306	0.298	0.237	7e-09
Q88VX7	867	Chaperone protein ClpB OS	yes	no	0.674	0.664	0.195	1e-08
Q9PGC1	861	Chaperone protein ClpB OS	yes	no	0.305	0.303	0.232	6e-08

>sp|P42730|CLPB1_ARATH Chaperone protein ClpB1 OS=Arabidopsis thaliana GN=CLPB1 PE=1 SV=2

 Score = 95.9 bits (237), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 85/288 (29%), Positives = 141/288 (48%), Gaps = 29/288 (10%)

Query: 20  VKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNR 79
           +  A  LA   GHAQ TPLH+A  +++  TG+   A + S       ++ E   N AL +
Sbjct: 14  IATAHELAVNAGHAQFTPLHLAGALISDPTGIFPQA-ISSAGGENAAQSAERVINQALKK 72

Query: 80  LPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQR-RGSIENQQQPLLAVKIELEQLIIS 138
           LP+ +  P        P  S++L+   +RAQA Q+ RG         LAV    +QLI+ 
Sbjct: 73  LPSQSPPP-----DDIPA-SSSLIKVIRRAQAAQKSRGDTH------LAV----DQLIMG 116

Query: 139 ILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKESNVLVLSQTASAT 198
           +L+D  +  ++ E G ++ +VKS VE+     +  +      + S ++N   L +T    
Sbjct: 117 LLEDSQIRDLLNEVGVATARVKSEVEK-----LRGKEGKKVESASGDTNFQAL-KTYGRD 170

Query: 199 KVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDV 256
            V +    LDP+  R+E++  V+  L  + K N V++GE       VV G+  +I KGDV
Sbjct: 171 LVEQAG-KLDPVIGRDEEIRRVVRILSRRTKNNPVLIGEPGVGKTAVVEGLAQRIVKGDV 229

Query: 257 PEALRDVKCLPLSISSF--RHMNRVEVEQRVEEIKNLVRSCLGRGIVL 302
           P +L DV+ + L + +       R E E+R++ +   V    G+ I+ 
Sbjct: 230 PNSLTDVRLISLDMGALVAGAKYRGEFEERLKSVLKEVEDAEGKVILF 277

Molecular chaperone that plays an important role in thermotolerance. Required for acquired thermotolerance in plants and naturally high basal thermotolerance observed in germinating seedlings.
Arabidopsis thaliana (taxid: 3702)

>sp|Q6F2Y7|CLPB1_ORYSJ Chaperone protein ClpB1 OS=Oryza sativa subsp. japonica GN=CLPB1 PE=2 SV=1

 Score = 80.9 bits (198), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 83/291 (28%), Positives = 139/291 (47%), Gaps = 39/291 (13%)

Query: 23  AMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQC-KALELCFNVALNRLP 81
           A  +A   GHAQ+TPLH+   + A   G+LR A  Q+         + E   + AL +LP
Sbjct: 17  AHEIASEAGHAQLTPLHLVAALAADKGGILRQAISQASGGDAGAPDSFERVVSGALKKLP 76

Query: 82  ASTSTPMLGGHCQFPTISNALVAAFKRAQ-AHQRRGSIENQQQPLLAVKIELEQLIISIL 140
           + +  P        P  S AL+   +RAQ A ++RG         LAV    +QL++ +L
Sbjct: 77  SQSPPP-----DSVPA-STALIKVIRRAQSAQKKRGDSH------LAV----DQLLLGLL 120

Query: 141 DDPSVSRVMREAGFSSTQVKSNVE-----QAVSLEICSQSTPVSSNKSKESNVLVLSQTA 195
           +D  +S  ++EAG S+ +V++ +E     +   +E  S  T   + K+   +++      
Sbjct: 121 EDSLISDCLKEAGVSAARVRAELEKLRGGEGRKVESASGDTNFQALKTYGRDLV-----E 175

Query: 196 SATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEK 253
            A K       LDP+  R+E++  V+  L  + K N V++GE       VV G+  +I +
Sbjct: 176 QAGK-------LDPVIGRDEEIRRVVRILSRRTKNNPVLIGEPGVGKTAVVEGLAQRIVR 228

Query: 254 GDVPEALRDVKCLPLSISSF--RHMNRVEVEQRVEEIKNLVRSCLGRGIVL 302
           GDVP  L DV+ + L + +       R E E+R++ +   V    G+ I+ 
Sbjct: 229 GDVPSNLLDVRLIALDMGALVAGAKYRGEFEERLKAVLKEVEEAEGKVILF 279

Molecular chaperone involved in heat stress response. May play a role in resolubilization of protein aggregates after heat shock.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8G4X4|CLPB_BIFLO Chaperone protein ClpB OS=Bifidobacterium longum (strain NCC 2705) GN=clpB PE=3 SV=1

 Score = 66.6 bits (161), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 87/368 (23%), Positives = 150/368 (40%), Gaps = 43/368 (11%)

Query: 8   IQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCK 67
           ++Q  T  A   V  A+  A   G+AQV  LHV + +L    G+ R+    +   P   +
Sbjct: 1   MEQKFTTMAQEAVGDAIQSASAAGNAQVETLHVMDALLRQENGVARSLIEAAGGDP---Q 57

Query: 68  ALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLA 127
           A+      AL  LP+++     G     P  S  L AA  +A         E + Q +  
Sbjct: 58  AIGAAVRNALVALPSAS-----GSSTSQPQASRQLTAAIAQA---------EKEMQQMGD 103

Query: 128 VKIELEQLIISIL-DDPSVS-RVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKE 185
             +  E L+I I    P+ S  ++ + G ++  ++  V         +      S K+ E
Sbjct: 104 EYVSTEHLLIGIAASKPNQSAEILEKNGVTAASLRKAVPGVRGGAKVTSPDAEGSYKALE 163

Query: 186 SNVLVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGV 243
                L+  A   K       LDP+  R++++  VI+ L  + K N V++GE       V
Sbjct: 164 KYSTDLTAAAKEGK-------LDPVIGRDQEIRRVIQILSRRTKNNPVLIGEPGVGKTAV 216

Query: 244 VRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMN--RVEVEQRVEEIKNLVRSCLGRGIV 301
           V G+  +I  GDVP  L+  K + L + S    +  R E E+R++ + N +++  G+  +
Sbjct: 217 VEGLAQRIVAGDVPTTLQGKKLISLDLGSMVAGSKYRGEFEERLKSVLNEIKNADGQ--I 274

Query: 302 LNLGDLEWAEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRC 361
           +   D       A ++E             M+ G ++  +       L+G  T   Y   
Sbjct: 275 ITFIDEIHTIVGAGAAEGS-----------MDAGNMLKPMLARGELRLIGATTLDEYREN 323

Query: 362 KSGHPSLE 369
               P+LE
Sbjct: 324 IEKDPALE 331

Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK.

Bifidobacterium longum (strain NCC 2705) (taxid: 206672)

>sp|P31540|HSP98_NEUCR Heat shock protein hsp98 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=hsp98 PE=1 SV=2

 Score = 65.1 bits (157), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 63/279 (22%), Positives = 123/279 (44%), Gaps = 39/279 (13%)

Query: 12  LTAEAASVVKQAMTLARRRGHAQVTPLHVANTML---------------AASTGLLRTAC 56
            T  A   ++ AM LA +  H+Q+ P+H+A  +L                A++ L R   
Sbjct: 7   FTDRAKKALEDAMALAEQYAHSQLLPVHLAVALLDPLPDPSKDQQNAPAGATSSLFRQVI 66

Query: 57  LQSHSHPLQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRG 116
            ++H  P   +  +     AL RLP+    P    H    +++ +     ++A   Q+  
Sbjct: 67  ERAHGDP---QLFDRALKKALVRLPSQDPPP---DHV---SMAPSFHTVLRKANELQK-- 115

Query: 117 SIENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQST 176
               Q+   +AV    + LI ++ ++PS+   ++EA     ++ ++  QA+     ++  
Sbjct: 116 ---TQKDTYIAV----DHLITALAEEPSIMNALKEANIPKPKLVTDAIQAIR---GTKRV 165

Query: 177 PVSSNKSKESNVLVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVG 234
              +  ++E +  +   T   T +++    +DP+  R E++  VI  L  + K N V++G
Sbjct: 166 DSRNADTEEEHENLAKFTIDMTAMAR-EGKIDPVIGREEEIRRVIRILSRRTKNNPVLIG 224

Query: 235 ECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSF 273
           E       VV G+  +I   DVP+ L + K L L + + 
Sbjct: 225 EPGVGKTTVVEGLAQRIVNADVPDNLANCKLLSLDVGAL 263

Required, in concert with Hsp40 and Hsp70 and small Hsps, for the dissociation, resolubilization and refolding of aggregates of damaged proteins after heat or other environmental stresses. Extracts proteins from aggregates by unfolding and threading them in an ATP-dependent process through the axial channel of the protein hexamer, after which they can be refolded by components of the Hsp70/Hsp40 chaperone system.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

>sp|F4JVJ1|CLPB2_ARATH Putative chaperone protein ClpB2, chloroplastic OS=Arabidopsis thaliana GN=CLPB2 PE=2 SV=1

 Score = 64.7 bits (156), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 71/298 (23%), Positives = 123/298 (41%), Gaps = 67/298 (22%)

Query: 17  ASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVA 76
           AS    AM+L+    H QVTPLH+  T+++  T +   A   +    +  +++    N +
Sbjct: 15  ASARSHAMSLS----HGQVTPLHLGVTLISDLTSVFYRAITSAGDGDISAQSVVNVINQS 70

Query: 77  LNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLI 136
           L +L                                         ++ L   K+ +  L+
Sbjct: 71  LYKL----------------------------------------TKRNLGDTKVGVAVLV 90

Query: 137 ISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKESNVLVLSQTAS 196
           IS+L+D  +S V++EAG    +VKS VE+                      V++ +    
Sbjct: 91  ISLLEDSQISDVLKEAGVVPEKVKSEVEKL------------------RGEVILRALKTY 132

Query: 197 ATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKG 254
            T + +    LDP+  R+ ++  VIE L  + K N V++GE       VV G+  +I KG
Sbjct: 133 GTDLVEQAGKLDPVIGRHREIRRVIEVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRILKG 192

Query: 255 DVPEALRDVKCLPLSISSFRHMN--RVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA 310
           DVP  L  VK + L   +       R + E+R++ +   V    G+ +VL + ++  A
Sbjct: 193 DVPINLTGVKLISLEFGAMVAGTTLRGQFEERLKSVLKAVEEAQGK-VVLFIDEIHMA 249

Arabidopsis thaliana (taxid: 3702)

>sp|Q6N1H2|CLPB_RHOPA Chaperone protein ClpB OS=Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) GN=clpB PE=3 SV=1

 Score = 64.3 bits (155), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 70/292 (23%), Positives = 130/292 (44%), Gaps = 27/292 (9%)

Query: 20  VKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNR 79
           ++ A +LA R GH Q +PLH+   +L  S GL      ++  +    +A+      AL +
Sbjct: 14  IQSAQSLAMREGHQQFSPLHILKVLLDDSEGLAGGLIDRAGGN---SRAILKATEEALGK 70

Query: 80  LPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISI 139
           +P  + +    G  Q   ++ A   AF  A+    +            V +E   L +S+
Sbjct: 71  MPKVSGS----GAGQV-YLAPATARAFDAAEKAAEKAGDS-------FVTVERLLLALSL 118

Query: 140 LDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKESNVLVLSQTASATK 199
             D    +++ + G +   + + +           +T  ++  + +     L+Q A   K
Sbjct: 119 DKDSEAGQLLTKGGVTPQNLNAAINALRKGRTADSATAENAYDALKKYARDLTQAARDGK 178

Query: 200 VSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVP 257
                  LDP+  R+E++   I+ L  + K N V++GE       +V G+  +I  GDVP
Sbjct: 179 -------LDPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEGLALRILNGDVP 231

Query: 258 EALRDVKCLPLSISSF--RHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDL 307
           E+L+D K L L + +       R E E+R++ + N V +  G GI+L + ++
Sbjct: 232 ESLKDKKLLALDMGALIAGAKYRGEFEERLKAVLNEVTAAEG-GIILFIDEM 282

Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK.

Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (taxid: 258594)

>sp|Q92MK7|CLPB_RHIME Chaperone protein ClpB OS=Rhizobium meliloti (strain 1021) GN=clpB PE=3 SV=1

 Score = 63.5 bits (153), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 77/289 (26%), Positives = 126/289 (43%), Gaps = 31/289 (10%)

Query: 20  VKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNR 79
           ++ A T A   GH Q TP HV   +L    G+  +   ++  +  + K   +    AL +
Sbjct: 14  LQSAQTYALAEGHQQFTPEHVLKVLLDDDQGMAASLIERAGGNAREAK---VGTAAALAK 70

Query: 80  LPASTSTPMLGGHCQFPTISNALVAAFKRAQ-AHQRRG-SIENQQQPLLAVKIELEQLII 137
           LP  T     GG+     +S  L   F  A+ A ++ G S    ++ LLA+ IE      
Sbjct: 71  LPKVT-----GGNGSV-YLSQPLAKVFTAAEDAAKKAGDSFVTVERLLLALAIESSAATA 124

Query: 138 SILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKESNVLVLSQTASA 197
           SIL          +AG + T++   +      EI    T  S+N   E     L + A  
Sbjct: 125 SILS---------KAGVTPTKLNQVIN-----EIRKGRTADSANA--EQGFDSLKKYARD 168

Query: 198 TKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGD 255
                    LDP+  R++++   I+ L  + K N V++GE       +  G+  +I  GD
Sbjct: 169 LTAEAREGKLDPVIGRDDEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIAEGLALRIVNGD 228

Query: 256 VPEALRDVKCLPLSISSF--RHMNRVEVEQRVEEIKNLVRSCLGRGIVL 302
           VPE+L+D + + L + +       R E E+R++ + N VRS  G  I+ 
Sbjct: 229 VPESLKDKRLMALDMGALIAGAKFRGEFEERLKAVLNEVRSEGGEIILF 277

Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK.

Rhizobium meliloti (strain 1021) (taxid: 266834)

>sp|O83110|CLPB_TREPA Chaperone protein ClpB OS=Treponema pallidum (strain Nichols) GN=clpB PE=3 SV=1

 Score = 63.5 bits (153), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 73/307 (23%), Positives = 137/307 (44%), Gaps = 45/307 (14%)

Query: 13  TAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHP-------LQ 65
           T +A+  +  A++LA    H QV   H+ + +L+   G++     +  + P       LQ
Sbjct: 7   TVKASEALNDAISLAEAENHGQVEEEHLLHALLSQKDGIISPLIEKIGAKPDFLYDELLQ 66

Query: 66  CKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPL 125
           C          L R P  T  P     C  PT+S A         A   R +++NQ +  
Sbjct: 67  C----------LRRKPRVTG-PAAQTRCA-PTLSKAC--------ARAERLALKNQDE-- 104

Query: 126 LAVKIELEQLIISILD-DPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSK 184
               +  E L+++I + D + +R++   G +S  + + ++     +  +   P S+ +  
Sbjct: 105 ---YVSCEHLLLAISETDSNTARLLHSQGITSKTISAALKDIRGSKRVTSQDPESTFQCL 161

Query: 185 ESNVLVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEG 242
           E     L+  A   K+       DP+  R+E++  V++ L  + K N V++GE       
Sbjct: 162 EKYCRDLTTLAREEKI-------DPVIGRDEEIRRVMQVLSRRTKNNPVLIGEPGVGKTA 214

Query: 243 VVRGVIDKIEKGDVPEALRDVKCLPLSISSF--RHMNRVEVEQRVEEIKNLVRSCLGRGI 300
           +V G+  +I  GDVPE+L+  + L L + +       R E E+R++ +   V+   G G+
Sbjct: 215 IVEGLARRIVSGDVPESLKGKRLLSLDLGALVAGAKFRGEFEERLKAVIEAVQKSDG-GV 273

Query: 301 VLNLGDL 307
           +L + +L
Sbjct: 274 ILFIDEL 280

Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK.

Treponema pallidum (strain Nichols) (taxid: 243276)

>sp|Q88VX7|CLPB_LACPL Chaperone protein ClpB OS=Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1) GN=clpB PE=3 SV=1

 Score = 62.4 bits (150), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 133/679 (19%), Positives = 251/679 (36%), Gaps = 103/679 (15%)

Query: 135 LIISILDDPS--VSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKESNVLVLS 192
           L ++++D     +++ + + G ++ QVK+ V++     I       S N+  +   L   
Sbjct: 112 LALALMDQTGDQLTKYLNQQGITAGQVKNAVDR-----IRGGQRVTSRNQEDQYQAL--- 163

Query: 193 QTASATKVSKPRV-SLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVID 249
           +      V + R  + DP+  R+E+++ VI  L  K K N V++GE       +V G+  
Sbjct: 164 EKYGVDLVKQARQGNQDPVIGRDEEILDVIRILSRKTKNNPVLIGEPGVGKTAIVEGLAQ 223

Query: 250 KIEKGDVPEALRDVKCLPLSISSF--RHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDL 307
           +I +GDVPE L+D     L + S       R E E+R++ +   ++   G          
Sbjct: 224 RIVRGDVPENLKDKTLFSLDMGSLIAGAKYRGEFEERLKAVLKEIKKSDG---------- 273

Query: 308 EWAEFRASSSEQVRGYYCSIEHII--------MEIGKLVCGIGENARFWLMGIATFQSYM 359
                      Q+  +   I +I+        M+ G L+  +       L+G  T   Y 
Sbjct: 274 -----------QIIMFIDEIHNIVGAGKTEGSMDAGNLLKPMLARGELHLIGATTLDEYR 322

Query: 360 RCKSGHPSLETLWSLHPLTIPAGSLSLSLITTDSDLQSQSTSKKAESGVSWLLFEGEEEN 419
           +      +LE  +    +  P+   ++S+      L+      +   GV          +
Sbjct: 323 QYMEKDKALERRFQKVLVAEPSVEDTISI------LRGLKERFEIHHGVRI-------HD 369

Query: 420 KQLTCCADCSAKF-------EAEARSLQSSSCNSDSPTSSLPAWLQQYKNE------KKA 466
             L   A  S ++       +     +  +S       +S P  L Q   +      ++A
Sbjct: 370 NALVAAAKLSDRYITDRYLPDKALDLVDEASAEIRVEMNSNPTELDQVNRQLMRLEVEEA 429

Query: 467 TLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFH 526
            L     D+ V+ L      + ++  KQ   SER  +   +  + S    + D+   +  
Sbjct: 430 ALKKETDDASVKRLADVQKELASAKEKQRTLSERWDSEKKSLQALSDKKSALDKAKHDLE 489

Query: 527 KTHRDWAVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNS 586
               ++ +   +Q+ +  H        +    E +       H+D     S   +   N 
Sbjct: 490 NAENNYDL---EQAAKLQHGTIPKLEQELKAMEAN-----DHHEDWLVEESVTPDQIANV 541

Query: 587 TSSSDIMEMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTM---R 643
            S    M    V K      E L  L + L ++V  Q   V  +++ VL+ R+G     R
Sbjct: 542 VSR---MTGIPVAKLVAGEREKLLHLADHLHERVVGQDAAVDAVSDAVLRSRAGLQDPNR 598

Query: 644 RKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADS 703
             G F             F G     K ++AK LA  +F + ++ V I +S +       
Sbjct: 599 PLGSF------------MFLGPTGVGKTELAKALAENLFDADDHMVRIDMSEYMEK---- 642

Query: 704 TEDSRNKRSRDEQSCSYIE--RFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRI 761
            E              Y E  +  EAV  NP+ + L +++E+A         + ++ GR+
Sbjct: 643 -ESVSRLVGAAPGYVGYEEGGQLTEAVRRNPYSIVLFDEIEKAHPDVFNILLQVLDDGRL 701

Query: 762 VTSSGDEVSLGDAIVILSC 780
               G  V   + I+I++ 
Sbjct: 702 TDGQGRTVDFKNTILIMTS 720

Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK.

Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1) (taxid: 220668)

>sp|Q9PGC1|CLPB_XYLFA Chaperone protein ClpB OS=Xylella fastidiosa (strain 9a5c) GN=clpB PE=3 SV=1

 Score = 60.5 bits (145), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 70/301 (23%), Positives = 128/301 (42%), Gaps = 40/301 (13%)

Query: 12  LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSH-PLQCKALE 70
           LT+   + +  A +LA  R H  + P+HV + +L    G  R   +Q+  + PL  + L 
Sbjct: 6   LTSRFQNALADAQSLAVGRDHTIIEPVHVFSALLDQQGGSTRPLLMQAGVNVPLLRERLT 65

Query: 71  LCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKR----AQAHQRRGSIENQQQPLL 126
                         + P + G     + SN L   F R    AQ H  +          +
Sbjct: 66  EILE----------ALPKVSGQTVNVSPSNELSRLFHRTDKLAQQHGDQ---------FM 106

Query: 127 AVKIELEQLIISILDDPS-VSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKE 185
           A     E  +++++DD   + + +R AG    ++++ +++    E           ++ E
Sbjct: 107 AS----EWFVLAVVDDSGGLGQALRAAGAEKKKIEAAIDKLRGGETVQTENAEEQRQALE 162

Query: 186 SNVLVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGV 243
              + L+  A + K       LDP+  R+E++   I+ L  + K N V++GE       +
Sbjct: 163 KYTIDLTARAESGK-------LDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAI 215

Query: 244 VRGVIDKIEKGDVPEALRDVKCLPLSISSF--RHMNRVEVEQRVEEIKNLVRSCLGRGIV 301
           V G+  +I  G+VPE LR  + L L + +       R E E+R++ + N +    GR I+
Sbjct: 216 VEGLAQRIVNGEVPEGLRSKRLLSLDLGALIAGAKFRGEFEERLKGVLNDLAKNEGRVIL 275

Query: 302 L 302
            
Sbjct: 276 F 276

Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK.

Xylella fastidiosa (taxid: 2371)

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	854
225440714	848	PREDICTED: chaperone protein ClpB1-like	0.983	0.990	0.764	0.0
147865471	828	hypothetical protein VITISV_031478 [Viti	0.957	0.987	0.739	0.0
224091901	841	predicted protein [Populus trichocarpa]	0.966	0.980	0.726	0.0
255583564	882	conserved hypothetical protein [Ricinus	0.982	0.951	0.707	0.0
356498707	867	PREDICTED: uncharacterized protein LOC10	0.989	0.974	0.649	0.0
15231233	815	heat shock protein-like protein [Arabido	0.933	0.977	0.592	0.0
51536536	837	At3g52490 [Arabidopsis thaliana]	0.933	0.952	0.577	0.0
147827418	861	hypothetical protein VITISV_031746 [Viti	0.983	0.975	0.552	0.0
225464404	840	PREDICTED: uncharacterized protein LOC10	0.967	0.983	0.551	0.0
224113403	854	predicted protein [Populus trichocarpa]	0.970	0.970	0.551	0.0

>gi|225440714|ref|XP_002275038.1| PREDICTED: chaperone protein ClpB1-like [Vitis vinifera]

 Score = 1281 bits (3316), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 659/862 (76%), Positives = 737/862 (85%), Gaps = 22/862 (2%)

Query: 1   MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSH 60
           MRAGGCT+QQ LTAEAA VVKQA+TLARRRGHAQVTPLHVANTMLAA+ GLLRTACLQSH
Sbjct: 1   MRAGGCTVQQALTAEAAGVVKQAVTLARRRGHAQVTPLHVANTMLAATNGLLRTACLQSH 60

Query: 61  SHPLQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIEN 120
           SHPLQCKALELCFNVALNRLPASTS+PMLG H Q P+ISNALVAAFKRAQAHQRRGSIEN
Sbjct: 61  SHPLQCKALELCFNVALNRLPASTSSPMLGPHSQHPSISNALVAAFKRAQAHQRRGSIEN 120

Query: 121 QQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSS 180
           QQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQ+  VSS
Sbjct: 121 QQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQAPSVSS 180

Query: 181 NKSKESNVLVLSQTAS----ATKVSKPRVSLDPIRNEDVMYVIENLMSKRKRNFVVVGEC 236
            KSKESN+LVLSQ+        K+ KP V  DP+RNEDVM VIENLM+KR++N V+VGEC
Sbjct: 181 -KSKESNLLVLSQSPPMGQIGVKLGKPTVP-DPVRNEDVMSVIENLMNKRRKNTVIVGEC 238

Query: 237 LASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCL 296
           LA+IEGVVRGV+DK++KGDVPEALRDVK + L + SF H +R EVEQ++ E+K+LV+SC+
Sbjct: 239 LATIEGVVRGVMDKVDKGDVPEALRDVKLISLPLFSFGHHSREEVEQKLGELKSLVKSCV 298

Query: 297 GRGIVLNLGDLEW-AEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATF 355
           GRG++L L DL+W  ++RASSSEQ R YYC +EH+IME+GKLVCG GEN RFWLMGIATF
Sbjct: 299 GRGVILYLEDLKWTTDYRASSSEQGRNYYCPVEHMIMELGKLVCGFGENGRFWLMGIATF 358

Query: 356 QSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLITTDSDLQSQSTSKKAESGVS-WLLFE 414
           Q+Y RC++GHPSLET+WSLHPLTIPA SL+LSL+       SQ +SKKA SG S WL+ E
Sbjct: 359 QTYSRCRTGHPSLETIWSLHPLTIPASSLALSLMP-----DSQFSSKKAGSGTSNWLMLE 413

Query: 415 GEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWLQQYKNEKKATLSNNDKD 474
           G  E KQLTCCADCSA FE EARS+ +S+CNSDS TS+LP WLQQYK+E K  LS ND+D
Sbjct: 414 GGAE-KQLTCCADCSANFENEARSIPTSTCNSDSTTSTLPTWLQQYKDENKK-LSRNDQD 471

Query: 475 S-GVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHKTHRDWA 533
              VRDLCKKWNSIC+S HKQP+ SE+TLTFSS SPSSSTSGFSYDQQYPN H+TH+ W 
Sbjct: 472 CVAVRDLCKKWNSICSSAHKQPHSSEKTLTFSSLSPSSSTSGFSYDQQYPNLHQTHQGWP 531

Query: 534 VVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNSTSSSDIM 593
           VVE KQSWR++HF  S EA +K T EPSLR+YIPEH D K   +SN NSTPNS SSSD+M
Sbjct: 532 VVEHKQSWRDNHFWVS-EALNK-TYEPSLRMYIPEHSDRK--YASNPNSTPNSASSSDVM 587

Query: 594 EMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSE 653
           EMEYV +FKELN+ENL +LCNALEKKVPWQKD + DIA+T+L+CRSG +RRKGK K+ SE
Sbjct: 588 EMEYVQRFKELNAENLNTLCNALEKKVPWQKDIIPDIASTILQCRSGMVRRKGKVKN-SE 646

Query: 654 VKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSR 713
            KEETW FFQGVD DAKEKIA+ELARLVFGS NNFVSIALSSFSSTRADSTED RNKRSR
Sbjct: 647 TKEETWFFFQGVDMDAKEKIARELARLVFGSQNNFVSIALSSFSSTRADSTEDLRNKRSR 706

Query: 714 DEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGD 773
           DEQSCSYIERFAEAV +NPHRVFL EDVEQADYCSQ G KRA E GRI  S+G+E+SL D
Sbjct: 707 DEQSCSYIERFAEAVGSNPHRVFLAEDVEQADYCSQMGIKRATERGRITNSNGEEISLSD 766

Query: 774 AIVILSCESFSSRSRACSPPTKQKSDG-CEEEKGAAMEGTSPSVSLDLNICIDDDSTEDQ 832
           AI+ILSCESFSSRSRACSPP KQKSD   EE+ G   E  SP VSLDLNICIDDD  ED+
Sbjct: 767 AIIILSCESFSSRSRACSPPIKQKSDEFEEEKGGGGGEEISPCVSLDLNICIDDDGVEDE 826

Query: 833 SIDDIGLLESVDKRIIFKIMEL 854
           SIDDIGLLESVD+RI FKI EL
Sbjct: 827 SIDDIGLLESVDRRITFKIQEL 848

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147865471|emb|CAN83664.1| hypothetical protein VITISV_031478 [Vitis vinifera]

 Score = 1217 bits (3149), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 639/864 (73%), Positives = 713/864 (82%), Gaps = 46/864 (5%)

Query: 1   MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSH 60
           MRAGGCT+QQ LTAEAA VVKQA+TLARRRGHAQVTPLHVANTMLAA+ GLLRTACLQSH
Sbjct: 1   MRAGGCTVQQALTAEAAGVVKQAVTLARRRGHAQVTPLHVANTMLAATNGLLRTACLQSH 60

Query: 61  SHPLQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIEN 120
           SHPLQCKALELCFNVALNRLPASTS+PMLG H Q P+ISNALVAAFKRAQAHQRRGSIEN
Sbjct: 61  SHPLQCKALELCFNVALNRLPASTSSPMLGPHSQHPSISNALVAAFKRAQAHQRRGSIEN 120

Query: 121 QQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSS 180
           QQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQ+  VSS
Sbjct: 121 QQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQAPSVSS 180

Query: 181 NKSKESNVLVLSQTAS----ATKVSKPRVSLDPIRNEDVMYVIENLMSKRKRNFVVVGEC 236
            KSKESN+LVLSQ+        K+ KP V  DP+RNEDVM                    
Sbjct: 181 -KSKESNLLVLSQSPPMGQIGVKLGKPTVP-DPVRNEDVMS------------------- 219

Query: 237 LASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISS--FRHMNRVEVEQRVEEIKNLVRS 294
                  VRGV+DK++KGDVPEALRDVK + L  SS  +  + R    +++ E+K+LV+S
Sbjct: 220 -------VRGVMDKVDKGDVPEALRDVKLISLPPSSDFWTSLQRRGPNRKLGELKSLVKS 272

Query: 295 CLGRGIVLNLGDLEW-AEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIA 353
           C+GRG++L L DL+W  ++RASSSEQ R YYC +EH+IME+GKLVCG GEN RFWLMGIA
Sbjct: 273 CVGRGVILYLEDLKWTTDYRASSSEQGRNYYCPVEHMIMELGKLVCGFGENGRFWLMGIA 332

Query: 354 TFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLITTDSDLQSQSTSKKAESGVS-WLL 412
           TFQ+Y RC++GHPSLET+WSLHPLTIPA SL+LSL+  DSDLQSQ +SKKA SG S WL+
Sbjct: 333 TFQTYSRCRTGHPSLETIWSLHPLTIPASSLALSLM-PDSDLQSQFSSKKAGSGTSNWLM 391

Query: 413 FEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWLQQYKNEKKATLSNND 472
            EG  E KQLTCCADCSA FE EARS+ +S+CNSDS TS+LP WLQQYK+E K  LS ND
Sbjct: 392 LEGGAE-KQLTCCADCSANFENEARSIPTSTCNSDSTTSTLPTWLQQYKDENK-KLSRND 449

Query: 473 KDS-GVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHKTHRD 531
           +D   VRDLCKKWNSIC+S HKQP+ SE+TLTFSS SPSSSTSGFSYDQQYPN H+TH+ 
Sbjct: 450 QDCVAVRDLCKKWNSICSSAHKQPHSSEKTLTFSSLSPSSSTSGFSYDQQYPNLHQTHQG 509

Query: 532 WAVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNSTSSSD 591
           W VVE KQSWR++HF  S EA +K T EPSLR+YIPEH D K   +SN NSTPNS SSSD
Sbjct: 510 WPVVEHKQSWRDNHFWVS-EALNK-TYEPSLRMYIPEHSDRK--YASNPNSTPNSASSSD 565

Query: 592 IMEMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDH 651
           +MEMEYV +FKELN+ENL +LCNALEKKVPWQKD + DIA+T+L+CRSG +RRKGK K+ 
Sbjct: 566 VMEMEYVQRFKELNAENLNTLCNALEKKVPWQKDIIPDIASTILQCRSGMVRRKGKVKN- 624

Query: 652 SEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKR 711
           SE KEETW FFQGVD DAKEKIA+ELARLVFGS NNFVSIALSSFSSTRADSTED RNKR
Sbjct: 625 SETKEETWFFFQGVDMDAKEKIARELARLVFGSQNNFVSIALSSFSSTRADSTEDLRNKR 684

Query: 712 SRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSL 771
           SRDEQSCSYIERFAEAV +NPHRVFL EDVEQADYCSQ G KRA E GRI  S+G+E+SL
Sbjct: 685 SRDEQSCSYIERFAEAVGSNPHRVFLAEDVEQADYCSQMGIKRATERGRITNSNGEEISL 744

Query: 772 GDAIVILSCESFSSRSRACSPPTKQKSDG-CEEEKGAAMEGTSPSVSLDLNICIDDDSTE 830
            DAI+ILSCESFSSRSRACSPP KQKSD   EE+ G   E  SP VSLDLNICIDDD  E
Sbjct: 745 SDAIIILSCESFSSRSRACSPPIKQKSDEFEEEKGGGGGEEISPCVSLDLNICIDDDGVE 804

Query: 831 DQSIDDIGLLESVDKRIIFKIMEL 854
           D+SIDDIGLLESVD+RI FKI EL
Sbjct: 805 DESIDDIGLLESVDRRITFKIQEL 828

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224091901|ref|XP_002309392.1| predicted protein [Populus trichocarpa] gi|222855368|gb|EEE92915.1| predicted protein [Populus trichocarpa]

 Score = 1176 bits (3041), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 631/869 (72%), Positives = 727/869 (83%), Gaps = 44/869 (5%)

Query: 1   MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSH 60
           MRAGGCT+QQ LTA+AASV+KQA+TLARRRGHAQVTPLHVANTML+ASTGL RTACLQSH
Sbjct: 1   MRAGGCTVQQALTADAASVIKQAVTLARRRGHAQVTPLHVANTMLSASTGLFRTACLQSH 60

Query: 61  SHPLQCKALELCFNVALNRLPASTSTPMLGGHCQ-FPTISNALVAAFKRAQAHQRRGSIE 119
           SHPLQCKALELCFNVALNRLPASTS+P+LG H Q FP+ISNALVAAFKRAQAHQRRGSIE
Sbjct: 61  SHPLQCKALELCFNVALNRLPASTSSPILGTHSQQFPSISNALVAAFKRAQAHQRRGSIE 120

Query: 120 NQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVS 179
           NQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQS P  
Sbjct: 121 NQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSAPSV 180

Query: 180 SNKSKESNVLVLSQTASATKVSKPRVSLDPIRNEDVMYVIENLMSKRKRNFVVVGECLAS 239
           S+KSKESN LVLSQ+ ++++V      LDPI+NEDVM VIENL++KR+R+FV+VGE LAS
Sbjct: 181 SSKSKESNGLVLSQSPTSSQVGAKATVLDPIKNEDVMCVIENLVNKRRRSFVIVGESLAS 240

Query: 240 IEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRG 299
           IE VV+GVIDK++KGDVPEALR+VK L + +SSF H +RVEVE ++EE+K  VRS +G+G
Sbjct: 241 IEVVVKGVIDKVQKGDVPEALREVKFLTIPVSSFGHFSRVEVEHKLEELKIHVRSYMGKG 300

Query: 300 IVLNLGDLEWA-EFRA--SSSEQVRGYYCSIEHIIMEIGKLVCGIGE--NARFWLMGIAT 354
           +VLNLGDL+WA E RA  SSSEQ R ++C +E++I+E+GKL CGIGE  N RFWLMGIAT
Sbjct: 301 VVLNLGDLKWAIENRASSSSSEQGRCFFCPMEYMIIELGKLACGIGENINGRFWLMGIAT 360

Query: 355 FQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLITTDSDLQSQSTSKKAESG-VSWLLF 413
           FQ+YM+CKSGHPS  T+  LHPLTIPAGSL LSLI +DSDL+ QST  KA +G  SW+L 
Sbjct: 361 FQTYMKCKSGHPSGGTVLGLHPLTIPAGSLRLSLI-SDSDLRCQSTRNKAGNGSSSWILH 419

Query: 414 EGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWLQQYKNEKKATLSNNDK 473
           EG E+ KQLTCCADCSAKFE+EARS  +S+C+SDS TS LPAWLQQ KNEK    S+N  
Sbjct: 420 EGGED-KQLTCCADCSAKFESEARSFPTSTCDSDSTTSGLPAWLQQCKNEKNLQNSDNQN 478

Query: 474 DSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHKTHRDWA 533
              ++DLC+KWNS C+SIH+Q Y+SE+TLTFSS SPSSST   SYDQQYP F +TH +W 
Sbjct: 479 SMSIKDLCRKWNSFCSSIHRQHYFSEKTLTFSSVSPSSST---SYDQQYPIFQQTHNEWP 535

Query: 534 VVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKD-LKQ-PLSSNRNSTPNSTSSSD 591
           +VEPK                       LR+YIPEHKD  KQ P SSN NSTPNSTSSSD
Sbjct: 536 IVEPKH----------------------LRMYIPEHKDHTKQLPFSSNPNSTPNSTSSSD 573

Query: 592 IMEMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDH 651
           +ME+ Y+HKFKELN+ENL  L  ALEKKVPWQ+D + +IA+T+L+CRSG +RRKGK K+ 
Sbjct: 574 VMEVVYLHKFKELNAENLKILSIALEKKVPWQRDIIPEIASTILQCRSGMIRRKGKMKN- 632

Query: 652 SEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKR 711
           SE KEETWLFFQGVD +AKEKIAKELARLVFGS+++F+S++LSSFSSTRADSTED RNKR
Sbjct: 633 SESKEETWLFFQGVDVEAKEKIAKELARLVFGSNDSFISVSLSSFSSTRADSTEDCRNKR 692

Query: 712 SRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSL 771
           SRDEQSCSYIERF+EA SNNP RVFL+EDVEQADYCSQ GFKRAIESGRI  S+G EV L
Sbjct: 693 SRDEQSCSYIERFSEAASNNPRRVFLVEDVEQADYCSQIGFKRAIESGRITNSNGQEVGL 752

Query: 772 GDAIVILSCESFSSRSRACSPPTKQKSDGCEEEK-----GAA-MEGTSPSVSLDLNICID 825
            DAI+ILSCESFSSRSRACSPP KQ++DG  EE+     GAA ME T+P +SLDLNI +D
Sbjct: 753 SDAIIILSCESFSSRSRACSPPIKQRTDGSYEEEDNAGAGAALMEDTTPCISLDLNISVD 812

Query: 826 DDST-EDQSIDDIGLLESVDKRIIFKIME 853
           DD+  EDQSIDDIGLLESVD+RIIFKI E
Sbjct: 813 DDNILEDQSIDDIGLLESVDRRIIFKIQE 841

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255583564|ref|XP_002532538.1| conserved hypothetical protein [Ricinus communis] gi|223527727|gb|EEF29832.1| conserved hypothetical protein [Ricinus communis]

 Score = 1111 bits (2873), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 632/893 (70%), Positives = 725/893 (81%), Gaps = 54/893 (6%)

Query: 1   MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSH 60
           MRAGGCT+QQ LT EAA+VVKQA+TLARRRGHAQVTPLHVANTML++STGLLRTACLQSH
Sbjct: 1   MRAGGCTVQQALTTEAATVVKQAVTLARRRGHAQVTPLHVANTMLSSSTGLLRTACLQSH 60

Query: 61  SHPLQCKALELCFNVALNRLPASTSTPMLGGHCQ-FPTISNALVAAFKRAQAHQRRGSIE 119
           SHPLQCKALELCFNVALNRLPASTS+P+LG H Q +P+ISNALVAAFKRAQAHQRRGSIE
Sbjct: 61  SHPLQCKALELCFNVALNRLPASTSSPVLGTHAQQYPSISNALVAAFKRAQAHQRRGSIE 120

Query: 120 NQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQ-STPV 178
           NQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQ S PV
Sbjct: 121 NQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQNSAPV 180

Query: 179 SSNKSKESN----VLVLSQTASATKVSKPRVS------LDPIRNEDVMYVIENLMSKRKR 228
           SS+KSKESN    VL LS T    + S           LDPIR EDVM VIENL++KRKR
Sbjct: 181 SSSKSKESNNNNSVLALSHTQVGARTSCRSSPTTSTTSLDPIRKEDVMSVIENLINKRKR 240

Query: 229 NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMN-RVEVEQRVEE 287
           + V+VGECL S+EGVV+GV+DK+ KGDVPEAL++VK +   +SS  H++ RVEV+Q++EE
Sbjct: 241 SVVIVGECLVSLEGVVKGVMDKVIKGDVPEALKEVKFISFPLSSLGHLSSRVEVDQKLEE 300

Query: 288 IKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGEN-A 345
           +K  +RS L +G+VLNLGDL+W  E+RA++          +EH+IMEIGKL  GI EN  
Sbjct: 301 LKVHIRSYLSKGVVLNLGDLKWVVEYRANN-------LSPMEHMIMEIGKLASGISENNG 353

Query: 346 RFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLITTDSDLQSQSTSKKAE 405
           +FWL GIATFQ+YM+CKSG+PSLET+W LH LTIPAGSL LSLIT DS+   Q  S+   
Sbjct: 354 KFWLTGIATFQTYMKCKSGNPSLETVWGLHALTIPAGSLRLSLIT-DSNKVGQDGSR--- 409

Query: 406 SGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSS-LPAWLQQYKNEK 464
               W++ EGEEE KQLTCC DC++KFE EARSLQSS+ NSDS T+S LPAWLQQYKNE 
Sbjct: 410 ---CWIMLEGEEE-KQLTCCVDCTSKFENEARSLQSSTSNSDSTTTSTLPAWLQQYKNEN 465

Query: 465 KATLSNNDKDS-GVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYP 523
           +   +NND+D   ++DLCKKWNSIC+SIH++PY SE+T+TFSS SPSS TS FSYD QYP
Sbjct: 466 QGVNNNNDQDCVSIKDLCKKWNSICSSIHQKPYSSEKTITFSSVSPSSFTSSFSYDHQYP 525

Query: 524 NFHKTH--RDWAVVEPKQSWREHHFLFSHEASDKSTS----EPSLRLYIPEHKDLKQP-- 575
           NFH T+  RDW VVE KQSWR+HHF    E  +K  S    EPSLR+YIPEH   + P  
Sbjct: 526 NFHHTYHQRDWPVVESKQSWRDHHFWVGSETVNKINSCISIEPSLRMYIPEHNRDQYPKP 585

Query: 576 ---LSSNRNSTPNSTSSSDIMEMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIAN 632
               SSN NSTPNSTSSSD+MEME+++KFKE+N+ENL  LCNALEKKV WQKD + DIA+
Sbjct: 586 TIPFSSNPNSTPNSTSSSDVMEMEHLNKFKEMNAENLKILCNALEKKVTWQKDIIPDIAS 645

Query: 633 TVLKCRSGTMRRKGKFKDHS---EVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFV 689
           T+L+CRSG +RRKGK   +S   + KEETWL FQGVD +AKEKIAKELA+L+FGS NNF+
Sbjct: 646 TILQCRSGMVRRKGKVTRNSSTEQAKEETWLLFQGVDVEAKEKIAKELAKLIFGSQNNFI 705

Query: 690 SIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQ 749
           SI+LSSFSSTRADSTED RNKRSRDEQSCSYIERFAEAVS+NPHRVFL+EDVEQADYCSQ
Sbjct: 706 SISLSSFSSTRADSTEDCRNKRSRDEQSCSYIERFAEAVSSNPHRVFLVEDVEQADYCSQ 765

Query: 750 KGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRACSPPTKQKSDGC------EE 803
            GFKRAIE GRI    G+EV L DAI+ILSCESFSSRSRACSPP KQK+D        EE
Sbjct: 766 VGFKRAIERGRITNVKGEEVGLSDAIIILSCESFSSRSRACSPPVKQKTDDYIISQDQEE 825

Query: 804 EK--GAAMEGTSPSVSLDLNICIDDDSTEDQSIDDIGLLESVDKRIIFKIMEL 854
           EK  GA ME +SP VSLDLNI IDDDS ED+SIDDIGLLESVD+RI+FKI EL
Sbjct: 826 EKGQGAKMEESSPCVSLDLNISIDDDSIEDRSIDDIGLLESVDRRIVFKIQEL 878

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356498707|ref|XP_003518191.1| PREDICTED: uncharacterized protein LOC100807485 [Glycine max]

 Score = 1041 bits (2691), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 569/876 (64%), Positives = 693/876 (79%), Gaps = 31/876 (3%)

Query: 1   MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSH 60
           MR G C +QQGLT EAAS+VKQA+TLA+RRGHAQVTPLHVANTML+ + GLLRTACLQSH
Sbjct: 1   MRTGSCAVQQGLTPEAASIVKQAVTLAKRRGHAQVTPLHVANTMLSITNGLLRTACLQSH 60

Query: 61  SHPLQCKALELCFNVALNRLPASTST-PMLGGHCQF-----PTISNALVAAFKRAQAHQR 114
           SHPLQCKALELCFNVALNRLPASTS+ PML G         P+ISNALVAAFKRAQAHQR
Sbjct: 61  SHPLQCKALELCFNVALNRLPASTSSSPMLQGSHHHHSHACPSISNALVAAFKRAQAHQR 120

Query: 115 RGSIENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQ 174
           RGS+ENQQQPLLAVKI+LEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQ
Sbjct: 121 RGSVENQQQPLLAVKIKLEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQ 180

Query: 175 STPVSSNKSKESNVLVLSQTASATKVSKPRVSLDPIRNEDVMYVIENLMSKRKRNFVVVG 234
                 N +  +     + +     V      LDPIR EDV  VIENL S+RKR+ V+VG
Sbjct: 181 DNGSGKNNNNSNKAKENNSSGEKGSV------LDPIRVEDVASVIENLGSERKRSVVIVG 234

Query: 235 ECLASIEGVVRGVIDKIEKGDVPE--ALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLV 292
           EC+ S+EGVVRGV++K++KGDV +   LR VK + LS+SSF +++RVEVEQ+V E+++LV
Sbjct: 235 ECVTSLEGVVRGVMEKVDKGDVGDECTLRGVKFISLSLSSFGNVSRVEVEQKVGELRSLV 294

Query: 293 RSC-LGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGEN-ARFWL 349
           ++    +G VL LGDL+W  +FRA  S Q  G YC ++H+++EIGKLV G+ EN ARFW+
Sbjct: 295 KASEHSKGYVLYLGDLKWVFDFRARGS-QGGGCYCPVDHMVVEIGKLVNGVEENGARFWV 353

Query: 350 MGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLITTDSDLQSQSTSKKAESGVS 409
           MG+ATFQ+YMRCK+G PSLETLW LHP+TIPAGSL LSLIT DS +Q+Q T++KA++  +
Sbjct: 354 MGVATFQAYMRCKNGQPSLETLWGLHPITIPAGSLRLSLIT-DSGVQNQPTNEKADNRTT 412

Query: 410 WLLFEG-EEENKQLTCCADCSAKFEA-EARSLQSSSCNSDSPTSSLPAWLQQYKNEKKAT 467
           WLL EG  +++KQ  C A+ S K E  E RSLQSSS  +   +S+LPAWLQQYKNE K  
Sbjct: 413 WLLLEGVGDDHKQQPCFAEPSTKNETTEVRSLQSSSTCNSDSSSTLPAWLQQYKNENKGI 472

Query: 468 LSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHK 527
             N+     V +LCKKWNS+C+SI KQPY S++TL+ SS SPSSS S FSY+QQ+PN  +
Sbjct: 473 THNDQNCVPVGELCKKWNSMCSSIQKQPYPSDKTLSLSSVSPSSSNSNFSYEQQHPNLLQ 532

Query: 528 THRDWAVVEP-KQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNS 586
           TH +W V EP K S   +HF  S+  ++ +T+EP+LR+YIPE+ + KQP SS   S+  +
Sbjct: 533 THHEWQVGEPPKDSLNNYHFWISNNGTNNNTNEPTLRVYIPENNN-KQPFSSPNPSSNPN 591

Query: 587 TSSS-DIMEMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRK 645
           ++SS DIME+E+V +FKELN+ENL +LCNALEKKVPWQKD + +IA+T+L+CRSG +RRK
Sbjct: 592 STSSSDIMEVEHVREFKELNTENLKTLCNALEKKVPWQKDIIPEIASTLLQCRSGMVRRK 651

Query: 646 GK-FKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADST 704
           GK  ++  EVKEETWLFFQGVD +AKEKIA+ELARLVFGS N+ VSIALS+F+STRADST
Sbjct: 652 GKVMRNSEEVKEETWLFFQGVDVEAKEKIARELARLVFGSQNDVVSIALSTFASTRADST 711

Query: 705 ED-SRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVT 763
           ED SRNKRSR+E SCSYIERFAEA++ NPHRVFL+ED+EQADYCSQ GFKRAIE GR+  
Sbjct: 712 EDYSRNKRSREETSCSYIERFAEAMACNPHRVFLVEDIEQADYCSQLGFKRAIERGRVAD 771

Query: 764 SSGDEVSLGDAIVILSCESFSSRSRACSPPTKQKSDGCEEEKG----AAMEGTSPSVSLD 819
           S G+EV+L DAI+ILSCESFSSRSRACSP  KQK    EE+ G    A +E TSP VSLD
Sbjct: 772 SKGEEVALCDAIIILSCESFSSRSRACSPSVKQKPLTEEEKNGGDMVATLEVTSPCVSLD 831

Query: 820 LNICIDDDS-TEDQSIDDIGLLESVDKRIIFKIMEL 854
           LNI IDD++  ED+S+D+IGLLESVDK++IF   EL
Sbjct: 832 LNISIDDENEVEDKSVDEIGLLESVDKKVIFNFQEL 867

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15231233|ref|NP_190817.1| heat shock protein-like protein [Arabidopsis thaliana] gi|4886278|emb|CAB43425.1| putative protein [Arabidopsis thaliana] gi|44917467|gb|AAS49058.1| At3g52490 [Arabidopsis thaliana] gi|332645430|gb|AEE78951.1| heat shock protein-like protein [Arabidopsis thaliana]

 Score =  919 bits (2376), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 512/864 (59%), Positives = 639/864 (73%), Gaps = 67/864 (7%)

Query: 1   MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSH 60
           MRAGGCT++Q LTA+AA+VVKQAM LARRRGHAQVTPLHVA+TML+A TGLLRTACLQSH
Sbjct: 1   MRAGGCTVEQALTADAANVVKQAMGLARRRGHAQVTPLHVASTMLSAPTGLLRTACLQSH 60

Query: 61  SHPLQCKALELCFNVALNRLPASTSTPMLG-GHCQFPTISNALVAAFKRAQAHQRRGSIE 119
           +HPLQC+ALELCFNVALNRLP ST +PMLG     FP+ISNAL AAFKRAQAHQRRGSIE
Sbjct: 61  THPLQCRALELCFNVALNRLPTSTGSPMLGVPTSPFPSISNALGAAFKRAQAHQRRGSIE 120

Query: 120 NQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVS 179
           +QQQP+LAVKIE+EQLIISILDDPSVSRVMREAGFSS QVK+ VEQAVSLEICS++T  S
Sbjct: 121 SQQQPILAVKIEVEQLIISILDDPSVSRVMREAGFSSPQVKTKVEQAVSLEICSKTT--S 178

Query: 180 SNKSKESNVLVLSQTASATKVSKPRVSLDPIRNEDVMYVIENLMSKRKRNFVVVGECLAS 239
           S+K KE  +L                   P+RNEDVM VI NL+ K++RNFV+VGECLA+
Sbjct: 179 SSKPKEGKLLT------------------PVRNEDVMNVINNLVDKKRRNFVIVGECLAT 220

Query: 240 IEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRG 299
           I+GVV+ V++K++K DVPE L+DVK + LS SSF   +R +VE+++EE++ LV+SC+G+G
Sbjct: 221 IDGVVKTVMEKVDKKDVPEVLKDVKFITLSFSSFGQPSRADVERKLEELETLVKSCVGKG 280

Query: 300 IVLNLGDLEW---AEFRASSSEQVRGYYCSIEHIIMEIGKLVCGI--GENARFWLMGIAT 354
           ++LNLGDL W   +  R SS       YC +EH+IMEIGKL CG+  G++ RFWLMG+AT
Sbjct: 281 VILNLGDLNWFVESRTRGSSLYNNNDSYCVVEHMIMEIGKLACGLVMGDHGRFWLMGLAT 340

Query: 355 FQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSL-ITTDSDLQSQSTSKKAESGVSWLLF 413
            Q+Y+RCKSG PSLE+LW L  LTIPA S SL L + ++S+L+     KK+E+ VS  L 
Sbjct: 341 SQTYVRCKSGQPSLESLWCLTTLTIPATSNSLRLSLVSESELEV----KKSEN-VSLQL- 394

Query: 414 EGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWLQQYKNEKKATLSNNDK 473
             ++ + QL+ C +CS KFE+EAR L+SS  NS+  T +LPAWLQQYK E +   S+ D 
Sbjct: 395 --QQSSDQLSFCEECSVKFESEARFLKSS--NSNVTTVALPAWLQQYKKENQN--SHTDS 448

Query: 474 DSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFH--KTHRD 531
           DS +++L  KWNSIC+SIHK+P     TL+  ++S S ST            H  +T+ D
Sbjct: 449 DS-IKELVVKWNSICDSIHKRPSLKTLTLSSPTSSFSGST-----QPSISTLHHLQTNGD 502

Query: 532 WAVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQP--LSSNRNSTPNS-TS 588
           W V+E       HH +  HE S        LRL+IPEH   ++   + SN NST NS  S
Sbjct: 503 WPVIETNT--HRHHSVV-HETSH-------LRLFIPEHDSEQKTELVCSNPNSTMNSEAS 552

Query: 589 SSDIMEMEYVH-KFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGK 647
           SSD ME+E+   +FKE+N+ENL +LC ALE KVPWQKD V ++A TVLKCRSG+  RK  
Sbjct: 553 SSDAMELEHASSRFKEMNAENLATLCAALESKVPWQKDLVPELAKTVLKCRSGSSTRK-- 610

Query: 648 FKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDS 707
              + + KE+TW+FFQG+D DAKEKIA+ELA+LVFGS ++FVSI LSSFSSTR+DS ED 
Sbjct: 611 INGNEDKKEDTWMFFQGLDVDAKEKIARELAKLVFGSQDSFVSICLSSFSSTRSDSAEDL 670

Query: 708 RNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGD 767
           RNKR RDEQS SYIERF+EAVS +P+RV L+ED+EQADY SQ GFKRA+E GR+  SSG+
Sbjct: 671 RNKRLRDEQSLSYIERFSEAVSLDPNRVILVEDIEQADYLSQVGFKRAVERGRVCNSSGE 730

Query: 768 EVSLGDAIVILSCESFSSRSRACSPPTKQKSDGCEEEKGAAMEGTSPSVSLDLNICIDDD 827
           E SL DAIVILSCE F SRSRACSPP+ QKSDG ++ +    +  +  V+LDLN+ ID  
Sbjct: 731 EASLKDAIVILSCERFRSRSRACSPPSNQKSDGSDQPED---KNVATCVALDLNLSIDSA 787

Query: 828 ST-EDQSIDDIGLLESVDKRIIFK 850
              E++S D+IGLLE+VD R  FK
Sbjct: 788 YVCEEESCDEIGLLEAVDARFHFK 811

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|51536536|gb|AAU05506.1| At3g52490 [Arabidopsis thaliana]

 Score =  907 bits (2343), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 512/886 (57%), Positives = 639/886 (72%), Gaps = 89/886 (10%)

Query: 1   MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSH 60
           MRAGGCT++Q LTA+AA+VVKQAM LARRRGHAQVTPLHVA+TML+A TGLLRTACLQSH
Sbjct: 1   MRAGGCTVEQALTADAANVVKQAMGLARRRGHAQVTPLHVASTMLSAPTGLLRTACLQSH 60

Query: 61  SHPLQCKALELCFNVALNRLPASTSTPMLG-GHCQFPTISNALVAAFKRAQAHQRRGSIE 119
           +HPLQC+ALELCFNVALNRLP ST +PMLG     FP+ISNAL AAFKRAQAHQRRGSIE
Sbjct: 61  THPLQCRALELCFNVALNRLPTSTGSPMLGVPTSPFPSISNALGAAFKRAQAHQRRGSIE 120

Query: 120 NQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVS 179
           +QQQP+LAVKIE+EQLIISILDDPSVSRVMREAGFSS QVK+ VEQAVSLEICS++T  S
Sbjct: 121 SQQQPILAVKIEVEQLIISILDDPSVSRVMREAGFSSPQVKTKVEQAVSLEICSKTT--S 178

Query: 180 SNKSKESNVLVLSQTASATKVSKPRVSLDPIRNEDVMYVIENLMSKRKRNFVVVGECLAS 239
           S+K KE  +L                   P+RNEDVM VI NL+ K++RNFV+VGECLA+
Sbjct: 179 SSKPKEGKLLT------------------PVRNEDVMNVINNLVDKKRRNFVIVGECLAT 220

Query: 240 IEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIK---------- 289
           I+GVV+ V++K++K DVPE L+DVK + LS SSF   +R +VE+++EE++          
Sbjct: 221 IDGVVKTVMEKVDKKDVPEVLKDVKFITLSFSSFGQPSRADVERKLEELEADVERKLEEL 280

Query: 290 ------------NLVRSCLGRGIVLNLGDLEW---AEFRASSSEQVRGYYCSIEHIIMEI 334
                        LV+SC+G+G++LNLGDL W   +  R SS       YC +EH+IMEI
Sbjct: 281 EADVERKLEELETLVKSCVGKGVILNLGDLNWFVESRTRGSSLYNNNDSYCVVEHMIMEI 340

Query: 335 GKLVCGI--GENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSL-ITT 391
           GKL CG+  G++ RFWLMG+AT Q+Y+RCKSG PSLE+LW L  LTIPA S SL L + +
Sbjct: 341 GKLACGLVMGDHGRFWLMGLATSQTYVRCKSGQPSLESLWCLTTLTIPATSNSLRLSLVS 400

Query: 392 DSDLQSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTS 451
           +S+L+     KK+E+ VS  L   ++ + QL+ C +CS KFE+EAR L+SS  NS+  T 
Sbjct: 401 ESELEV----KKSEN-VSLQL---QQSSDQLSFCEECSVKFESEARFLKSS--NSNVTTV 450

Query: 452 SLPAWLQQYKNEKKATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSS 511
           +LPAWLQQYK E +   S+ D DS +++L  KWNSIC+SIHK+P     TL+  ++S S 
Sbjct: 451 ALPAWLQQYKKENQN--SHTDSDS-IKELVVKWNSICDSIHKRPSLKTLTLSSPTSSFSG 507

Query: 512 STSGFSYDQQYPNFH--KTHRDWAVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEH 569
           ST            H  +T+ DW V+E       HH +  HE S        LRL+IPEH
Sbjct: 508 ST-----QPSISTLHHLQTNGDWPVIETNT--HRHHSVV-HETSH-------LRLFIPEH 552

Query: 570 KDLKQP--LSSNRNSTPNS-TSSSDIMEMEYVH-KFKELNSENLTSLCNALEKKVPWQKD 625
              ++   + SN NST NS  SSSD ME+E+   +FKE+N+ENL +LC ALE KVPWQKD
Sbjct: 553 DSEQKTELVCSNPNSTMNSEASSSDAMELEHASSRFKEMNAENLATLCAALESKVPWQKD 612

Query: 626 TVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH 685
            V ++A TVLKCRSG+  RK     + + KE+TW+FFQG+D DAKEKIA+ELA+LVFGS 
Sbjct: 613 LVPELAKTVLKCRSGSSTRK--INGNEDKKEDTWMFFQGLDVDAKEKIARELAKLVFGSQ 670

Query: 686 NNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQAD 745
           ++FVSI LSSFSSTR+DS ED RNKR RDEQS SYIERF+EAVS +P+RV L+ED+EQAD
Sbjct: 671 DSFVSICLSSFSSTRSDSAEDLRNKRLRDEQSLSYIERFSEAVSLDPNRVILVEDIEQAD 730

Query: 746 YCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRACSPPTKQKSDGCEEEK 805
           Y SQ GFKRA+E GR+  SSG+E SL DAIVILSCE F SRSRACSPP+ QKSDG ++ +
Sbjct: 731 YLSQVGFKRAVERGRVCNSSGEEASLKDAIVILSCERFRSRSRACSPPSNQKSDGSDQPE 790

Query: 806 GAAMEGTSPSVSLDLNICIDDDST-EDQSIDDIGLLESVDKRIIFK 850
               +  +  V+LDLN+ ID     E++S D+IGLLE+VD R  FK
Sbjct: 791 D---KNVATCVALDLNLSIDSAYVCEEESCDEIGLLEAVDARFHFK 833

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147827418|emb|CAN62072.1| hypothetical protein VITISV_031746 [Vitis vinifera]

 Score =  865 bits (2235), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 483/875 (55%), Positives = 634/875 (72%), Gaps = 35/875 (4%)

Query: 1   MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSH 60
           MRAG C++QQ LTA+AAS VKQA+TLARRRGHAQVTPLHVA+ MLA+S+GLLR+ACL+SH
Sbjct: 1   MRAGVCSVQQVLTADAASXVKQAVTLARRRGHAQVTPLHVASVMLASSSGLLRSACLRSH 60

Query: 61  SHPLQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIEN 120
           SHPLQCKALELCFNVALNRLPAS+S+P+L  H   P++SNALVAAFKRAQAHQRR SIEN
Sbjct: 61  SHPLQCKALELCFNVALNRLPASSSSPLLAPHSSHPSLSNALVAAFKRAQAHQRRASIEN 120

Query: 121 QQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSS 180
           QQQP+LA+K+E+EQLIISIL DPSVSRVMREAGFSSTQ+++N+EQAVSL++CSQS P  S
Sbjct: 121 QQQPILALKVEIEQLIISILHDPSVSRVMREAGFSSTQLRTNIEQAVSLDVCSQS-PAVS 179

Query: 181 NKSKESN---VLVLSQTASATKVSKPRVSL----DPIRNEDVMYVIENLMSKRKRNFVVV 233
           + SKESN   +++ +  + ++   +  V+L    D  + EDV  +++   SKR+RN VVV
Sbjct: 180 SLSKESNNPPLILGTNVSQSSTFIQFGVTLNNPFDEAQEEDVKSLLDAFTSKRRRNTVVV 239

Query: 234 GECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVR 293
           GE LAS EGVVRG+++K E+GDVP  LR V+ + L + S +++++ EVEQ++ ++  L++
Sbjct: 240 GETLASAEGVVRGLMNKFERGDVPGDLRYVQFISLPLFSLKNLSK-EVEQKLVKLNCLLK 298

Query: 294 SCLGRGIVLNLGDLEW-AEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGI 352
           S + RG+VL LGDL+W +EF ++  E+ R Y   +EHIIME+G+++CGIG+  R WL+G 
Sbjct: 299 SYVCRGVVLYLGDLKWVSEFESNYGER-RNYCSPVEHIIMELGRMMCGIGDRGRMWLLGT 357

Query: 353 ATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLITTDSDLQSQSTSKKAESGVSWLL 412
           ATFQ+YMRCK+GHPSLET+W LHPLTIP GSL L L   DS+LQ +  SK +  G SW L
Sbjct: 358 ATFQTYMRCKAGHPSLETIWELHPLTIPVGSLGLGL-NLDSNLQGRFQSKASGDGTSWSL 416

Query: 413 FEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSD-------SPTSSLPAWLQQYKNEKK 465
            +    +K LTC  +CS  F+ E++S+  S  N +       S +SSLP+WLQ+   EK+
Sbjct: 417 LQS--GDKHLTCSTNCSDNFDKESQSIACSFRNGESTTTITTSTSSSLPSWLQK---EKR 471

Query: 466 ATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNF 525
             + ++ +   VRDLC KWNS C+S+HK+ + +E+ L FSS S  SSTS  SYDQ  PN 
Sbjct: 472 RKIMDDQECVQVRDLCNKWNSFCSSVHKKAHSTEKALNFSSPS-PSSTSISSYDQCSPNL 530

Query: 526 HKTHRDW-AVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQP--LSSNRNS 582
            + H  W A++EPK   +EH F  S    +    EP   ++I E ++   P  LS+  +S
Sbjct: 531 QQNHLSWPAIIEPKPPLKEHQFWISENVDE--GLEPKFSMHIAE-RNFPIPDLLSNPNSS 587

Query: 583 TPNSTSSSDIMEMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTM 642
             +++SS  I + E ++ FKELN+ENL  LCNALE++VPWQKD + +IA+T+L+CRSGT+
Sbjct: 588 PNSASSSEAIEDGEGLYGFKELNAENLRILCNALERRVPWQKDIIPEIASTILECRSGTL 647

Query: 643 RRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRAD 702
           R K K K   E KEETWL F GVD   KEKIA+E+A+LVFGS + F+SI LSS  STRAD
Sbjct: 648 RGKNKLKQR-EDKEETWLLFLGVDFQGKEKIAREIAKLVFGSXSKFISIGLSSLGSTRAD 706

Query: 703 STEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIV 762
           STED  +K++RDE   SYIE+FAEAV  NPHRVF IEDVEQ DY SQ G KR IESGRI 
Sbjct: 707 STEDFLSKQARDEPVGSYIEKFAEAVHENPHRVFFIEDVEQLDYSSQMGVKRGIESGRIQ 766

Query: 763 TSSGDEVSLGDAIVILSCESFSSRSRACSPPTK--QKSDGCEEEKGAAMEGTSPSVSLDL 820
            + G+  SL DAI+I SCESFSS SRA SPP    +  +  E+++   +E  SP VSLDL
Sbjct: 767 IAGGEAFSLEDAIIIFSCESFSSVSRASSPPPMGLKSEENEEKDRDNELEKRSPCVSLDL 826

Query: 821 NICIDDDSTEDQ-SIDDIGLLESVDKRIIFKIMEL 854
           N+  +D+    Q S+ D G+L+SVD++ IFKI EL
Sbjct: 827 NLSAEDNQEYGQNSVADTGVLDSVDRQXIFKIQEL 861

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225464404|ref|XP_002269046.1| PREDICTED: uncharacterized protein LOC100254987 [Vitis vinifera]

 Score =  863 bits (2230), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 479/868 (55%), Positives = 625/868 (72%), Gaps = 42/868 (4%)

Query: 1   MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSH 60
           MRAG C++QQ LTA+AAS+VKQA+TLARRRGHAQVTPLHVA+ MLA+S+GLLR+ACL+SH
Sbjct: 1   MRAGVCSVQQVLTADAASMVKQAVTLARRRGHAQVTPLHVASVMLASSSGLLRSACLRSH 60

Query: 61  SHPLQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIEN 120
           SHPLQCKALELCFNVALNRLPAS+S+P+L  H   P++SNALVAAFKRAQAHQRR SIEN
Sbjct: 61  SHPLQCKALELCFNVALNRLPASSSSPLLAPHSSHPSLSNALVAAFKRAQAHQRRASIEN 120

Query: 121 QQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSS 180
           QQQP+LA+K+E+EQLIISIL DPSVSRVMREAGFSSTQ+++N+EQAVSL++CSQS P  S
Sbjct: 121 QQQPILALKVEIEQLIISILHDPSVSRVMREAGFSSTQLRTNIEQAVSLDVCSQS-PAVS 179

Query: 181 NKSKESNVLVLSQTASATKVSKPRVSLDPIRNEDVMYVIENLMSKRKRNFVVVGECLASI 240
           + SKE              ++ P    D  + EDV  +++   SKR+RN VVVGE LAS 
Sbjct: 180 SLSKE------------ITLNNP---FDEAQEEDVKSLLDAFTSKRRRNTVVVGETLASA 224

Query: 241 EGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGI 300
           EGVVRG+++K E+GDVP  LR V+ + L + S +++++ EVEQ++ ++  L++S + RG+
Sbjct: 225 EGVVRGLMNKFERGDVPGDLRYVQFISLPLFSLKNLSKEEVEQKLVKLTCLLKSYVCRGV 284

Query: 301 VLNLGDLEW-AEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYM 359
           VL LGDL+W +EF ++  E+ R Y   +EHIIME+G+++CGIG+  R WL+G ATFQ+YM
Sbjct: 285 VLYLGDLKWVSEFESNYGER-RNYCSPVEHIIMELGRMMCGIGDRGRMWLLGTATFQTYM 343

Query: 360 RCKSGHPSLETLWSLHPLTIPAGSLSLSLITTDSDLQSQSTSKKAESGVSWLLFEGEEEN 419
           RCK+GHPSLET+W LHPLTIP GSL L L   DS+LQ +  SK +  G SW L +    +
Sbjct: 344 RCKAGHPSLETIWELHPLTIPVGSLGLGL-NLDSNLQGRFQSKASGDGTSWSLLQS--GD 400

Query: 420 KQLTCCADCSAKFEAEARSLQSSSCNSD-------SPTSSLPAWLQQYKNEKKATLSNND 472
           K LTC  +CS  F+ E++S+  S  N +       S +SSLP+WLQ+   EK+  + ++ 
Sbjct: 401 KHLTCSTNCSDNFDKESQSIACSFRNGESTTTITTSTSSSLPSWLQK---EKRRKIMDDQ 457

Query: 473 KDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHKTHRDW 532
           +   VRDLC KWNS C+S+HK+ + +E+ L FSS S  SSTS  SYDQ  PN  + H  W
Sbjct: 458 ECVQVRDLCNKWNSFCSSVHKKAHSTEKALNFSSPS-PSSTSISSYDQCSPNLQQNHLSW 516

Query: 533 -AVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQP--LSSNRNSTPNSTSS 589
            A++EPK   +EH F  S    +    EP   ++I E ++   P  LS+  +S  +++SS
Sbjct: 517 PAIIEPKPPLKEHQFWISENVDE--GLEPKFSMHIAE-RNFPIPDLLSNPNSSPNSASSS 573

Query: 590 SDIMEMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFK 649
             I + E ++ FKELN+ENL  LCNALE++VPWQKD + +IA+T+L+CRSGT+R K K K
Sbjct: 574 EAIEDGEGLYGFKELNAENLRILCNALERRVPWQKDIIPEIASTILECRSGTLRGKNKLK 633

Query: 650 DHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRN 709
              E KEETWL F GVD   K+KIA+E+A+LVFGS + F+SI LSS  STRADSTED  +
Sbjct: 634 -QREDKEETWLLFLGVDFQGKDKIAREIAKLVFGSQSKFISIGLSSLGSTRADSTEDFLS 692

Query: 710 KRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV 769
           K++RDE   SYIE+FAEAV  NPHRVF IEDVEQ DY SQ G KR IESGRI  + G+  
Sbjct: 693 KQARDEPVGSYIEKFAEAVHENPHRVFFIEDVEQLDYSSQMGVKRGIESGRIQIAGGEAF 752

Query: 770 SLGDAIVILSCESFSSRSRACSPPTK--QKSDGCEEEKGAAMEGTSPSVSLDLNICIDDD 827
           SL DAI+I SCESFSS SRA SPP    +  +  E+++   +E  SP VSLDLN+  +D+
Sbjct: 753 SLEDAIIIFSCESFSSVSRASSPPPMGLKSEENEEKDRDNELEKRSPCVSLDLNLSAEDN 812

Query: 828 STEDQ-SIDDIGLLESVDKRIIFKIMEL 854
               Q S+ D G+L+SVD++ IFKI EL
Sbjct: 813 QEYGQNSVADTGVLDSVDRQFIFKIQEL 840

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224113403|ref|XP_002316485.1| predicted protein [Populus trichocarpa] gi|222865525|gb|EEF02656.1| predicted protein [Populus trichocarpa]

 Score =  862 bits (2228), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 484/878 (55%), Positives = 618/878 (70%), Gaps = 49/878 (5%)

Query: 1   MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSH 60
           MRAG C++QQ LT EA S+VKQA+ LARRRGHAQVTPLHVA+TMLA+STGLLR ACLQSH
Sbjct: 1   MRAGICSVQQALTPEAVSLVKQAVGLARRRGHAQVTPLHVASTMLASSTGLLRRACLQSH 60

Query: 61  SHPLQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIEN 120
           SHPLQCKALELCFNVALNRLPASTS+ +LG H  +P++SNALVAAFKRAQAHQRRGSIEN
Sbjct: 61  SHPLQCKALELCFNVALNRLPASTSSALLGPHSSYPSLSNALVAAFKRAQAHQRRGSIEN 120

Query: 121 QQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSS 180
           QQQP+LA+KIE+EQLIISILDDPSVSRVM+EAGFSSTQVK+ VEQ VSLEIC QS+   S
Sbjct: 121 QQQPILALKIEIEQLIISILDDPSVSRVMKEAGFSSTQVKNKVEQTVSLEICPQSSLTVS 180

Query: 181 NKSKESNVLVLSQTASATKV------------SKPRVSLDPIRNEDVMYVIENLMSKRKR 228
            + KE   ++  Q  SA+              SKP   LD +RN+DVM V+  L+ K KR
Sbjct: 181 CQPKE---IIKPQVLSASVSQSLPFSQFGIIHSKP---LDQVRNDDVMSVLNTLVGK-KR 233

Query: 229 NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEI 288
           N ++ GECLA+ E VVRGV+DK E+G+V   LR V+   L + SFR +++ ++EQ++ E+
Sbjct: 234 NTIITGECLATAESVVRGVMDKFERGEVSGDLRSVRFKNLPLFSFRSLSKEDLEQKLMEL 293

Query: 289 KNLVRSCLGRGIVLNLGDLEW-AEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARF 347
           + +V+S +  G+VL LGDL+W A+F +S  EQ R YYC+ +HII+E+ +LV G  E  R 
Sbjct: 294 RCIVKSYISTGVVLYLGDLKWIADFWSSYGEQRRSYYCTADHIILELKRLVHGFSETGRL 353

Query: 348 WLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLITTDSDLQS-QSTSKKAES 406
           WLMGIATFQ+YM+CK+GHPSLET+W L+P+TIP GSL+LSL   DSD QS QS SK + +
Sbjct: 354 WLMGIATFQTYMKCKAGHPSLETMWELNPVTIPVGSLNLSL-KLDSDSQSHQSRSKASLN 412

Query: 407 GVSWLLFEGEEENKQLTCCADCSAKFEAEARSL-------QSSSCNSDSPTSSLPAWLQQ 459
           G SW L E   +N  LTC  D S  F  EA+SL       +S+S  + S  SSLP WLQQ
Sbjct: 413 GSSWPLLESRVDN-HLTCWTDYSVNFNKEAQSLVGRTHNKESTSSVTISNNSSLPLWLQQ 471

Query: 460 YKNEKKATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYD 519
            K  ++ T   ND++     LC K  S+  S+HKQ YY E+T+ F+S+ PS ++      
Sbjct: 472 CKETERNT--TNDQEY----LCNKGISLFGSVHKQSYYPEKTIKFASSPPSPNSFSSQER 525

Query: 520 QQYPNFHKTHRDWAVV-EPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSS 578
              P   +TH  W V+ E KQ  +E+    S E S++   E SLR  +P+  DL    +S
Sbjct: 526 NTDP--QQTHLSWPVIFEHKQFEKENQIWIS-ECSNEGY-ESSLR-NVPK-PDLLSNPNS 579

Query: 579 NRNSTPNSTSSSDIMEMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCR 638
           + NS  +S +  DI   E V  FKE N  +L +L + LEKKVPWQKD + +IA T+L+CR
Sbjct: 580 SPNSASSSEAMDDI---EGVQSFKEFNDYSLKNLRSGLEKKVPWQKDIIPEIATTILECR 636

Query: 639 SGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS 698
           SG  +RKGK  +H E K ETWLFF GVD + KEKIA+ELA+LVFGS +NFVSI LS+FSS
Sbjct: 637 SGMRKRKGKL-NHIEDKAETWLFFLGVDFEGKEKIARELAKLVFGSQSNFVSIGLSNFSS 695

Query: 699 TRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIES 758
           +RADS E+S+NKR+RDE  CSY+ER   A++ NPHRVF +EDV+Q D CSQKG K+AIE+
Sbjct: 696 SRADSIEESKNKRARDELGCSYLERLGLALNENPHRVFFMEDVDQVDNCSQKGIKQAIEN 755

Query: 759 GRIVTSSGDEVSLGDAIVILSCESFSSRSRACSPPTKQKSDGCEEEK--GAAMEGTSPSV 816
           G +    G++V L DAI+I SCESF S SR CSPP +QK+    E+K     ME  S  +
Sbjct: 756 GNVTLPDGEKVPLKDAIIIFSCESFCSVSRTCSPPRRQKTGDNHEDKEDEDVMEEKSLVL 815

Query: 817 SLDLNICIDDDSTEDQSIDDIGLLESVDKRIIFKIMEL 854
           SLDLNI   D+  +  S+ + G+LESVD++++FKI EL
Sbjct: 816 SLDLNISFGDNGDDQCSLAEYGILESVDRQVVFKIQEL 853

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	854
TAIR|locus:2079904	815	AT3G52490 [Arabidopsis thalian	0.480	0.503	0.5	2.6e-195
TAIR|locus:2172585	990	AT5G57710 [Arabidopsis thalian	0.857	0.739	0.335	1.7e-91
TAIR|locus:2123944	1017	AT4G29920 [Arabidopsis thalian	0.193	0.162	0.619	1.9e-90
TAIR|locus:2118806	924	AT4G30350 "AT4G30350" [Arabido	0.553	0.511	0.373	4.4e-88
TAIR|locus:2175589	1028	AT5G57130 "AT5G57130" [Arabido	0.166	0.138	0.563	3.9e-61
TAIR|locus:2045653	1002	AT2G29970 [Arabidopsis thalian	0.545	0.465	0.299	1.6e-49
TAIR|locus:2065074	910	AT2G40130 [Arabidopsis thalian	0.402	0.378	0.329	4.9e-40
TAIR|locus:2007412	979	AT1G07200 "AT1G07200" [Arabido	0.409	0.357	0.301	6e-34
TAIR|locus:2019667	911	HSP101 "heat shock protein 101	0.223	0.209	0.299	1.2e-16
UNIPROTKB|Q6F2Y7	912	CLPB1 "Chaperone protein ClpB1	0.223	0.209	0.285	3.8e-15

TAIR|locus:2079904 AT3G52490 [Arabidopsis thaliana (taxid:3702)]

 Score = 987 (352.5 bits), Expect = 2.6e-195, Sum P(2) = 2.6e-195
 Identities = 221/442 (50%), Positives = 278/442 (62%)

Query:   416 EEENKQLTCCADCSAKFEAEARSLQXXXXXXXXXXXXLPAWLQQYKNEKKATLSNNDKDS 475
             ++ + QL+ C +CS KFE+EAR L+            LPAWLQQYK E +   S+ D DS
Sbjct:   395 QQSSDQLSFCEECSVKFESEARFLKSSNSNVTTVA--LPAWLQQYKKENQN--SHTDSDS 450

Query:   476 GVRDLCKKWNSICNSIHKQPYYSERTLTFXXXXXXXXXXXXXYDQQYPNFH--KTHRDWA 533
              +++L  KWNSIC+SIHK+P  S +TLT                      H  +T+ DW 
Sbjct:   451 -IKELVVKWNSICDSIHKRP--SLKTLTLSSPTSSFSGST---QPSISTLHHLQTNGDWP 504

Query:   534 VVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEH-KDLKQPLXXXX--XXXXXXXXXX 590
             V+E       HH +  HE S        LRL+IPEH  + K  L                
Sbjct:   505 VIETNT--HRHHSVV-HETSH-------LRLFIPEHDSEQKTELVCSNPNSTMNSEASSS 554

Query:   591 DIMEMEYVH-KFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFK 649
             D ME+E+   +FKE+N+ENL +LC ALE KVPWQKD V ++A TVLKCRSG+  RK    
Sbjct:   555 DAMELEHASSRFKEMNAENLATLCAALESKVPWQKDLVPELAKTVLKCRSGSSTRK--IN 612

Query:   650 DHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRN 709
              + + KE+TW+FFQG+D DAKEKIA+ELA+LVFGS ++FVSI LSSFSSTR+DS ED RN
Sbjct:   613 GNEDKKEDTWMFFQGLDVDAKEKIARELAKLVFGSQDSFVSICLSSFSSTRSDSAEDLRN 672

Query:   710 KRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV 769
             KR RDEQS SYIERF+EAVS +P+RV L+ED+EQADY SQ GFKRA+E GR+  SSG+E 
Sbjct:   673 KRLRDEQSLSYIERFSEAVSLDPNRVILVEDIEQADYLSQVGFKRAVERGRVCNSSGEEA 732

Query:   770 SLGDAIVILSCESFSSRSRACSPPTKQKSDGCEEEKGAAMEGTSPSVSLDLNICXXXXXX 829
             SL DAIVILSCE F SRSRACSPP+ QKSDG ++ +    +  +  V+LDLN+       
Sbjct:   733 SLKDAIVILSCERFRSRSRACSPPSNQKSDGSDQPED---KNVATCVALDLNLSIDSAYV 789

Query:   830 XXXXX-XXXGLLESVDKRIIFK 850
                      GLLE+VD R  FK
Sbjct:   790 CEEESCDEIGLLEAVDARFHFK 811

GO:0005737 "cytoplasm" evidence=ISM

GO:0019538 "protein metabolic process" evidence=IEA

TAIR|locus:2172585 AT5G57710 [Arabidopsis thaliana (taxid:3702)]

 Score = 912 (326.1 bits), Expect = 1.7e-91, P = 1.7e-91
 Identities = 272/810 (33%), Positives = 402/810 (49%)

Query:     1 MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSH 60
             MRAG  TIQQ LT EAA+V+ Q++  A RR H Q TPLHVA T+LA+  G LR AC++SH
Sbjct:     1 MRAGLSTIQQTLTPEAATVLNQSIAEAARRNHGQTTPLHVAATLLASPAGFLRRACIRSH 60

Query:    61 ---SHPLQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGS 117
                SHPLQC+ALELCF+VAL RLP +T+TP  G     P ISNAL+AA KRAQAHQRRG 
Sbjct:    61 PNSSHPLQCRALELCFSVALERLPTATTTP--GND---PPISNALMAALKRAQAHQRRGC 115

Query:   118 IENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTP 177
              E QQQPLLAVK+ELEQLIISILDDPSVSRVMREA FSS  VK+ +EQ+++  +    TP
Sbjct:   116 PEQQQQPLLAVKVELEQLIISILDDPSVSRVMREASFSSPAVKATIEQSLNNSVTP--TP 173

Query:   178 VSSNKSKESNVLVLSQTASATKVS--KPRVSLDPI-------RNEDVMYVIENLMSKRKR 228
             + S  S   N          T+ S   PR+  +         +N+DV  V++ L   +K+
Sbjct:   174 IPSVSSVGLNFRP-GGGGPMTRNSYLNPRLQQNASSVQSGVSKNDDVERVMDILGRAKKK 232

Query:   229 NFVVVGECLASIEG-VVRGVIDKIEKGDVPE-ALRDVKCLPLS-ISSFRHMNRVEVEQRV 285
             N V+VG+   S  G V+R ++ KIE G+V   A+++ K + L  ISS + +   E++  +
Sbjct:   233 NPVLVGD---SEPGRVIREILKKIEVGEVGNLAVKNSKVVSLEEISSDKALRIKELDGLL 289

Query:   286 E-EIKNLVRSCLGRGIVLNLGDLEWAEFRASSSEQVRGYYCSIEHI-IMEIGKLVCGIGE 343
             +  +KN      G G++L+LGDL+W   + SS++        I    ++E+ +L+     
Sbjct:   290 QTRLKNS-DPIGGGGVILDLGDLKWLVEQPSSTQPPATVAVEIGRTAVVELRRLLEKF-- 346

Query:   344 NARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGXXXXXXXXXXXXXXXXXXXKK 403
               R W +G AT ++Y+RC+  HPS+ET W L  +++ A                      
Sbjct:   347 EGRLWFIGTATCETYLRCQVYHPSVETDWDLQAVSVAA--------KAPASGVFPRLANN 398

Query:   404 AESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQXXXXXXXXXXXXLPAWLQQYKNE 463
              ES      F     N+ L CC  C   +E E   +              P  L Q+  +
Sbjct:   399 LESFTPLKSFV--PANRTLKCCPQCLQSYERELAEIDSVSSPEVKSEVAQPKQLPQWLLK 456

Query:   464 KKATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFXXXXXXXXXXXXXYDQQYP 523
              K    +    + + ++ KKWN  C  +H  P +  +                 Y    P
Sbjct:   457 AKPV--DRLPQAKIEEVQKKWNDACVRLH--PSFHNKNERIVPIPVPITLTTSPYS---P 509

Query:   524 NFHKTHRDWAVVEPKQSWREH-HF-----LFSHEASDKST--SEPSLRLYIPEHKDLKQP 575
             N          ++P +  RE  H      L + +A  KS   S     L +   +D ++ 
Sbjct:   510 NMLLRQPLQPKLQPNRELRERVHLKPMSPLVAEQAKKKSPPGSPVQTDLVLGRAEDSEKA 569

Query:   576 LXXXXXXXXXXXXXXDIMEMEYVHKFKELNSEN------LTSLCNALEKKVPWQKDTVYD 629
                             +     +   ++ N  N         L   + +KV WQ D    
Sbjct:   570 GDVQVRDFLGCISSESVQNNNNISVLQKENLGNSLDIDLFKKLLKGMTEKVWWQNDAAAA 629

Query:   630 IANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFV 689
             +A TV +C+ G  +R+G        K + WL F G D   K K+   L+ LV+G+  N +
Sbjct:   630 VAATVSQCKLGNGKRRGVLS-----KGDVWLLFSGPDRVGKRKMVSALSSLVYGT--NPI 682

Query:   690 SIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQ 749
              I L S    R D+ + + + R +     + +++ AE V  +P  V L+ED+++AD   +
Sbjct:   683 MIQLGS----RQDAGDGNSSFRGK-----TALDKIAETVKRSPFSVILLEDIDEADMLVR 733

Query:   750 KGFKRAIESGRIVTSSGDEVSLGDAIVILS 779
                K+A++ GRI  S G E+SLG+ I +++
Sbjct:   734 GSIKQAMDRGRIRDSHGREISLGNVIFVMT 763

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0080167 "response to karrikin" evidence=IEP

TAIR|locus:2123944 AT4G29920 [Arabidopsis thaliana (taxid:3702)]

 Score = 511 (184.9 bits), Expect = 1.9e-90, Sum P(3) = 1.9e-90
 Identities = 114/184 (61%), Positives = 139/184 (75%)

Query:     1 MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAAS-TGLLRTACLQS 59
             MR G  T+ Q LT EAASV+KQ++TLARRRGH+QVTPLHVA+T+L +S + L R ACL+S
Sbjct:     1 MRTGAYTVHQTLTPEAASVLKQSLTLARRRGHSQVTPLHVASTLLTSSRSNLFRRACLKS 60

Query:    60 H---------SHP-LQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRA 109
             +         +HP L C+ALELCFNV+LNRLP + + P+     Q P++SNALVAA KRA
Sbjct:    61 NPFTALGRQMAHPSLHCRALELCFNVSLNRLPTNPN-PLF--QTQ-PSLSNALVAALKRA 116

Query:   110 QAHQRRGSIENQQ----QPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQ 165
             QAHQRRG +E QQ    QP LAVK+ELEQL++SILDDPSVSRVMREAG SS  VKSN+E 
Sbjct:   117 QAHQRRGCVEQQQSQQNQPFLAVKVELEQLVVSILDDPSVSRVMREAGLSSVSVKSNIED 176

Query:   166 AVSL 169
               S+
Sbjct:   177 DSSV 180

GO:0005737 "cytoplasm" evidence=ISM

GO:0019538 "protein metabolic process" evidence=IEA

GO:0009507 "chloroplast" evidence=IDA

TAIR|locus:2118806 AT4G30350 "AT4G30350" [Arabidopsis thaliana (taxid:3702)]

 Score = 693 (249.0 bits), Expect = 4.4e-88, Sum P(2) = 4.4e-88
 Identities = 200/536 (37%), Positives = 279/536 (52%)

Query:     1 MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSH 60
             MRA   TIQQ LT EAA+V+ Q++  A RR H   TPLHVA T+L++S+G LR AC++SH
Sbjct:     1 MRADLITIQQTLTPEAATVLNQSIAEATRRNHGHTTPLHVAATLLSSSSGYLRQACIKSH 60

Query:    61 ---SHPLQCKALELCFNVALNRLPA-STSTPMLGG-------HCQFPTISNALVAAFKRA 109
                SHPLQC+ALELCF+VAL RLP  ST+T              Q P +SNAL AA KRA
Sbjct:    61 PNSSHPLQCRALELCFSVALERLPTTSTTTTTTSSSSSSSPSQTQEPLLSNALTAALKRA 120

Query:   110 QAHQRRGSIENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSL 169
             QAHQRRG  E QQQPLLAVK+ELEQLIISILDDPSVSRVMREA FSS  VKS +EQ++  
Sbjct:   121 QAHQRRGCPEQQQQPLLAVKVELEQLIISILDDPSVSRVMREASFSSPAVKSAIEQSLIG 180

Query:   170 EICSQSTPVSSNKSKESNVLVLSQTASATKVSK-----PRVSLDPI---------RNEDV 215
                S S    S      + +     +    V++     PR+    +         R ++ 
Sbjct:   181 NSVSNSRQTGSPGIINPSAIGFGYRSVPAPVNRNLYLNPRLQQPGVGMQSGMMIQRTDEA 240

Query:   216 MYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPE-ALRDVKCLPLSISSFR 274
               VIE ++  RKRN V+VG+    I  +V+ +++KIE G+  + ALR+ + + L      
Sbjct:   241 KRVIEIMIRTRKRNPVLVGDSEPHI--LVKEILEKIENGEFSDGALRNFQVIRLEKELVS 298

Query:   275 HMNRVEVEQRVEEIKNLVRSCLGRG-IVLNLGDLEW-AEFRASSSEQVRGYYCSIEHIIM 332
                  ++  R+ EI  LV + +G G +VL+LGDL+W  E  A++   V           +
Sbjct:   299 -----QLATRLGEISGLVETRIGGGGVVLDLGDLKWLVEHPAANGGAV-----------V 342

Query:   333 EIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGXXXXXXXXXX 392
             E+ KL+       R   +G AT ++Y+RC+  +PS+E  W L  + I A           
Sbjct:   343 EMRKLLERY--KGRLCFIGTATCETYLRCQVYYPSMENDWDLQAIPIAAKSSLPAIFPRL 400

Query:   393 XXXXXXXXXKKAESGVSWLLFEGEEENK----QLTCCADCSAKFEAEARSLQXXXXXXXX 448
                        + + +S          +    +++CC+ C   +E +   ++        
Sbjct:   401 GSNNNNNAMLLSNNIISIESISPTRSFQIPMSKMSCCSRCLQSYENDVAKVEKDLTGDNR 460

Query:   449 XXXXLPAWLQQYK----NEKKATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSER 500
                 LP WLQ  K     +KK T     KD  + +L KKWN +C  +H     SER
Sbjct:   461 SV--LPQWLQNAKANDDGDKKLT-----KDQQIVELQKKWNDLCLRLHPNQSVSER 509

GO:0003674 "molecular_function" evidence=ND

GO:0005737 "cytoplasm" evidence=ISM

GO:0007623 "circadian rhythm" evidence=IEP

TAIR|locus:2175589 AT5G57130 "AT5G57130" [Arabidopsis thaliana (taxid:3702)]

 Score = 352 (129.0 bits), Expect = 3.9e-61, Sum P(3) = 3.9e-61
 Identities = 89/158 (56%), Positives = 104/158 (65%)

Query:    17 ASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVA 76
             A+ +  + T   RR   +  P    N   A S   L+     + +HPLQC+ALELCFNVA
Sbjct:    41 AATLLSSRTSLLRRACIKSHPGFSTNYQFAPSR--LQHHHHHNQNHPLQCRALELCFNVA 98

Query:    77 LNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQ----P------LL 126
             LNRLP +   PM  G    P+++NALVAA KRAQAHQRRG IE QQQ    P      LL
Sbjct:    99 LNRLP-TVPGPMFHGQ---PSLANALVAALKRAQAHQRRGCIEQQQQTQTHPQTQQTQLL 154

Query:   127 AVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVE 164
             AVK+ELEQL+ISILDDPSVSRVMREAGF+ST VKS VE
Sbjct:   155 AVKVELEQLVISILDDPSVSRVMREAGFNSTAVKSCVE 192

GO:0005575 "cellular_component" evidence=ND

GO:0019538 "protein metabolic process" evidence=IEA

GO:0009855 "determination of bilateral symmetry" evidence=RCA

GO:0009887 "organ morphogenesis" evidence=RCA

GO:0009944 "polarity specification of adaxial/abaxial axis" evidence=RCA

GO:0010014 "meristem initiation" evidence=RCA

GO:0010051 "xylem and phloem pattern formation" evidence=RCA

GO:0010075 "regulation of meristem growth" evidence=RCA

GO:0048439 "flower morphogenesis" evidence=RCA

GO:0048519 "negative regulation of biological process" evidence=RCA

TAIR|locus:2045653 AT2G29970 [Arabidopsis thaliana (taxid:3702)]

 Score = 433 (157.5 bits), Expect = 1.6e-49, Sum P(2) = 1.6e-49
 Identities = 155/518 (29%), Positives = 252/518 (48%)

Query:     7 TIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQ--SHSHP- 63
             T +Q LT E A  +  A+++ARRR HAQ T LH  + +L   + +LR  C+   +H+ P 
Sbjct:     7 TARQCLTEETARALDDAVSVARRRSHAQTTSLHAVSGLLTMPSSILREVCISRAAHNTPY 66

Query:    64 ---LQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRG---- 116
                LQ +ALELC  V+L+RLP+S STP      + P +SN+L+AA KR+QA QRR     
Sbjct:    67 SSRLQFRALELCVGVSLDRLPSSKSTPTTTVE-EDPPVSNSLMAAIKRSQATQRRHPETY 125

Query:   117 ---SIE--NQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNV-EQAVSLE 170
                 I   N  +    +K+EL+  I+SILDDP VSRV  EAGF ST +K +V    V+ +
Sbjct:   126 HLHQIHGNNNTETTSVLKVELKYFILSILDDPIVSRVFGEAGFRSTDIKLDVLHPPVTSQ 185

Query:   171 ICSQSTPVSSNKSKESNVLVLSQTASA-TKVSKPRVSLDPIRNEDVMYVIENLMSKRKRN 229
               S+ T  S ++     +  L ++ S   +   P   LD    E+   + E L  K K+N
Sbjct:   186 FSSRFT--SRSRIPPLFLCNLPESDSGRVRFGFPFGDLD----ENCRRIGEVLARKDKKN 239

Query:   230 FVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVE-QRVE-E 287
              ++VG C   +E + +   D I +G        ++   LS+ S + ++ V V+  R++ +
Sbjct:   240 PLLVGVC--GVEAL-KTFTDSINRGKF--GFLPLEISGLSVVSIK-ISEVLVDGSRIDIK 293

Query:   288 IKNLVRSCLGRGIVLNLGDLEWAEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARF 347
               +L R  L  G+VLNLG+L+     AS    V      IE  ++++  L+    E  + 
Sbjct:   294 FDDLGR--LKSGMVLNLGELK---VLASDVFSVD----VIEKFVLKLADLLKLHRE--KL 342

Query:   348 WLMG-IATFQSYMRCKSGHPSLETLWSLHPLTIPAGXXXXXXXXXXXXXXXXXXXKKAES 406
             W +G +++ ++Y++     P+++  W+LH L I +                      + +
Sbjct:   343 WFIGSVSSNETYLKLIERFPTIDKDWNLHLLPITSSSQGLYPKSSLMGSFVPFGGFFSST 402

Query:   407 GVSWLLFEGEEENKQLTCCADCSAKFEAEARSL-QXXXXXXXXXXXXLPAWLQQYKNE-K 464
                + +      N+ L  C  C+ K+E E  +  +            LP+WL+  ++E +
Sbjct:   403 S-DFRIPSSSSMNQTLPRCHLCNEKYEQEVTAFAKSGSMIDDQCSEKLPSWLRNVEHEHE 461

Query:   465 KATLSNNDKD-----SGVRDLCKKWNSICNSIHKQPYY 497
             K  L     D     S +  L KKW+ IC  IH+ P +
Sbjct:   462 KGNLGKVKDDPNVLASRIPALQKKWDDICQRIHQTPAF 499

GO:0005737 "cytoplasm" evidence=ISM

TAIR|locus:2065074 AT2G40130 [Arabidopsis thaliana (taxid:3702)]

 Score = 362 (132.5 bits), Expect = 4.9e-40, Sum P(2) = 4.9e-40
 Identities = 132/401 (32%), Positives = 202/401 (50%)

Query:     9 QQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQ----SHSHPL 64
             +Q LTAEA+  +++A+ +ARRRGH+Q T LH  + +L+  T +LR AC +    ++S  L
Sbjct:     9 KQCLTAEASYALEEAVNVARRRGHSQTTSLHAISALLSLPTSVLRDACARVRNSAYSPRL 68

Query:    65 QCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRR--------- 115
             Q KAL+LC +V+L+R+    S   LG     P +SN+L+AA KR+QAHQRR         
Sbjct:    69 QFKALDLCLSVSLDRIQ---SGHQLGSD-DSPPVSNSLMAAIKRSQAHQRRLPENFRIYQ 124

Query:   116 -GSIENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVS--LEIC 172
               S    Q  L  VK+EL QLI+SILDDP VSRV  EAGF S+++K ++ + V   L   
Sbjct:   125 EMSQSQNQNSLSCVKVELRQLILSILDDPVVSRVFGEAGFRSSELKLSIIRPVPHLLRYS 184

Query:   173 SQSTPVSSNKS--KESNVLVLSQTASATKVSKPRVSLDPIRNEDVMYV-IENLMSKRK-R 228
             SQ      N +   E N +    T        P ++     N D+ Y  I  + +K K R
Sbjct:   185 SQQPLFLCNLTGNPEPNPVRWGFTV-------PSLNF----NGDLDYRRISAVFTKDKGR 233

Query:   229 NFVVVGECLASIEGVVRGVIDKIEKGD-----VPEALRDVKCLPLS--ISSFRHM--NRV 279
             N ++VG    S  GV+   ++ +EK       +P  L  +  + +   IS    +  ++ 
Sbjct:   234 NPLLVG---VSAYGVLTSYLNSLEKNQTDGMILPTKLHGLTAVNIGSEISDQISVKFDKT 290

Query:   280 EVEQRVEEIKNLVRSCLGRGIVLNLGDLEWAEFRASSSEQVRGYYCSIEHIIMEIGKLVC 339
               + R  ++  L     G G++L+ GDL     R  ++ +  G   +  +I+  I +L+ 
Sbjct:   291 YTDTRFHDLGKLAEQGSGPGLLLHYGDL-----RVFTNGE--GNVPAANYIVNRISELLR 343

Query:   340 GIGENARFWLMGIATFQS-YMRCKSGHPSLETLWSLHPLTI 379
               G   R WL+G  T    Y +     P++E  W L  LTI
Sbjct:   344 RHGR--RVWLIGATTSNEVYEKMMRRFPNVEKDWDLQLLTI 382

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2007412 AT1G07200 "AT1G07200" [Arabidopsis thaliana (taxid:3702)]

 Score = 331 (121.6 bits), Expect = 6.0e-34, Sum P(2) = 6.0e-34
 Identities = 122/404 (30%), Positives = 198/404 (49%)

Query:     7 TIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQS------H 60
             T ++ LT EAA  +  A+ +ARRR HAQ T LH  + +LA  + +LR  C+        +
Sbjct:     7 TARECLTEEAARALDDAVVVARRRSHAQTTSLHAVSALLAMPSSILREVCVSRAARSVPY 66

Query:    61 SHPLQCKALELCFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIEN 120
             S  LQ +ALELC  V+L+RLP+S S P      + P +SN+L+AA KR+QA+QRR     
Sbjct:    67 SSRLQFRALELCVGVSLDRLPSSKS-PATE---EDPPVSNSLMAAIKRSQANQRRHPESY 122

Query:   121 QQQPLLA------------VKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVS 168
               Q + A            +K+EL+  I+SILDDP V+RV  EAGF S+++K +V     
Sbjct:   123 HLQQIHASNNGGGGCQTTVLKVELKYFILSILDDPIVNRVFGEAGFRSSEIKLDV----- 177

Query:   169 LEICSQSTPVSSNKSK-ESNVLVLSQTASATKVSKPRVSLDPIRNEDVMYVIENLMSKRK 227
               +    T +SS  S+     L L    ++    +   S     +E+   + E L  K K
Sbjct:   178 --LHPPVTQLSSRFSRGRCPPLFLCNLPNSDPNREFPFSGSSGFDENSRRIGEVLGRKDK 235

Query:   228 RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPL-----SISSFR---HMNRV 279
             +N +++G C       ++   D I  G +     D+  L L      IS        N  
Sbjct:   236 KNPLLIGNCANE---ALKTFTDSINSGKLGFLQMDISGLSLISIEKEISEILADGSKNEE 292

Query:   280 EVEQRVEEIKNLVRSCLGR-GIVLNLGDLEWAEFRASSSEQVRGYYCSIEHIIMEIGKLV 338
             E+  +V+++   V     + GIVLNLG+L+     A+++         +E ++ ++  L+
Sbjct:   293 EIRMKVDDLGRTVEQSGSKSGIVLNLGELKVLTSEANAA---------LEILVSKLSDLL 343

Query:   339 CGIGENARFWLMG-IATFQSYMRCKSGHPSLETLWSLHPLTIPA 381
                 E+ +   +G +++ ++Y +     P++E  W LH L I A
Sbjct:   344 KH--ESKQLSFIGCVSSNETYTKLIDRFPTIEKDWDLHVLPITA 385

GO:0005524 "ATP binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2019667 HSP101 "heat shock protein 101" [Arabidopsis thaliana (taxid:3702)]

 Score = 184 (69.8 bits), Expect = 1.2e-16, Sum P(2) = 1.2e-16
 Identities = 64/214 (29%), Positives = 109/214 (50%)

Query:    99 SNALVAAFKRAQAHQR-RGSIENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSST 157
             S++L+   +RAQA Q+ RG         LAV    +QLI+ +L+D  +  ++ E G ++ 
Sbjct:    86 SSSLIKVIRRAQAAQKSRGDTH------LAV----DQLIMGLLEDSQIRDLLNEVGVATA 135

Query:   158 QVKSNVEQAVSLEICSQSTPVSSNKSKESNVLVLSQTASATKVSKPRVSLDPI--RNEDV 215
             +VKS VE+    E       V S  S ++N   L +T     V +    LDP+  R+E++
Sbjct:   136 RVKSEVEKLRGKE----GKKVES-ASGDTNFQAL-KTYGRDLVEQAG-KLDPVIGRDEEI 188

Query:   216 MYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSF-- 273
               V+  L  + K N V++GE       VV G+  +I KGDVP +L DV+ + L + +   
Sbjct:   189 RRVVRILSRRTKNNPVLIGEPGVGKTAVVEGLAQRIVKGDVPNSLTDVRLISLDMGALVA 248

Query:   274 RHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDL 307
                 R E E+R++ +   V    G+ ++L + ++
Sbjct:   249 GAKYRGEFEERLKSVLKEVEDAEGK-VILFIDEI 281

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0009408 "response to heat" evidence=IEP;IGI;RCA;IMP

GO:0043335 "protein unfolding" evidence=IMP

GO:0009644 "response to high light intensity" evidence=IEP;RCA

GO:0042542 "response to hydrogen peroxide" evidence=IEP;RCA

GO:0005515 "protein binding" evidence=IPI

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0006457 "protein folding" evidence=RCA

GO:0010286 "heat acclimation" evidence=RCA

GO:0034976 "response to endoplasmic reticulum stress" evidence=RCA

GO:0045727 "positive regulation of translation" evidence=IMP

UNIPROTKB|Q6F2Y7 CLPB1 "Chaperone protein ClpB1" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 174 (66.3 bits), Expect = 3.8e-15, Sum P(2) = 3.8e-15
 Identities = 61/214 (28%), Positives = 109/214 (50%)

Query:    99 SNALVAAFKRAQ-AHQRRGSIENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSST 157
             S AL+   +RAQ A ++RG         LAV    +QL++ +L+D  +S  ++EAG S+ 
Sbjct:    88 STALIKVIRRAQSAQKKRGDSH------LAV----DQLLLGLLEDSLISDCLKEAGVSAA 137

Query:   158 QVKSNVEQAVSLEICSQSTPVSSNKSKESNVLVLSQTASATKVSKPRVSLDPI--RNEDV 215
             +V++ +E+        +   V S  S ++N   L +T     V +    LDP+  R+E++
Sbjct:   138 RVRAELEKLRG----GEGRKVES-ASGDTNFQAL-KTYGRDLVEQAG-KLDPVIGRDEEI 190

Query:   216 MYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSF-- 273
               V+  L  + K N V++GE       VV G+  +I +GDVP  L DV+ + L + +   
Sbjct:   191 RRVVRILSRRTKNNPVLIGEPGVGKTAVVEGLAQRIVRGDVPSNLLDVRLIALDMGALVA 250

Query:   274 RHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDL 307
                 R E E+R++ +   V    G+ ++L + ++
Sbjct:   251 GAKYRGEFEERLKAVLKEVEEAEGK-VILFIDEI 283

GO:0034605 "cellular response to heat" evidence=IGI

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.VI.2232.1 hypothetical protein (841 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	854
COG0542	786	COG0542, clpA, ATP-binding subunits of Clp proteas	3e-15
TIGR03346	852	TIGR03346, chaperone_ClpB, ATP-dependent chaperone	5e-14
TIGR03345	852	TIGR03345, VI_ClpV1, type VI secretion ATPase, Clp	6e-09
PRK10865	857	PRK10865, PRK10865, protein disaggregation chapero	3e-06
COG0542	786	COG0542, clpA, ATP-binding subunits of Clp proteas	9e-06
CHL00095	821	CHL00095, clpC, Clp protease ATP binding subunit	4e-05

>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

 Score = 80.0 bits (198), Expect = 3e-15
 Identities = 63/270 (23%), Positives = 106/270 (39%), Gaps = 44/270 (16%)

Query: 12  LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALEL 71
           LT  A   ++ A  LAR R H  VTP H+   +L    G             +    L  
Sbjct: 2   LTERAQKALELAQELARMRRHEYVTPEHLLLALLDQPKGDELLNLC-----GIDLDKLRQ 56

Query: 72  CFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIE 131
                +++LP    +         P +S  L    +RA             Q L    + 
Sbjct: 57  ELEEFIDKLPKVLGS---------PYLSPRLKRVLERAWLL---------AQSLGDEYVS 98

Query: 132 LEQLIISILDDPS--VSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKESNVL 189
            E L++++L++P    + ++++ G +   V+  +E+                 + E    
Sbjct: 99  TEHLLLALLNEPESVAAYILKKLGVTRKDVEELIEELRGGNEVDSKNAEEDQDALEKYTR 158

Query: 190 VLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGV---- 243
            L++ A   K       LDP+  R+E++   I+ L  + K N V+VGE      GV    
Sbjct: 159 DLTELAREGK-------LDPVIGRDEEIRRTIQILSRRTKNNPVLVGE-----PGVGKTA 206

Query: 244 -VRGVIDKIEKGDVPEALRDVKCLPLSISS 272
            V G+  +I  GDVPE+L+D +   L + S
Sbjct: 207 IVEGLAQRIVNGDVPESLKDKRIYSLDLGS 236

Length = 786

>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB

 Score = 75.8 bits (187), Expect = 5e-14
 Identities = 62/262 (23%), Positives = 111/262 (42%), Gaps = 32/262 (12%)

Query: 12  LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALEL 71
            T +    ++ A +LA  R H Q+ P H+   +L    GL R   LQ     +   AL  
Sbjct: 1   FTEKFQEALQAAQSLALGRDHQQIEPEHLLKALLDQEGGLAR-RLLQKAGVNVG--ALRQ 57

Query: 72  CFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRA--QAHQRRGSIENQQQPLLAVK 129
                L +LP       + G      +S  L      A   A +R               
Sbjct: 58  ALEKELEKLPK------VSGPGGQVYLSPELNRLLNLAEKLAQKRGDEF----------- 100

Query: 130 IELEQLIISILDDPS-VSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKESNV 188
           I  E L++++LDD   + ++++EAG ++  +++ +      +  + +      ++ E   
Sbjct: 101 ISSEHLLLALLDDKGTLGKLLKEAGATADALEAAINAVRGGQKVTSANAEDQYEALEKYA 160

Query: 189 LVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRG 246
             L++ A   K       LDP+  R+E++   I+ L  + K N V++GE       +V G
Sbjct: 161 RDLTERAREGK-------LDPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEG 213

Query: 247 VIDKIEKGDVPEALRDVKCLPL 268
           +  +I  GDVPE+L++ + L L
Sbjct: 214 LAQRIVNGDVPESLKNKRLLAL 235

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 [Protein fate, Protein folding and stabilization]. Length = 852

>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family

 Score = 59.2 bits (144), Expect = 6e-09
 Identities = 63/273 (23%), Positives = 111/273 (40%), Gaps = 36/273 (13%)

Query: 12  LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALEL 71
           L   +   ++QA  L   RGH +V   H    +L      L            + KA +L
Sbjct: 1   LNPTSRRALEQAAALCVARGHPEVELEHWLLALLDQPDSDLAAILRHFGVDLGRLKA-DL 59

Query: 72  CFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIE 131
               AL++LP         G+ + P  S  LV   + A       S+E         +I 
Sbjct: 60  --ARALDKLPR--------GNTRTPVFSPHLVELLQEAWLL---ASLELGDG-----RIR 101

Query: 132 LEQLIISILDDPSVSRVMREAGFSSTQVKSNVE---QAVSLEICSQSTPVSSNKSKESNV 188
              L++++L DP + R++     S    K + E   +A+   +   S   S+  +     
Sbjct: 102 SGHLLLALLTDPELRRLLGSI--SPELAKIDREALREALP-ALVEGSAEASAAAADAGPA 158

Query: 189 LVLSQTASATKVSKPRVSL---------DPI--RNEDVMYVIENLMSKRKRNFVVVGECL 237
              +  A  + + +    L         DP+  R++++  +I+ L+ +R+ N ++ GE  
Sbjct: 159 AAAAGAAGTSALDQYTTDLTAQAREGKIDPVLGRDDEIRQMIDILLRRRQNNPILTGEAG 218

Query: 238 ASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSI 270
                VV G+  +I  GDVP ALR+V+ L L +
Sbjct: 219 VGKTAVVEGLALRIAAGDVPPALRNVRLLSLDL 251

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 [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis]. Length = 852

>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional

 Score = 51.0 bits (122), Expect = 3e-06
 Identities = 66/274 (24%), Positives = 118/274 (43%), Gaps = 32/274 (11%)

Query: 23  AMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPA 82
           A +LA    +  + PLH+ + +L    G +R   L S    +    L    N AL+RLP 
Sbjct: 17  AQSLALGHDNQFIEPLHLMSALLNQEGGSVR-PLLTSAG--INAGQLRTDINQALSRLPQ 73

Query: 83  STSTPMLGGHCQFPTISNALVAAFKRA-QAHQRRGSIENQQQPLLAVKIELEQLIISILD 141
              T   GG  Q    S  LV       +  Q+RG             I  E  +++ L+
Sbjct: 74  VEGT---GGDVQ---PSQDLVRVLNLCDKLAQKRGD----------NFISSELFVLAALE 117

Query: 142 DP-SVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKESNVLVLSQTASATKV 200
              +++ +++ AG ++  +   +EQ    E  +        ++ +   + L++ A   K 
Sbjct: 118 SRGTLADILKAAGATTANITQAIEQMRGGESVNDQGAEDQRQALKKYTIDLTERAEQGK- 176

Query: 201 SKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPE 258
                 LDP+  R+E++   I+ L  + K N V++GE       +V G+  +I  G+VPE
Sbjct: 177 ------LDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPE 230

Query: 259 ALRDVKCLPLSISSF--RHMNRVEVEQRVEEIKN 290
            L+  + L L + +       R E E+R++ + N
Sbjct: 231 GLKGRRVLALDMGALVAGAKYRGEFEERLKGVLN 264

Length = 857

>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

 Score = 49.2 bits (118), Expect = 9e-06
 Identities = 43/187 (22%), Positives = 78/187 (41%), Gaps = 22/187 (11%)

Query: 598 VHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEE 657
           V K  E   E L +L   L+K+V  Q + V  +++ + + R+G         D +  +  
Sbjct: 471 VAKLLEDEKEKLLNLERRLKKRVIGQDEAVEAVSDAIRRARAG-------LGDPN--RPI 521

Query: 658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQS 717
               F G     K ++AK LA  +FG     + I +S +    +     SR   +     
Sbjct: 522 GSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHS----VSRLIGAPP--- 574

Query: 718 CSYI---ER--FAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLG 772
             Y+   E     EAV   P+ V L++++E+A         + ++ GR+    G  V   
Sbjct: 575 -GYVGYEEGGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVLDDGRLTDGQGRTVDFR 633

Query: 773 DAIVILS 779
           + I+I++
Sbjct: 634 NTIIIMT 640

Length = 786

>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit

 Score = 47.0 bits (112), Expect = 4e-05
 Identities = 25/93 (26%), Positives = 46/93 (49%), Gaps = 4/93 (4%)

Query: 206 SLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDV 263
           +LDP+  R +++  VI+ L  + K N +++GE       +  G+  +I   DVP+ L D 
Sbjct: 177 NLDPVIGREKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDK 236

Query: 264 KCLPLSISSF--RHMNRVEVEQRVEEIKNLVRS 294
             + L I         R E E+R++ I + ++ 
Sbjct: 237 LVITLDIGLLLAGTKYRGEFEERLKRIFDEIQE 269

Length = 821

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	854
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	100.0
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	100.0
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	100.0
CHL00095	821	clpC Clp protease ATP binding subunit	100.0
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	100.0
PRK10865	857	protein disaggregation chaperone; Provisional	100.0
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	100.0
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	100.0
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	99.89
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.89
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.77
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	99.75
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.75
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.64
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	99.56
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.48
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.41
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.41
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.37
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	99.37
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	99.36
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	99.35
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.33
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.32
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.31
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	99.31
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.29
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.27
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.26
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	99.26
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.25
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.24
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.24
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	99.22
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	99.22
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.22
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	99.21
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.2
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.2
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.19
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.18
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	99.18
CHL00181	287	cbbX CbbX; Provisional	99.18
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.17
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.17
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.16
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.16
PRK13531	498	regulatory ATPase RavA; Provisional	99.15
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.15
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.15
PLN03025	319	replication factor C subunit; Provisional	99.14
PF00004	132	AAA: ATPase family associated with various cellula	99.14
) 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	99.14
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.14
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	99.13
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.13
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	99.13
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	99.12
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.12
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	99.12
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.11
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.1
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.1
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.09
CHL00195	489	ycf46 Ycf46; Provisional	99.09
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.09
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.09
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.07
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.07
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	99.06
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	99.06
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.06
CHL00181	287	cbbX CbbX; Provisional	99.05
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.05
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	99.05
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.04
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	99.04
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.04
PRK07471	365	DNA polymerase III subunit delta'; Validated	99.04
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.04
CHL00176	638	ftsH cell division protein; Validated	99.03
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.02
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.02
COG0714	329	MoxR-like ATPases [General function prediction onl	99.01
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.01
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	99.01
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	99.0
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.0
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.99
PRK07399	314	DNA polymerase III subunit delta'; Validated	98.99
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	98.99
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	98.99
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.98
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	98.97
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	98.97
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	98.97
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	98.96
PRK06871	325	DNA polymerase III subunit delta'; Validated	98.96
PRK09112	351	DNA polymerase III subunit delta'; Validated	98.96
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	98.95
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	98.95
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	98.94
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	98.94
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	98.93
PRK08058	329	DNA polymerase III subunit delta'; Validated	98.93
PRK08769	319	DNA polymerase III subunit delta'; Validated	98.93
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	98.93
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	98.93
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	98.92
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	98.92
PRK06090	319	DNA polymerase III subunit delta'; Validated	98.91
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	98.91
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.91
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	98.91
PF07726	131	AAA_3: ATPase family associated with various cellu	98.9
PRK07993	334	DNA polymerase III subunit delta'; Validated	98.9
CHL00206	2281	ycf2 Ycf2; Provisional	98.89
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	98.89
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	98.88
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	98.88
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	98.88
PF00004	132	AAA: ATPase family associated with various cellula	98.87
PRK05707	328	DNA polymerase III subunit delta'; Validated	98.87
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	98.87
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	98.83
PRK03992	389	proteasome-activating nucleotidase; Provisional	98.83
PRK12402	337	replication factor C small subunit 2; Reviewed	98.82
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	98.82
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	98.82
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	98.81
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	98.81
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	98.8
PRK13342	413	recombination factor protein RarA; Reviewed	98.78
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.78
PRK05022	509	anaerobic nitric oxide reductase transcription reg	98.77
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	98.77
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	98.77
COG2204	464	AtoC Response regulator containing CheY-like recei	98.77
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	98.76
PRK06964	342	DNA polymerase III subunit delta'; Validated	98.76
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	98.75
KOG2028	554	consensus ATPase related to the helicase subunit o	98.74
CHL00195	489	ycf46 Ycf46; Provisional	98.74
PRK11608	326	pspF phage shock protein operon transcriptional ac	98.74
PRK15424	538	propionate catabolism operon regulatory protein Pr	98.73
PHA02244	383	ATPase-like protein	98.73
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	98.72
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.72
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.72
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	98.7
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	98.7
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	98.69
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	98.68
PHA02544	316	44 clamp loader, small subunit; Provisional	98.68
KOG2028	554	consensus ATPase related to the helicase subunit o	98.68
PRK04195	482	replication factor C large subunit; Provisional	98.67
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	98.67
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	98.67
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	98.67
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	98.67
PF02861	53	Clp_N: Clp amino terminal domain; InterPro: IPR004	98.66
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.65
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	98.65
PRK08699	325	DNA polymerase III subunit delta'; Validated	98.64
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	98.63
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	98.62
COG1221	403	PspF Transcriptional regulators containing an AAA-	98.62
PRK00440	319	rfc replication factor C small subunit; Reviewed	98.62
PRK05917	290	DNA polymerase III subunit delta'; Validated	98.62
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	98.61
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	98.59
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	98.59
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	98.59
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	98.54
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	98.53
PRK13342	413	recombination factor protein RarA; Reviewed	98.53
PRK07276	290	DNA polymerase III subunit delta'; Validated	98.53
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	98.52
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.52
PRK13341	725	recombination factor protein RarA/unknown domain f	98.52
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	98.51
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.51
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	98.51
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	98.5
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.49
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	98.49
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	98.47
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	98.46
CHL00176	638	ftsH cell division protein; Validated	98.46
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.44
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	98.44
PRK05818	261	DNA polymerase III subunit delta'; Validated	98.44
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.44
smart00382	148	AAA ATPases associated with a variety of cellular	98.42
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.4
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	98.4
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	98.4
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	98.4
PRK04132	846	replication factor C small subunit; Provisional	98.39
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	98.37
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	98.37
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	98.36
PRK13341	725	recombination factor protein RarA/unknown domain f	98.35
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	98.35
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	98.35
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.34
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	98.33
PRK10865	857	protein disaggregation chaperone; Provisional	98.31
PRK15115	444	response regulator GlrR; Provisional	98.29
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	98.28
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	98.28
smart00350	509	MCM minichromosome maintenance proteins.	98.28
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	98.27
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	98.26
PRK08903	227	DnaA regulatory inactivator Hda; Validated	98.26
PRK06893	229	DNA replication initiation factor; Validated	98.25
CHL00095	821	clpC Clp protease ATP binding subunit	98.23
PRK08084	235	DNA replication initiation factor; Provisional	98.19
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	98.19
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.19
PRK12377	248	putative replication protein; Provisional	98.19
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.19
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	98.18
PRK08084	235	DNA replication initiation factor; Provisional	98.18
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.16
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	98.15
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	98.15
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	98.15
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.14
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	98.14
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	98.13
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	98.12
CHL00206	2281	ycf2 Ycf2; Provisional	98.12
PRK08116	268	hypothetical protein; Validated	98.1
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	98.08
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	98.08
PRK07132	299	DNA polymerase III subunit delta'; Validated	98.07
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	98.07
PRK10365	441	transcriptional regulatory protein ZraR; Provision	98.07
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	98.05
PRK09862	506	putative ATP-dependent protease; Provisional	98.05
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.05
PHA02544	316	44 clamp loader, small subunit; Provisional	98.03
smart00382	148	AAA ATPases associated with a variety of cellular	98.03
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.03
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	98.03
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	98.01
PRK06893	229	DNA replication initiation factor; Validated	98.01
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	98.0
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.0
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	97.99
PF13173	128	AAA_14: AAA domain	97.98
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	97.97
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	97.97
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	97.96
PRK08727	233	hypothetical protein; Validated	97.96
PRK05642	234	DNA replication initiation factor; Validated	97.96
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	97.94
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	97.93
PRK12402	337	replication factor C small subunit 2; Reviewed	97.93
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	97.92
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.92
PRK06526	254	transposase; Provisional	97.92
COG0606	490	Predicted ATPase with chaperone activity [Posttran	97.91
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	97.91
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.88
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.87
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	97.86
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	97.86
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	97.85
PRK05642	234	DNA replication initiation factor; Validated	97.85
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	97.85
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	97.84
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	97.82
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.82
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	97.8
PRK08181	269	transposase; Validated	97.8
COG4650	531	RtcR Sigma54-dependent transcription regulator con	97.79
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	97.78
PRK12422	445	chromosomal replication initiation protein; Provis	97.78
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.77
PRK06835	329	DNA replication protein DnaC; Validated	97.77
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	97.77
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.76
PRK07952	244	DNA replication protein DnaC; Validated	97.76
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.75
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	97.74
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	97.74
PRK13765	637	ATP-dependent protease Lon; Provisional	97.73
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	97.73
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	97.72
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	97.72
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	97.71
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.71
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	97.7
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	97.69
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.69
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.68
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.68
PRK08939	306	primosomal protein DnaI; Reviewed	97.68
PRK04195	482	replication factor C large subunit; Provisional	97.67
PLN03025	319	replication factor C subunit; Provisional	97.64
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.64
PRK06921	266	hypothetical protein; Provisional	97.64
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.64
PRK06581	263	DNA polymerase III subunit delta'; Validated	97.64
KOG1969	877	consensus DNA replication checkpoint protein CHL12	97.61
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.61
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.61
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	97.6
PRK08727	233	hypothetical protein; Validated	97.6
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	97.6
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	97.59
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.59
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.59
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.57
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.55
PRK09183	259	transposase/IS protein; Provisional	97.55
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.55
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.53
PRK08181	269	transposase; Validated	97.53
PRK06526	254	transposase; Provisional	97.53
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.53
PHA02244	383	ATPase-like protein	97.52
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.51
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	97.49
PRK09183	259	transposase/IS protein; Provisional	97.49
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.49
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.48
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.48
PRK12422	445	chromosomal replication initiation protein; Provis	97.48
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.47
PRK12377	248	putative replication protein; Provisional	97.45
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.45
PRK06620	214	hypothetical protein; Validated	97.45
PRK13531	498	regulatory ATPase RavA; Provisional	97.45
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	97.45
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.44
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	97.4
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	97.4
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.4
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	97.4
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	97.39
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	97.39
COG0714	329	MoxR-like ATPases [General function prediction onl	97.38
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.38
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.38
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.36
PRK06921	266	hypothetical protein; Provisional	97.36
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	97.35
PRK06835	329	DNA replication protein DnaC; Validated	97.34
PRK08116	268	hypothetical protein; Validated	97.33
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.33
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.32
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	97.32
PRK07952	244	DNA replication protein DnaC; Validated	97.32
PF13173	128	AAA_14: AAA domain	97.31
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.31
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	97.31
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	97.3
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	97.29
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.28
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.28
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.27
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.24
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	97.24
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.23
COG1221	403	PspF Transcriptional regulators containing an AAA-	97.22
PRK11608	326	pspF phage shock protein operon transcriptional ac	97.2
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	97.2
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	97.19
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	97.19
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	97.18
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.16
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	97.15
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	97.14
PRK15455	644	PrkA family serine protein kinase; Provisional	97.14
PRK08939	306	primosomal protein DnaI; Reviewed	97.13
PRK09087	226	hypothetical protein; Validated	97.13
PRK09376	416	rho transcription termination factor Rho; Provisio	97.12
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	97.11
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	97.11
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.1
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.1
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	97.08
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	97.08
PF05729	166	NACHT: NACHT domain	97.08
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	97.05
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.04
PF02861	53	Clp_N: Clp amino terminal domain; InterPro: IPR004	97.02
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	97.02
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.02
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.02
PHA00729	226	NTP-binding motif containing protein	97.01
cd01128	249	rho_factor Transcription termination factor rho is	97.0
KOG0480	764	consensus DNA replication licensing factor, MCM6 c	96.99
TIGR02533	486	type_II_gspE general secretory pathway protein E.	96.99
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	96.97
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	96.96
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	96.96
PRK06620	214	hypothetical protein; Validated	96.91
PRK09087	226	hypothetical protein; Validated	96.9
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	96.89
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.89
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	96.88
PRK09112	351	DNA polymerase III subunit delta'; Validated	96.87
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	96.87
PRK12608	380	transcription termination factor Rho; Provisional	96.86
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	96.85
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	96.84
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	96.83
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	96.83
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.83
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	96.82
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	96.82
COG2204	464	AtoC Response regulator containing CheY-like recei	96.81
PRK07471	365	DNA polymerase III subunit delta'; Validated	96.8
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.79
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	96.78
PRK10436	462	hypothetical protein; Provisional	96.77
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	96.76
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	96.72
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	96.71
PRK15424	538	propionate catabolism operon regulatory protein Pr	96.69
PRK04296	190	thymidine kinase; Provisional	96.65
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	96.63
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	96.61
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	96.59
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	96.58
PRK05022	509	anaerobic nitric oxide reductase transcription reg	96.54
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	96.54
PF05729	166	NACHT: NACHT domain	96.49
TIGR00767	415	rho transcription termination factor Rho. Members	96.46
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	96.45
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	96.44
KOG0477	854	consensus DNA replication licensing factor, MCM2 c	96.44
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	96.44
PRK14974	336	cell division protein FtsY; Provisional	96.42
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	96.42
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	96.41
COG1241	682	MCM2 Predicted ATPase involved in replication cont	96.41
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.39
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.37
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	96.33
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.32
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	96.31
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.28
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	96.28
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.24
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.23
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	96.2
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.19
PRK05564	313	DNA polymerase III subunit delta'; Validated	96.18
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	96.17
PLN02165	334	adenylate isopentenyltransferase	96.13
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.13
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.12
KOG1969	877	consensus DNA replication checkpoint protein CHL12	96.12
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	96.11
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	96.1
PRK08118	167	topology modulation protein; Reviewed	96.09
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	96.09
PRK06696	223	uridine kinase; Validated	96.08
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	96.07
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	96.04
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	95.98
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	95.96
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	95.96
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	95.92
PRK10867	433	signal recognition particle protein; Provisional	95.91
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	95.91
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	95.9
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.87
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	95.85
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	95.85
COG0593	408	DnaA ATPase involved in DNA replication initiation	95.84
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	95.84
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	95.84
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	95.84
PHA00729	226	NTP-binding motif containing protein	95.83
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	95.83
PRK13851	344	type IV secretion system protein VirB11; Provision	95.76
PHA02774	613	E1; Provisional	95.75
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	95.73
PRK08058	329	DNA polymerase III subunit delta'; Validated	95.72
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	95.67
PRK15455	644	PrkA family serine protein kinase; Provisional	95.67
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.66
PRK04296	190	thymidine kinase; Provisional	95.65
TIGR00959	428	ffh signal recognition particle protein. This mode	95.65
PRK00131	175	aroK shikimate kinase; Reviewed	95.63
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	95.62
KOG1808	1856	consensus AAA ATPase containing von Willebrand fac	95.62
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	95.6
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	95.59
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	95.59
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	95.56
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	95.55
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	95.54
PRK06217	183	hypothetical protein; Validated	95.54

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

Probab=100.00  E-value=4.4e-119  Score=1049.93  Aligned_cols=603  Identities=21%  Similarity=0.302  Sum_probs=495.1

Q ss_pred             hhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCCCCCCCCC
Q 003038           11 GLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTSTPMLG   90 (854)
Q Consensus        11 ~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~~~~~~~~   90 (854)
                      +||+.++.+|..|+++|+.++|.+|+++|||++|+.++.+.  .++..+|++.   +.++..++..+.++|...+.    
T Consensus         1 ~~~~~~~~~l~~a~~~a~~~~h~~~~~eHll~~ll~~~~~~--~~l~~~~~~~---~~l~~~~~~~~~~~~~~~~~----   71 (786)
T COG0542           1 KLTERAQKALELAQELARMRRHEYVTPEHLLLALLDQPKGD--ELLNLCGIDL---DKLRQELEEFIDKLPKVLGS----   71 (786)
T ss_pred             CcCHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHcCCchH--HHHHHcCCCH---HHHHHHHHHHHhccCCCCCC----
Confidence            58999999999999999999999999999999999999886  8999999886   89999999999998876531    


Q ss_pred             CCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC--hHHHHHHHhCCCHHHHHHHHHHHhh
Q 003038           91 GHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP--SVSRVMREAGFSSTQVKSNVEQAVS  168 (854)
Q Consensus        91 ~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~--~~~~iL~~~Gi~~~~l~~~v~~~l~  168 (854)
                       ..+++.+.+.++.+...|+..++    +         +|+++|||+|++.++  .+.++|...|++...+...+. .++
T Consensus        72 -~~~s~~~~~~~~~a~~~a~~~~~----~---------~v~~~~llla~~~~~~~~~~~~l~~~~~~~~~~~~~~~-~~~  136 (786)
T COG0542          72 -PYLSPRLKRVLERAWLLAQSLGD----E---------YVSTEHLLLALLNEPESVAAYILKKLGVTRKDVEELIE-ELR  136 (786)
T ss_pred             -CCCCHHHHHHHHHHHHHHHhccC----c---------cccHHHHHHHHhcccchHHHHHHHhccCCHHHHHHHHH-HHh
Confidence             22456666666666666665421    3         599999999999986  678999999999998865555 344


Q ss_pred             hhhccCCCCCCCCCcccccccccccccccccccCCCCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHH
Q 003038          169 LEICSQSTPVSSNKSKESNVLVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRG  246 (854)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~  246 (854)
                      +   +....+..   .......+.+|+.|+|+.|++|+||||  ||+||+|+|+||+||+||||||||||||||||||+|
T Consensus       137 ~---~~~~~~~~---~~~~~~~L~~y~~dlt~~Ar~gklDPvIGRd~EI~r~iqIL~RR~KNNPvLiGEpGVGKTAIvEG  210 (786)
T COG0542         137 G---GNEVDSKN---AEEDQDALEKYTRDLTELAREGKLDPVIGRDEEIRRTIQILSRRTKNNPVLVGEPGVGKTAIVEG  210 (786)
T ss_pred             c---ccccCCcc---cccchhhHHHHhhhhHHHHhcCCCCCCcChHHHHHHHHHHHhccCCCCCeEecCCCCCHHHHHHH
Confidence            3   11111110   011235789999999999999999999  999999999999999999999999999999999999


Q ss_pred             HHHHHHcCCCCcccCCceEEEccccccccc--chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-ccccccccccccc
Q 003038          247 VIDKIEKGDVPEALRDVKCLPLSISSFRHM--NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGY  323 (854)
Q Consensus       247 la~~i~~~~vp~~L~~~~~~~l~~~~l~~~--~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~  323 (854)
                      ||+||++|+||+.|+++++++||+++|++|  ||||||+||+.|++++++. + ++||||||||++ |+|+++       
T Consensus       211 LA~rIv~g~VP~~L~~~~i~sLD~g~LvAGakyRGeFEeRlk~vl~ev~~~-~-~vILFIDEiHtiVGAG~~~-------  281 (786)
T COG0542         211 LAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFEERLKAVLKEVEKS-K-NVILFIDEIHTIVGAGATE-------  281 (786)
T ss_pred             HHHHHhcCCCCHHHcCCEEEEecHHHHhccccccCcHHHHHHHHHHHHhcC-C-CeEEEEechhhhcCCCccc-------
Confidence            999999999999999999999999999998  9999999999999999987 4 999999999999 998763       


Q ss_pred             chhhhHH-HHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHHHhh-------------
Q 003038          324 YCSIEHI-IMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLI-------------  389 (854)
Q Consensus       324 ~~~~~~~-~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~al~-------------  389 (854)
                            | +||++|+|||+..+|+|+||||||++||+|||++|+||+|  |||+|.|.+|+++.++.             
T Consensus       282 ------G~a~DAaNiLKPaLARGeL~~IGATT~~EYRk~iEKD~AL~R--RFQ~V~V~EPs~e~ti~ILrGlk~~yE~hH  353 (786)
T COG0542         282 ------GGAMDAANLLKPALARGELRCIGATTLDEYRKYIEKDAALER--RFQKVLVDEPSVEDTIAILRGLKERYEAHH  353 (786)
T ss_pred             ------ccccchhhhhHHHHhcCCeEEEEeccHHHHHHHhhhchHHHh--cCceeeCCCCCHHHHHHHHHHHHHHHHHcc
Confidence                  2 5899999999555558999999999999999999999999  99999999999887653             


Q ss_pred             ---cccchh------hhccccCCcCCCcccccccchhhhhhhcccccchhhhHHHHhhhhcccCCCCCCCCCChHHHHhh
Q 003038          390 ---TTDSDL------QSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWLQQY  460 (854)
Q Consensus       390 ---~~~s~~------~~~~~~~~~~pdkaidlld~a~~~~~~~c~~~~~~~~e~e~~~~~~~~~~~~~~~~~lp~~l~~~  460 (854)
                         ++|+++      +.||+++|++|||||||+|+|++++.+            +              .. .|..|+.+
T Consensus       354 ~V~i~D~Al~aAv~LS~RYI~dR~LPDKAIDLiDeA~a~~~l------------~--------------~~-~p~~l~~~  406 (786)
T COG0542         354 GVRITDEALVAAVTLSDRYIPDRFLPDKAIDLLDEAGARVRL------------E--------------ID-KPEELDEL  406 (786)
T ss_pred             CceecHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHh------------c--------------cc-CCcchhHH
Confidence               455553      459999999999999999999888442            1              11 34444444


Q ss_pred             HHHHhhcccCCCcccchhhHHHHHHHHhhhcccCccccccccccccCCCCCCCCcccccccCcchhhhhhhhhccccccc
Q 003038          461 KNEKKATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHKTHRDWAVVEPKQS  540 (854)
Q Consensus       461 ~~~~~~~~~~~d~~~~~~~L~~~w~~~~~~~~~~~~~~~~~~~~~s~~~~s~~~~~~~~~~~~~l~~~~~~~~~~~~~~p  540 (854)
                      +.+...+..  ++....   +..+...+..                      +.  ..    ..+..         ..+|
T Consensus       407 ~~~~~~l~~--e~~~~~---~e~~~~~k~~----------------------~~--~~----~~~~~---------~~~~  444 (786)
T COG0542         407 ERELAQLEI--EKEALE---REQDEKEKKL----------------------ID--EI----IKLKE---------GRIP  444 (786)
T ss_pred             HHHHHHHHH--HHHHHh---hhhhHHHHHH----------------------HH--HH----HHHhh---------hhhh
Confidence            432211000  000000   0000000000                      00  00    00000         0111


Q ss_pred             hhccccccccccccCCCCCcccccccccccccccccccCCCCCCCCCCccccccc--hhh----hhhhhhhHHHHHHHHH
Q 003038          541 WREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNSTSSSDIMEM--EYV----HKFKELNSENLTSLCN  614 (854)
Q Consensus       541 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~~~v--~~~----~~~~~~~~e~l~~L~~  614 (854)
                      ..++ +                             + .     . .|+.++|++|  +||    .++.+.+.+.|.+|++
T Consensus       445 ~~~~-~-----------------------------~-~-----~-~v~~~~Ia~vv~~~TgIPv~~l~~~e~~kll~le~  487 (786)
T COG0542         445 ELEK-E-----------------------------L-E-----A-EVDEDDIAEVVARWTGIPVAKLLEDEKEKLLNLER  487 (786)
T ss_pred             hHHH-H-----------------------------H-h-----h-ccCHHHHHHHHHHHHCCChhhhchhhHHHHHHHHH
Confidence            1110 0                             0 0     0 1556677777  887    7788999999999999


Q ss_pred             hhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          615 ALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       615 ~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      .|.++|+||++||..|+.+|++.|+|+.+|+         ||.|+|||+||||||||+|||+||+.|||++.++|+||||
T Consensus       488 ~L~~rViGQd~AV~avs~aIrraRaGL~dp~---------rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMS  558 (786)
T COG0542         488 RLKKRVIGQDEAVEAVSDAIRRARAGLGDPN---------RPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMS  558 (786)
T ss_pred             HHhcceeChHHHHHHHHHHHHHHhcCCCCCC---------CCceEEEeeCCCcccHHHHHHHHHHHhcCCCccceeechH
Confidence            9999999999999999999999999999986         8999999999999999999999999999999999999999


Q ss_pred             cccCcCCCccccccccccC-CCCCC-chHH--HHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceee
Q 003038          695 SFSSTRADSTEDSRNKRSR-DEQSC-SYIE--RFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVS  770 (854)
Q Consensus       695 ~~~~~~~~s~e~~~~~rl~-~~~g~-g~~e--~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~  770 (854)
                      +|+       ++|+++||+ +|||| ||.+  +|+|+||++||+||||||||||||+|+|.|||+||+|++||++|++||
T Consensus       559 Ey~-------EkHsVSrLIGaPPGYVGyeeGG~LTEaVRr~PySViLlDEIEKAHpdV~nilLQVlDdGrLTD~~Gr~Vd  631 (786)
T COG0542         559 EYM-------EKHSVSRLIGAPPGYVGYEEGGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVLDDGRLTDGQGRTVD  631 (786)
T ss_pred             HHH-------HHHHHHHHhCCCCCCceeccccchhHhhhcCCCeEEEechhhhcCHHHHHHHHHHhcCCeeecCCCCEEe
Confidence            999       999999999 59999 9998  999999999999999999999999999999999999999999999999


Q ss_pred             cCCeEEEEecCC
Q 003038          771 LGDAIVILSCES  782 (854)
Q Consensus       771 ~~~aIiIlTsn~  782 (854)
                      |+|||||||||.
T Consensus       632 FrNtiIImTSN~  643 (786)
T COG0542         632 FRNTIIIMTSNA  643 (786)
T ss_pred             cceeEEEEeccc
Confidence            999999999995

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=9e-112  Score=999.19  Aligned_cols=681  Identities=38%  Similarity=0.551  Sum_probs=530.9

Q ss_pred             CCCCccchHHhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccC
Q 003038            1 MRAGGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRL   80 (854)
Q Consensus         1 mr~~~~~~~~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rl   80 (854)
                      ||+|++++++.||++|+.+|..|+.+|+++||++|||+|++.+||.+++|.++++|.+.+-  +||.+++.|+++.|+++
T Consensus         1 m~t~~~t~~q~lT~~Aa~~L~~a~~~Arrrgh~qvtplH~~~~LLs~~t~~lr~ac~~~~~--l~~ralelc~~v~l~rl   78 (898)
T KOG1051|consen    1 MRTGVYTVQQTLTEEAATVLKQAVTEARRRGHAQVTPLHVASTLLSSPTGILRRACIKSHP--LQCRALELCFNVSLNRL   78 (898)
T ss_pred             CCCcccchHhhhCHHHHHHHHHHHHHHHHcCCCCcchHHHHHHHHcCCchHHHHHHHhcCc--ccHHHHHHHHHHHHHhc
Confidence            9999999999999999999999999999999999999999999999999999999999983  46899999999999999


Q ss_pred             CCCCCCCCCCCCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCChHHHHHHHhCCCHHHHH
Q 003038           81 PASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVK  160 (854)
Q Consensus        81 p~~~~~~~~~~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~~~~~iL~~~Gi~~~~l~  160 (854)
                      |++.          +|+.++.|..|+++|++++++++.+++||   +++|..+.|++++++||.++++|+++|+++..++
T Consensus        79 pt~~----------~p~~sn~l~aalkr~qa~qrr~~~~~~~~---~vkvE~~~li~silDdp~vsrv~reag~~s~~vK  145 (898)
T KOG1051|consen   79 PTSY----------GPPVSNALMAALKRAQAHQRRGCEEQQQQ---AVKVELEQLILSILDDPSVSRVMREAGFSSSAVK  145 (898)
T ss_pred             cCCC----------CCccchHhHHHHHHHHHHHHhcchhhccc---hhhHhHHhhheeeecCchHHHHHHHhcCChHHHH
Confidence            9864          37889999999999999999998777666   4566666678888999999999999999999999


Q ss_pred             HHHHHHhhhhhccCCCCCCCCCcccccccccccccccccccCCCCCCCCC--c-HHHHHHHHHHhhccCcCCceeecCCC
Q 003038          161 SNVEQAVSLEICSQSTPVSSNKSKESNVLVLSQTASATKVSKPRVSLDPI--R-NEDVMYVIENLMSKRKRNFVVVGECL  237 (854)
Q Consensus       161 ~~v~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~ldpv--r-~~ei~~v~~~L~r~~k~n~vLvGe~G  237 (854)
                      ..|++....    .+.+. .++  ......+.+|+.+++..+++|++|||  | ++||+|||+||+||+||||||||+||
T Consensus       146 ~~ve~~~g~----~~~~~-~~~--~~~~~~L~~~~~dl~p~a~~gkldPvigr~deeirRvi~iL~Rrtk~NPvLVG~~g  218 (898)
T KOG1051|consen  146 SAVEQPVGQ----FRSPS-RGP--LWPLLFLENYGTDLTPRARQGKLDPVIGRHDEEIRRVIEILSRKTKNNPVLVGEPG  218 (898)
T ss_pred             HHHHhhccc----cCCCC-cCC--ccchhHHHhcccccChhhhccCCCCccCCchHHHHHHHHHHhccCCCCceEEecCC
Confidence            999974421    11111 011  11234577889999999989999999  6 99999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc--chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccc
Q 003038          238 ASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM--NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRA  314 (854)
Q Consensus       238 vGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~--~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~  314 (854)
                      ||||++|+++|+||++|+||..|.+++++.|+++.+.+|  +|||||.|+++|+++|++. ++++|||||||||+ +.+.
T Consensus       219 vgktaiv~gla~ri~~G~vp~~l~~~~l~~l~~g~l~aGa~~rge~E~rlk~l~k~v~~~-~~gvILfigelh~lvg~g~  297 (898)
T KOG1051|consen  219 VGKTAIVEGLAQRIATGDVPETLKDKKLIALDFGSLVAGAKRRGEFEERLKELLKEVESG-GGGVILFLGELHWLVGSGS  297 (898)
T ss_pred             CCchhHHHHHHHHhhcCCCCccccccceEEEEhhhcccCcccchHHHHHHHHHHHHHhcC-CCcEEEEecceeeeecCCC
Confidence            999999999999999999999999999999999999887  9999999999999999975 78999999999999 8876


Q ss_pred             cccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCch-HHHHhh----
Q 003038          315 SSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGS-LSLSLI----  389 (854)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~s-l~~al~----  389 (854)
                      +             ++.|+++++|+|..++|.||||||||++||+||+++||+|||+|.+|.|++|..+ +...|+    
T Consensus       298 ~-------------~~~~d~~nlLkp~L~rg~l~~IGatT~e~Y~k~iekdPalErrw~l~~v~~pS~~~~~~iL~~l~~  364 (898)
T KOG1051|consen  298 N-------------YGAIDAANLLKPLLARGGLWCIGATTLETYRKCIEKDPALERRWQLVLVPIPSVENLSLILPGLSE  364 (898)
T ss_pred             c-------------chHHHHHHhhHHHHhcCCeEEEecccHHHHHHHHhhCcchhhCcceeEeccCcccchhhhhhhhhh
Confidence            4             2578999999984444469999999999999999999999997777777777532 121121    


Q ss_pred             ---------cccch------hhhccccCCcCCCcccccccchhhhhhhcccccchhhhHHHHhhhhcccCCCCCCCCCCh
Q 003038          390 ---------TTDSD------LQSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLP  454 (854)
Q Consensus       390 ---------~~~s~------~~~~~~~~~~~pdkaidlld~a~~~~~~~c~~~~~~~~e~e~~~~~~~~~~~~~~~~~lp  454 (854)
                               +.+++      ++.+|++.+++||+|+|++|+|++.++.                          ...++|
T Consensus       365 ~~e~~hg~~~s~~a~~~a~~~s~~~~t~r~lpd~aidl~dEa~a~~~~--------------------------~~~~lP  418 (898)
T KOG1051|consen  365 RYEVHHGVRISDESLFSAAQLSARYITLSFLPDCAIDLEDEAAALVKS--------------------------QAESLP  418 (898)
T ss_pred             hhccccCCcccccccccccchhhhhcccCcCchhcccHHHHHHHHHhh--------------------------hhhhCC
Confidence                     22322      4458999999999999999999877442                          123699


Q ss_pred             HHHHhhHHHHhhcccCCCcccchhhHHHHHHHHhhhcccCccccccccccccCCCCCCCCcccccccCcchhhhhhhhhc
Q 003038          455 AWLQQYKNEKKATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHKTHRDWAV  534 (854)
Q Consensus       455 ~~l~~~~~~~~~~~~~~d~~~~~~~L~~~w~~~~~~~~~~~~~~~~~~~~~s~~~~s~~~~~~~~~~~~~l~~~~~~~~~  534 (854)
                      +|||.++.....      .......|+++|+   ..+|+.+......-.+....|   .. .+++. ...+.....   .
T Consensus       419 ~wL~~~~~~~~~------~~~e~~~L~kk~d---~~~h~r~~~~~~~~~~~~~~~---l~-~~~~~-~~s~~~~l~---~  481 (898)
T KOG1051|consen  419 PWLQNLERVDIK------LQDEISELQKKWN---QALHKRPSLESLAPSKPTQQP---LS-ASVDS-ERSVIEELK---L  481 (898)
T ss_pred             HHHHhhhhhhhh------hHHHHHHHHHhhh---hhhcccccccccccccccccc---ch-hhhcc-chhHHhhhc---c
Confidence            999999854421      0111228999999   334543321110000000000   00 01111 000100000   0


Q ss_pred             cccccchhcccc-ccccccccCCCCCcccccccccccccccccccCCCCCCCCCCccccccc--hhh----hhhhhhhHH
Q 003038          535 VEPKQSWREHHF-LFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNSTSSSDIMEM--EYV----HKFKELNSE  607 (854)
Q Consensus       535 ~~~~~p~~~~~~-l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~~~v--~~~----~~~~~~~~e  607 (854)
                      . .+.+...  . +...+...+.+.+.++...-.+ ....  ..+    ..+..+++++..+  +|+    .++++.+.+
T Consensus       482 ~-~~~~~~~--~~~~k~~r~~d~~~~~~l~~~~~p-~~~~--~~~----~~~~~~~~~i~~~~s~~tgip~~~~~~~e~~  551 (898)
T KOG1051|consen  482 K-KNSLDRN--SLLAKAHRPNDYTRETDLRYGRIP-DELS--EKS----NDNQGGESDISEVVSRWTGIPVDRLAEAEAE  551 (898)
T ss_pred             c-cCCcccc--hhhhcccCCCCcchhhhccccccc-hhhh--hhc----ccccCCccchhhhhhhhcCCchhhhhhhHHH
Confidence            0 0000000  0 0001111111111111000000 0000  001    1122355567666  776    567788999


Q ss_pred             HHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc
Q 003038          608 NLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN  687 (854)
Q Consensus       608 ~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~  687 (854)
                      +|+.|++.|.++|+||++||+.|+.+|.+||.|+.+|          +|.+||||+||||||||+||++||..+||++++
T Consensus       552 ~l~~L~~~L~~~V~gQ~eAv~aIa~AI~~sr~gl~~~----------~~~awflflGpdgvGKt~lAkaLA~~~Fgse~~  621 (898)
T KOG1051|consen  552 RLKKLEERLHERVIGQDEAVAAIAAAIRRSRAGLKDP----------NPDAWFLFLGPDGVGKTELAKALAEYVFGSEEN  621 (898)
T ss_pred             HHHHHHHHHHhhccchHHHHHHHHHHHHhhhcccCCC----------CCCeEEEEECCCchhHHHHHHHHHHHHcCCccc
Confidence            9999999999999999999999999999999999885          588999999999999999999999999999999


Q ss_pred             eEEEccccccCcCCCccccccccccC-CCCCC-chHH--HHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEec
Q 003038          688 FVSIALSSFSSTRADSTEDSRNKRSR-DEQSC-SYIE--RFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVT  763 (854)
Q Consensus       688 ~i~id~s~~~~~~~~s~e~~~~~rl~-~~~g~-g~~e--~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d  763 (854)
                      ||+||||+|+       +   +++++ +|+|| ||.+  +|+|+|+++||+|||||||||||+++++.|+|+||+|+++|
T Consensus       622 ~IriDmse~~-------e---vskligsp~gyvG~e~gg~LteavrrrP~sVVLfdeIEkAh~~v~n~llq~lD~GrltD  691 (898)
T KOG1051|consen  622 FIRLDMSEFQ-------E---VSKLIGSPPGYVGKEEGGQLTEAVKRRPYSVVLFEEIEKAHPDVLNILLQLLDRGRLTD  691 (898)
T ss_pred             eEEechhhhh-------h---hhhccCCCcccccchhHHHHHHHHhcCCceEEEEechhhcCHHHHHHHHHHHhcCcccc
Confidence            9999999999       5   78888 58899 9987  99999999999999999999999999999999999999999


Q ss_pred             CCCceeecCCeEEEEecCCCCCCCCCC
Q 003038          764 SSGDEVSLGDAIVILSCESFSSRSRAC  790 (854)
Q Consensus       764 ~~G~~v~~~~aIiIlTsn~f~~~s~~~  790 (854)
                      ++|++|||+|||||||||...+....+
T Consensus       692 s~Gr~Vd~kN~I~IMTsn~~~~~i~~~  718 (898)
T KOG1051|consen  692 SHGREVDFKNAIFIMTSNVGSSAIAND  718 (898)
T ss_pred             CCCcEeeccceEEEEecccchHhhhcc
Confidence            999999999999999999876644444

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=100.00  E-value=1e-90  Score=844.66  Aligned_cols=655  Identities=19%  Similarity=0.252  Sum_probs=487.9

Q ss_pred             hhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCCCCCCCCCC
Q 003038           12 LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTSTPMLGG   91 (854)
Q Consensus        12 fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~~~~~~~~~   91 (854)
                      ||+.++++|+.|+++|++++|++|+++|||++||.++++.+.++|..+|+++   +.|+..++..+.+.|.+.+    + 
T Consensus         1 Lt~~a~~~L~~A~~~A~~~~h~~I~~eHLLlaLL~~~~~~~~~iL~~~Gvd~---~~Lr~~le~~l~~~p~~~~----~-   72 (852)
T TIGR03345         1 LNPTSRRALEQAAALCVARGHPEVELEHWLLALLDQPDSDLAAILRHFGVDL---GRLKADLARALDKLPRGNT----R-   72 (852)
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHhccCcHHHHHHHHcCCCH---HHHHHHHHHHhccCCCCCC----C-
Confidence            6899999999999999999999999999999999998889999999999986   7899999999887775321    1 


Q ss_pred             CccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC----hHHHHHHHh-CCCHHHHHHHHHHH
Q 003038           92 HCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP----SVSRVMREA-GFSSTQVKSNVEQA  166 (854)
Q Consensus        92 ~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~----~~~~iL~~~-Gi~~~~l~~~v~~~  166 (854)
                         .+.+++.+..+++.|+.+...   .+++     .+|+++|||+||++++    .+..++..+ |++.+.+...+.+.
T Consensus        73 ---~~~~S~~l~~vL~~A~~~~a~---~~g~-----~~I~teHLLlALl~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  141 (852)
T TIGR03345        73 ---TPVFSPHLVELLQEAWLLASL---ELGD-----GRIRSGHLLLALLTDPELRRLLGSISPELAKIDREALREALPAL  141 (852)
T ss_pred             ---CCCcCHHHHHHHHHHHHHHHH---HcCC-----CcccHHHHHHHHHccccchhHHHHHHHHHhCCCHHHHHHHHHHH
Confidence               244555566666666542110   1111     1599999999999975    245678887 99999888777642


Q ss_pred             hhhhhccCCC-CCCCC---CcccccccccccccccccccCCCCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCH
Q 003038          167 VSLEICSQST-PVSSN---KSKESNVLVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASI  240 (854)
Q Consensus       167 l~~~~~~~~~-~~~~~---~~~~~~~~~~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGK  240 (854)
                      ..+....... .+...   .......+.+.+|+.|+++.++.|++||+  |++||++++++|+|++||||||+|||||||
T Consensus       142 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~L~~~~r~~~ld~~iGr~~ei~~~i~~l~r~~~~n~lLvG~pGvGK  221 (852)
T TIGR03345       142 VEGSAEASAAAADAGPAAAAAGAAGTSALDQYTTDLTAQAREGKIDPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGK  221 (852)
T ss_pred             hcCCccccccccccccccccccccchhhHHHHhhhHHHHhcCCCCCcccCCHHHHHHHHHHHhcCCcCceeEECCCCCCH
Confidence            1210000000 00000   00011235788999999999999999998  999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHcCCCCcccCCceEEEccccccccc--chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-ccccccc
Q 003038          241 EGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM--NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSS  317 (854)
Q Consensus       241 ta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~--~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~  317 (854)
                      |++|++||++|..|+||..|++.++++++++++.++  |+|+||+||+.++++++.. ++++||||||+|.+ ++|++. 
T Consensus       222 Tal~~~La~~i~~~~v~~~l~~~~i~~l~l~~l~ag~~~~ge~e~~lk~ii~e~~~~-~~~~ILfIDEih~l~~~g~~~-  299 (852)
T TIGR03345       222 TAVVEGLALRIAAGDVPPALRNVRLLSLDLGLLQAGASVKGEFENRLKSVIDEVKAS-PQPIILFIDEAHTLIGAGGQA-  299 (852)
T ss_pred             HHHHHHHHHHHhhCCCCccccCCeEEEeehhhhhcccccchHHHHHHHHHHHHHHhc-CCCeEEEEeChHHhccCCCcc-
Confidence            999999999999999999999999999999999975  9999999999999999865 57899999999999 887542 


Q ss_pred             ccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHHHhh--------
Q 003038          318 EQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLI--------  389 (854)
Q Consensus       318 ~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~al~--------  389 (854)
                                  +.+|++++|+|...+|+++||||||++||++|++.||||.|  |||.|.|++|+...+..        
T Consensus       300 ------------~~~d~~n~Lkp~l~~G~l~~IgaTT~~e~~~~~~~d~AL~r--Rf~~i~v~eps~~~~~~iL~~~~~~  365 (852)
T TIGR03345       300 ------------GQGDAANLLKPALARGELRTIAATTWAEYKKYFEKDPALTR--RFQVVKVEEPDEETAIRMLRGLAPV  365 (852)
T ss_pred             ------------ccccHHHHhhHHhhCCCeEEEEecCHHHHhhhhhccHHHHH--hCeEEEeCCCCHHHHHHHHHHHHHh
Confidence                        34678899988444557999999999999999999999999  99999999998655332        


Q ss_pred             --------cccch------hhhccccCCcCCCcccccccchhhhhhhcccccchhhhHHHHhhhhcccCCCCCCCCCChH
Q 003038          390 --------TTDSD------LQSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPA  455 (854)
Q Consensus       390 --------~~~s~------~~~~~~~~~~~pdkaidlld~a~~~~~~~c~~~~~~~~e~e~~~~~~~~~~~~~~~~~lp~  455 (854)
                              +++.+      ++.+|++++++|||||||||+||+.+.++-..    .. .++..              +..
T Consensus       366 ~e~~~~v~i~d~al~~~~~ls~ryi~~r~LPDKAIdlldea~a~~~~~~~~----~p-~~~~~--------------~~~  426 (852)
T TIGR03345       366 LEKHHGVLILDEAVVAAVELSHRYIPGRQLPDKAVSLLDTACARVALSQNA----TP-AALED--------------LRR  426 (852)
T ss_pred             hhhcCCCeeCHHHHHHHHHHcccccccccCccHHHHHHHHHHHHHHHhccC----Cc-hhHHH--------------HHH
Confidence                    22332      34589999999999999999998875532100    00 00000              111


Q ss_pred             HHHhhHHHHhhcccCC----Ccc-c------------chh-hHHHHHHHHhhhcccCccccccccccccCCCCCCCCccc
Q 003038          456 WLQQYKNEKKATLSNN----DKD-S------------GVR-DLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFS  517 (854)
Q Consensus       456 ~l~~~~~~~~~~~~~~----d~~-~------------~~~-~L~~~w~~~~~~~~~~~~~~~~~~~~~s~~~~s~~~~~~  517 (854)
                      .+..++.+.......+    +.. .            .++ .|..+|+..+.....   ...........     ..  .
T Consensus       427 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~-----~~--~  496 (852)
T TIGR03345       427 RIAALELELDALEREAALGADHDERLAELRAELAALEAELAALEARWQQEKELVEA---ILALRAELEAD-----AD--A  496 (852)
T ss_pred             HHHHHHHHHHHHhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhhhc-----cc--c
Confidence            1111111110000000    000 0            000 455667655421110   00000000000     00  0


Q ss_pred             ccccCcchhhhhhhhhccccccchhccccccccccccCCCCCcccccccccccccccccccCCCCCCCCCCccccccc--
Q 003038          518 YDQQYPNFHKTHRDWAVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNSTSSSDIMEM--  595 (854)
Q Consensus       518 ~~~~~~~l~~~~~~~~~~~~~~p~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~~~v--  595 (854)
                      .+. ..++..         ..+|..+. ++....                    ....+.      ...|+.+++++|  
T Consensus       497 ~~~-~~~~~~---------~~~~~~~~-~~~~~~--------------------~~~~~~------~~~v~~~~i~~vv~  539 (852)
T TIGR03345       497 PAD-DDAALR---------AQLAELEA-ALASAQ--------------------GEEPLV------FPEVDAQAVAEVVA  539 (852)
T ss_pred             hhh-hhHHHH---------HHHHHHHH-HHHHHh--------------------hccccc------cceecHHHHHHHHH
Confidence            000 000000         01111100 000000                    000111      146778888888  


Q ss_pred             hhh----hhhhhhhHHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHH
Q 003038          596 EYV----HKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKE  671 (854)
Q Consensus       596 ~~~----~~~~~~~~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt  671 (854)
                      +||    .++...+.++|.+|++.|.++|+||++|+..|+.+|.++++|+.+|+         ||.+||||+||+|||||
T Consensus       540 ~~tgip~~~~~~~e~~~l~~l~~~L~~~v~GQ~~Av~~v~~~i~~~~~gl~~~~---------~p~~~~lf~Gp~GvGKT  610 (852)
T TIGR03345       540 DWTGIPVGRMVRDEIEAVLSLPDRLAERVIGQDHALEAIAERIRTARAGLEDPR---------KPLGVFLLVGPSGVGKT  610 (852)
T ss_pred             HHHCCCchhhchhHHHHHHHHHHHhcCeEcChHHHHHHHHHHHHHHhcCCCCCC---------CCceEEEEECCCCCCHH
Confidence            898    67888999999999999999999999999999999999999999875         89999999999999999


Q ss_pred             HHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccC-CCCCC-chHH--HHHHHHHcCCCEEEEEecCCCCCHH
Q 003038          672 KIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSR-DEQSC-SYIE--RFAEAVSNNPHRVFLIEDVEQADYC  747 (854)
Q Consensus       672 ~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~-~~~g~-g~~e--~L~eav~~~p~~ViliDEieka~~~  747 (854)
                      ++|++||+.+|++...|+++||++|+       +.|++++++ .++|| ||.+  .|+++++++||+||+||||||+|++
T Consensus       611 ~lA~~La~~l~~~~~~~~~~dmse~~-------~~~~~~~l~g~~~gyvg~~~~g~L~~~v~~~p~svvllDEieka~~~  683 (852)
T TIGR03345       611 ETALALAELLYGGEQNLITINMSEFQ-------EAHTVSRLKGSPPGYVGYGEGGVLTEAVRRKPYSVVLLDEVEKAHPD  683 (852)
T ss_pred             HHHHHHHHHHhCCCcceEEEeHHHhh-------hhhhhccccCCCCCcccccccchHHHHHHhCCCcEEEEechhhcCHH
Confidence            99999999999999999999999999       888999998 57888 9976  7999999999999999999999999


Q ss_pred             HHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCC
Q 003038          748 SQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       748 v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                      +++.|+++|++|+++|+.|+.|+|+|+|||||||..
T Consensus       684 v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TSNlg  719 (852)
T TIGR03345       684 VLELFYQVFDKGVMEDGEGREIDFKNTVILLTSNAG  719 (852)
T ss_pred             HHHHHHHHhhcceeecCCCcEEeccccEEEEeCCCc
Confidence            999999999999999999999999999999999964

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=100.00  E-value=1.4e-89  Score=838.47  Aligned_cols=616  Identities=19%  Similarity=0.281  Sum_probs=485.8

Q ss_pred             hHHhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCCCCCC
Q 003038            8 IQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTSTP   87 (854)
Q Consensus         8 ~~~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~~~~~   87 (854)
                      |+++||+.++++|..|+++|++++|.+|++||||++||.++.+.+.++|.++|+++   ..++..++..+.+.+...  +
T Consensus         1 m~~rfT~~a~~vL~~A~~~A~~~~h~~V~~EHLLLaLL~~~~~~a~~iL~~~gid~---~~l~~~l~~~l~~~~~~~--~   75 (821)
T CHL00095          1 MFERFTEKAIKVIMLSQEEARRLGHNFVGTEQILLGLIGEGTGIAARALKSMGVTL---KDARIEVEKIIGRGTGFV--A   75 (821)
T ss_pred             ChhhHhHHHHHHHHHHHHHHHHhCCCcCcHHHHHHHHHhCCCchHHHHHHHcCCCH---HHHHHHHHHHHhcCCCCC--c
Confidence            57899999999999999999999999999999999999999999999999999986   788888888876543211  0


Q ss_pred             CCCCCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC--hHHHHHHHhCCCHHHHHHHHHH
Q 003038           88 MLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP--SVSRVMREAGFSSTQVKSNVEQ  165 (854)
Q Consensus        88 ~~~~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~--~~~~iL~~~Gi~~~~l~~~v~~  165 (854)
                        +.+++++.+.++|..|...|...++    .         +|+++|||+||++++  .+.++|..+|++...++..+.+
T Consensus        76 --~~~~~S~~~~~vL~~A~~~A~~~~~----~---------~I~~eHLLlALL~~~ds~a~~iL~~~gvd~~~L~~~l~~  140 (821)
T CHL00095         76 --VEIPFTPRAKRVLEMSLEEARDLGH----N---------YIGTEHLLLALLEEGEGVAARVLENLGVDLSKIRSLILN  140 (821)
T ss_pred             --cccccCHHHHHHHHHHHHHHHHhCC----C---------cccHHHHHHHHHhCCCchHHHHHHHcCCCHHHHHHHHHH
Confidence              1234566666666666666655421    2         599999999999975  4678999999999999888775


Q ss_pred             HhhhhhccCCCCCCCCCcccccccccccccccccccCCCCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCHHHH
Q 003038          166 AVSLEICSQSTPVSSNKSKESNVLVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGV  243 (854)
Q Consensus       166 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~  243 (854)
                      .+.....  ......  ......+.+.+|+.|++..+++|++||+  |++||++++++|+|++||||||+||||||||++
T Consensus       141 ~l~~~~e--~~~~~~--~~~~~~~~l~~~~~~l~~~a~~~~~~~~igr~~ei~~~~~~L~r~~~~n~lL~G~pGvGKTal  216 (821)
T CHL00095        141 LIGEIIE--AILGAE--QSRSKTPTLEEFGTNLTKEAIDGNLDPVIGREKEIERVIQILGRRTKNNPILIGEPGVGKTAI  216 (821)
T ss_pred             Hhccccc--cccccc--cccccchHHHHHHHHHHHHHHcCCCCCCCCcHHHHHHHHHHHcccccCCeEEECCCCCCHHHH
Confidence            3321000  000000  0011234688999999999999999998  999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCCCCcccCCceEEEccccccccc--chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccc
Q 003038          244 VRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM--NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQV  320 (854)
Q Consensus       244 v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~--~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~  320 (854)
                      |++||++|..++||..|++.+||+++++++++|  |+||||+|++.++++++..  +++||||||||.| ++|.+.    
T Consensus       217 ~~~la~~i~~~~vp~~l~~~~i~~l~~~~l~ag~~~~ge~e~rl~~i~~~~~~~--~~~ILfiDEih~l~~~g~~~----  290 (821)
T CHL00095        217 AEGLAQRIVNRDVPDILEDKLVITLDIGLLLAGTKYRGEFEERLKRIFDEIQEN--NNIILVIDEVHTLIGAGAAE----  290 (821)
T ss_pred             HHHHHHHHHhCCCChhhcCCeEEEeeHHHHhccCCCccHHHHHHHHHHHHHHhc--CCeEEEEecHHHHhcCCCCC----
Confidence            999999999999999999999999999999976  9999999999999999865  6899999999999 887532    


Q ss_pred             cccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHHHh---h--------
Q 003038          321 RGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSL---I--------  389 (854)
Q Consensus       321 ~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~al---~--------  389 (854)
                               +.++++++|+|...+|+|+||||||+++|++|++.||+|++  +|++|.+++++.....   +        
T Consensus       291 ---------g~~~~a~lLkp~l~rg~l~~IgaTt~~ey~~~ie~D~aL~r--Rf~~I~v~ep~~~e~~aILr~l~~~~e~  359 (821)
T CHL00095        291 ---------GAIDAANILKPALARGELQCIGATTLDEYRKHIEKDPALER--RFQPVYVGEPSVEETIEILFGLRSRYEK  359 (821)
T ss_pred             ---------CcccHHHHhHHHHhCCCcEEEEeCCHHHHHHHHhcCHHHHh--cceEEecCCCCHHHHHHHHHHHHHHHHH
Confidence                     33588999988434447999999999999999999999999  9999999988743321   1        


Q ss_pred             -----cccch------hhhccccCCcCCCcccccccchhhhhhhcccccchhhhHHHHhhhhcccCCCCCCCCCChHHHH
Q 003038          390 -----TTDSD------LQSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWLQ  458 (854)
Q Consensus       390 -----~~~s~------~~~~~~~~~~~pdkaidlld~a~~~~~~~c~~~~~~~~e~e~~~~~~~~~~~~~~~~~lp~~l~  458 (854)
                           +.+..      ++.+|+++|++|||||||||+|++.+++.                          ..+.|..++
T Consensus       360 ~~~v~i~deal~~i~~ls~~yi~~r~lPdkaidlld~a~a~~~~~--------------------------~~~~~~~~~  413 (821)
T CHL00095        360 HHNLSISDKALEAAAKLSDQYIADRFLPDKAIDLLDEAGSRVRLI--------------------------NSRLPPAAR  413 (821)
T ss_pred             HcCCCCCHHHHHHHHHHhhccCccccCchHHHHHHHHHHHHHHhh--------------------------ccCCchhHH
Confidence                 12222      34589999999999999999998774421                          013454444


Q ss_pred             hhHHHHhhc-------ccCCCcccchhhHHHHHHHHhhhcccCccccccccccccCCCCCCCCcccccccCcchhhhhhh
Q 003038          459 QYKNEKKAT-------LSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHKTHRD  531 (854)
Q Consensus       459 ~~~~~~~~~-------~~~~d~~~~~~~L~~~w~~~~~~~~~~~~~~~~~~~~~s~~~~s~~~~~~~~~~~~~l~~~~~~  531 (854)
                      .++.+...+       ....+-+.. ..++.++..+                                  ...+......
T Consensus       414 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~----------------------------------~~~~~~~~~~  458 (821)
T CHL00095        414 ELDKELREILKDKDEAIREQDFETA-KQLRDREMEV----------------------------------RAQIAAIIQS  458 (821)
T ss_pred             HHHHHHHHHHHHHHHHHhCcchHHH-HHHHHHHHHH----------------------------------HHHHHHHHHH
Confidence            443222110       000000000 0000000000                                  0001110011


Q ss_pred             hhccccccchhccccccccccccCCCCCcccccccccccccccccccCCCCCCCCCCccccccc--hhh----hhhhhhh
Q 003038          532 WAVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNSTSSSDIMEM--EYV----HKFKELN  605 (854)
Q Consensus       532 ~~~~~~~~p~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~~~v--~~~----~~~~~~~  605 (854)
                      |.-..               .                     ...      ....|+.+++++|  +||    .++.+.+
T Consensus       459 ~~~~~---------------~---------------------~~~------~~~~v~~~~i~~~~~~~tgip~~~~~~~~  496 (821)
T CHL00095        459 KKTEE---------------E---------------------KRL------EVPVVTEEDIAEIVSAWTGIPVNKLTKSE  496 (821)
T ss_pred             HHhhh---------------c---------------------ccc------cCCccCHHHHHHHHHHHHCCCchhhchhH
Confidence            21100               0                     000      0145677778887  887    6788899


Q ss_pred             HHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC
Q 003038          606 SENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH  685 (854)
Q Consensus       606 ~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~  685 (854)
                      .++|.+|++.|.++|+||++|+..|+.+|.++++|+.+++         ||.++|||+||+|||||++|++||+.+||+.
T Consensus       497 ~~~l~~l~~~L~~~v~GQ~~ai~~l~~~i~~~~~gl~~~~---------~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~  567 (821)
T CHL00095        497 SEKLLHMEETLHKRIIGQDEAVVAVSKAIRRARVGLKNPN---------RPIASFLFSGPTGVGKTELTKALASYFFGSE  567 (821)
T ss_pred             HHHHHHHHHHhcCcCcChHHHHHHHHHHHHHHhhcccCCC---------CCceEEEEECCCCCcHHHHHHHHHHHhcCCc
Confidence            9999999999999999999999999999999999998875         8999999999999999999999999999999


Q ss_pred             CceEEEccccccCcCCCccccccccccC-CCCCC-chHH--HHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeE
Q 003038          686 NNFVSIALSSFSSTRADSTEDSRNKRSR-DEQSC-SYIE--RFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRI  761 (854)
Q Consensus       686 ~~~i~id~s~~~~~~~~s~e~~~~~rl~-~~~g~-g~~e--~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l  761 (854)
                      .+++++||++|.       +.|.+++++ .|+|| ||.+  .|+++++++||+|||||||||||+++++.|+++||+|++
T Consensus       568 ~~~~~~d~s~~~-------~~~~~~~l~g~~~gyvg~~~~~~l~~~~~~~p~~VvllDeieka~~~v~~~Llq~le~g~~  640 (821)
T CHL00095        568 DAMIRLDMSEYM-------EKHTVSKLIGSPPGYVGYNEGGQLTEAVRKKPYTVVLFDEIEKAHPDIFNLLLQILDDGRL  640 (821)
T ss_pred             cceEEEEchhcc-------ccccHHHhcCCCCcccCcCccchHHHHHHhCCCeEEEECChhhCCHHHHHHHHHHhccCce
Confidence            999999999999       788888888 47888 8876  799999999999999999999999999999999999999


Q ss_pred             ecCCCceeecCCeEEEEecCCC
Q 003038          762 VTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       762 ~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                      +|+.|+.|+|+|+|||||||..
T Consensus       641 ~d~~g~~v~~~~~i~I~Tsn~g  662 (821)
T CHL00095        641 TDSKGRTIDFKNTLIIMTSNLG  662 (821)
T ss_pred             ecCCCcEEecCceEEEEeCCcc
Confidence            9999999999999999999964

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=100.00  E-value=1.6e-85  Score=804.93  Aligned_cols=656  Identities=22%  Similarity=0.320  Sum_probs=491.5

Q ss_pred             hhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCCCCCCCCCC
Q 003038           12 LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTSTPMLGG   91 (854)
Q Consensus        12 fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~~~~~~~~~   91 (854)
                      ||+.++.+|..|+++|++++|.+|+++|||++|+.+++|.+.++|.++|+++   +.++..+...+.+.|...+.+  +.
T Consensus         1 fT~~a~~vL~~A~~~A~~~~h~~V~~EHLLlaLl~~~~g~a~~iL~~~Gvd~---~~l~~~l~~~l~~~~~~~~~~--~~   75 (852)
T TIGR03346         1 FTEKFQEALQAAQSLALGRDHQQIEPEHLLKALLDQEGGLARRLLQKAGVNV---GALRQALEKELEKLPKVSGPG--GQ   75 (852)
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCCccHHHHHHHHcCCCH---HHHHHHHHHHhcccccCCCCC--CC
Confidence            7999999999999999999999999999999999999999999999999986   789999999888776533211  23


Q ss_pred             CccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC-hHHHHHHHhCCCHHHHHHHHHHHhhhh
Q 003038           92 HCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP-SVSRVMREAGFSSTQVKSNVEQAVSLE  170 (854)
Q Consensus        92 ~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~-~~~~iL~~~Gi~~~~l~~~v~~~l~~~  170 (854)
                      ++++|.+.++|+.|...|...+    .+         +|+++|||+||++++ .+.++|..+|++.+.++..+.+ +.+ 
T Consensus        76 ~~~S~~~~~vLe~A~~~A~~~g----~~---------~I~teHLLlALl~e~~~a~~iL~~~gi~~~~l~~~l~~-~~~-  140 (852)
T TIGR03346        76 VYLSPELNRLLNLAEKLAQKRG----DE---------FISSEHLLLALLDDKGTLGKLLKEAGATADALEAAINA-VRG-  140 (852)
T ss_pred             CCcCHHHHHHHHHHHHHHHHcC----CC---------cccHHHHHHHHHcCCccHHHHHHHcCCCHHHHHHHHHh-hcc-
Confidence            4456666666666666665432    12         599999999999985 4568999999999999877763 221 


Q ss_pred             hccCCCCCCCCCcccccccccccccccccccCCCCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHH
Q 003038          171 ICSQSTPVSSNKSKESNVLVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la  248 (854)
                        +.......   .....+.+.+|+.++++.++.|++||+  |++||++++++|+|++||||||+||||||||++|++||
T Consensus       141 --~~~~~~~~---~~~~~~~l~~~~~~l~~~~~~~~~~~~igr~~ei~~~~~~l~r~~~~n~lL~G~pGvGKT~l~~~la  215 (852)
T TIGR03346       141 --GQKVTSAN---AEDQYEALEKYARDLTERAREGKLDPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEGLA  215 (852)
T ss_pred             --Cccccccc---cccchhHHHHHhhhHHHHhhCCCCCcCCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHH
Confidence              11111000   011235789999999999999999998  99999999999999999999999999999999999999


Q ss_pred             HHHHcCCCCcccCCceEEEccccccccc--chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccch
Q 003038          249 DKIEKGDVPEALRDVKCLPLSISSFRHM--NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYC  325 (854)
Q Consensus       249 ~~i~~~~vp~~L~~~~~~~l~~~~l~~~--~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~  325 (854)
                      ++|..|+||..|++.+++.++++++.++  |+|+||++++.+++++... ++++||||||||.| ++|.+.         
T Consensus       216 ~~i~~~~~p~~l~~~~~~~l~~~~l~a~~~~~g~~e~~l~~~l~~~~~~-~~~~ILfIDEih~l~~~g~~~---------  285 (852)
T TIGR03346       216 QRIVNGDVPESLKNKRLLALDMGALIAGAKYRGEFEERLKAVLNEVTKS-EGQIILFIDELHTLVGAGKAE---------  285 (852)
T ss_pred             HHHhccCCchhhcCCeEEEeeHHHHhhcchhhhhHHHHHHHHHHHHHhc-CCCeEEEeccHHHhhcCCCCc---------
Confidence            9999999999999999999999999876  9999999999999999765 56899999999999 877542         


Q ss_pred             hhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHHHhh----------------
Q 003038          326 SIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLI----------------  389 (854)
Q Consensus       326 ~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~al~----------------  389 (854)
                          +.++++++|+|...+|++.||||||.++|++|++.||+|+|  ||++|.|++|+....+.                
T Consensus       286 ----~~~d~~~~Lk~~l~~g~i~~IgaTt~~e~r~~~~~d~al~r--Rf~~i~v~~p~~~~~~~iL~~~~~~~e~~~~v~  359 (852)
T TIGR03346       286 ----GAMDAGNMLKPALARGELHCIGATTLDEYRKYIEKDAALER--RFQPVFVDEPTVEDTISILRGLKERYEVHHGVR  359 (852)
T ss_pred             ----chhHHHHHhchhhhcCceEEEEeCcHHHHHHHhhcCHHHHh--cCCEEEeCCCCHHHHHHHHHHHHHHhccccCCC
Confidence                45789999988444457999999999999999999999999  99999999998655432                


Q ss_pred             cccch------hhhccccCCcCCCcccccccchhhhhhhcccccchhhhHHHHhhhhcccCCCCCCCCCChHHHHhh---
Q 003038          390 TTDSD------LQSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWLQQY---  460 (854)
Q Consensus       390 ~~~s~------~~~~~~~~~~~pdkaidlld~a~~~~~~~c~~~~~~~~e~e~~~~~~~~~~~~~~~~~lp~~l~~~---  460 (854)
                      +.+.+      ++++|+++|++|||||||||+||+++++.-                          ...|..++.+   
T Consensus       360 ~~d~~i~~~~~ls~~yi~~r~lPdkAidlld~a~a~~~~~~--------------------------~~~~~~~~~~~~~  413 (852)
T TIGR03346       360 ITDPAIVAAATLSHRYITDRFLPDKAIDLIDEAAARIRMEI--------------------------DSKPEELDELDRR  413 (852)
T ss_pred             CCHHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHhhc--------------------------cCCchhHHHHHHH
Confidence            12222      456999999999999999999988855310                          0122222222   


Q ss_pred             ----HHHHhhcccCCCcccc---------------h-hhHHHHHHHHhhhcccCccccccccccccCCCCCCCCcccccc
Q 003038          461 ----KNEKKATLSNNDKDSG---------------V-RDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQ  520 (854)
Q Consensus       461 ----~~~~~~~~~~~d~~~~---------------~-~~L~~~w~~~~~~~~~~~~~~~~~~~~~s~~~~s~~~~~~~~~  520 (854)
                          +.+........+....               + ..+...|......+.....+.+. +.....    ...  ..+.
T Consensus       414 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~----~~~--~~~~  486 (852)
T TIGR03346       414 IIQLEIEREALKKEKDEASKERLEDLEKELAELEEEYADLEEQWKAEKAAIQGIQQIKEE-IEQVRL----ELE--QAER  486 (852)
T ss_pred             HHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH----HHH--HHHh
Confidence                1111111000010000               0 03455565543221110000000 000000    000  0000


Q ss_pred             cCcchhhhhhhhhccccccchhccccccccccccCCCCCcccccccccccccccccccCCCCCCCCCCccccccc--hhh
Q 003038          521 QYPNFHKTHRDWAVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNSTSSSDIMEM--EYV  598 (854)
Q Consensus       521 ~~~~l~~~~~~~~~~~~~~p~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~~~v--~~~  598 (854)
                       ..++....+   +.....|...+ .+...+....            +  .....+.      ...|+.++++.|  +||
T Consensus       487 -~~~~~~~~~---~~~~~~~~~~~-~~~~~~~~~~------------~--~~~~~l~------~~~v~~~~i~~v~~~~t  541 (852)
T TIGR03346       487 -EGDLAKAAE---LQYGKLPELEK-RLQAAEAKLG------------E--ETKPRLL------REEVTAEEIAEVVSRWT  541 (852)
T ss_pred             -hhhHHHHHH---hhhcchHHHHH-HHHHHHHHhh------------h--ccccccc------cCCcCHHHHHHHHHHhc
Confidence             000000000   00001111100 0000000000            0  0001111      145777888888  787


Q ss_pred             ----hhhhhhhHHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHH
Q 003038          599 ----HKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIA  674 (854)
Q Consensus       599 ----~~~~~~~~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lA  674 (854)
                          .++.+.+.++|.+|++.|.++|+||++||..|+.+|.++++|+.+|+         ||.++|||+||+|||||++|
T Consensus       542 gip~~~~~~~e~~~l~~l~~~l~~~v~GQ~~av~~v~~~i~~~~~gl~~~~---------~p~~~~Lf~Gp~GvGKt~lA  612 (852)
T TIGR03346       542 GIPVSKMLEGEREKLLHMEEVLHERVVGQDEAVEAVSDAIRRSRAGLSDPN---------RPIGSFLFLGPTGVGKTELA  612 (852)
T ss_pred             CCCcccccHHHHHHHHHHHHHhhcccCCChHHHHHHHHHHHHHhccCCCCC---------CCCeEEEEEcCCCCCHHHHH
Confidence                56788899999999999999999999999999999999999999875         88999999999999999999


Q ss_pred             HHHHHHHhCCCCceEEEccccccCcCCCccccccccccC-CCCCC-chHH--HHHHHHHcCCCEEEEEecCCCCCHHHHH
Q 003038          675 KELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSR-DEQSC-SYIE--RFAEAVSNNPHRVFLIEDVEQADYCSQK  750 (854)
Q Consensus       675 r~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~-~~~g~-g~~e--~L~eav~~~p~~ViliDEieka~~~v~~  750 (854)
                      ++||+.+|++..+|+++||++|.       +.+.+++++ +++|| ||.+  .|+++++++|++|||||||||+|+++|+
T Consensus       613 ~~La~~l~~~~~~~i~~d~s~~~-------~~~~~~~l~g~~~g~~g~~~~g~l~~~v~~~p~~vlllDeieka~~~v~~  685 (852)
T TIGR03346       613 KALAEFLFDDEDAMVRIDMSEYM-------EKHSVARLIGAPPGYVGYEEGGQLTEAVRRKPYSVVLFDEVEKAHPDVFN  685 (852)
T ss_pred             HHHHHHhcCCCCcEEEEechhhc-------ccchHHHhcCCCCCccCcccccHHHHHHHcCCCcEEEEeccccCCHHHHH
Confidence            99999999999999999999998       788888887 47888 9976  8999999999999999999999999999


Q ss_pred             HHHHhhhcCeEecCCCceeecCCeEEEEecCC
Q 003038          751 GFKRAIESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       751 ~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      .|+++|++|+++|+.|+.++|+|+|||||||.
T Consensus       686 ~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~  717 (852)
T TIGR03346       686 VLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNL  717 (852)
T ss_pred             HHHHHHhcCceecCCCeEEecCCcEEEEeCCc
Confidence            99999999999999999999999999999995

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=100.00  E-value=2.7e-85  Score=799.59  Aligned_cols=657  Identities=20%  Similarity=0.285  Sum_probs=494.7

Q ss_pred             chHHhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCCCCC
Q 003038            7 TIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTST   86 (854)
Q Consensus         7 ~~~~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~~~~   86 (854)
                      |++++||+.++.+|+.|+.+|++++|.+|+++|||++|+.++.+.+..+|.++|++.   ..|+..++..+.+.|...++
T Consensus         1 ~~~~~~~~~~~~~l~~a~~~a~~~~~~~~~~~hll~~l~~~~~~~~~~~l~~~~~~~---~~l~~~~~~~~~~~~~~~~~   77 (857)
T PRK10865          1 MRLDRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVRPLLTSAGINA---GQLRTDINQALSRLPQVEGT   77 (857)
T ss_pred             CChHHhCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCCccHHHHHHHHcCCCH---HHHHHHHHHHHhhCCCCCCC
Confidence            357899999999999999999999999999999999999999899999999999986   79999999999887753221


Q ss_pred             CCCCCCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC-hHHHHHHHhCCCHHHHHHHHHH
Q 003038           87 PMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP-SVSRVMREAGFSSTQVKSNVEQ  165 (854)
Q Consensus        87 ~~~~~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~-~~~~iL~~~Gi~~~~l~~~v~~  165 (854)
                      +      ..+.++..+..+++.|+.+++..+..         +|+++|||+|++.++ ....+|..+|++.+.++..+.+
T Consensus        78 ~------~~~~~~~~~~~~l~~a~~~~~~~~~~---------~i~~~~ll~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  142 (857)
T PRK10865         78 G------GDVQPSQDLVRVLNLCDKLAQKRGDN---------FISSELFVLAALESRGTLADILKAAGATTANITQAIEQ  142 (857)
T ss_pred             C------CCCCcCHHHHHHHHHHHHHHHHcCCC---------cccHHHHHHHHHcCcchHHHHHHHcCCCHHHHHHHHHH
Confidence            1      12445555556666666554322212         599999999999985 4567899999999999877653


Q ss_pred             HhhhhhccCCCCCCCCCcccccccccccccccccccCCCCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCHHHH
Q 003038          166 AVSLEICSQSTPVSSNKSKESNVLVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGV  243 (854)
Q Consensus       166 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~  243 (854)
                       +.+    ........+  ....+.+.+|+.++++.++.|++|||  |+.||+++++||+||+|+||||+||||||||++
T Consensus       143 -~~~----~~~~~~~~~--~~~~~~l~~~~~~l~~~~r~~~l~~vigr~~ei~~~i~iL~r~~~~n~lL~G~pGvGKT~l  215 (857)
T PRK10865        143 -MRG----GESVNDQGA--EDQRQALKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAI  215 (857)
T ss_pred             -hhc----ccccccccc--ccchhHHHHHhhhHHHHHhcCCCCcCCCCHHHHHHHHHHHhcCCcCceEEECCCCCCHHHH
Confidence             221    110000000  11235789999999999999999998  999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCCCCcccCCceEEEccccccccc--chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccc
Q 003038          244 VRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM--NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQV  320 (854)
Q Consensus       244 v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~--~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~  320 (854)
                      |++||+++..|+||..|++.+++.+++++++++  |+|+||+|++.+++++... ++++||||||+|.| ++|.+.    
T Consensus       216 ~~~la~~i~~~~vp~~l~~~~~~~l~l~~l~ag~~~~g~~e~~lk~~~~~~~~~-~~~~ILfIDEih~l~~~~~~~----  290 (857)
T PRK10865        216 VEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQ-EGNVILFIDELHTMVGAGKAD----  290 (857)
T ss_pred             HHHHHHHhhcCCCchhhCCCEEEEEehhhhhhccchhhhhHHHHHHHHHHHHHc-CCCeEEEEecHHHhccCCCCc----
Confidence            999999999999999999999999999999876  9999999999999998765 57899999999999 887542    


Q ss_pred             cccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHHHhh-----------
Q 003038          321 RGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLI-----------  389 (854)
Q Consensus       321 ~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~al~-----------  389 (854)
                               +.++++++|+|...+|+|+||||||+++|++|++.||+|+|  |||.|.|++|+...++.           
T Consensus       291 ---------~~~d~~~~lkp~l~~g~l~~IgaTt~~e~r~~~~~d~al~r--Rf~~i~v~eP~~~~~~~iL~~l~~~~e~  359 (857)
T PRK10865        291 ---------GAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALER--RFQKVFVAEPSVEDTIAILRGLKERYEL  359 (857)
T ss_pred             ---------cchhHHHHhcchhhcCCCeEEEcCCCHHHHHHhhhcHHHHh--hCCEEEeCCCCHHHHHHHHHHHhhhhcc
Confidence                     45789999998544558999999999999999999999999  99999999998655432           


Q ss_pred             -----cccc------hhhhccccCCcCCCcccccccchhhhhhhcccccchhhhHHHHhhhhcccCCCCCCCCCChHHHH
Q 003038          390 -----TTDS------DLQSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWLQ  458 (854)
Q Consensus       390 -----~~~s------~~~~~~~~~~~~pdkaidlld~a~~~~~~~c~~~~~~~~e~e~~~~~~~~~~~~~~~~~lp~~l~  458 (854)
                           +.+.      +++++|++++++||||++|+|.+++.+.+.-                          .+.|..|+
T Consensus       360 ~~~v~~~d~a~~~a~~ls~ry~~~~~~pdkAi~LiD~aaa~~rl~~--------------------------~~kp~~L~  413 (857)
T PRK10865        360 HHHVQITDPAIVAAATLSHRYIADRQLPDKAIDLIDEAASSIRMQI--------------------------DSKPEELD  413 (857)
T ss_pred             CCCCCcCHHHHHHHHHHhhccccCCCCChHHHHHHHHHhccccccc--------------------------ccChHHHH
Confidence                 1222      2566999999999999999999877744310                          11222222


Q ss_pred             -------hhHHHHhhcccCCCcc---------------cchh-hHHHHHHHHhhhcccCcccc-ccc-cccccCCCCCCC
Q 003038          459 -------QYKNEKKATLSNNDKD---------------SGVR-DLCKKWNSICNSIHKQPYYS-ERT-LTFSSASPSSST  513 (854)
Q Consensus       459 -------~~~~~~~~~~~~~d~~---------------~~~~-~L~~~w~~~~~~~~~~~~~~-~~~-~~~~s~~~~s~~  513 (854)
                             .++.+...+....+..               ..+. .|+.+|..+...+....... +.. +..       .+
T Consensus       414 rLer~l~~L~~E~e~l~~e~~~~~~~~~~~l~~~l~~lq~e~~~L~eq~k~~k~el~~~~~~~~ele~l~~-------ki  486 (857)
T PRK10865        414 RLDRRIIQLKLEQQALMKESDEASKKRLDMLNEELSDKERQYSELEEEWKAEKASLSGTQTIKAELEQAKI-------AI  486 (857)
T ss_pred             HHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH-------HH
Confidence                   1111111110000000               0001 36777776643321100000 000 000       00


Q ss_pred             CcccccccCcchhhhhhhhhccccccchhccccccccccccCCCCCcccccccccccccccccccCCCCCCCCCCccccc
Q 003038          514 SGFSYDQQYPNFHKTHRDWAVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNSTSSSDIM  593 (854)
Q Consensus       514 ~~~~~~~~~~~l~~~~~~~~~~~~~~p~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~~  593 (854)
                      .  ..+. ..+.....+   +....+|...+ ++...+..                ......++.      ..|+.++++
T Consensus       487 e--~a~~-~~~~~~~~~---~~~~~~~~~~~-~~~~~~~~----------------~~~~~~~~~------~~v~~~~i~  537 (857)
T PRK10865        487 E--QARR-VGDLARMSE---LQYGKIPELEK-QLAAATQL----------------EGKTMRLLR------NKVTDAEIA  537 (857)
T ss_pred             H--HHHh-hhhhhhHHH---hhhhhhHHHHH-HHHHHHhh----------------hcccccccc------CccCHHHHH
Confidence            0  0000 000000000   00001111100 00000000                000011221      568888898


Q ss_pred             cc--hhh----hhhhhhhHHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCC
Q 003038          594 EM--EYV----HKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDA  667 (854)
Q Consensus       594 ~v--~~~----~~~~~~~~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~G  667 (854)
                      .|  +||    .++.+.+.++|..|++.|.++|+||+.|+..|..+|.++++|+.+|+         ||.++|||+||+|
T Consensus       538 ~vv~~~tgip~~~~~~~~~~~l~~l~~~l~~~viGQ~~ai~~l~~~i~~~~~gl~~~~---------~p~~~~Lf~Gp~G  608 (857)
T PRK10865        538 EVLARWTGIPVSRMLESEREKLLRMEQELHHRVIGQNEAVEAVSNAIRRSRAGLSDPN---------RPIGSFLFLGPTG  608 (857)
T ss_pred             HHHHHHHCCCchhhhhhHHHHHHHHHHHhCCeEeCCHHHHHHHHHHHHHHHhcccCCC---------CCCceEEEECCCC
Confidence            88  998    77889999999999999999999999999999999999999999875         7889999999999


Q ss_pred             chHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccC-CCCCC-chHH--HHHHHHHcCCCEEEEEecCCC
Q 003038          668 DAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSR-DEQSC-SYIE--RFAEAVSNNPHRVFLIEDVEQ  743 (854)
Q Consensus       668 vGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~-~~~g~-g~~e--~L~eav~~~p~~ViliDEiek  743 (854)
                      ||||++|++||+.+|++...|+++||++|.       +.+..++++ .++|| ||.+  .|+++++.+|++|||||||||
T Consensus       609 ~GKT~lA~aLa~~l~~~~~~~i~id~se~~-------~~~~~~~LiG~~pgy~g~~~~g~l~~~v~~~p~~vLllDEiek  681 (857)
T PRK10865        609 VGKTELCKALANFMFDSDDAMVRIDMSEFM-------EKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEK  681 (857)
T ss_pred             CCHHHHHHHHHHHhhcCCCcEEEEEhHHhh-------hhhhHHHHhCCCCcccccchhHHHHHHHHhCCCCeEEEeehhh
Confidence            999999999999999998999999999998       677777877 47788 8875  799999999999999999999


Q ss_pred             CCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCC
Q 003038          744 ADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       744 a~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      +|+++|+.|+++|++|+++|+.|++++|+|+|||||||.
T Consensus       682 a~~~v~~~Ll~ile~g~l~d~~gr~vd~rn~iiI~TSN~  720 (857)
T PRK10865        682 AHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNL  720 (857)
T ss_pred             CCHHHHHHHHHHHhhCceecCCceEEeecccEEEEeCCc
Confidence            999999999999999999999999999999999999985

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

Probab=100.00  E-value=5.4e-82  Score=763.96  Aligned_cols=569  Identities=17%  Similarity=0.241  Sum_probs=453.6

Q ss_pred             hhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhc-cCCCCCCCCCCC
Q 003038           12 LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALN-RLPASTSTPMLG   90 (854)
Q Consensus        12 fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~-rlp~~~~~~~~~   90 (854)
                      ||+.++++|..|+++|++++|.+|++||||++||.++.  ..++|.++|+++   +.+++.+...+. .+|...+.. .+
T Consensus         1 ~~~~a~~~L~~A~~~A~~~~h~~V~~EHLLlaLL~~~~--~~~iL~~~gid~---~~l~~~l~~~l~~~~p~~~~~~-~~   74 (731)
T TIGR02639         1 ISEELERILDAALEEAKKRRHEFVTLEHILLALLFDSD--AIEILEECGGDV---EALRKDLEDYLENNLPSITEEN-EA   74 (731)
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCcCcHHHHHHHHHcCch--HHHHHHHcCCCH---HHHHHHHHHHHhhcCCCCCCCC-CC
Confidence            68999999999999999999999999999999999876  568999999986   789999988887 555432110 12


Q ss_pred             CCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC--hHHHHHHHhCCCHHHHHHHHHHHhh
Q 003038           91 GHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP--SVSRVMREAGFSSTQVKSNVEQAVS  168 (854)
Q Consensus        91 ~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~--~~~~iL~~~Gi~~~~l~~~v~~~l~  168 (854)
                      .+++++.+.+.|+.|.+.|..+++    +         +|+++|||+||++++  .+.++|..+|++.+.+...+.....
T Consensus        75 ~~~~S~~lk~vL~~A~~~A~~~g~----~---------~I~teHLLLALl~~~~~~a~~lL~~~gi~~~~l~~~l~~~~~  141 (731)
T TIGR02639        75 DPEQTVGVQRVLQRALLHVKSAGK----K---------EIGIGDILVALFDEEDSHASYFLKSQGITRLDILEYISHGIP  141 (731)
T ss_pred             CCCcCHHHHHHHHHHHHHHHHcCC----C---------ccCHHHHHHHHhcCcccHHHHHHHHcCCCHHHHHHHHHhhcc
Confidence            344566666666666666655421    2         599999999999974  4567999999999988776652111


Q ss_pred             hhhccCCCCCCCC-CcccccccccccccccccccCCCCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHH
Q 003038          169 LEICSQSTPVSSN-KSKESNVLVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVR  245 (854)
Q Consensus       169 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~  245 (854)
                      ............. .......+.+++|+.++++.++.|++||+  |++||++++++|+|++|+||||+||||||||++|+
T Consensus       142 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~r~~~l~~~igr~~ei~~~~~~L~~~~~~n~lL~G~pG~GKT~l~~  221 (731)
T TIGR02639       142 KDDGKNRDAEEAGKEEAKKQEDALEKYTVDLTEKAKNGKIDPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAE  221 (731)
T ss_pred             cccccccccccccccccccchhHHHHHhhhHHHHHhcCCCCcccCcHHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHH
Confidence            0000000000000 00001234688999999999999999998  99999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCCCcccCCceEEEccccccccc--chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccc
Q 003038          246 GVIDKIEKGDVPEALRDVKCLPLSISSFRHM--NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRG  322 (854)
Q Consensus       246 ~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~--~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~  322 (854)
                      +||++|..++||..|++.+|++++++++.++  |+|+||+|+++++++++..  +++||||||||.| ++|...      
T Consensus       222 ~la~~~~~~~~p~~l~~~~~~~~~~~~l~a~~~~~g~~e~~l~~i~~~~~~~--~~~ILfiDEih~l~~~g~~~------  293 (731)
T TIGR02639       222 GLALRIAEGKVPENLKNAKIYSLDMGSLLAGTKYRGDFEERLKAVVSEIEKE--PNAILFIDEIHTIVGAGATS------  293 (731)
T ss_pred             HHHHHHHhCCCchhhcCCeEEEecHHHHhhhccccchHHHHHHHHHHHHhcc--CCeEEEEecHHHHhccCCCC------
Confidence            9999999999999999999999999999975  9999999999999999875  5899999999999 876532      


Q ss_pred             cchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHHHhh-------------
Q 003038          323 YYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLI-------------  389 (854)
Q Consensus       323 ~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~al~-------------  389 (854)
                            .+.++++++|+|...+|+|.||||||++||++|++.||+|.|  ||+.|.|++++......             
T Consensus       294 ------~~~~~~~~~L~~~l~~g~i~~IgaTt~~e~~~~~~~d~al~r--Rf~~i~v~~p~~~~~~~il~~~~~~~e~~~  365 (731)
T TIGR02639       294 ------GGSMDASNLLKPALSSGKLRCIGSTTYEEYKNHFEKDRALSR--RFQKIDVGEPSIEETVKILKGLKEKYEEFH  365 (731)
T ss_pred             ------CccHHHHHHHHHHHhCCCeEEEEecCHHHHHHHhhhhHHHHH--hCceEEeCCCCHHHHHHHHHHHHHHHHhcc
Confidence                  134678899987333447999999999999999999999999  99999999998554332             


Q ss_pred             ---cccch------hhhccccCCcCCCcccccccchhhhhhhcccccchhhhHHHHhhhhcccCCCCCCCCCChHHHHhh
Q 003038          390 ---TTDSD------LQSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWLQQY  460 (854)
Q Consensus       390 ---~~~s~------~~~~~~~~~~~pdkaidlld~a~~~~~~~c~~~~~~~~e~e~~~~~~~~~~~~~~~~~lp~~l~~~  460 (854)
                         +.+.+      ++.+|++++++|||||||+|+|++.+.+        ..           .       ..+      
T Consensus       366 ~v~i~~~al~~~~~ls~ryi~~r~~P~kai~lld~a~a~~~~--------~~-----------~-------~~~------  413 (731)
T TIGR02639       366 HVKYSDEALEAAVELSARYINDRFLPDKAIDVIDEAGASFRL--------RP-----------K-------AKK------  413 (731)
T ss_pred             CcccCHHHHHHHHHhhhcccccccCCHHHHHHHHHhhhhhhc--------Cc-----------c-------ccc------
Confidence               22222      3458999999999999999998665221        00           0       000      


Q ss_pred             HHHHhhcccCCCcccchhhHHHHHHHHhhhcccCccccccccccccCCCCCCCCcccccccCcchhhhhhhhhccccccc
Q 003038          461 KNEKKATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHKTHRDWAVVEPKQS  540 (854)
Q Consensus       461 ~~~~~~~~~~~d~~~~~~~L~~~w~~~~~~~~~~~~~~~~~~~~~s~~~~s~~~~~~~~~~~~~l~~~~~~~~~~~~~~p  540 (854)
                         .         .                                     .+.       ..++......|.    .+|
T Consensus       414 ---~---------~-------------------------------------~v~-------~~~i~~~i~~~t----giP  433 (731)
T TIGR02639       414 ---K---------A-------------------------------------NVS-------VKDIENVVAKMA----HIP  433 (731)
T ss_pred             ---c---------c-------------------------------------ccC-------HHHHHHHHHHHh----CCC
Confidence               0         0                                     000       011111111111    112


Q ss_pred             hhccccccccccccCCCCCcccccccccccccccccccCCCCCCCCCCccccccchhhhhhhhhhHHHHHHHHHhhcCcc
Q 003038          541 WREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNSTSSSDIMEMEYVHKFKELNSENLTSLCNALEKKV  620 (854)
Q Consensus       541 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~~~v~~~~~~~~~~~e~l~~L~~~L~~~V  620 (854)
                      +                                                         .++...+.++|..|++.|.++|
T Consensus       434 ~---------------------------------------------------------~~~~~~~~~~l~~l~~~l~~~v  456 (731)
T TIGR02639       434 V---------------------------------------------------------KTVSVDDREKLKNLEKNLKAKI  456 (731)
T ss_pred             h---------------------------------------------------------hhhhhHHHHHHHHHHHHHhcce
Confidence            1                                                         2344557889999999999999


Q ss_pred             cccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcC
Q 003038          621 PWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTR  700 (854)
Q Consensus       621 ~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~  700 (854)
                      +||++|+..|+.+|.+.+.|+.+++         ||.++|||+||+|||||++|++||+.++   .+|+++||++|.   
T Consensus       457 ~GQ~~ai~~l~~~i~~~~~g~~~~~---------~p~~~~lf~Gp~GvGKT~lA~~la~~l~---~~~~~~d~se~~---  521 (731)
T TIGR02639       457 FGQDEAIDSLVSSIKRSRAGLGNPN---------KPVGSFLFTGPTGVGKTELAKQLAEALG---VHLERFDMSEYM---  521 (731)
T ss_pred             eCcHHHHHHHHHHHHHHhcCCCCCC---------CCceeEEEECCCCccHHHHHHHHHHHhc---CCeEEEeCchhh---
Confidence            9999999999999999999998864         8899999999999999999999999984   579999999999   


Q ss_pred             CCccccccccccC-CCCCC-chHH--HHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEE
Q 003038          701 ADSTEDSRNKRSR-DEQSC-SYIE--RFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIV  776 (854)
Q Consensus       701 ~~s~e~~~~~rl~-~~~g~-g~~e--~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIi  776 (854)
                          +.|.+++++ .++|| ||.+  .|+++++++|++|||||||||+|+++++.|+++||+|+++|+.|+.|+|+|+||
T Consensus       522 ----~~~~~~~lig~~~gyvg~~~~~~l~~~~~~~p~~VvllDEieka~~~~~~~Ll~~ld~g~~~d~~g~~vd~~~~ii  597 (731)
T TIGR02639       522 ----EKHTVSRLIGAPPGYVGFEQGGLLTEAVRKHPHCVLLLDEIEKAHPDIYNILLQVMDYATLTDNNGRKADFRNVIL  597 (731)
T ss_pred             ----hcccHHHHhcCCCCCcccchhhHHHHHHHhCCCeEEEEechhhcCHHHHHHHHHhhccCeeecCCCcccCCCCCEE
Confidence                788888888 47788 8876  799999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCCC
Q 003038          777 ILSCESF  783 (854)
Q Consensus       777 IlTsn~f  783 (854)
                      |||||..
T Consensus       598 i~Tsn~g  604 (731)
T TIGR02639       598 IMTSNAG  604 (731)
T ss_pred             EECCCcc
Confidence            9999863

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=100.00  E-value=4.9e-80  Score=738.11  Aligned_cols=568  Identities=16%  Similarity=0.240  Sum_probs=446.5

Q ss_pred             hhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhcc-CCCCCCCCCCC
Q 003038           12 LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNR-LPASTSTPMLG   90 (854)
Q Consensus        12 fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~r-lp~~~~~~~~~   90 (854)
                      ||+.+..+|..|+.+|++++|.+|+++|||++|+.++.  +..+|..+|++.   ..+++.+...+.. .|.....+..+
T Consensus         2 ~~~~~~~~l~~a~~~a~~~~~~~~~~~h~l~~l~~~~~--~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~   76 (758)
T PRK11034          2 LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPS--AREALEACSVDL---VALRQELEAFIEQTTPVLPASEEER   76 (758)
T ss_pred             cCHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHcChh--HHHHHHHcCCCH---HHHHHHHHHHHhhcCCcCCCCCCcC
Confidence            78999999999999999999999999999999998765  889999999985   7889999888763 33211100001


Q ss_pred             CCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC--hHHHHHHHhCCCHHHHHHHHHHHhh
Q 003038           91 GHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP--SVSRVMREAGFSSTQVKSNVEQAVS  168 (854)
Q Consensus        91 ~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~--~~~~iL~~~Gi~~~~l~~~v~~~l~  168 (854)
                      +.++++.+.+.|..|...|...    +..         +|+++|||+||++++  .+..+|..+|++...+...+... .
T Consensus        77 ~~~~~~~~~~~l~~a~~~~~~~----~~~---------~i~~~~ll~a~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~-~  142 (758)
T PRK11034         77 DTQPTLSFQRVLQRAVFHVQSS----GRS---------EVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHG-T  142 (758)
T ss_pred             CcCCCHHHHHHHHHHHHHHHHc----CCC---------cccHHHHHHHHhcCCcchHHHHHHHcCCCHHHHHHHHHhC-C
Confidence            1223444444444444444432    112         599999999999974  45679999999988775553310 0


Q ss_pred             hhhc-c-CCCCCCC--CCcccccccccccccccccccCCCCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCHHH
Q 003038          169 LEIC-S-QSTPVSS--NKSKESNVLVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEG  242 (854)
Q Consensus       169 ~~~~-~-~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta  242 (854)
                      .... . .+..+..  ..........+.+|+.|+++.|++|++||+  |+++|++++++|+|++++||+|+||||||||+
T Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~a~~g~~~~liGR~~ei~~~i~iL~r~~~~n~LLvGppGvGKT~  222 (758)
T PRK11034        143 RKDEPSQSSDPGSQPNSEEQAGGEERMENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTA  222 (758)
T ss_pred             ccccccccccccccccccccccchhHHHHHHHhHHHHHHcCCCCcCcCCCHHHHHHHHHHhccCCCCeEEECCCCCCHHH
Confidence            0000 0 0000000  000001124788999999999999999998  99999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCCCcccCCceEEEccccccccc--chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-ccccccccc
Q 003038          243 VVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM--NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQ  319 (854)
Q Consensus       243 ~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~--~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~  319 (854)
                      +|+++|++|..+++|..+.++.+++++++++++|  |+|+||+|++.++++++..  +++||||||||.| +++.+.   
T Consensus       223 lae~la~~i~~~~vP~~l~~~~~~~l~~~~llaG~~~~Ge~e~rl~~l~~~l~~~--~~~ILfIDEIh~L~g~g~~~---  297 (758)
T PRK11034        223 IAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQD--TNSILFIDEIHTIIGAGAAS---  297 (758)
T ss_pred             HHHHHHHHHHhcCCCchhcCCeEEeccHHHHhcccchhhhHHHHHHHHHHHHHhc--CCCEEEeccHHHHhccCCCC---
Confidence            9999999999999999999999999999999976  8999999999999999875  5789999999999 877532   


Q ss_pred             ccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHHHhh----------
Q 003038          320 VRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLI----------  389 (854)
Q Consensus       320 ~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~al~----------  389 (854)
                               .+.++++++|+|...+|++.||||||+++|+++++.||+|+|  ||+.|.|++|+...++.          
T Consensus       298 ---------~g~~d~~nlLkp~L~~g~i~vIgATt~~E~~~~~~~D~AL~r--RFq~I~v~ePs~~~~~~IL~~~~~~ye  366 (758)
T PRK11034        298 ---------GGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALAR--RFQKIDITEPSIEETVQIINGLKPKYE  366 (758)
T ss_pred             ---------CcHHHHHHHHHHHHhCCCeEEEecCChHHHHHHhhccHHHHh--hCcEEEeCCCCHHHHHHHHHHHHHHhh
Confidence                     145789999988333447999999999999999999999999  99999999998765432          


Q ss_pred             ------cccch------hhhccccCCcCCCcccccccchhhhhhhcccccchhhhHHHHhhhhcccCCCCCCCCCChHHH
Q 003038          390 ------TTDSD------LQSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWL  457 (854)
Q Consensus       390 ------~~~s~------~~~~~~~~~~~pdkaidlld~a~~~~~~~c~~~~~~~~e~e~~~~~~~~~~~~~~~~~lp~~l  457 (854)
                            +.+.+      ++.+|++++++|||||||||+|++.+.+                              .|.. 
T Consensus       367 ~~h~v~i~~~al~~a~~ls~ryi~~r~lPdKaidlldea~a~~~~------------------------------~~~~-  415 (758)
T PRK11034        367 AHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARL------------------------------MPVS-  415 (758)
T ss_pred             hccCCCcCHHHHHHHHHHhhccccCccChHHHHHHHHHHHHhhcc------------------------------Cccc-
Confidence                  23333      2458999999999999999998765221                              0100 


Q ss_pred             HhhHHHHhhcccCCCcccchhhHHHHHHHHhhhcccCccccccccccccCCCCCCCCcccccccCcchhhhhhhhhcccc
Q 003038          458 QQYKNEKKATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHKTHRDWAVVEP  537 (854)
Q Consensus       458 ~~~~~~~~~~~~~~d~~~~~~~L~~~w~~~~~~~~~~~~~~~~~~~~~s~~~~s~~~~~~~~~~~~~l~~~~~~~~~~~~  537 (854)
                           ...                                  ..           +.       ..++.+....|.    
T Consensus       416 -----~~~----------------------------------~~-----------v~-------~~~i~~v~~~~t----  434 (758)
T PRK11034        416 -----KRK----------------------------------KT-----------VN-------VADIESVVARIA----  434 (758)
T ss_pred             -----ccc----------------------------------cc-----------cC-------hhhHHHHHHHHh----
Confidence                 000                                  00           00       011121111121    


Q ss_pred             ccchhccccccccccccCCCCCcccccccccccccccccccCCCCCCCCCCccccccchhhhhhhhhhHHHHHHHHHhhc
Q 003038          538 KQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNSTSSSDIMEMEYVHKFKELNSENLTSLCNALE  617 (854)
Q Consensus       538 ~~p~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~~~v~~~~~~~~~~~e~l~~L~~~L~  617 (854)
                      .+|                                                      +   .++.+.+.++++.|++.|.
T Consensus       435 gip------------------------------------------------------~---~~~~~~~~~~l~~l~~~L~  457 (758)
T PRK11034        435 RIP------------------------------------------------------E---KSVSQSDRDTLKNLGDRLK  457 (758)
T ss_pred             CCC------------------------------------------------------h---hhhhhhHHHHHHHHHHHhc
Confidence            111                                                      1   3344567889999999999


Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ++|+||++|+..|+.+|.+.++|+.+++         ||.++|||+||+|||||++|++||+.+   +.+|+++||++|.
T Consensus       458 ~~ViGQ~~ai~~l~~~i~~~~~gl~~~~---------kp~~~~Lf~GP~GvGKT~lAk~LA~~l---~~~~i~id~se~~  525 (758)
T PRK11034        458 MLVFGQDKAIEALTEAIKMSRAGLGHEH---------KPVGSFLFAGPTGVGKTEVTVQLSKAL---GIELLRFDMSEYM  525 (758)
T ss_pred             ceEeCcHHHHHHHHHHHHHHhccccCCC---------CCcceEEEECCCCCCHHHHHHHHHHHh---CCCcEEeechhhc
Confidence            9999999999999999999999998864         889999999999999999999999998   3689999999998


Q ss_pred             CcCCCccccccccccCC-CCCC-chHH--HHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCC
Q 003038          698 STRADSTEDSRNKRSRD-EQSC-SYIE--RFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGD  773 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~-~~g~-g~~e--~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~  773 (854)
                             +.+.++++++ ++|| ||.+  .|+++++++|++|||||||||+|+++|+.|+++||+|+++|..|++++|+|
T Consensus       526 -------~~~~~~~LiG~~~gyvg~~~~g~L~~~v~~~p~sVlllDEieka~~~v~~~LLq~ld~G~ltd~~g~~vd~rn  598 (758)
T PRK11034        526 -------ERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNLLLQVMDNGTLTDNNGRKADFRN  598 (758)
T ss_pred             -------ccccHHHHcCCCCCcccccccchHHHHHHhCCCcEEEeccHhhhhHHHHHHHHHHHhcCeeecCCCceecCCC
Confidence                   7777888884 6788 8875  799999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEecCC
Q 003038          774 AIVILSCES  782 (854)
Q Consensus       774 aIiIlTsn~  782 (854)
                      +|||||||.
T Consensus       599 ~iiI~TsN~  607 (758)
T PRK11034        599 VVLVMTTNA  607 (758)
T ss_pred             cEEEEeCCc
Confidence            999999983

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=99.89  E-value=1.6e-23  Score=210.70  Aligned_cols=116  Identities=22%  Similarity=0.342  Sum_probs=97.2

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHh-CCCCceEEEccccccCcCCCccccccccccC-CCCCC-chHHHHHHHHHcC
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVF-GSHNNFVSIALSSFSSTRADSTEDSRNKRSR-DEQSC-SYIERFAEAVSNN  731 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lf-g~~~~~i~id~s~~~~~~~~s~e~~~~~rl~-~~~g~-g~~e~L~eav~~~  731 (854)
                      ||.++|||+||+|||||+||++||+.+| ++..+|+++||++|+...+   ..+.+.+++ .+++| ++.          
T Consensus         1 ~p~~~~ll~GpsGvGKT~la~~la~~l~~~~~~~~~~~d~s~~~~~~~---~~~~~~~l~~~~~~~v~~~----------   67 (171)
T PF07724_consen    1 RPKSNFLLAGPSGVGKTELAKALAELLFVGSERPLIRIDMSEYSEGDD---VESSVSKLLGSPPGYVGAE----------   67 (171)
T ss_dssp             S-SEEEEEESSTTSSHHHHHHHHHHHHT-SSCCEEEEEEGGGHCSHHH---CSCHCHHHHHHTTCHHHHH----------
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHhccCCccchHHHhhhcccccch---HHhhhhhhhhcccceeecc----------
Confidence            4788999999999999999999999999 8999999999999992000   055566655 34444 332          


Q ss_pred             CCEEEEEecCCCCCH-----------HHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCC
Q 003038          732 PHRVFLIEDVEQADY-----------CSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       732 p~~ViliDEieka~~-----------~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                      ++.|||||||||+|+           .||+.||++||+|+++|.+|++|+|+|+|||||||..
T Consensus        68 ~~gVVllDEidKa~~~~~~~~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~~  130 (171)
T PF07724_consen   68 EGGVVLLDEIDKAHPSNSGGADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNFG  130 (171)
T ss_dssp             HHTEEEEETGGGCSHTTTTCSHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESSS
T ss_pred             chhhhhhHHHhhccccccccchhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEecccc
Confidence            233999999999999           9999999999999999999999999999999999853

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.89  E-value=9.9e-22  Score=220.53  Aligned_cols=134  Identities=13%  Similarity=0.123  Sum_probs=105.2

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      -.+.++|+||||||||.+++++|..          .++.|++++...+++|+.||.|+++++||+.+++.  .|||+|||
T Consensus       222 PprGvLlHGPPGCGKT~lA~AiAge----------l~vPf~~isApeivSGvSGESEkkiRelF~~A~~~--aPcivFiD  289 (802)
T KOG0733|consen  222 PPRGVLLHGPPGCGKTSLANAIAGE----------LGVPFLSISAPEIVSGVSGESEKKIRELFDQAKSN--APCIVFID  289 (802)
T ss_pred             CCCceeeeCCCCccHHHHHHHHhhh----------cCCceEeecchhhhcccCcccHHHHHHHHHHHhcc--CCeEEEee
Confidence            4567899999999999999999976          47899999999999999999999999999999987  79999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcc-c----CCCCceEEEEEecCHHHHHHhhccCCchhhhhcc---CC
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVC-G----IGENARFWLMGIATFQSYMRCKSGHPSLETLWSL---HP  376 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~-~----~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~---~~  376 (854)
                      ||+.+ ..+..+.      .....+.|..+-+.+- .    ..| ..+.+||||+-..     ..||+|.|.-||   -.
T Consensus       290 eIDAI~pkRe~aq------reMErRiVaQLlt~mD~l~~~~~~g-~~VlVIgATnRPD-----slDpaLRRaGRFdrEI~  357 (802)
T KOG0733|consen  290 EIDAITPKREEAQ------REMERRIVAQLLTSMDELSNEKTKG-DPVLVIGATNRPD-----SLDPALRRAGRFDREIC  357 (802)
T ss_pred             cccccccchhhHH------HHHHHHHHHHHHHhhhcccccccCC-CCeEEEecCCCCc-----ccCHHHhccccccceee
Confidence            99999 6554321      2233466666555552 1    112 2699999999655     579999997777   34


Q ss_pred             CCCCCch
Q 003038          377 LTIPAGS  383 (854)
Q Consensus       377 v~i~~~s  383 (854)
                      +.||+..
T Consensus       358 l~vP~e~  364 (802)
T KOG0733|consen  358 LGVPSET  364 (802)
T ss_pred             ecCCchH
Confidence            5666554

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.77  E-value=4.3e-17  Score=199.08  Aligned_cols=135  Identities=11%  Similarity=0.140  Sum_probs=97.3

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..++++|+||||+|||++++++|...          +..++.++...+.+.+.|+.+++++.+++.+...  .|.|||||
T Consensus       211 ~~~giLL~GppGtGKT~laraia~~~----------~~~~i~i~~~~i~~~~~g~~~~~l~~lf~~a~~~--~p~il~iD  278 (733)
T TIGR01243       211 PPKGVLLYGPPGTGKTLLAKAVANEA----------GAYFISINGPEIMSKYYGESEERLREIFKEAEEN--APSIIFID  278 (733)
T ss_pred             CCceEEEECCCCCChHHHHHHHHHHh----------CCeEEEEecHHHhcccccHHHHHHHHHHHHHHhc--CCcEEEee
Confidence            34689999999999999999999864          4578999988888889999999999999999875  68999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCch
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGS  383 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~s  383 (854)
                      ||+.+ ..+......      .-......+.+++.....++.+.+||+|+..+.     .||+|.|.-|| ..+.++.|+
T Consensus       279 Eid~l~~~r~~~~~~------~~~~~~~~Ll~~ld~l~~~~~vivI~atn~~~~-----ld~al~r~gRfd~~i~i~~P~  347 (733)
T TIGR01243       279 EIDAIAPKREEVTGE------VEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDA-----LDPALRRPGRFDREIVIRVPD  347 (733)
T ss_pred             hhhhhcccccCCcch------HHHHHHHHHHHHhhccccCCCEEEEeecCChhh-----cCHHHhCchhccEEEEeCCcC
Confidence            99999 554321000      011234455555533123346999999987653     48888774455 234555444

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.

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=99.75  E-value=5.4e-18  Score=191.16  Aligned_cols=151  Identities=13%  Similarity=0.153  Sum_probs=116.9

Q ss_pred             HHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCc--ccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC
Q 003038          609 LTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMR--RKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN  686 (854)
Q Consensus       609 l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~--~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~  686 (854)
                      .+.|++.|.+.|+||++|+..++.+|.+.+.++..  ......  --..+.+++||.||+|+|||++|++||+.+   ..
T Consensus        68 p~~i~~~L~~~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~--~~~~~~~~iLL~GP~GsGKT~lAraLA~~l---~~  142 (413)
T TIGR00382        68 PKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDN--GVELSKSNILLIGPTGSGKTLLAQTLARIL---NV  142 (413)
T ss_pred             HHHHHHHhcceecCHHHHHHHHHHHHHHHHhhhcccccccccc--ccccCCceEEEECCCCcCHHHHHHHHHHhc---CC
Confidence            46899999999999999999999999887777654  110000  000124689999999999999999999877   34


Q ss_pred             ceEEEccccccCcCCCccccccccccCCCCCC-chH--HHHHHHHHcCCC-------EEEEEecCCCCCH----------
Q 003038          687 NFVSIALSSFSSTRADSTEDSRNKRSRDEQSC-SYI--ERFAEAVSNNPH-------RVFLIEDVEQADY----------  746 (854)
Q Consensus       687 ~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~~--e~L~eav~~~p~-------~ViliDEieka~~----------  746 (854)
                      +|+.++++.+.                 +++| |+.  ..|.++++..++       .|||||||||+++          
T Consensus       143 pf~~~da~~L~-----------------~~gyvG~d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~~~~~~~s~~~d  205 (413)
T TIGR00382       143 PFAIADATTLT-----------------EAGYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRD  205 (413)
T ss_pred             CeEEechhhcc-----------------ccccccccHHHHHHHHHHhCcccHHhcccceEEecccchhchhhcccccccc
Confidence            67777766443                 2344 553  256666665444       5999999999998          


Q ss_pred             ----HHHHHHHHhhhcCeEec---CCCceeecCCeEEEEecCC
Q 003038          747 ----CSQKGFKRAIESGRIVT---SSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       747 ----~v~~~Ll~~le~G~l~d---~~G~~v~~~~aIiIlTsn~  782 (854)
                          .+|+.||++| +|.++|   ..|+.++|+|+|+|+|||.
T Consensus       206 vsg~~vq~~LL~iL-eG~~~~v~~~~gr~~~~~~~i~i~TsNi  247 (413)
T TIGR00382       206 VSGEGVQQALLKII-EGTVANVPPQGGRKHPYQEFIQIDTSNI  247 (413)
T ss_pred             ccchhHHHHHHHHh-hccceecccCCCccccCCCeEEEEcCCc
Confidence                6999999999 599987   6789999999999999996

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.75  E-value=3.2e-17  Score=187.36  Aligned_cols=134  Identities=12%  Similarity=0.094  Sum_probs=102.3

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      -.++++++||||+|||.+|+++|++          .+++++.++...++..+-||.|..|+..++++.+. ..|.|+|||
T Consensus       217 ~prg~Ll~gppg~Gkt~l~~aVa~e----------~~a~~~~i~~peli~k~~gEte~~LR~~f~~a~k~-~~psii~Id  285 (693)
T KOG0730|consen  217 PPRGLLLYGPPGTGKTFLVRAVANE----------YGAFLFLINGPELISKFPGETESNLRKAFAEALKF-QVPSIIFID  285 (693)
T ss_pred             CCCCccccCCCCCChHHHHHHHHHH----------hCceeEecccHHHHHhcccchHHHHHHHHHHHhcc-CCCeeEeHH
Confidence            5678999999999999999999987          57899999999999999999999999999999987 339999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCch
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGS  383 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~s  383 (854)
                      ||+.+ +.+....       ......+..+-.|+....+.+.+.+|++|.-..     ..||++.| -|| +-|.|.-|+
T Consensus       286 Eld~l~p~r~~~~-------~~e~Rv~sqlltL~dg~~~~~~vivl~atnrp~-----sld~alRR-gRfd~ev~IgiP~  352 (693)
T KOG0730|consen  286 ELDALCPKREGAD-------DVESRVVSQLLTLLDGLKPDAKVIVLAATNRPD-----SLDPALRR-GRFDREVEIGIPG  352 (693)
T ss_pred             hHhhhCCcccccc-------hHHHHHHHHHHHHHhhCcCcCcEEEEEecCCcc-----ccChhhhc-CCCcceeeecCCC
Confidence            99999 5443210       123356666667764322233699999997544     47899886 455 444444333

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=99.64  E-value=8.7e-16  Score=174.22  Aligned_cols=152  Identities=13%  Similarity=0.139  Sum_probs=112.5

Q ss_pred             HHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCce
Q 003038          609 LTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNF  688 (854)
Q Consensus       609 l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~  688 (854)
                      .+.+...|.+.|+||++|+..|+.+|.....++.......  .....+..++||.||+|+|||++|++||+.+   ..+|
T Consensus        62 p~~i~~~L~~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~--~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l---~~pf  136 (412)
T PRK05342         62 PKEIKAHLDQYVIGQERAKKVLSVAVYNHYKRLRHGDKKD--DDVELQKSNILLIGPTGSGKTLLAQTLARIL---DVPF  136 (412)
T ss_pred             HHHHHHHHhhHeeChHHHHHHHHHHHHHHHHhhhcccccc--cccccCCceEEEEcCCCCCHHHHHHHHHHHh---CCCc
Confidence            4688899999999999999999999865433332211000  0001245689999999999999999999987   4689


Q ss_pred             EEEccccccCcCCCccccccccccCCCCCC-chH-H-HHHHH-------HHcCCCEEEEEecCCCCCH------------
Q 003038          689 VSIALSSFSSTRADSTEDSRNKRSRDEQSC-SYI-E-RFAEA-------VSNNPHRVFLIEDVEQADY------------  746 (854)
Q Consensus       689 i~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~~-e-~L~ea-------v~~~p~~ViliDEieka~~------------  746 (854)
                      +++|++.++.                 .+| |.. + .+...       +...+++||||||||++++            
T Consensus       137 ~~id~~~l~~-----------------~gyvG~d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~~~~~~~~~~~d~s  199 (412)
T PRK05342        137 AIADATTLTE-----------------AGYVGEDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIARKSENPSITRDVS  199 (412)
T ss_pred             eecchhhccc-----------------CCcccchHHHHHHHHHHhccccHHHcCCcEEEEechhhhccccCCCCcCCCcc
Confidence            9999987761                 123 332 1 23332       3445789999999999986            


Q ss_pred             --HHHHHHHHhhhcCe--EecCCCceeecCCeEEEEecCC
Q 003038          747 --CSQKGFKRAIESGR--IVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       747 --~v~~~Ll~~le~G~--l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                        .+|+.||++||.+.  +++..|+..++.+.|+|+|+|.
T Consensus       200 ~~~vQ~~LL~~Leg~~~~v~~~gg~~~~~~~~~~i~t~ni  239 (412)
T PRK05342        200 GEGVQQALLKILEGTVASVPPQGGRKHPQQEFIQVDTTNI  239 (412)
T ss_pred             cHHHHHHHHHHHhcCeEEeCCCCCcCcCCCCeEEeccCCc
Confidence              39999999998543  3567889999999999999996

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=99.56  E-value=1.3e-14  Score=152.91  Aligned_cols=148  Identities=18%  Similarity=0.141  Sum_probs=111.6

Q ss_pred             HHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc
Q 003038          608 NLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN  687 (854)
Q Consensus       608 ~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~  687 (854)
                      ++..|++.|..+++||.-++..|..+|.....   +++       |.|| .++-|+|++|+||..+++.||+.+|.... 
T Consensus        72 ~~~~Le~dL~~~lfGQHla~~~Vv~alk~~~~---n~~-------p~KP-LvLSfHG~tGTGKN~Va~iiA~n~~~~Gl-  139 (344)
T KOG2170|consen   72 DLDGLEKDLARALFGQHLAKQLVVNALKSHWA---NPN-------PRKP-LVLSFHGWTGTGKNYVAEIIAENLYRGGL-  139 (344)
T ss_pred             cchHHHHHHHHHhhchHHHHHHHHHHHHHHhc---CCC-------CCCC-eEEEecCCCCCchhHHHHHHHHHHHhccc-
Confidence            36789999999999999999999999988765   222       2366 48999999999999999999999985431 


Q ss_pred             eEEEccccccCcCCCccccccccccCCC-CCC--chHHH----HHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCe
Q 003038          688 FVSIALSSFSSTRADSTEDSRNKRSRDE-QSC--SYIER----FAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       688 ~i~id~s~~~~~~~~s~e~~~~~rl~~~-~g~--g~~e~----L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~  760 (854)
                           +|.|.        .+.+.++-.| +.+  .|.++    +.+-++.++.++++|||+||+|+.+.+.|...+|...
T Consensus       140 -----~S~~V--------~~fvat~hFP~~~~ie~Yk~eL~~~v~~~v~~C~rslFIFDE~DKmp~gLld~lkpfLdyyp  206 (344)
T KOG2170|consen  140 -----RSPFV--------HHFVATLHFPHASKIEDYKEELKNRVRGTVQACQRSLFIFDEVDKLPPGLLDVLKPFLDYYP  206 (344)
T ss_pred             -----cchhH--------HHhhhhccCCChHHHHHHHHHHHHHHHHHHHhcCCceEEechhhhcCHhHHHHHhhhhcccc
Confidence                 12221        1112222111 222  45554    5555667899999999999999999999999999755


Q ss_pred             EecCCCceeecCCeEEEEecCCCC
Q 003038          761 IVTSSGDEVSLGDAIVILSCESFS  784 (854)
Q Consensus       761 l~d~~G~~v~~~~aIiIlTsn~f~  784 (854)
                      ..++    ++|++|||||-||.-.
T Consensus       207 ~v~g----v~frkaIFIfLSN~gg  226 (344)
T KOG2170|consen  207 QVSG----VDFRKAIFIFLSNAGG  226 (344)
T ss_pred             cccc----ccccceEEEEEcCCcc
Confidence            5443    9999999999998543

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=99.48  E-value=1.6e-12  Score=150.46  Aligned_cols=155  Identities=17%  Similarity=0.167  Sum_probs=105.7

Q ss_pred             CCCCCC-cHHHHHHHHHHhhccCcC---------CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc
Q 003038          205 VSLDPI-RNEDVMYVIENLMSKRKR---------NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR  274 (854)
Q Consensus       205 g~ldpv-r~~ei~~v~~~L~r~~k~---------n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~  274 (854)
                      +.+.+. ++.-+..+.++|.-+...         .++|+|+||+|||++|+.+|..+          |.+|+.+|..+|.
T Consensus       399 n~~~~~~~~~~~~~l~~vl~p~~~~s~~~~~~~~~vLLhG~~g~GK~t~V~~vas~l----------g~h~~evdc~el~  468 (953)
T KOG0736|consen  399 NSLSPPGLEAKVLELVAVLSPQKQPSGALLTLNPSVLLHGPPGSGKTTVVRAVASEL----------GLHLLEVDCYELV  468 (953)
T ss_pred             ccCCCccchHHHHHHHHHhCcccCcchhccccceEEEEeCCCCCChHHHHHHHHHHh----------CCceEeccHHHHh
Confidence            444444 777788888998754222         26899999999999999999884          8899999999999


Q ss_pred             ccchHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcc---cCCCCceEEEE
Q 003038          275 HMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVC---GIGENARFWLM  350 (854)
Q Consensus       275 ~~~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~---~~~g~g~l~lI  350 (854)
                      +...+-.|.++...+..++.+  .|+|||+-.+..+ ....++     +..    ....-+..++.   .....+.+.+|
T Consensus       469 ~~s~~~~etkl~~~f~~a~~~--~pavifl~~~dvl~id~dgg-----ed~----rl~~~i~~~ls~e~~~~~~~~~ivv  537 (953)
T KOG0736|consen  469 AESASHTETKLQAIFSRARRC--SPAVLFLRNLDVLGIDQDGG-----EDA----RLLKVIRHLLSNEDFKFSCPPVIVV  537 (953)
T ss_pred             hcccchhHHHHHHHHHHHhhc--CceEEEEeccceeeecCCCc-----hhH----HHHHHHHHHHhcccccCCCCceEEE
Confidence            999999999999999999986  7999999999988 222211     000    01111111222   11112369999


Q ss_pred             EecCHHHHHHhhccCCchhhhhccCCCCCCCchHHH
Q 003038          351 GIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSL  386 (854)
Q Consensus       351 gatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~  386 (854)
                      |+|+..+      .=|+--+---+|.+.|+.++-+.
T Consensus       538 ~t~~s~~------~lp~~i~~~f~~ei~~~~lse~q  567 (953)
T KOG0736|consen  538 ATTSSIE------DLPADIQSLFLHEIEVPALSEEQ  567 (953)
T ss_pred             Eeccccc------cCCHHHHHhhhhhccCCCCCHHH
Confidence            9998644      22333332245777777766444

>TIGR00763 lon ATP-dependent protease La

Probab=99.41  E-value=8.9e-13  Score=161.89  Aligned_cols=160  Identities=15%  Similarity=0.199  Sum_probs=111.6

Q ss_pred             HHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC
Q 003038          606 SENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH  685 (854)
Q Consensus       606 ~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~  685 (854)
                      ..+++.+++.|.+.++||++++..|...+...+.. ...          +. ..++|+||+|||||++|++||+.+   .
T Consensus       308 ~~~~~~~~~~l~~~~~G~~~~k~~i~~~~~~~~~~-~~~----------~~-~~lll~GppG~GKT~lAk~iA~~l---~  372 (775)
T TIGR00763       308 NLDLKRAKEILDEDHYGLKKVKERILEYLAVQKLR-GKM----------KG-PILCLVGPPGVGKTSLGKSIAKAL---N  372 (775)
T ss_pred             hhhHHHHHHHhhhhcCChHHHHHHHHHHHHHHHhh-cCC----------CC-ceEEEECCCCCCHHHHHHHHHHHh---c
Confidence            56789999999999999999999999866543220 010          11 279999999999999999999998   3


Q ss_pred             CceEEEccccccCcCCCccccccccccCCCCCCchH-HHHHHHHHcCCCEEEEEecCCCCCHHH----HHHHHHhhhc--
Q 003038          686 NNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYI-ERFAEAVSNNPHRVFLIEDVEQADYCS----QKGFKRAIES--  758 (854)
Q Consensus       686 ~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~-e~L~eav~~~p~~ViliDEieka~~~v----~~~Ll~~le~--  758 (854)
                      .+|++++++........  ..|. ...++ ...|+. +.+..+.+.+|  |||||||||+++..    .+.|+++||.  
T Consensus       373 ~~~~~i~~~~~~~~~~i--~g~~-~~~~g-~~~g~i~~~l~~~~~~~~--villDEidk~~~~~~~~~~~aLl~~ld~~~  446 (775)
T TIGR00763       373 RKFVRFSLGGVRDEAEI--RGHR-RTYVG-AMPGRIIQGLKKAKTKNP--LFLLDEIDKIGSSFRGDPASALLEVLDPEQ  446 (775)
T ss_pred             CCeEEEeCCCcccHHHH--cCCC-CceeC-CCCchHHHHHHHhCcCCC--EEEEechhhcCCccCCCHHHHHHHhcCHHh
Confidence            57899987755410000  0111 11111 111332 23334333444  99999999997754    4899999984  


Q ss_pred             -CeEecCC-CceeecCCeEEEEecCCCCCC
Q 003038          759 -GRIVTSS-GDEVSLGDAIVILSCESFSSR  786 (854)
Q Consensus       759 -G~l~d~~-G~~v~~~~aIiIlTsn~f~~~  786 (854)
                       +.++|.. +..+++++++||+|+|..+..
T Consensus       447 ~~~f~d~~~~~~~d~s~v~~I~TtN~~~~i  476 (775)
T TIGR00763       447 NNAFSDHYLDVPFDLSKVIFIATANSIDTI  476 (775)
T ss_pred             cCccccccCCceeccCCEEEEEecCCchhC
Confidence             7888864 788999999999999976543

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.

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=99.41  E-value=5.4e-13  Score=154.40  Aligned_cols=144  Identities=13%  Similarity=0.147  Sum_probs=108.9

Q ss_pred             HHHHHHHHHH-------hhcc--CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHH
Q 003038          212 NEDVMYVIEN-------LMSK--RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVE  282 (854)
Q Consensus       212 ~~ei~~v~~~-------L~r~--~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E  282 (854)
                      ..||...|+.       +..+  ++..++|+||||+|||-+|+++|-.          ....|+++....|+.||.||.|
T Consensus       681 K~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATE----------csL~FlSVKGPELLNMYVGqSE  750 (953)
T KOG0736|consen  681 KTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATE----------CSLNFLSVKGPELLNMYVGQSE  750 (953)
T ss_pred             HHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhh----------ceeeEEeecCHHHHHHHhcchH
Confidence            3455555544       4443  4567999999999999999999987          3678999999999999999999


Q ss_pred             HHHHHHHHHHHhhhCCCeEEEeCccccc-c-ccccccccccccchhhhHHHHHHHhhc-ccC-CCCceEEEEEecCHHHH
Q 003038          283 QRVEEIKNLVRSCLGRGIVLNLGDLEWA-E-FRASSSEQVRGYYCSIEHIIMEIGKLV-CGI-GENARFWLMGIATFQSY  358 (854)
Q Consensus       283 ~rl~~l~~~~~~~~~~~~ILfidel~~l-~-~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~~-~g~g~l~lIgatT~~ey  358 (854)
                      +.++++|+.+++.  .|||+|+|||+.+ . .|.++..|     .+||+.|..+-.=| +.. .....+.+||||+....
T Consensus       751 ~NVR~VFerAR~A--~PCVIFFDELDSlAP~RG~sGDSG-----GVMDRVVSQLLAELDgls~~~s~~VFViGATNRPDL  823 (953)
T KOG0736|consen  751 ENVREVFERARSA--APCVIFFDELDSLAPNRGRSGDSG-----GVMDRVVSQLLAELDGLSDSSSQDVFVIGATNRPDL  823 (953)
T ss_pred             HHHHHHHHHhhcc--CCeEEEeccccccCccCCCCCCcc-----ccHHHHHHHHHHHhhcccCCCCCceEEEecCCCccc
Confidence            9999999999987  7999999999999 4 44333222     35667665543333 221 12247999999997663


Q ss_pred             HHhhccCCchhhhhccCCC
Q 003038          359 MRCKSGHPSLETLWSLHPL  377 (854)
Q Consensus       359 ~k~~~~~pale~~~~~~~v  377 (854)
                           -||||-|--||..+
T Consensus       824 -----LDpALLRPGRFDKL  837 (953)
T KOG0736|consen  824 -----LDPALLRPGRFDKL  837 (953)
T ss_pred             -----cChhhcCCCcccee
Confidence                 69999987777544

>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=99.37  E-value=7.8e-12  Score=129.05  Aligned_cols=107  Identities=16%  Similarity=0.212  Sum_probs=70.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +.++||++++..+.-.+...+.    +         ..+..++||+||||+|||+||+.||+.+   ..+|..+......
T Consensus        24 ~efiGQ~~l~~~l~i~i~aa~~----r---------~~~l~h~lf~GPPG~GKTTLA~IIA~e~---~~~~~~~sg~~i~   87 (233)
T PF05496_consen   24 DEFIGQEHLKGNLKILIRAAKK----R---------GEALDHMLFYGPPGLGKTTLARIIANEL---GVNFKITSGPAIE   87 (233)
T ss_dssp             CCS-S-HHHHHHHHHHHHHHHC----T---------TS---EEEEESSTTSSHHHHHHHHHHHC---T--EEEEECCC--
T ss_pred             HHccCcHHHHhhhHHHHHHHHh----c---------CCCcceEEEECCCccchhHHHHHHHhcc---CCCeEeccchhhh
Confidence            5689999999987766665543    1         1456799999999999999999999988   2345443322111


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHc-CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSN-NPHRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~-~p~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                                           .. ..|...+.. .+..|+||||||++++.+|+.|+.+||+|.+.
T Consensus        88 ---------------------k~-~dl~~il~~l~~~~ILFIDEIHRlnk~~qe~LlpamEd~~id  131 (233)
T PF05496_consen   88 ---------------------KA-GDLAAILTNLKEGDILFIDEIHRLNKAQQEILLPAMEDGKID  131 (233)
T ss_dssp             ---------------------SC-HHHHHHHHT--TT-EEEECTCCC--HHHHHHHHHHHHCSEEE
T ss_pred             ---------------------hH-HHHHHHHHhcCCCcEEEEechhhccHHHHHHHHHHhccCeEE
Confidence                                 00 112222222 45779999999999999999999999999985

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.

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=99.37  E-value=1.2e-12  Score=138.73  Aligned_cols=136  Identities=18%  Similarity=0.243  Sum_probs=92.9

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC---CceEEEcccc
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH---NNFVSIALSS  695 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~---~~~i~id~s~  695 (854)
                      .+.||+++|..+.+++.+ |-                 ..++||+||+|+|||..|+++|+.+|+..   ..+...+.|.
T Consensus        37 e~~gQe~vV~~L~~a~~~-~~-----------------lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSd   98 (346)
T KOG0989|consen   37 ELAGQEHVVQVLKNALLR-RI-----------------LPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASD   98 (346)
T ss_pred             hhcchHHHHHHHHHHHhh-cC-----------------CceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccc
Confidence            479999999999999987 32                 34899999999999999999999999832   1112222221


Q ss_pred             ccCcCCCccccccccccCCCCCCchHHHHHHHH------HcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIERFAEAV------SNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav------~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      ..   ..+        .+....++|.. +....      -..|+.||+|||.|-|..+.|++|++.||+           
T Consensus        99 er---Gis--------vvr~Kik~fak-l~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~-----------  155 (346)
T KOG0989|consen   99 ER---GIS--------VVREKIKNFAK-LTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMED-----------  155 (346)
T ss_pred             cc---ccc--------chhhhhcCHHH-HhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhc-----------
Confidence            11   000        11111112222 11111      124679999999999999999999999995           


Q ss_pred             ecCCeEEEEecCCCCCCCCC-CCCCcc
Q 003038          770 SLGDAIVILSCESFSSRSRA-CSPPTK  795 (854)
Q Consensus       770 ~~~~aIiIlTsn~f~~~s~~-~sp~~~  795 (854)
                      .-+++.|||-||..+-..+. .|.|+|
T Consensus       156 ~s~~trFiLIcnylsrii~pi~SRC~K  182 (346)
T KOG0989|consen  156 FSRTTRFILICNYLSRIIRPLVSRCQK  182 (346)
T ss_pred             cccceEEEEEcCChhhCChHHHhhHHH
Confidence            23578899999887655555 466665

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=99.36  E-value=1.7e-12  Score=144.87  Aligned_cols=147  Identities=16%  Similarity=0.180  Sum_probs=116.8

Q ss_pred             HHHHHHHHHHhhc---------cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHH
Q 003038          212 NEDVMYVIENLMS---------KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVE  282 (854)
Q Consensus       212 ~~ei~~v~~~L~r---------~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E  282 (854)
                      ..|+..|++-|.-         +-.+.++||||||+|||-+++++|-.          .++.|+...-+.|--+|.|.-.
T Consensus       313 K~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGE----------A~VPFF~~sGSEFdEm~VGvGA  382 (752)
T KOG0734|consen  313 KQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGE----------AGVPFFYASGSEFDEMFVGVGA  382 (752)
T ss_pred             HHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcc----------cCCCeEeccccchhhhhhcccH
Confidence            4678888887653         34578999999999999999999854          6788999999989889999999


Q ss_pred             HHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcc-c--CCCCceEEEEEecCHHHH
Q 003038          283 QRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVC-G--IGENARFWLMGIATFQSY  358 (854)
Q Consensus       283 ~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~-~--~~g~g~l~lIgatT~~ey  358 (854)
                      .|+++||..+++.  .|||+|||||+.+ +.+...         ...|+-+.+.+||- .  ...+-.|.+||||++.+ 
T Consensus       383 rRVRdLF~aAk~~--APcIIFIDEiDavG~kR~~~---------~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe-  450 (752)
T KOG0734|consen  383 RRVRDLFAAAKAR--APCIIFIDEIDAVGGKRNPS---------DQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNFPE-  450 (752)
T ss_pred             HHHHHHHHHHHhc--CCeEEEEechhhhcccCCcc---------HHHHHHHHHHHHHHHhcCcCcCCceEEEeccCChh-
Confidence            9999999999986  7999999999999 655432         22367778888882 2  11222599999999988 


Q ss_pred             HHhhccCCchhhhhcc-CCCCCCCchH
Q 003038          359 MRCKSGHPSLETLWSL-HPLTIPAGSL  384 (854)
Q Consensus       359 ~k~~~~~pale~~~~~-~~v~i~~~sl  384 (854)
                          .-||||-|--|| -.|+||-|.+
T Consensus       451 ----~LD~AL~RPGRFD~~v~Vp~PDv  473 (752)
T KOG0734|consen  451 ----ALDKALTRPGRFDRHVTVPLPDV  473 (752)
T ss_pred             ----hhhHHhcCCCccceeEecCCCCc
Confidence                468999986666 4567776664

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=99.35  E-value=4e-13  Score=154.43  Aligned_cols=175  Identities=17%  Similarity=0.158  Sum_probs=124.5

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..|.+++...|.                 .+.+||.||.|||||++||.+|+.|-.. ..-..-=|.++.
T Consensus        16 ~evvGQe~v~~~L~nal~~~ri-----------------~hAYlfsG~RGvGKTt~Ari~AkalNC~-~~~~~ePC~~C~   77 (515)
T COG2812          16 DDVVGQEHVVKTLSNALENGRI-----------------AHAYLFSGPRGVGKTTIARILAKALNCE-NGPTAEPCGKCI   77 (515)
T ss_pred             HHhcccHHHHHHHHHHHHhCcc-----------------hhhhhhcCCCCcCchhHHHHHHHHhcCC-CCCCCCcchhhh
Confidence            3469999999999999998654                 4689999999999999999999999432 110000011111


Q ss_pred             CcCCCccccccccccC--CCCCC-chHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCce
Q 003038          698 STRADSTEDSRNKRSR--DEQSC-SYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDE  768 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~--~~~g~-g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~  768 (854)
                      .+...  ...+...++  +.... |.++  .|.+.+...|    |.|++|||+|.++...+|+||+.+|+          
T Consensus        78 ~Ck~I--~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS~~afNALLKTLEE----------  145 (515)
T COG2812          78 SCKEI--NEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSKQAFNALLKTLEE----------  145 (515)
T ss_pred             hhHhh--hcCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhhHHHHHHHhccccc----------
Confidence            00000  111122222  22222 5555  7888888877    78999999999999999999999997          


Q ss_pred             eecCCeEEEE-ecCCCCCCCCCCCCCcc---CCCCC------------------ch-------hhcccccCCCCCceeee
Q 003038          769 VSLGDAIVIL-SCESFSSRSRACSPPTK---QKSDG------------------CE-------EEKGAAMEGTSPSVSLD  819 (854)
Q Consensus       769 v~~~~aIiIl-Tsn~f~~~s~~~sp~~~---~~~~~------------------~~-------~~~~~~~~~~~~~~~~~  819 (854)
                       ...+++||| |++....+.+..|.|++   +|+..                  ++       ...+|+++|.-+-+|+=
T Consensus       146 -PP~hV~FIlATTe~~Kip~TIlSRcq~f~fkri~~~~I~~~L~~i~~~E~I~~e~~aL~~ia~~a~Gs~RDalslLDq~  224 (515)
T COG2812         146 -PPSHVKFILATTEPQKIPNTILSRCQRFDFKRLDLEEIAKHLAAILDKEGINIEEDALSLIARAAEGSLRDALSLLDQA  224 (515)
T ss_pred             -CccCeEEEEecCCcCcCchhhhhccccccccCCCHHHHHHHHHHHHHhcCCccCHHHHHHHHHHcCCChhhHHHHHHHH
Confidence             467888888 55667888888999987   66651                  11       26677889988889998


Q ss_pred             ccCC
Q 003038          820 LNIC  823 (854)
Q Consensus       820 l~~~  823 (854)
                      ++++
T Consensus       225 i~~~  228 (515)
T COG2812         225 IAFG  228 (515)
T ss_pred             HHcc
Confidence            8886

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.33  E-value=3.8e-11  Score=134.19  Aligned_cols=122  Identities=13%  Similarity=0.144  Sum_probs=84.2

Q ss_pred             HHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhh-
Q 003038          218 VIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCL-  296 (854)
Q Consensus       218 v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~-  296 (854)
                      |++-|.-+.-+.++|+||||+|||-+|+.+...+ ++.-|.-..|.+        +.+.|.||.|+.++.||..+++.. 
T Consensus       247 vie~lGi~HVKGiLLyGPPGTGKTLiARqIGkML-NArePKIVNGPe--------IL~KYVGeSE~NvR~LFaDAEeE~r  317 (744)
T KOG0741|consen  247 VIEQLGIKHVKGILLYGPPGTGKTLIARQIGKML-NAREPKIVNGPE--------ILNKYVGESEENVRKLFADAEEEQR  317 (744)
T ss_pred             HHHHcCccceeeEEEECCCCCChhHHHHHHHHHh-cCCCCcccCcHH--------HHHHhhcccHHHHHHHHHhHHHHHH
Confidence            4555666677889999999999999999998654 444465544444        556799999999999999998642 


Q ss_pred             -----CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhc-cc----CCCCceEEEEEecCHHH
Q 003038          297 -----GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CG----IGENARFWLMGIATFQS  357 (854)
Q Consensus       297 -----~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~----~~g~g~l~lIgatT~~e  357 (854)
                           .+=.|+.+|||+.+ ..+++.. |.++   +-+..|   .+|| |.    ...  .+-+||-|+...
T Consensus       318 ~~g~~SgLHIIIFDEiDAICKqRGS~~-g~TG---VhD~VV---NQLLsKmDGVeqLN--NILVIGMTNR~D  380 (744)
T KOG0741|consen  318 RLGANSGLHIIIFDEIDAICKQRGSMA-GSTG---VHDTVV---NQLLSKMDGVEQLN--NILVIGMTNRKD  380 (744)
T ss_pred             hhCccCCceEEEehhhHHHHHhcCCCC-CCCC---ccHHHH---HHHHHhcccHHhhh--cEEEEeccCchh
Confidence                 22378889999999 5443221 1122   222333   3455 43    233  599999998655

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.32  E-value=1.1e-11  Score=146.44  Aligned_cols=137  Identities=12%  Similarity=0.109  Sum_probs=86.8

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||+++++.|.+.+...                 +....+||+||+|+|||++|++||+.|+... ......|..+.
T Consensus        16 dEVIGQe~Vv~~L~~aL~~g-----------------RL~HAyLFtGPpGvGKTTlAriLAKaLnCe~-~~~~~PCG~C~   77 (830)
T PRK07003         16 ASLVGQEHVVRALTHALDGG-----------------RLHHAYLFTGTRGVGKTTLSRIFAKALNCET-GVTSQPCGVCR   77 (830)
T ss_pred             HHHcCcHHHHHHHHHHHhcC-----------------CCCeEEEEECCCCCCHHHHHHHHHHHhcCcc-CCCCCCCcccH
Confidence            45799999999998887642                 2245789999999999999999999997431 11111111111


Q ss_pred             CcCCCcccccc-ccccCCCC-CCchHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDSR-NKRSRDEQ-SCSYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~~-~~rl~~~~-g~g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .+.......|. +.. ++.. ..|.++  .+.+.+..    ..++||||||+|+++...+|.||+.||+           
T Consensus        78 sCr~I~~G~h~DviE-IDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEE-----------  145 (830)
T PRK07003         78 ACREIDEGRFVDYVE-MDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEE-----------  145 (830)
T ss_pred             HHHHHhcCCCceEEE-ecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHh-----------
Confidence            00000000110 000 1111 114433  44454443    3579999999999999999999999996           


Q ss_pred             ecCCeEEEEecCCCC
Q 003038          770 SLGDAIVILSCESFS  784 (854)
Q Consensus       770 ~~~~aIiIlTsn~f~  784 (854)
                      .-.+++|||+||...
T Consensus       146 PP~~v~FILaTtd~~  160 (830)
T PRK07003        146 PPPHVKFILATTDPQ  160 (830)
T ss_pred             cCCCeEEEEEECChh
Confidence            235778999987643

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.31  E-value=4.9e-12  Score=147.74  Aligned_cols=148  Identities=11%  Similarity=0.096  Sum_probs=92.4

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC----ceEEEcc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN----NFVSIAL  693 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~----~~i~id~  693 (854)
                      ..|+||++++..|.+++...|                 -.+.+||+||.|+|||++|+.||+.|+....    .+..-.|
T Consensus        16 ddVIGQe~vv~~L~~al~~gR-----------------LpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PC   78 (700)
T PRK12323         16 TTLVGQEHVVRALTHALEQQR-----------------LHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPC   78 (700)
T ss_pred             HHHcCcHHHHHHHHHHHHhCC-----------------CceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCC
Confidence            458999999999999988643                 2457899999999999999999999975311    0000001


Q ss_pred             ccccCcCCCcccccc-ccccCCCC-CCchHH--HHHHHHHcC----CCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCC
Q 003038          694 SSFSSTRADSTEDSR-NKRSRDEQ-SCSYIE--RFAEAVSNN----PHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSS  765 (854)
Q Consensus       694 s~~~~~~~~s~e~~~-~~rl~~~~-g~g~~e--~L~eav~~~----p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~  765 (854)
                      ..+..+.......|. +.. +.+. ..|.++  .|.+.+...    .|+||||||+|+++...+|.||+.||+       
T Consensus        79 G~C~sC~~I~aG~hpDviE-IdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEE-------  150 (700)
T PRK12323         79 GQCRACTEIDAGRFVDYIE-MDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEE-------  150 (700)
T ss_pred             cccHHHHHHHcCCCCcceE-ecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhcc-------
Confidence            111100000000110 000 1111 114443  455555544    479999999999999999999999997       


Q ss_pred             CceeecCCeEEEEecCCCCCC-CCCCCCCc
Q 003038          766 GDEVSLGDAIVILSCESFSSR-SRACSPPT  794 (854)
Q Consensus       766 G~~v~~~~aIiIlTsn~f~~~-s~~~sp~~  794 (854)
                          .-.+++|||+||..... .+..|.|+
T Consensus       151 ----PP~~v~FILaTtep~kLlpTIrSRCq  176 (700)
T PRK12323        151 ----PPEHVKFILATTDPQKIPVTVLSRCL  176 (700)
T ss_pred             ----CCCCceEEEEeCChHhhhhHHHHHHH
Confidence                22567799988754333 23344443

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.31  E-value=7.1e-12  Score=135.26  Aligned_cols=139  Identities=12%  Similarity=0.058  Sum_probs=108.7

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      -.+.++|+||||+|||-+|+++|..          -++.|+.+-.+.|+..|.||--.-++++|..++..  .|+|+|||
T Consensus       184 PPKGVLLYGPPGTGKTLLAkAVA~~----------T~AtFIrvvgSElVqKYiGEGaRlVRelF~lArek--aPsIIFiD  251 (406)
T COG1222         184 PPKGVLLYGPPGTGKTLLAKAVANQ----------TDATFIRVVGSELVQKYIGEGARLVRELFELAREK--APSIIFID  251 (406)
T ss_pred             CCCceEeeCCCCCcHHHHHHHHHhc----------cCceEEEeccHHHHHHHhccchHHHHHHHHHHhhc--CCeEEEEe
Confidence            5678999999999999999999987          57899999999999999999999999999999986  79999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCC
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPA  381 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~  381 (854)
                      ||+.+ ..+-..   .++...-|.+..|++-+=|-+  .+|  .+.+|+||+--.     .-||||-|--|| ..|.+|-
T Consensus       252 EIDAIg~kR~d~---~t~gDrEVQRTmleLL~qlDGFD~~~--nvKVI~ATNR~D-----~LDPALLRPGR~DRkIEfpl  321 (406)
T COG1222         252 EIDAIGAKRFDS---GTSGDREVQRTMLELLNQLDGFDPRG--NVKVIMATNRPD-----ILDPALLRPGRFDRKIEFPL  321 (406)
T ss_pred             chhhhhcccccC---CCCchHHHHHHHHHHHHhccCCCCCC--CeEEEEecCCcc-----ccChhhcCCCcccceeecCC
Confidence            99999 443211   111223355677776666633  344  699999998655     479999986666 4566666


Q ss_pred             chHHH
Q 003038          382 GSLSL  386 (854)
Q Consensus       382 ~sl~~  386 (854)
                      |+...
T Consensus       322 Pd~~g  326 (406)
T COG1222         322 PDEEG  326 (406)
T ss_pred             CCHHH
Confidence            65443

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.29  E-value=5.6e-12  Score=144.91  Aligned_cols=139  Identities=12%  Similarity=0.118  Sum_probs=109.8

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEe
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      ...+.++|+||||||||.+|+++|..          .++.|+++....|.++|.||.|.-++++|+.+++.  .|+|+|+
T Consensus       466 ~ppkGVLlyGPPGC~KT~lAkalAne----------~~~nFlsvkgpEL~sk~vGeSEr~ir~iF~kAR~~--aP~IiFf  533 (693)
T KOG0730|consen  466 SPPKGVLLYGPPGCGKTLLAKALANE----------AGMNFLSVKGPELFSKYVGESERAIREVFRKARQV--APCIIFF  533 (693)
T ss_pred             CCCceEEEECCCCcchHHHHHHHhhh----------hcCCeeeccCHHHHHHhcCchHHHHHHHHHHHhhc--CCeEEeh
Confidence            35678999999999999999999976          57899999999999999999999999999999997  6899999


Q ss_pred             Cccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCC
Q 003038          305 GDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIP  380 (854)
Q Consensus       305 del~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~  380 (854)
                      |||+.+ +.+++.++      .+.++....+-+-+-+  ..  ..|.+||||+...     ..||||-|--|| +.+.||
T Consensus       534 DEiDsi~~~R~g~~~------~v~~RVlsqLLtEmDG~e~~--k~V~ViAATNRpd-----~ID~ALlRPGRlD~iiyVp  600 (693)
T KOG0730|consen  534 DEIDALAGSRGGSSS------GVTDRVLSQLLTEMDGLEAL--KNVLVIAATNRPD-----MIDPALLRPGRLDRIIYVP  600 (693)
T ss_pred             hhHHhHhhccCCCcc------chHHHHHHHHHHHccccccc--CcEEEEeccCChh-----hcCHHHcCCcccceeEeec
Confidence            999999 76653322      3445665554444422  22  2699999999765     579999885566 567777


Q ss_pred             CchHHHHh
Q 003038          381 AGSLSLSL  388 (854)
Q Consensus       381 ~~sl~~al  388 (854)
                      -|.+..-+
T Consensus       601 lPD~~aR~  608 (693)
T KOG0730|consen  601 LPDLEARL  608 (693)
T ss_pred             CccHHHHH
Confidence            77766543

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.27  E-value=1.2e-11  Score=139.95  Aligned_cols=145  Identities=13%  Similarity=0.151  Sum_probs=93.0

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..+.+++...+.+.....        .+..+.+||+||+|+|||.+|+++|+.++.....  .-.|..+.
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~--------~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~--~~~Cg~C~   74 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAG--------SGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPD--EPGCGECR   74 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccC--------CCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCC--CCCCCCCH
Confidence            4689999999999999988765433322        1234689999999999999999999999764321  01111111


Q ss_pred             CcCCCccccccccccCCCCC--CchHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDSRNKRSRDEQS--CSYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g--~g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .+.......|.--..+.+.+  .+..+  .+.+.+...|    ++|+||||+|++++..+|.|++.||+.          
T Consensus        75 ~C~~~~~~~hpD~~~i~~~~~~i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m~~~aanaLLk~LEep----------  144 (394)
T PRK07940         75 ACRTVLAGTHPDVRVVAPEGLSIGVDEVRELVTIAARRPSTGRWRIVVIEDADRLTERAANALLKAVEEP----------  144 (394)
T ss_pred             HHHHHhcCCCCCEEEeccccccCCHHHHHHHHHHHHhCcccCCcEEEEEechhhcCHHHHHHHHHHhhcC----------
Confidence            10000001121111122222  24444  4666665544    689999999999999999999999973          


Q ss_pred             ecCCeEEEEecCCC
Q 003038          770 SLGDAIVILSCESF  783 (854)
Q Consensus       770 ~~~~aIiIlTsn~f  783 (854)
                       -.+++|||+|+..
T Consensus       145 -~~~~~fIL~a~~~  157 (394)
T PRK07940        145 -PPRTVWLLCAPSP  157 (394)
T ss_pred             -CCCCeEEEEECCh
Confidence             1356677766543

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

Probab=99.26  E-value=1.2e-11  Score=135.65  Aligned_cols=130  Identities=18%  Similarity=0.203  Sum_probs=92.8

Q ss_pred             HHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHH
Q 003038          213 EDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLV  292 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~  292 (854)
                      .=|+|+++-   ..-.+.||+||||||||++++.+|...          ++.|..++..  .++.     +.++++++.+
T Consensus        37 ~~lrr~v~~---~~l~SmIl~GPPG~GKTTlA~liA~~~----------~~~f~~~sAv--~~gv-----kdlr~i~e~a   96 (436)
T COG2256          37 KPLRRAVEA---GHLHSMILWGPPGTGKTTLARLIAGTT----------NAAFEALSAV--TSGV-----KDLREIIEEA   96 (436)
T ss_pred             chHHHHHhc---CCCceeEEECCCCCCHHHHHHHHHHhh----------CCceEEeccc--cccH-----HHHHHHHHHH
Confidence            446777754   677899999999999999999999864          5577777543  3322     2477777777


Q ss_pred             Hhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchh
Q 003038          293 RSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLE  369 (854)
Q Consensus       293 ~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale  369 (854)
                      ++..  |...||||||||.+ ...+.                    .||+. -.+|.|.+|||||.+.|   |+.+|||-
T Consensus        97 ~~~~~~gr~tiLflDEIHRfnK~QQD--------------------~lLp~-vE~G~iilIGATTENPs---F~ln~ALl  152 (436)
T COG2256          97 RKNRLLGRRTILFLDEIHRFNKAQQD--------------------ALLPH-VENGTIILIGATTENPS---FELNPALL  152 (436)
T ss_pred             HHHHhcCCceEEEEehhhhcChhhhh--------------------hhhhh-hcCCeEEEEeccCCCCC---eeecHHHh
Confidence            6543  56899999999999 65432                    25543 23447999999999996   57899997


Q ss_pred             h---hhccCCCCCCCchHHHHh
Q 003038          370 T---LWSLHPLTIPAGSLSLSL  388 (854)
Q Consensus       370 ~---~~~~~~v~i~~~sl~~al  388 (854)
                      +   +|.|.+++-.  .|...+
T Consensus       153 SR~~vf~lk~L~~~--di~~~l  172 (436)
T COG2256         153 SRARVFELKPLSSE--DIKKLL  172 (436)
T ss_pred             hhhheeeeecCCHH--HHHHHH
Confidence            5   3555655543  455444

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=99.26  E-value=2.2e-11  Score=136.36  Aligned_cols=81  Identities=19%  Similarity=0.240  Sum_probs=65.2

Q ss_pred             HHHHHHhhcCcccccHHHHHHHHHHHHH--hhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC
Q 003038          609 LTSLCNALEKKVPWQKDTVYDIANTVLK--CRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN  686 (854)
Q Consensus       609 l~~L~~~L~~~V~GQ~~av~~Ia~~v~~--~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~  686 (854)
                      .+.+.+.|.+.|+||++|+..|+.++..  .|.++..+.+.      ..+...+||+||+|+|||++|+.||+.+   ..
T Consensus         6 p~~I~~~Ld~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~------e~~~~~ILliGp~G~GKT~LAr~LAk~l---~~   76 (443)
T PRK05201          6 PREIVSELDKYIIGQDDAKRAVAIALRNRWRRMQLPEELRD------EVTPKNILMIGPTGVGKTEIARRLAKLA---NA   76 (443)
T ss_pred             HHHHHHHhccccCCHHHHHHHHHHHHHHHHHHhcCCccccc------ccCCceEEEECCCCCCHHHHHHHHHHHh---CC
Confidence            3578899999999999999999999976  34444432210      1223689999999999999999999998   57


Q ss_pred             ceEEEccccccC
Q 003038          687 NFVSIALSSFSS  698 (854)
Q Consensus       687 ~~i~id~s~~~~  698 (854)
                      +|+++|+++|.+
T Consensus        77 ~fi~vD~t~f~e   88 (443)
T PRK05201         77 PFIKVEATKFTE   88 (443)
T ss_pred             hheeecchhhcc
Confidence            899999998885

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.25  E-value=3.2e-11  Score=143.08  Aligned_cols=138  Identities=17%  Similarity=0.155  Sum_probs=86.4

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..|.+++...|                 -...+||+||+|+|||++|++||+.+++.. .....-|..+.
T Consensus        16 ~divGQe~vv~~L~~~l~~~r-----------------l~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~-~~~~~pCg~C~   77 (647)
T PRK07994         16 AEVVGQEHVLTALANALDLGR-----------------LHHAYLFSGTRGVGKTTIARLLAKGLNCET-GITATPCGECD   77 (647)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----------------CCeEEEEECCCCCCHHHHHHHHHHhhhhcc-CCCCCCCCCCH
Confidence            458999999999998887643                 235689999999999999999999997631 10000011110


Q ss_pred             CcCCCccccccccccCCCCCC-chHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceee
Q 003038          698 STRADSTEDSRNKRSRDEQSC-SYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVS  770 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~-g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~  770 (854)
                      .+.......|.--..+.+... +.++  .|.+.+..    .+++|+||||+|+++...+|.||+.||+           .
T Consensus        78 ~C~~i~~g~~~D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEE-----------P  146 (647)
T PRK07994         78 NCREIEQGRFVDLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEE-----------P  146 (647)
T ss_pred             HHHHHHcCCCCCceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHc-----------C
Confidence            000000001100000111111 3333  44454443    4578999999999999999999999997           2


Q ss_pred             cCCeEEEEecCCCC
Q 003038          771 LGDAIVILSCESFS  784 (854)
Q Consensus       771 ~~~aIiIlTsn~f~  784 (854)
                      -.+++|||+|+.-.
T Consensus       147 p~~v~FIL~Tt~~~  160 (647)
T PRK07994        147 PEHVKFLLATTDPQ  160 (647)
T ss_pred             CCCeEEEEecCCcc
Confidence            34667999886533

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.24  E-value=2.9e-11  Score=138.22  Aligned_cols=148  Identities=16%  Similarity=0.113  Sum_probs=91.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..|..++...+                 -.+.+||+||+|+|||++|+.||+.++..... ...-|..+.
T Consensus        18 ~dvVGQe~iv~~L~~~i~~~r-----------------i~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~-~~~pCg~C~   79 (484)
T PRK14956         18 RDVIHQDLAIGALQNALKSGK-----------------IGHAYIFFGPRGVGKTTIARILAKRLNCENPI-GNEPCNECT   79 (484)
T ss_pred             HHHhChHHHHHHHHHHHHcCC-----------------CCeEEEEECCCCCCHHHHHHHHHHhcCccccc-CccccCCCc
Confidence            458999999999888887532                 23469999999999999999999999653210 000111111


Q ss_pred             CcCCCccccc-cccccCCC-CCCchHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDS-RNKRSRDE-QSCSYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~-~~~rl~~~-~g~g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .+.......+ .+- .+.+ ...|..+  .+.+.+..    ..+.|++|||+|+++.+.+|.||+.||+-          
T Consensus        80 sC~~i~~g~~~dvi-EIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEP----------  148 (484)
T PRK14956         80 SCLEITKGISSDVL-EIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEEP----------  148 (484)
T ss_pred             HHHHHHccCCccce-eechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhcC----------
Confidence            0000000000 000 0111 1113433  34444443    45789999999999999999999999862          


Q ss_pred             ecCCeEEEEecCCCCC-CCCCCCCCcc
Q 003038          770 SLGDAIVILSCESFSS-RSRACSPPTK  795 (854)
Q Consensus       770 ~~~~aIiIlTsn~f~~-~s~~~sp~~~  795 (854)
                       -.+++|||+|+.... ..+..|.|++
T Consensus       149 -p~~viFILaTte~~kI~~TI~SRCq~  174 (484)
T PRK14956        149 -PAHIVFILATTEFHKIPETILSRCQD  174 (484)
T ss_pred             -CCceEEEeecCChhhccHHHHhhhhe
Confidence             246789998876433 3444566653

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.24  E-value=2.9e-11  Score=145.41  Aligned_cols=138  Identities=14%  Similarity=0.147  Sum_probs=85.7

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..|.+++...|                 -...+||+||+|+|||++||+||+.|++... .--..|..+.
T Consensus        16 ddIIGQe~Iv~~LknaI~~~r-----------------l~HAyLFtGPpGtGKTTLARiLAk~Lnce~~-~~~~pCg~C~   77 (944)
T PRK14949         16 EQMVGQSHVLHALTNALTQQR-----------------LHHAYLFTGTRGVGKTSLARLFAKGLNCEQG-VTATPCGVCS   77 (944)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC-----------------CCeEEEEECCCCCCHHHHHHHHHHhccCccC-CCCCCCCCch
Confidence            458999999999988887532                 2456799999999999999999999976421 0000111111


Q ss_pred             CcCCCccccccccccCCCCC-CchHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceee
Q 003038          698 STRADSTEDSRNKRSRDEQS-CSYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVS  770 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g-~g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~  770 (854)
                      .+.......|..--.+.+.. .+..+  .|.+.+..    .+++||||||+|+++...+|.||+.||+.           
T Consensus        78 sC~~i~~g~~~DviEidAas~~kVDdIReLie~v~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEEP-----------  146 (944)
T PRK14949         78 SCVEIAQGRFVDLIEVDAASRTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEEP-----------  146 (944)
T ss_pred             HHHHHhcCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcc-----------
Confidence            00000000010000011111 13332  45555544    45789999999999999999999999972           


Q ss_pred             cCCeEEEEecCCCC
Q 003038          771 LGDAIVILSCESFS  784 (854)
Q Consensus       771 ~~~aIiIlTsn~f~  784 (854)
                      -.+++|||+|+...
T Consensus       147 P~~vrFILaTTe~~  160 (944)
T PRK14949        147 PEHVKFLLATTDPQ  160 (944)
T ss_pred             CCCeEEEEECCCch
Confidence            23566888776543

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=99.22  E-value=2e-11  Score=122.66  Aligned_cols=139  Identities=13%  Similarity=0.158  Sum_probs=94.9

Q ss_pred             ccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc
Q 003038          620 VPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST  699 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~  699 (854)
                      ++|.+.++..+...+.+.-.                ....+|++|++|+||+.+|++|...-.....+|+.+||+.+.  
T Consensus         1 liG~s~~m~~~~~~~~~~a~----------------~~~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~~~~--   62 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAAS----------------SDLPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCAALP--   62 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTT----------------STS-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETTTS---
T ss_pred             CEeCCHHHHHHHHHHHHHhC----------------CCCCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehhhhh--
Confidence            57889888888888776522                125789999999999999999999776678899999999886  


Q ss_pred             CCCccccccccccCC-CCC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEE
Q 003038          700 RADSTEDSRNKRSRD-EQS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIV  776 (854)
Q Consensus       700 ~~~s~e~~~~~rl~~-~~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIi  776 (854)
                           ++.....+.+ ..+ + |-...-...+.......+|||||+.+++.+|..|+++|++|.++--.+.+.--.|+.|
T Consensus        63 -----~~~~e~~LFG~~~~~~~~~~~~~~G~l~~A~~GtL~Ld~I~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~Ri  137 (168)
T PF00158_consen   63 -----EELLESELFGHEKGAFTGARSDKKGLLEQANGGTLFLDEIEDLPPELQAKLLRVLEEGKFTRLGSDKPVPVDVRI  137 (168)
T ss_dssp             -----HHHHHHHHHEBCSSSSTTTSSEBEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEECCTSSSEEE--EEE
T ss_pred             -----cchhhhhhhccccccccccccccCCceeeccceEEeecchhhhHHHHHHHHHHHHhhchhccccccccccccceE
Confidence                 2221111211 000 0 1000012455667789999999999999999999999999999865444444459999


Q ss_pred             EEecC
Q 003038          777 ILSCE  781 (854)
Q Consensus       777 IlTsn  781 (854)
                      |+||+
T Consensus       138 I~st~  142 (168)
T PF00158_consen  138 IASTS  142 (168)
T ss_dssp             EEEES
T ss_pred             EeecC
Confidence            99886

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>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=99.22  E-value=2.8e-11  Score=121.05  Aligned_cols=131  Identities=17%  Similarity=0.168  Sum_probs=79.9

Q ss_pred             ccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCC
Q 003038          622 WQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRA  701 (854)
Q Consensus       622 GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~  701 (854)
                      ||+++++.+.+.+...+                 -...+||+||+|+||+++|+++|+.+++....-.  -+........
T Consensus         1 gq~~~~~~L~~~~~~~~-----------------l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~--~c~~c~~c~~   61 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGR-----------------LPHALLFHGPSGSGKKTLALAFARALLCSNPNED--PCGECRSCRR   61 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC-------------------SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT----SSSHHHHH
T ss_pred             CcHHHHHHHHHHHHcCC-----------------cceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCC--CCCCCHHHHH
Confidence            89999999998887642                 2457999999999999999999999998653311  0000000000


Q ss_pred             CccccccccccCCCCC----CchHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeec
Q 003038          702 DSTEDSRNKRSRDEQS----CSYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSL  771 (854)
Q Consensus       702 ~s~e~~~~~rl~~~~g----~g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~  771 (854)
                      .....|.--..+.+.+    .+.++  .+.+.+..    ++++||+|||+|+++.+.+|+||+.||+.           -
T Consensus        62 ~~~~~~~d~~~~~~~~~~~~i~i~~ir~i~~~~~~~~~~~~~KviiI~~ad~l~~~a~NaLLK~LEep-----------p  130 (162)
T PF13177_consen   62 IEEGNHPDFIIIKPDKKKKSIKIDQIREIIEFLSLSPSEGKYKVIIIDEADKLTEEAQNALLKTLEEP-----------P  130 (162)
T ss_dssp             HHTT-CTTEEEEETTTSSSSBSHHHHHHHHHHCTSS-TTSSSEEEEEETGGGS-HHHHHHHHHHHHST-----------T
T ss_pred             HHhccCcceEEEecccccchhhHHHHHHHHHHHHHHHhcCCceEEEeehHhhhhHHHHHHHHHHhcCC-----------C
Confidence            0000010000111111    13332  34444433    46789999999999999999999999973           3


Q ss_pred             CCeEEEEecCC
Q 003038          772 GDAIVILSCES  782 (854)
Q Consensus       772 ~~aIiIlTsn~  782 (854)
                      .+++|||+|+.
T Consensus       131 ~~~~fiL~t~~  141 (162)
T PF13177_consen  131 ENTYFILITNN  141 (162)
T ss_dssp             TTEEEEEEES-
T ss_pred             CCEEEEEEECC
Confidence            68889998853

...

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.22  E-value=6.6e-10  Score=128.16  Aligned_cols=119  Identities=11%  Similarity=0.085  Sum_probs=80.0

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      +.-|++|.|++|+|||.+|++++....+.      ..+++.-++++.+......-+..-+..++.+...+  .|.|+++|
T Consensus       430 ~~~~Ill~G~~GsGKT~L~kal~~~~~k~------~~~hv~~v~Cs~l~~~~~e~iQk~l~~vfse~~~~--~PSiIvLD  501 (952)
T KOG0735|consen  430 RHGNILLNGPKGSGKTNLVKALFDYYSKD------LIAHVEIVSCSTLDGSSLEKIQKFLNNVFSEALWY--APSIIVLD  501 (952)
T ss_pred             ccccEEEeCCCCCCHhHHHHHHHHHhccc------cceEEEEEechhccchhHHHHHHHHHHHHHHHHhh--CCcEEEEc
Confidence            67899999999999999999999988743      24577777887776555566777788888888877  79999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecC
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIAT  354 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT  354 (854)
                      +++.| +.....+++-+.++-.+-+...++-.... ..++ .+.+||+..
T Consensus       502 dld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~-~~~~-~ia~Iat~q  549 (952)
T KOG0735|consen  502 DLDCLASASSNENGQDGVVSERLAAFLNQVIKIYL-KRNR-KIAVIATGQ  549 (952)
T ss_pred             chhhhhccCcccCCcchHHHHHHHHHHHHHHHHHH-ccCc-EEEEEEech
Confidence            99999 73322222212223333333333333321 1233 578887754

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.21  E-value=2.9e-11  Score=131.30  Aligned_cols=136  Identities=15%  Similarity=0.139  Sum_probs=96.9

Q ss_pred             ccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEE
Q 003038          224 SKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLN  303 (854)
Q Consensus       224 r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILf  303 (854)
                      ||-=+.+|+|||||+|||-++++||-.          .+..|+.++.+.|.+.||||.|+-++=||+.++.+  .|.++|
T Consensus       242 rrPWkgvLm~GPPGTGKTlLAKAvATE----------c~tTFFNVSsstltSKwRGeSEKlvRlLFemARfy--APStIF  309 (491)
T KOG0738|consen  242 RRPWKGVLMVGPPGTGKTLLAKAVATE----------CGTTFFNVSSSTLTSKWRGESEKLVRLLFEMARFY--APSTIF  309 (491)
T ss_pred             ccccceeeeeCCCCCcHHHHHHHHHHh----------hcCeEEEechhhhhhhhccchHHHHHHHHHHHHHh--CCceee
Confidence            455678999999999999999999976          57899999999999999999999999999999998  799999


Q ss_pred             eCccccc-cccccccccccccchhhhHHHHHHHhhc-ccCCC---CceEEEEEecCHHHHHHhhccCCchhhhhcc-CCC
Q 003038          304 LGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CGIGE---NARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPL  377 (854)
Q Consensus       304 idel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~~~g---~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v  377 (854)
                      ||||+.| ..+++.++.     .+..+.-.++--.+ +..+.   .-.|.+++||++..     ..|-||.|  || ..|
T Consensus       310 iDEIDslcs~RG~s~EH-----EaSRRvKsELLvQmDG~~~t~e~~k~VmVLAATN~PW-----diDEAlrR--RlEKRI  377 (491)
T KOG0738|consen  310 IDEIDSLCSQRGGSSEH-----EASRRVKSELLVQMDGVQGTLENSKVVMVLAATNFPW-----DIDEALRR--RLEKRI  377 (491)
T ss_pred             hhhHHHHHhcCCCccch-----hHHHHHHHHHHHHhhccccccccceeEEEEeccCCCc-----chHHHHHH--HHhhhe
Confidence            9999999 554432111     11223333433333 21111   11366777777543     46777777  66 344


Q ss_pred             CCCCch
Q 003038          378 TIPAGS  383 (854)
Q Consensus       378 ~i~~~s  383 (854)
                      .||=|+
T Consensus       378 yIPLP~  383 (491)
T KOG0738|consen  378 YIPLPD  383 (491)
T ss_pred             eeeCCC
Confidence            454443

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.20  E-value=6.2e-11  Score=139.81  Aligned_cols=137  Identities=13%  Similarity=0.123  Sum_probs=87.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..|.+.+...                 +..+.+||+||+|+|||++|++||+.++..... ..--|..+.
T Consensus        13 ~eivGq~~i~~~L~~~i~~~-----------------r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~-~~~pCg~C~   74 (584)
T PRK14952         13 AEVVGQEHVTEPLSSALDAG-----------------RINHAYLFSGPRGCGKTSSARILARSLNCAQGP-TATPCGVCE   74 (584)
T ss_pred             HHhcCcHHHHHHHHHHHHcC-----------------CCCeEEEEECCCCCCHHHHHHHHHHHhccccCC-CCCcccccH
Confidence            45799999999999988752                 234578999999999999999999999753210 000111111


Q ss_pred             CcCCCcccccccccc--CCCCCC-chHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCce
Q 003038          698 STRADSTEDSRNKRS--RDEQSC-SYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDE  768 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl--~~~~g~-g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~  768 (854)
                      .+.......+.....  +..... |.++  .|.+.+..    .+|+||+|||+|.++...+|.|++.||+          
T Consensus        75 ~C~~i~~~~~~~~dvieidaas~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEE----------  144 (584)
T PRK14952         75 SCVALAPNGPGSIDVVELDAASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEE----------  144 (584)
T ss_pred             HHHHhhcccCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhc----------
Confidence            111000000000011  122112 4443  45555544    4588999999999999999999999997          


Q ss_pred             eecCCeEEEEecCCC
Q 003038          769 VSLGDAIVILSCESF  783 (854)
Q Consensus       769 v~~~~aIiIlTsn~f  783 (854)
                       .-.+++|||+|+..
T Consensus       145 -pp~~~~fIL~tte~  158 (584)
T PRK14952        145 -PPEHLIFIFATTEP  158 (584)
T ss_pred             -CCCCeEEEEEeCCh
Confidence             22477899877644

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.20  E-value=9.6e-11  Score=136.95  Aligned_cols=136  Identities=15%  Similarity=0.150  Sum_probs=86.4

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..|.+++...+                 -.+.+||+||+|+|||++|+.||+.+++... .-.--|..+.
T Consensus        16 ~divGq~~v~~~L~~~~~~~~-----------------l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~-~~~~pCg~C~   77 (509)
T PRK14958         16 QEVIGQAPVVRALSNALDQQY-----------------LHHAYLFTGTRGVGKTTISRILAKCLNCEKG-VSANPCNDCE   77 (509)
T ss_pred             HHhcCCHHHHHHHHHHHHhCC-----------------CCeeEEEECCCCCCHHHHHHHHHHHhcCCCC-CCcccCCCCH
Confidence            458999999999999987632                 3457999999999999999999999975321 1000011111


Q ss_pred             CcCCCccccccccccCCCCCC-chHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceee
Q 003038          698 STRADSTEDSRNKRSRDEQSC-SYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVS  770 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~-g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~  770 (854)
                      .+.......|.--..+.+... |..+  .+.+.+..    .+|+|++|||+|++++..+|.|++.||+-           
T Consensus        78 ~C~~i~~g~~~d~~eidaas~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls~~a~naLLk~LEep-----------  146 (509)
T PRK14958         78 NCREIDEGRFPDLFEVDAASRTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHMLSGHSFNALLKTLEEP-----------  146 (509)
T ss_pred             HHHHHhcCCCceEEEEcccccCCHHHHHHHHHHHhhccccCCcEEEEEEChHhcCHHHHHHHHHHHhcc-----------
Confidence            000000001100000111112 4433  44555444    45789999999999999999999999962           


Q ss_pred             cCCeEEEEecCC
Q 003038          771 LGDAIVILSCES  782 (854)
Q Consensus       771 ~~~aIiIlTsn~  782 (854)
                      -.+++|||+|+.
T Consensus       147 p~~~~fIlattd  158 (509)
T PRK14958        147 PSHVKFILATTD  158 (509)
T ss_pred             CCCeEEEEEECC
Confidence            356778887764

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.19  E-value=3.3e-11  Score=129.79  Aligned_cols=139  Identities=14%  Similarity=0.052  Sum_probs=98.4

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ...|++|+||||+|||++|+.+|..+..-.   .+....++.++.+.+.+.|.|+.+.+++++++.+.     +.|||||
T Consensus        41 ~~~~vll~GppGtGKTtlA~~ia~~l~~~~---~~~~~~~v~~~~~~l~~~~~g~~~~~~~~~~~~a~-----~~VL~ID  112 (261)
T TIGR02881        41 QVLHMIFKGNPGTGKTTVARILGKLFKEMN---VLSKGHLIEVERADLVGEYIGHTAQKTREVIKKAL-----GGVLFID  112 (261)
T ss_pred             CcceEEEEcCCCCCHHHHHHHHHHHHHhcC---cccCCceEEecHHHhhhhhccchHHHHHHHHHhcc-----CCEEEEe
Confidence            345789999999999999999998875422   22344788899999988899999999998887653     3489999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhccc-CCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCc
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAG  382 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~  382 (854)
                      |+|.| ..+...            ++...+..|+.. ...++.+.+|+++++.+...+...+|+|.+  || +.|.+++.
T Consensus       113 E~~~L~~~~~~~------------~~~~~i~~Ll~~~e~~~~~~~vila~~~~~~~~~~~~~p~L~s--Rf~~~i~f~~~  178 (261)
T TIGR02881       113 EAYSLARGGEKD------------FGKEAIDTLVKGMEDNRNEFVLILAGYSDEMDYFLSLNPGLRS--RFPISIDFPDY  178 (261)
T ss_pred             chhhhccCCccc------------hHHHHHHHHHHHHhccCCCEEEEecCCcchhHHHHhcChHHHh--ccceEEEECCC
Confidence            99999 422110            111223334432 222336888888887766666778999999  77 45777766


Q ss_pred             hHHH
Q 003038          383 SLSL  386 (854)
Q Consensus       383 sl~~  386 (854)
                      +...
T Consensus       179 ~~~e  182 (261)
T TIGR02881       179 TVEE  182 (261)
T ss_pred             CHHH
Confidence            5443

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.

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

Probab=99.18  E-value=7.3e-11  Score=137.00  Aligned_cols=159  Identities=14%  Similarity=0.206  Sum_probs=113.2

Q ss_pred             hHHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC
Q 003038          605 NSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS  684 (854)
Q Consensus       605 ~~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~  684 (854)
                      +...|+...+.|.+.=.|=+++.+.|.+.+.-.+-  .+          ......++|+||||||||.|++.+|+.+   
T Consensus       310 ~~~Dl~~a~~iLd~dHYGLekVKeRIlEyLAV~~l--~~----------~~kGpILcLVGPPGVGKTSLgkSIA~al---  374 (782)
T COG0466         310 DKLDLKKAEKILDKDHYGLEKVKERILEYLAVQKL--TK----------KLKGPILCLVGPPGVGKTSLGKSIAKAL---  374 (782)
T ss_pred             hhhhHHHHHHHhcccccCchhHHHHHHHHHHHHHH--hc----------cCCCcEEEEECCCCCCchhHHHHHHHHh---
Confidence            55678899999999999999999999887653221  00          0112379999999999999999999999   


Q ss_pred             CCceEEEccccccCcCCCccccccccccCCCCCCchH-HHHHHHHHc----CCCEEEEEecCCCCCHHHH----HHHHHh
Q 003038          685 HNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYI-ERFAEAVSN----NPHRVFLIEDVEQADYCSQ----KGFKRA  755 (854)
Q Consensus       685 ~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~-e~L~eav~~----~p~~ViliDEieka~~~v~----~~Ll~~  755 (854)
                      ...|+|+.+....+-..+.  .|+.. .+     |.. .++.+.+++    ||  ||+||||||+..+.+    .+||.+
T Consensus       375 ~RkfvR~sLGGvrDEAEIR--GHRRT-YI-----GamPGrIiQ~mkka~~~NP--v~LLDEIDKm~ss~rGDPaSALLEV  444 (782)
T COG0466         375 GRKFVRISLGGVRDEAEIR--GHRRT-YI-----GAMPGKIIQGMKKAGVKNP--VFLLDEIDKMGSSFRGDPASALLEV  444 (782)
T ss_pred             CCCEEEEecCccccHHHhc--ccccc-cc-----ccCChHHHHHHHHhCCcCC--eEEeechhhccCCCCCChHHHHHhh
Confidence            5789999887655210000  12110 11     111 145555543    55  999999999977644    589999


Q ss_pred             hh---cCeEecCC-CceeecCCeEEEEecCCCCCCCC
Q 003038          756 IE---SGRIVTSS-GDEVSLGDAIVILSCESFSSRSR  788 (854)
Q Consensus       756 le---~G~l~d~~-G~~v~~~~aIiIlTsn~f~~~s~  788 (854)
                      +|   +-.|.|.. .-..|+++++||.|+|+.++.+.
T Consensus       445 LDPEQN~~F~DhYLev~yDLS~VmFiaTANsl~tIP~  481 (782)
T COG0466         445 LDPEQNNTFSDHYLEVPYDLSKVMFIATANSLDTIPA  481 (782)
T ss_pred             cCHhhcCchhhccccCccchhheEEEeecCccccCCh
Confidence            97   57777764 56789999999999998876543

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=99.18  E-value=9.9e-11  Score=142.98  Aligned_cols=140  Identities=14%  Similarity=0.096  Sum_probs=87.7

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..||||++++..|.+.+...|                 -.+.+||+||+|+|||++|++||+.|+..... ..--|..+.
T Consensus        15 ~eiiGqe~v~~~L~~~i~~~r-----------------i~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~-~~~pCg~C~   76 (824)
T PRK07764         15 AEVIGQEHVTEPLSTALDSGR-----------------INHAYLFSGPRGCGKTSSARILARSLNCVEGP-TSTPCGECD   76 (824)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC-----------------CCceEEEECCCCCCHHHHHHHHHHHhCcccCC-CCCCCcccH
Confidence            458999999999999887532                 23579999999999999999999999742210 000111111


Q ss_pred             CcCCCcccccccccc--CCCCCC-chHH--HHHHHHH----cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCce
Q 003038          698 STRADSTEDSRNKRS--RDEQSC-SYIE--RFAEAVS----NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDE  768 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl--~~~~g~-g~~e--~L~eav~----~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~  768 (854)
                      ++.......+....+  +..... |.++  .|.+.+.    ...|+||||||+|+++...+|.||++||+          
T Consensus        77 sC~~~~~g~~~~~dv~eidaas~~~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEE----------  146 (824)
T PRK07764         77 SCVALAPGGPGSLDVTEIDAASHGGVDDARELRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEE----------  146 (824)
T ss_pred             HHHHHHcCCCCCCcEEEecccccCCHHHHHHHHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhC----------
Confidence            110000000000001  111111 3333  3333332    35689999999999999999999999997          


Q ss_pred             eecCCeEEEEecCCCCCC
Q 003038          769 VSLGDAIVILSCESFSSR  786 (854)
Q Consensus       769 v~~~~aIiIlTsn~f~~~  786 (854)
                       .-.+++|||+|+..+..
T Consensus       147 -pP~~~~fIl~tt~~~kL  163 (824)
T PRK07764        147 -PPEHLKFIFATTEPDKV  163 (824)
T ss_pred             -CCCCeEEEEEeCChhhh
Confidence             22477899988765543

>CHL00181 cbbX CbbX; Provisional

Probab=99.18  E-value=1.2e-10  Score=126.86  Aligned_cols=139  Identities=12%  Similarity=0.162  Sum_probs=96.0

Q ss_pred             hHHHHHHHHHhhcCcccccHHHHHHHHHHHHH-------hhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHH
Q 003038          605 NSENLTSLCNALEKKVPWQKDTVYDIANTVLK-------CRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKEL  677 (854)
Q Consensus       605 ~~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~-------~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~L  677 (854)
                      +...++.+.+.|.+.++|++++...|...+..       .+.|+..+          ++...++|+||||||||++|+++
T Consensus        10 ~~~~~~~~~~~l~~~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~----------~~~~~ill~G~pGtGKT~lAr~l   79 (287)
T CHL00181         10 EKTQIQEVLDILDEELVGLAPVKTRIREIAALLLIDRLRKNLGLTSS----------NPGLHMSFTGSPGTGKTTVALKM   79 (287)
T ss_pred             cccCHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCC----------CCCceEEEECCCCCCHHHHHHHH
Confidence            34557789999999999999988877665421       23454332          33447999999999999999999


Q ss_pred             HHHHhCC----CCceEEEccccccCcCCCccccccccccCCCCCCchH-HHHHHHHHcCCCEEEEEecCCCC--------
Q 003038          678 ARLVFGS----HNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYI-ERFAEAVSNNPHRVFLIEDVEQA--------  744 (854)
Q Consensus       678 A~~lfg~----~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~-e~L~eav~~~p~~ViliDEieka--------  744 (854)
                      |+.++..    ...++.++.+.+.       ..     +.     |.. ....+.+.+....|+||||++.+        
T Consensus        80 a~~~~~~g~~~~~~~~~v~~~~l~-------~~-----~~-----g~~~~~~~~~l~~a~ggVLfIDE~~~l~~~~~~~~  142 (287)
T CHL00181         80 ADILYKLGYIKKGHLLTVTRDDLV-------GQ-----YI-----GHTAPKTKEVLKKAMGGVLFIDEAYYLYKPDNERD  142 (287)
T ss_pred             HHHHHHcCCCCCCceEEecHHHHH-------HH-----Hh-----ccchHHHHHHHHHccCCEEEEEccchhccCCCccc
Confidence            9988642    2346666644332       00     01     211 13445556666789999999985        


Q ss_pred             -CHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecC
Q 003038          745 -DYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       745 -~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn  781 (854)
                       .+++++.|++.|++++           .+.+||++++
T Consensus       143 ~~~e~~~~L~~~me~~~-----------~~~~vI~ag~  169 (287)
T CHL00181        143 YGSEAIEILLQVMENQR-----------DDLVVIFAGY  169 (287)
T ss_pred             hHHHHHHHHHHHHhcCC-----------CCEEEEEeCC
Confidence             5789999999998642           5678888764

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.17  E-value=7.3e-11  Score=134.03  Aligned_cols=127  Identities=9%  Similarity=0.107  Sum_probs=97.0

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ....++|.||||||||-+++++|..          .++.|+++-...|.++|.||.|.-++.+|..++.+  .|||+|+|
T Consensus       544 ~PsGvLL~GPPGCGKTLlAKAVANE----------ag~NFisVKGPELlNkYVGESErAVR~vFqRAR~s--aPCVIFFD  611 (802)
T KOG0733|consen  544 APSGVLLCGPPGCGKTLLAKAVANE----------AGANFISVKGPELLNKYVGESERAVRQVFQRARAS--APCVIFFD  611 (802)
T ss_pred             CCCceEEeCCCCccHHHHHHHHhhh----------ccCceEeecCHHHHHHHhhhHHHHHHHHHHHhhcC--CCeEEEec
Confidence            4667999999999999999999976          68899999999999999999999999999999986  79999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccC
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLH  375 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~  375 (854)
                      ||+.| ..++.+.      .....+.+..+-.=|-+-.+|..+.+||||+-..     ..|||+-|--||.
T Consensus       612 EiDaL~p~R~~~~------s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPD-----iIDpAiLRPGRlD  671 (802)
T KOG0733|consen  612 EIDALVPRRSDEG------SSVSSRVVNQLLTELDGLEERRGVYVIAATNRPD-----IIDPAILRPGRLD  671 (802)
T ss_pred             chhhcCcccCCCC------chhHHHHHHHHHHHhcccccccceEEEeecCCCc-----ccchhhcCCCccC
Confidence            99999 5443210      1122234333222221111223599999999766     4799998866663

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.17  E-value=1.2e-10  Score=136.13  Aligned_cols=135  Identities=15%  Similarity=0.140  Sum_probs=84.0

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..+.+++...                 +....+||+||+|+|||++|+.||+.++..... -.-.|..+.
T Consensus        16 ~diiGq~~~v~~L~~~i~~~-----------------rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~-~~~pCg~C~   77 (546)
T PRK14957         16 AEVAGQQHALNSLVHALETQ-----------------KVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGV-TAEPCNKCE   77 (546)
T ss_pred             HHhcCcHHHHHHHHHHHHcC-----------------CCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCC-CCCCCcccH
Confidence            45899999999998888653                 224578999999999999999999999752110 000011110


Q ss_pred             CcCCCccccc-cccccCCCCC-CchHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDS-RNKRSRDEQS-CSYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~-~~~rl~~~~g-~g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .+.......| .+-. +.... .|..+  .+.+.+..    ..++||+|||+|+++...++.|++.||+.          
T Consensus        78 sC~~i~~~~~~dlie-idaas~~gvd~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEep----------  146 (546)
T PRK14957         78 NCVAINNNSFIDLIE-IDAASRTGVEETKEILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEP----------  146 (546)
T ss_pred             HHHHHhcCCCCceEE-eecccccCHHHHHHHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcC----------
Confidence            0000000000 0000 01111 14433  45455544    45789999999999999999999999973          


Q ss_pred             ecCCeEEEEecCC
Q 003038          770 SLGDAIVILSCES  782 (854)
Q Consensus       770 ~~~~aIiIlTsn~  782 (854)
                       -.+++|||+|+.
T Consensus       147 -p~~v~fIL~Ttd  158 (546)
T PRK14957        147 -PEYVKFILATTD  158 (546)
T ss_pred             -CCCceEEEEECC
Confidence             145668887754

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.16  E-value=2.4e-10  Score=132.43  Aligned_cols=153  Identities=11%  Similarity=0.096  Sum_probs=103.7

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhh--CCCeEEE
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCL--GRGIVLN  303 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~--~~~~ILf  303 (854)
                      ..++++|+||||+|||++++++|..+...-.-.......|+.+....+...|.|+.+.+++.+++.++...  +.++|||
T Consensus       215 ~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~fl~v~~~eLl~kyvGete~~ir~iF~~Ar~~a~~g~p~IIf  294 (512)
T TIGR03689       215 PPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASDGRPVIVF  294 (512)
T ss_pred             CCcceEEECCCCCcHHHHHHHHHHhhccccccccCCceeEEeccchhhcccccchHHHHHHHHHHHHHHHhhcCCCceEE
Confidence            56789999999999999999999987432110111234566777778888899999999999999988632  4689999


Q ss_pred             eCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccC-CCCCCC
Q 003038          304 LGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLH-PLTIPA  381 (854)
Q Consensus       304 idel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~-~v~i~~  381 (854)
                      |||++.+ ..+..+.   .+  ......+..+-+.+..-...+.+.+||||+..+     ..||||-|-.||. .|.++.
T Consensus       295 IDEiD~L~~~R~~~~---s~--d~e~~il~~LL~~LDgl~~~~~ViVI~ATN~~d-----~LDpALlRpGRfD~~I~~~~  364 (512)
T TIGR03689       295 FDEMDSIFRTRGSGV---SS--DVETTVVPQLLSELDGVESLDNVIVIGASNRED-----MIDPAILRPGRLDVKIRIER  364 (512)
T ss_pred             EehhhhhhcccCCCc---cc--hHHHHHHHHHHHHhcccccCCceEEEeccCChh-----hCCHhhcCccccceEEEeCC
Confidence            9999999 6543210   00  001122334444442211123699999998866     3599998855663 378887


Q ss_pred             chHHHHh
Q 003038          382 GSLSLSL  388 (854)
Q Consensus       382 ~sl~~al  388 (854)
                      |+.....
T Consensus       365 Pd~e~r~  371 (512)
T TIGR03689       365 PDAEAAA  371 (512)
T ss_pred             CCHHHHH
Confidence            7765543

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.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.16  E-value=1.2e-10  Score=137.86  Aligned_cols=137  Identities=15%  Similarity=0.180  Sum_probs=87.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc----eEEEcc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN----FVSIAL  693 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~----~i~id~  693 (854)
                      ..|+||++++..|.+++...|                 -...+||+||+|+|||++|+.||+.++.....    ...--|
T Consensus        16 ~dviGQe~vv~~L~~~l~~~r-----------------l~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pC   78 (618)
T PRK14951         16 SEMVGQEHVVQALTNALTQQR-----------------LHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPC   78 (618)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----------------CCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCC
Confidence            457999999999999887643                 24578999999999999999999999742110    000001


Q ss_pred             ccccCcCCCccccccccccCCCC-CCchHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCC
Q 003038          694 SSFSSTRADSTEDSRNKRSRDEQ-SCSYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSG  766 (854)
Q Consensus       694 s~~~~~~~~s~e~~~~~rl~~~~-g~g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G  766 (854)
                      ..+..+.......|.-...+.+. ..|.++  .+.+.+...|    |+||+|||+|+++...+|.|++.||+.       
T Consensus        79 g~C~~C~~i~~g~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEP-------  151 (618)
T PRK14951         79 GVCQACRDIDSGRFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEP-------  151 (618)
T ss_pred             CccHHHHHHHcCCCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhcccC-------
Confidence            11110000000111100011111 124443  4556666555    799999999999999999999999972       


Q ss_pred             ceeecCCeEEEEecCC
Q 003038          767 DEVSLGDAIVILSCES  782 (854)
Q Consensus       767 ~~v~~~~aIiIlTsn~  782 (854)
                          -.+++|||+|+.
T Consensus       152 ----P~~~~fIL~Ttd  163 (618)
T PRK14951        152 ----PEYLKFVLATTD  163 (618)
T ss_pred             ----CCCeEEEEEECC
Confidence                246778888754

>PRK13531 regulatory ATPase RavA; Provisional

Probab=99.15  E-value=1.8e-10  Score=131.35  Aligned_cols=147  Identities=16%  Similarity=0.201  Sum_probs=101.3

Q ss_pred             HHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC
Q 003038          606 SENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH  685 (854)
Q Consensus       606 ~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~  685 (854)
                      .+.+..|.+.|.+.|+||+++|+.+..++..                    .+++||.||||+|||.+|++|+..+-.. 
T Consensus         8 ~~~i~~l~~~l~~~i~gre~vI~lll~aala--------------------g~hVLL~GpPGTGKT~LAraLa~~~~~~-   66 (498)
T PRK13531          8 AERISRLSSALEKGLYERSHAIRLCLLAALS--------------------GESVFLLGPPGIAKSLIARRLKFAFQNA-   66 (498)
T ss_pred             HHHHHHHHHHHhhhccCcHHHHHHHHHHHcc--------------------CCCEEEECCCChhHHHHHHHHHHHhccc-
Confidence            4678899999999999999999988887653                    3578999999999999999999987433 


Q ss_pred             CceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCC---CEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          686 NNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNP---HRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       686 ~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p---~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                      ..|..+... |+.+.+.- +..++..+.. .| .|    . .....|   ..|+|+|||.++++.+|+.|+++|+++.++
T Consensus        67 ~~F~~~~~~-fttp~DLf-G~l~i~~~~~-~g-~f----~-r~~~G~L~~A~lLfLDEI~rasp~~QsaLLeam~Er~~t  137 (498)
T PRK13531         67 RAFEYLMTR-FSTPEEVF-GPLSIQALKD-EG-RY----Q-RLTSGYLPEAEIVFLDEIWKAGPAILNTLLTAINERRFR  137 (498)
T ss_pred             Ccceeeeee-ecCcHHhc-CcHHHhhhhh-cC-ch----h-hhcCCccccccEEeecccccCCHHHHHHHHHHHHhCeEe
Confidence            255544332 11000000 0000000000 00 01    0 111111   239999999999999999999999999999


Q ss_pred             cCCCceeecCCeEEEEecCCC
Q 003038          763 TSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       763 d~~G~~v~~~~aIiIlTsn~f  783 (854)
                      . .|+...+.--+||.+||..
T Consensus       138 ~-g~~~~~lp~rfiv~ATN~L  157 (498)
T PRK13531        138 N-GAHEEKIPMRLLVTASNEL  157 (498)
T ss_pred             c-CCeEEeCCCcEEEEECCCC
Confidence            6 5788888888888888843

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.15  E-value=1.3e-10  Score=136.36  Aligned_cols=135  Identities=14%  Similarity=0.158  Sum_probs=84.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..|.+++...                 +....+||+||+|+|||++|++||+.++... ..-..-|..+.
T Consensus        15 ddVIGQe~vv~~L~~aI~~g-----------------rl~HAyLF~GPpGvGKTTlAriLAK~LnC~~-~~~~~pCg~C~   76 (702)
T PRK14960         15 NELVGQNHVSRALSSALERG-----------------RLHHAYLFTGTRGVGKTTIARILAKCLNCET-GVTSTPCEVCA   76 (702)
T ss_pred             HHhcCcHHHHHHHHHHHHcC-----------------CCCeEEEEECCCCCCHHHHHHHHHHHhCCCc-CCCCCCCccCH
Confidence            45899999999999988743                 3346889999999999999999999996421 10000011111


Q ss_pred             CcCCCccccc-cccccCCCCCC-chHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDS-RNKRSRDEQSC-SYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~-~~~rl~~~~g~-g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .+.....+.| .+-. +.+... +..+  .+.+.+..    ..++|++|||+|+++...++.|++.||+.          
T Consensus        77 sC~~I~~g~hpDviE-IDAAs~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEP----------  145 (702)
T PRK14960         77 TCKAVNEGRFIDLIE-IDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEP----------  145 (702)
T ss_pred             HHHHHhcCCCCceEE-ecccccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcC----------
Confidence            0000000011 0000 111111 3332  34444433    35789999999999999999999999972          


Q ss_pred             ecCCeEEEEecCC
Q 003038          770 SLGDAIVILSCES  782 (854)
Q Consensus       770 ~~~~aIiIlTsn~  782 (854)
                       -.+++|||+|+.
T Consensus       146 -P~~v~FILaTtd  157 (702)
T PRK14960        146 -PEHVKFLFATTD  157 (702)
T ss_pred             -CCCcEEEEEECC
Confidence             145678888864

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.15  E-value=2.6e-10  Score=131.73  Aligned_cols=138  Identities=14%  Similarity=0.096  Sum_probs=87.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..+.+++...                 +....+||+||+|+|||++|+.||+.+......-. -.|..+.
T Consensus        13 ~dliGQe~vv~~L~~a~~~~-----------------ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~-~pCg~C~   74 (491)
T PRK14964         13 KDLVGQDVLVRILRNAFTLN-----------------KIPQSILLVGASGVGKTTCARIISLCLNCSNGPTS-DPCGTCH   74 (491)
T ss_pred             HHhcCcHHHHHHHHHHHHcC-----------------CCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCC-CCccccH
Confidence            45799999999988887653                 23458999999999999999999998853211000 0000000


Q ss_pred             CcCCCccccc-cccccCCCCCC-chHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDS-RNKRSRDEQSC-SYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~-~~~rl~~~~g~-g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .+.......| .+.. +.+... |.++  .+.+.+...|    ++||+|||+|.++...+|.|++.||+-          
T Consensus        75 ~C~~i~~~~~~Dv~e-idaas~~~vddIR~Iie~~~~~P~~~~~KVvIIDEah~Ls~~A~NaLLK~LEeP----------  143 (491)
T PRK14964         75 NCISIKNSNHPDVIE-IDAASNTSVDDIKVILENSCYLPISSKFKVYIIDEVHMLSNSAFNALLKTLEEP----------  143 (491)
T ss_pred             HHHHHhccCCCCEEE-EecccCCCHHHHHHHHHHHHhccccCCceEEEEeChHhCCHHHHHHHHHHHhCC----------
Confidence            0000000000 0000 111111 4444  4566666555    689999999999999999999999972          


Q ss_pred             ecCCeEEEEecCCCCC
Q 003038          770 SLGDAIVILSCESFSS  785 (854)
Q Consensus       770 ~~~~aIiIlTsn~f~~  785 (854)
                       -.+++|||+|+..+.
T Consensus       144 -p~~v~fIlatte~~K  158 (491)
T PRK14964        144 -APHVKFILATTEVKK  158 (491)
T ss_pred             -CCCeEEEEEeCChHH
Confidence             246789998865433

>PLN03025 replication factor C subunit; Provisional

Probab=99.14  E-value=1.8e-10  Score=127.67  Aligned_cols=116  Identities=13%  Similarity=0.229  Sum_probs=78.9

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC--CceEEEccccc
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH--NNFVSIALSSF  696 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~--~~~i~id~s~~  696 (854)
                      .|+||++++..|...+...                  ...+++|+||+|+|||++|+++|+.++|..  ..++.++.+..
T Consensus        14 ~~~g~~~~~~~L~~~~~~~------------------~~~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~eln~sd~   75 (319)
T PLN03025         14 DIVGNEDAVSRLQVIARDG------------------NMPNLILSGPPGTGKTTSILALAHELLGPNYKEAVLELNASDD   75 (319)
T ss_pred             HhcCcHHHHHHHHHHHhcC------------------CCceEEEECCCCCCHHHHHHHHHHHHhcccCccceeeeccccc
Confidence            4689999988877664421                  123689999999999999999999998753  23344443311


Q ss_pred             cCcCCCccccccccccCCCCCCchHH-HHHHHHH------cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          697 SSTRADSTEDSRNKRSRDEQSCSYIE-RFAEAVS------NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       697 ~~~~~~s~e~~~~~rl~~~~g~g~~e-~L~eav~------~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .                   +..... .+.....      ...+.||+|||+|+++...|+.|++.||..          
T Consensus        76 ~-------------------~~~~vr~~i~~~~~~~~~~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~----------  126 (319)
T PLN03025         76 R-------------------GIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTSGAQQALRRTMEIY----------  126 (319)
T ss_pred             c-------------------cHHHHHHHHHHHHhccccCCCCCeEEEEEechhhcCHHHHHHHHHHHhcc----------
Confidence            1                   001111 1111111      134789999999999999999999999851          


Q ss_pred             ecCCeEEEEecCC
Q 003038          770 SLGDAIVILSCES  782 (854)
Q Consensus       770 ~~~~aIiIlTsn~  782 (854)
                       -.++.|||+||.
T Consensus       127 -~~~t~~il~~n~  138 (319)
T PLN03025        127 -SNTTRFALACNT  138 (319)
T ss_pred             -cCCceEEEEeCC
Confidence             134668999984

>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=99.14  E-value=2.7e-10  Score=108.37  Aligned_cols=118  Identities=12%  Similarity=0.142  Sum_probs=87.1

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCcccc
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEW  309 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~  309 (854)
                      ++|+||||+|||++|+.+|+.+          +.+++.++...+.+.+.++.++++..++..++.. .+++||||||+|.
T Consensus         1 ill~G~~G~GKT~l~~~la~~l----------~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~-~~~~vl~iDe~d~   69 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYL----------GFPFIEIDGSELISSYAGDSEQKIRDFFKKAKKS-AKPCVLFIDEIDK   69 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHT----------TSEEEEEETTHHHTSSTTHHHHHHHHHHHHHHHT-STSEEEEEETGGG
T ss_pred             CEEECcCCCCeeHHHHHHHhhc----------cccccccccccccccccccccccccccccccccc-ccceeeeeccchh
Confidence            5899999999999999999885          5789999999999889999999999999999876 3389999999999


Q ss_pred             c-cccccccccccccchhhhHHHHHHHhhccc-CCCCceEEEEEecCHHHHHHhhccCCchh
Q 003038          310 A-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGENARFWLMGIATFQSYMRCKSGHPSLE  369 (854)
Q Consensus       310 l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~g~l~lIgatT~~ey~k~~~~~pale  369 (854)
                      + .......      ..........+.+.+.. ...++.+.+|++|+..+     ..+|+|.
T Consensus        70 l~~~~~~~~------~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~-----~i~~~l~  120 (132)
T PF00004_consen   70 LFPKSQPSS------SSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPD-----KIDPALL  120 (132)
T ss_dssp             TSHHCSTSS------SHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGG-----GSCHHHH
T ss_pred             ccccccccc------ccccccccceeeecccccccccccceeEEeeCChh-----hCCHhHH
Confidence            9 5441110      11112233444444522 22123699999998722     4677777

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 ....

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=99.14  E-value=1.4e-10  Score=109.56  Aligned_cols=107  Identities=21%  Similarity=0.252  Sum_probs=78.3

Q ss_pred             HHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC--C
Q 003038          608 NLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS--H  685 (854)
Q Consensus       608 ~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~--~  685 (854)
                      ++..|+..|.++++||..|++.|..+|......- .|         .|| .+|.|+||+||||+.+++.||+.+|.+  .
T Consensus        15 ~~~~L~~~L~~~l~GQhla~~~v~~ai~~~l~~~-~p---------~Kp-LVlSfHG~tGtGKn~v~~liA~~ly~~G~~   83 (127)
T PF06309_consen   15 NITGLEKDLQRNLFGQHLAVEVVVNAIKGHLANP-NP---------RKP-LVLSFHGWTGTGKNFVSRLIAEHLYKSGMK   83 (127)
T ss_pred             CHHHHHHHHHHHccCcHHHHHHHHHHHHHHHcCC-CC---------CCC-EEEEeecCCCCcHHHHHHHHHHHHHhcccC
Confidence            4679999999999999999999999999886532 22         366 599999999999999999999999964  4


Q ss_pred             CceEEEccccccCcCCCccccccccccCCCCCCchHH----HHHHHHHcCCCEEEEE
Q 003038          686 NNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIE----RFAEAVSNNPHRVFLI  738 (854)
Q Consensus       686 ~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e----~L~eav~~~p~~Vili  738 (854)
                      .++|..=.+...       .++.      .....|.+    .+.+.+.++|.++++|
T Consensus        84 S~~V~~f~~~~h-------FP~~------~~v~~Yk~~L~~~I~~~v~~C~rslFIF  127 (127)
T PF06309_consen   84 SPFVHQFIATHH-------FPHN------SNVDEYKEQLKSWIRGNVSRCPRSLFIF  127 (127)
T ss_pred             CCceeeeccccc-------CCCc------hHHHHHHHHHHHHHHHHHHhCCcCeeeC
Confidence            555544333211       0110      01115655    4667777899999886

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

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.14  E-value=2.2e-10  Score=129.22  Aligned_cols=136  Identities=18%  Similarity=0.149  Sum_probs=84.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..+.+++...                 +....+||+||+|+|||++|+++|+.+++.... ..--+..+.
T Consensus        16 ~~iiGq~~~~~~l~~~~~~~-----------------~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~-~~~pc~~c~   77 (363)
T PRK14961         16 RDIIGQKHIVTAISNGLSLG-----------------RIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGI-TSNPCRKCI   77 (363)
T ss_pred             hhccChHHHHHHHHHHHHcC-----------------CCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCC-CCCCCCCCH
Confidence            45899999999998888653                 223578999999999999999999999743210 000000000


Q ss_pred             CcCCCccccc-cccccCCCCC-CchHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDS-RNKRSRDEQS-CSYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~-~~~rl~~~~g-~g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .+.......| .+.. +.+.. .+..+  .+.+.+...|    ++||+|||+|+++...++.|++.+++.          
T Consensus        78 ~c~~~~~~~~~d~~~-~~~~~~~~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe~----------  146 (363)
T PRK14961         78 ICKEIEKGLCLDLIE-IDAASRTKVEEMREILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEEP----------  146 (363)
T ss_pred             HHHHHhcCCCCceEE-ecccccCCHHHHHHHHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhcC----------
Confidence            0000000000 0000 11111 12322  4555555444    679999999999999999999999972          


Q ss_pred             ecCCeEEEEecCCC
Q 003038          770 SLGDAIVILSCESF  783 (854)
Q Consensus       770 ~~~~aIiIlTsn~f  783 (854)
                       -.+++|||+|+..
T Consensus       147 -~~~~~fIl~t~~~  159 (363)
T PRK14961        147 -PQHIKFILATTDV  159 (363)
T ss_pred             -CCCeEEEEEcCCh
Confidence             1366788888643

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.13  E-value=1.6e-10  Score=137.28  Aligned_cols=136  Identities=14%  Similarity=0.131  Sum_probs=88.1

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..+.+++...                 +....+||+||+|+|||++|++||+.++..... -.--|..+.
T Consensus        16 ~~iiGq~~v~~~L~~~i~~~-----------------~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~-~~~~c~~c~   77 (576)
T PRK14965         16 SDLTGQEHVSRTLQNAIDTG-----------------RVAHAFLFTGARGVGKTSTARILAKALNCEQGL-TAEPCNVCP   77 (576)
T ss_pred             HHccCcHHHHHHHHHHHHcC-----------------CCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCC-CCCCCCccH
Confidence            46899999999999988753                 234578999999999999999999999753210 000011110


Q ss_pred             CcCCCccccc-cccccCCCCC-CchHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDS-RNKRSRDEQS-CSYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~-~~~rl~~~~g-~g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .+.......+ .+.. +.+.+ .|..+  .|.+.+...|    |+||+|||+|+++...+|.|+++||+-          
T Consensus        78 ~c~~i~~g~~~d~~e-id~~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~~a~naLLk~LEep----------  146 (576)
T PRK14965         78 PCVEITEGRSVDVFE-IDGASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEEP----------  146 (576)
T ss_pred             HHHHHhcCCCCCeee-eeccCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCCHHHHHHHHHHHHcC----------
Confidence            0000000000 0000 11221 24444  5666666555    689999999999999999999999972          


Q ss_pred             ecCCeEEEEecCCC
Q 003038          770 SLGDAIVILSCESF  783 (854)
Q Consensus       770 ~~~~aIiIlTsn~f  783 (854)
                       -.+++|||+|+..
T Consensus       147 -p~~~~fIl~t~~~  159 (576)
T PRK14965        147 -PPHVKFIFATTEP  159 (576)
T ss_pred             -CCCeEEEEEeCCh
Confidence             3578899988643

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.13  E-value=1.4e-10  Score=133.59  Aligned_cols=127  Identities=9%  Similarity=0.117  Sum_probs=102.1

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEe
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      |-+.+++|+||||||||-+|.++|..          .+.+|+++-...|.+.|.|..|+.+++||..+++.  +|||||+
T Consensus       699 r~~~giLLyGppGcGKT~la~a~a~~----------~~~~fisvKGPElL~KyIGaSEq~vR~lF~rA~~a--~PCiLFF  766 (952)
T KOG0735|consen  699 RLRTGILLYGPPGCGKTLLASAIASN----------SNLRFISVKGPELLSKYIGASEQNVRDLFERAQSA--KPCILFF  766 (952)
T ss_pred             ccccceEEECCCCCcHHHHHHHHHhh----------CCeeEEEecCHHHHHHHhcccHHHHHHHHHHhhcc--CCeEEEe
Confidence            35678999999999999999999976          58899999999999999999999999999999986  8999999


Q ss_pred             Cccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc
Q 003038          305 GDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL  374 (854)
Q Consensus       305 del~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~  374 (854)
                      ||++.+ ..++..+.|      +.++.|..+-.=|.++-|=+.+.++|||+..+.     .||||-|--||
T Consensus       767 DEfdSiAPkRGhDsTG------VTDRVVNQlLTelDG~Egl~GV~i~aaTsRpdl-----iDpALLRpGRl  826 (952)
T KOG0735|consen  767 DEFDSIAPKRGHDSTG------VTDRVVNQLLTELDGAEGLDGVYILAATSRPDL-----IDPALLRPGRL  826 (952)
T ss_pred             ccccccCcccCCCCCC------chHHHHHHHHHhhccccccceEEEEEecCCccc-----cCHhhcCCCcc
Confidence            999999 655444333      455777665554532222235999999997773     69999885555

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.13  E-value=1.5e-10  Score=121.73  Aligned_cols=129  Identities=12%  Similarity=0.120  Sum_probs=96.3

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGD  306 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfide  306 (854)
                      -+.++|+||||+||+-+++++|..          .|-.|++++.+.|++.+.||.|+-++.||+.++++  +|.|+||||
T Consensus       166 wrgiLLyGPPGTGKSYLAKAVATE----------AnSTFFSvSSSDLvSKWmGESEkLVknLFemARe~--kPSIIFiDE  233 (439)
T KOG0739|consen  166 WRGILLYGPPGTGKSYLAKAVATE----------ANSTFFSVSSSDLVSKWMGESEKLVKNLFEMAREN--KPSIIFIDE  233 (439)
T ss_pred             ceeEEEeCCCCCcHHHHHHHHHhh----------cCCceEEeehHHHHHHHhccHHHHHHHHHHHHHhc--CCcEEEeeh
Confidence            357899999999999999999976          56799999999999999999999999999999997  899999999


Q ss_pred             cccc-cccccccccccccchhhhHHHHHHHhhc-cc-CCC--CceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCC
Q 003038          307 LEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CG-IGE--NARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIP  380 (854)
Q Consensus       307 l~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~-~~g--~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~  380 (854)
                      |+.+ +.+..+.      ..+.++.-.+   +| .. .-|  ++.+-++|||+...     ..|.|+.|  || ..|.||
T Consensus       234 iDslcg~r~enE------seasRRIKTE---fLVQMqGVG~d~~gvLVLgATNiPw-----~LDsAIRR--RFekRIYIP  297 (439)
T KOG0739|consen  234 IDSLCGSRSENE------SEASRRIKTE---FLVQMQGVGNDNDGVLVLGATNIPW-----VLDSAIRR--RFEKRIYIP  297 (439)
T ss_pred             hhhhccCCCCCc------hHHHHHHHHH---HHHhhhccccCCCceEEEecCCCch-----hHHHHHHH--Hhhcceecc
Confidence            9999 7765321      1111222222   22 11 122  24699999998654     35778888  66 445555


Q ss_pred             Cch
Q 003038          381 AGS  383 (854)
Q Consensus       381 ~~s  383 (854)
                      =|.
T Consensus       298 LPe  300 (439)
T KOG0739|consen  298 LPE  300 (439)
T ss_pred             CCc
Confidence            443

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.12  E-value=1.7e-10  Score=120.68  Aligned_cols=137  Identities=19%  Similarity=0.259  Sum_probs=101.9

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCcccccccccc----CCCCCCchHH--HHHHHHH-
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRS----RDEQSCSYIE--RFAEAVS-  729 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl----~~~~g~g~~e--~L~eav~-  729 (854)
                      ..+++|+||+|.||.+.+.+|-+.+||..-.=++|+...|.+++.-..|-..++..    +.|..+|+.+  .+.+.++ 
T Consensus        34 ~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEistvsS~yHlEitPSDaG~~DRvViQellKe  113 (351)
T KOG2035|consen   34 FPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEISTVSSNYHLEITPSDAGNYDRVVIQELLKE  113 (351)
T ss_pred             CCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEEEEecccceEEeChhhcCcccHHHHHHHHHH
Confidence            45899999999999999999999999977777888888777432211111111111    1233345444  1222222 


Q ss_pred             -----------cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCCCCCCCCccCCC
Q 003038          730 -----------NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRACSPPTKQKS  798 (854)
Q Consensus       730 -----------~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~~sp~~~~~~  798 (854)
                                 +.++.||+|.|+|++..+.|.+|.+.||           ..-+|+.+||.||   |.|+...|.     
T Consensus       114 vAQt~qie~~~qr~fKvvvi~ead~LT~dAQ~aLRRTME-----------kYs~~~RlIl~cn---s~SriIepI-----  174 (351)
T KOG2035|consen  114 VAQTQQIETQGQRPFKVVVINEADELTRDAQHALRRTME-----------KYSSNCRLILVCN---STSRIIEPI-----  174 (351)
T ss_pred             HHhhcchhhccccceEEEEEechHhhhHHHHHHHHHHHH-----------HHhcCceEEEEec---CcccchhHH-----
Confidence                       3679999999999999999999999999           4557888999995   678888999     


Q ss_pred             CCchhhcccccCCCCCceeeeccCCCC
Q 003038          799 DGCEEEKGAAMEGTSPSVSLDLNICID  825 (854)
Q Consensus       799 ~~~~~~~~~~~~~~~~~~~~~l~~~~~  825 (854)
                                   +||||-++++++.+
T Consensus       175 -------------rSRCl~iRvpaps~  188 (351)
T KOG2035|consen  175 -------------RSRCLFIRVPAPSD  188 (351)
T ss_pred             -------------hhheeEEeCCCCCH
Confidence                         99999999999844

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

Probab=99.12  E-value=1.8e-10  Score=126.50  Aligned_cols=101  Identities=13%  Similarity=0.238  Sum_probs=73.3

Q ss_pred             cccccHHHHHH---HHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          619 KVPWQKDTVYD---IANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       619 ~V~GQ~~av~~---Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      .|+||++.+..   |-.+|..                  +..++++|+||||||||++|+.||...   ...|..++...
T Consensus        25 e~vGQ~HLlg~~~~lrr~v~~------------------~~l~SmIl~GPPG~GKTTlA~liA~~~---~~~f~~~sAv~   83 (436)
T COG2256          25 EVVGQEHLLGEGKPLRRAVEA------------------GHLHSMILWGPPGTGKTTLARLIAGTT---NAAFEALSAVT   83 (436)
T ss_pred             HhcChHhhhCCCchHHHHHhc------------------CCCceeEEECCCCCCHHHHHHHHHHhh---CCceEEecccc
Confidence            47999988843   2233322                  346799999999999999999999976   45677776431


Q ss_pred             ccCcCCCccccccccccCCCCCCchHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                      .                      |..+  .+.+.-++    ....|+|+||||+.+..-|+.||..||+|.++
T Consensus        84 ~----------------------gvkdlr~i~e~a~~~~~~gr~tiLflDEIHRfnK~QQD~lLp~vE~G~ii  134 (436)
T COG2256          84 S----------------------GVKDLREIIEEARKNRLLGRRTILFLDEIHRFNKAQQDALLPHVENGTII  134 (436)
T ss_pred             c----------------------cHHHHHHHHHHHHHHHhcCCceEEEEehhhhcChhhhhhhhhhhcCCeEE
Confidence            1                      2222  22222221    23579999999999999999999999999887

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=99.12  E-value=3.3e-10  Score=126.93  Aligned_cols=80  Identities=19%  Similarity=0.254  Sum_probs=62.9

Q ss_pred             HHHHHhhcCcccccHHHHHHHHHHHHHh--hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc
Q 003038          610 TSLCNALEKKVPWQKDTVYDIANTVLKC--RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN  687 (854)
Q Consensus       610 ~~L~~~L~~~V~GQ~~av~~Ia~~v~~~--rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~  687 (854)
                      +.+.+.|.+.|+||++|+..++-++...  |.++....+.      .-+...+||+||+|+|||++|++||+.+   ..+
T Consensus         4 ~~I~~~Ld~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~------e~~p~~ILLiGppG~GKT~lAraLA~~l---~~~   74 (441)
T TIGR00390         4 REIVAELDKYIIGQDNAKKSVAIALRNRYRRSQLNEELKD------EVTPKNILMIGPTGVGKTEIARRLAKLA---NAP   74 (441)
T ss_pred             HHHHHHHhhhccCHHHHHHHHHHHHHhhhhhhcccccccc------ccCCceEEEECCCCCCHHHHHHHHHHHh---CCe
Confidence            4788899999999999999999999864  3333221110      1123579999999999999999999998   578


Q ss_pred             eEEEccccccC
Q 003038          688 FVSIALSSFSS  698 (854)
Q Consensus       688 ~i~id~s~~~~  698 (854)
                      |+.+|++.|.+
T Consensus        75 fi~vdat~~~e   85 (441)
T TIGR00390        75 FIKVEATKFTE   85 (441)
T ss_pred             EEEeecceeec
Confidence            99999987763

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.

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=99.11  E-value=2.6e-10  Score=125.21  Aligned_cols=129  Identities=12%  Similarity=0.022  Sum_probs=93.6

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhh---CCCeE
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCL---GRGIV  301 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~---~~~~I  301 (854)
                      +-.+-++|+||||||||.+++++|..+          |+.++.++.+.|.++|.||.|+++++++.+++...   ++|+|
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~el----------g~~~i~vsa~eL~sk~vGEsEk~IR~~F~~A~~~a~~~~aPcV  215 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKM----------GIEPIVMSAGELESENAGEPGKLIRQRYREAADIIKKKGKMSC  215 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHc----------CCCeEEEEHHHhhcCcCCcHHHHHHHHHHHHHHHhhccCCCeE
Confidence            455667899999999999999999884          77899999999999999999999999999998531   57999


Q ss_pred             EEeCccccc-cccccccccccccchhhhHHH-HHHHhhc-ccC-----------CCCceEEEEEecCHHHHHHhhccCCc
Q 003038          302 LNLGDLEWA-EFRASSSEQVRGYYCSIEHII-MEIGKLV-CGI-----------GENARFWLMGIATFQSYMRCKSGHPS  367 (854)
Q Consensus       302 Lfidel~~l-~~~~~~~~~~~~~~~~~~~~~-~~~~~ll-~~~-----------~g~g~l~lIgatT~~ey~k~~~~~pa  367 (854)
                      ||||||+.+ +...+..      +....+.+ ..+.+++ .+.           ....++.+|+||+--.     ..||+
T Consensus       216 LFIDEIDA~~g~r~~~~------~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~VIaTTNrpd-----~LDpA  284 (413)
T PLN00020        216 LFINDLDAGAGRFGTTQ------YTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGNDFS-----TLYAP  284 (413)
T ss_pred             EEEehhhhcCCCCCCCC------cchHHHHHHHHHHHHhcCCccccccccccccccCCCceEEEeCCCcc-----cCCHh
Confidence            999999999 6543211      11112333 3444544 210           1123688999996433     46888


Q ss_pred             hhhhhcc
Q 003038          368 LETLWSL  374 (854)
Q Consensus       368 le~~~~~  374 (854)
                      |-|-=||
T Consensus       285 LlRpGRf  291 (413)
T PLN00020        285 LIRDGRM  291 (413)
T ss_pred             HcCCCCC
Confidence            8774334

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.10  E-value=5.1e-10  Score=122.00  Aligned_cols=139  Identities=16%  Similarity=0.188  Sum_probs=95.4

Q ss_pred             hHHHHHHHHHhhcCcccccHHHHHHHHHHHHH-------hhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHH
Q 003038          605 NSENLTSLCNALEKKVPWQKDTVYDIANTVLK-------CRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKEL  677 (854)
Q Consensus       605 ~~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~-------~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~L  677 (854)
                      +...++.+.+.|...++|.+++.+.|.+.+..       .+.|+...          .|...++|+||+|||||++|+++
T Consensus         9 ~~~~~~~~~~~l~~~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~----------~~~~~vll~G~pGTGKT~lA~~i   78 (284)
T TIGR02880         9 EASGITEVLDQLDRELIGLKPVKTRIREIAALLLVERLRQRLGLASA----------APTLHMSFTGNPGTGKTTVALRM   78 (284)
T ss_pred             hhccHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcC----------CCCceEEEEcCCCCCHHHHHHHH
Confidence            34456778888888899999998887665432       23444321          34457999999999999999999


Q ss_pred             HHHHhCC----CCceEEEccccccCcCCCccccccccccCCCCCCchH-HHHHHHHHcCCCEEEEEecCCCC--------
Q 003038          678 ARLVFGS----HNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYI-ERFAEAVSNNPHRVFLIEDVEQA--------  744 (854)
Q Consensus       678 A~~lfg~----~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~-e~L~eav~~~p~~ViliDEieka--------  744 (854)
                      |+.+...    ...|+.+++++..       .     .+.     |.. ..+.+.+.+...+|+|||||+.+        
T Consensus        79 a~~l~~~g~~~~~~~v~v~~~~l~-------~-----~~~-----g~~~~~~~~~~~~a~~gvL~iDEi~~L~~~~~~~~  141 (284)
T TIGR02880        79 AQILHRLGYVRKGHLVSVTRDDLV-------G-----QYI-----GHTAPKTKEILKRAMGGVLFIDEAYYLYRPDNERD  141 (284)
T ss_pred             HHHHHHcCCcccceEEEecHHHHh-------H-----hhc-----ccchHHHHHHHHHccCcEEEEechhhhccCCCccc
Confidence            9988642    2357777654332       1     111     211 13445555555689999999976        


Q ss_pred             -CHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecC
Q 003038          745 -DYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       745 -~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn  781 (854)
                       ..++++.|++.|++++           .+.+||++++
T Consensus       142 ~~~~~~~~Ll~~le~~~-----------~~~~vI~a~~  168 (284)
T TIGR02880       142 YGQEAIEILLQVMENQR-----------DDLVVILAGY  168 (284)
T ss_pred             hHHHHHHHHHHHHhcCC-----------CCEEEEEeCC
Confidence             4678999999998643           5677888764

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.

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.10  E-value=4.9e-10  Score=127.40  Aligned_cols=155  Identities=12%  Similarity=0.099  Sum_probs=106.6

Q ss_pred             cHHHHHHHHHHhh----c---------cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccc
Q 003038          211 RNEDVMYVIENLM----S---------KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMN  277 (854)
Q Consensus       211 r~~ei~~v~~~L~----r---------~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~  277 (854)
                      +++.++.+.+.+.    +         ...++++|+||||||||.+|+++|...          +..++.++.+.+...|
T Consensus       136 l~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~----------~~~~i~v~~~~l~~~~  205 (389)
T PRK03992        136 LEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHET----------NATFIRVVGSELVQKF  205 (389)
T ss_pred             cHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHh----------CCCEEEeehHHHhHhh
Confidence            5666666655432    1         346789999999999999999999874          4578999999888889


Q ss_pred             hHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcc---cCCCCceEEEEEec
Q 003038          278 RVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVC---GIGENARFWLMGIA  353 (854)
Q Consensus       278 rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~---~~~g~g~l~lIgat  353 (854)
                      .|+.+..++.+++.++..  .|+||||||++.+ +.+......   ....+..   .+..++.   .....+.+++||||
T Consensus       206 ~g~~~~~i~~~f~~a~~~--~p~IlfiDEiD~l~~~r~~~~~~---~~~~~~~---~l~~lL~~ld~~~~~~~v~VI~aT  277 (389)
T PRK03992        206 IGEGARLVRELFELAREK--APSIIFIDEIDAIAAKRTDSGTS---GDREVQR---TLMQLLAEMDGFDPRGNVKIIAAT  277 (389)
T ss_pred             ccchHHHHHHHHHHHHhc--CCeEEEEechhhhhcccccCCCC---ccHHHHH---HHHHHHHhccccCCCCCEEEEEec
Confidence            999999999999999875  6899999999999 554321100   0001112   2334442   11122369999999


Q ss_pred             CHHHHHHhhccCCchhhhhcc-CCCCCCCchHHHHh
Q 003038          354 TFQSYMRCKSGHPSLETLWSL-HPLTIPAGSLSLSL  388 (854)
Q Consensus       354 T~~ey~k~~~~~pale~~~~~-~~v~i~~~sl~~al  388 (854)
                      +..+     ..||+|-|-=|| +.|.|+.|+.....
T Consensus       278 n~~~-----~ld~allRpgRfd~~I~v~~P~~~~R~  308 (389)
T PRK03992        278 NRID-----ILDPAILRPGRFDRIIEVPLPDEEGRL  308 (389)
T ss_pred             CChh-----hCCHHHcCCccCceEEEECCCCHHHHH
Confidence            8764     468888762234 34777777765533

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.09  E-value=3.8e-10  Score=132.39  Aligned_cols=154  Identities=14%  Similarity=0.133  Sum_probs=104.4

Q ss_pred             HHHHHHHHHhhc---------cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHH
Q 003038          213 EDVMYVIENLMS---------KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQ  283 (854)
Q Consensus       213 ~ei~~v~~~L~r---------~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~  283 (854)
                      ++++.+++.|..         +..++++|+||||||||.+++++|..          .++.++.++.+.+...+.|+.+.
T Consensus        65 ~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~----------~~~~~~~i~~~~~~~~~~g~~~~  134 (495)
T TIGR01241        65 EELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGE----------AGVPFFSISGSDFVEMFVGVGAS  134 (495)
T ss_pred             HHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHH----------cCCCeeeccHHHHHHHHhcccHH
Confidence            345666665432         24568999999999999999999976          36789999999888889999999


Q ss_pred             HHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhh
Q 003038          284 RVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCK  362 (854)
Q Consensus       284 rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~  362 (854)
                      +++++++.++..  .|+|||||||+.+ ..+..+..+   .....++.+..+-..+....+++.+.+||||+..+     
T Consensus       135 ~l~~~f~~a~~~--~p~Il~iDEid~l~~~r~~~~~~---~~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~~~-----  204 (495)
T TIGR01241       135 RVRDLFEQAKKN--APCIIFIDEIDAVGRQRGAGLGG---GNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPD-----  204 (495)
T ss_pred             HHHHHHHHHHhc--CCCEEEEechhhhhhccccCcCC---ccHHHHHHHHHHHhhhccccCCCCeEEEEecCChh-----
Confidence            999999999875  6899999999999 543321000   00111123223222232112233599999998765     


Q ss_pred             ccCCchhhhhcc-CCCCCCCchHHH
Q 003038          363 SGHPSLETLWSL-HPLTIPAGSLSL  386 (854)
Q Consensus       363 ~~~pale~~~~~-~~v~i~~~sl~~  386 (854)
                      ..||+|.|.=|| +.|.|+.|+...
T Consensus       205 ~ld~al~r~gRfd~~i~i~~Pd~~~  229 (495)
T TIGR01241       205 VLDPALLRPGRFDRQVVVDLPDIKG  229 (495)
T ss_pred             hcCHHHhcCCcceEEEEcCCCCHHH
Confidence            468999873334 346666666543

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.

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.09  E-value=2.4e-10  Score=132.56  Aligned_cols=134  Identities=10%  Similarity=0.093  Sum_probs=95.3

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..+.++|+||||||||.+|+++|...          +..++.++.+.+.++|.|+.|.+++++++.++..  .|+|||||
T Consensus       258 ~pkGILL~GPpGTGKTllAkaiA~e~----------~~~~~~l~~~~l~~~~vGese~~l~~~f~~A~~~--~P~IL~ID  325 (489)
T CHL00195        258 TPRGLLLVGIQGTGKSLTAKAIANDW----------QLPLLRLDVGKLFGGIVGESESRMRQMIRIAEAL--SPCILWID  325 (489)
T ss_pred             CCceEEEECCCCCcHHHHHHHHHHHh----------CCCEEEEEhHHhcccccChHHHHHHHHHHHHHhc--CCcEEEeh
Confidence            45779999999999999999999873          6789999999999999999999999999999876  79999999


Q ss_pred             ccccc-cccc-cccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccC-CCCCCCc
Q 003038          306 DLEWA-EFRA-SSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLH-PLTIPAG  382 (854)
Q Consensus       306 el~~l-~~~~-~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~-~v~i~~~  382 (854)
                      ||+.+ .... .+..+      ...+....+-..+..  .+..+.+||||+.-+     .-||+|-|--||. .+.|+-|
T Consensus       326 EID~~~~~~~~~~d~~------~~~rvl~~lL~~l~~--~~~~V~vIaTTN~~~-----~Ld~allR~GRFD~~i~v~lP  392 (489)
T CHL00195        326 EIDKAFSNSESKGDSG------TTNRVLATFITWLSE--KKSPVFVVATANNID-----LLPLEILRKGRFDEIFFLDLP  392 (489)
T ss_pred             hhhhhhccccCCCCch------HHHHHHHHHHHHHhc--CCCceEEEEecCChh-----hCCHHHhCCCcCCeEEEeCCc
Confidence            99988 4322 11111      111222222223321  122599999998654     4688887643552 3445544


Q ss_pred             hH
Q 003038          383 SL  384 (854)
Q Consensus       383 sl  384 (854)
                      +.
T Consensus       393 ~~  394 (489)
T CHL00195        393 SL  394 (489)
T ss_pred             CH
Confidence            43

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=99.09  E-value=5.2e-10  Score=136.75  Aligned_cols=157  Identities=11%  Similarity=0.175  Sum_probs=108.3

Q ss_pred             hHHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC
Q 003038          605 NSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS  684 (854)
Q Consensus       605 ~~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~  684 (854)
                      +..+++.-++.|.+..+|++.+.+.|...+..... ...           .+...++|+||+|+|||++++.+|+.+ + 
T Consensus       309 ~~~~~~~~~~~l~~~~~g~~~vK~~i~~~l~~~~~-~~~-----------~~g~~i~l~GppG~GKTtl~~~ia~~l-~-  374 (784)
T PRK10787        309 VKKDLRQAQEILDTDHYGLERVKDRILEYLAVQSR-VNK-----------IKGPILCLVGPPGVGKTSLGQSIAKAT-G-  374 (784)
T ss_pred             ccccHHHHHHHhhhhccCHHHHHHHHHHHHHHHHh-ccc-----------CCCceEEEECCCCCCHHHHHHHHHHHh-C-
Confidence            34578888999999999999999999877663321 111           112268999999999999999999987 3 


Q ss_pred             CCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHc--CCCEEEEEecCCCCCHHH----HHHHHHhhhc
Q 003038          685 HNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSN--NPHRVFLIEDVEQADYCS----QKGFKRAIES  758 (854)
Q Consensus       685 ~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~--~p~~ViliDEieka~~~v----~~~Ll~~le~  758 (854)
                       .+|++++++...+.....  .|.  +...+...|   .+..++.+  ....|||||||||++++.    ++.|++++|.
T Consensus       375 -~~~~~i~~~~~~d~~~i~--g~~--~~~~g~~~G---~~~~~l~~~~~~~~villDEidk~~~~~~g~~~~aLlevld~  446 (784)
T PRK10787        375 -RKYVRMALGGVRDEAEIR--GHR--RTYIGSMPG---KLIQKMAKVGVKNPLFLLDEIDKMSSDMRGDPASALLEVLDP  446 (784)
T ss_pred             -CCEEEEEcCCCCCHHHhc--cch--hccCCCCCc---HHHHHHHhcCCCCCEEEEEChhhcccccCCCHHHHHHHHhcc
Confidence             568888877554110000  010  111111112   23444433  234599999999999876    5999999997


Q ss_pred             C---eEecCC-CceeecCCeEEEEecCCC
Q 003038          759 G---RIVTSS-GDEVSLGDAIVILSCESF  783 (854)
Q Consensus       759 G---~l~d~~-G~~v~~~~aIiIlTsn~f  783 (854)
                      +   .++|.. .-.+|+++++||+|+|++
T Consensus       447 ~~~~~~~d~~~~~~~dls~v~~i~TaN~~  475 (784)
T PRK10787        447 EQNVAFSDHYLEVDYDLSDVMFVATSNSM  475 (784)
T ss_pred             ccEEEEecccccccccCCceEEEEcCCCC
Confidence            5   677754 346799999999999986

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.09  E-value=5.2e-10  Score=132.45  Aligned_cols=135  Identities=18%  Similarity=0.168  Sum_probs=87.5

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..+.+++...                 +....+||+||+|+|||++|+.||+.+++.... -.-.|..+.
T Consensus        16 ~~viGq~~v~~~L~~~i~~~-----------------~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~-~~~pC~~C~   77 (559)
T PRK05563         16 EDVVGQEHITKTLKNAIKQG-----------------KISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPP-DGEPCNECE   77 (559)
T ss_pred             HhccCcHHHHHHHHHHHHcC-----------------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCC-CCCCCCccH
Confidence            46899999999999888763                 234579999999999999999999999743210 000111111


Q ss_pred             CcCCCccccc-cccccCCCCC-CchHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDS-RNKRSRDEQS-CSYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~-~~~rl~~~~g-~g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .+.......| .+- .+++.. .|..+  .+.+.+...|    |+||+|||+|+++...+|.|++.+|+.          
T Consensus        78 ~C~~i~~g~~~dv~-eidaas~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~~a~naLLKtLEep----------  146 (559)
T PRK05563         78 ICKAITNGSLMDVI-EIDAASNNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLSTGAFNALLKTLEEP----------  146 (559)
T ss_pred             HHHHHhcCCCCCeE-EeeccccCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHhcCC----------
Confidence            0000000000 000 011111 24443  5666666544    789999999999999999999999963          


Q ss_pred             ecCCeEEEEecCC
Q 003038          770 SLGDAIVILSCES  782 (854)
Q Consensus       770 ~~~~aIiIlTsn~  782 (854)
                       -.+++|||+|+.
T Consensus       147 -p~~~ifIlatt~  158 (559)
T PRK05563        147 -PAHVIFILATTE  158 (559)
T ss_pred             -CCCeEEEEEeCC
Confidence             246789987753

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.07  E-value=4.6e-10  Score=132.85  Aligned_cols=136  Identities=13%  Similarity=0.089  Sum_probs=84.4

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..|.+++...                 +....+||+||+|+|||++|++||+.|++... ....-|..+.
T Consensus        16 ddIIGQe~vv~~L~~ai~~~-----------------rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~-~~~~pCg~C~   77 (709)
T PRK08691         16 ADLVGQEHVVKALQNALDEG-----------------RLHHAYLLTGTRGVGKTTIARILAKSLNCENA-QHGEPCGVCQ   77 (709)
T ss_pred             HHHcCcHHHHHHHHHHHHcC-----------------CCCeEEEEECCCCCcHHHHHHHHHHHhcccCC-CCCCCCcccH
Confidence            45799999999999988753                 23457899999999999999999999975321 1101111111


Q ss_pred             CcCCCccccc-cccccCCCCCCchHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceee
Q 003038          698 STRADSTEDS-RNKRSRDEQSCSYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVS  770 (854)
Q Consensus       698 ~~~~~s~e~~-~~~rl~~~~g~g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~  770 (854)
                      .+.......| .+..+-.....|..+  .+.+.+..    ..++||||||+|+++...++.|++.||+-           
T Consensus        78 sCr~i~~g~~~DvlEidaAs~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls~~A~NALLKtLEEP-----------  146 (709)
T PRK08691         78 SCTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEP-----------  146 (709)
T ss_pred             HHHHHhccCccceEEEeccccCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccCHHHHHHHHHHHHhC-----------
Confidence            0000000001 000000011113322  34444433    34689999999999999999999999961           


Q ss_pred             cCCeEEEEecCC
Q 003038          771 LGDAIVILSCES  782 (854)
Q Consensus       771 ~~~aIiIlTsn~  782 (854)
                      -.+++|||+|+.
T Consensus       147 p~~v~fILaTtd  158 (709)
T PRK08691        147 PEHVKFILATTD  158 (709)
T ss_pred             CCCcEEEEEeCC
Confidence            245778998864

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=99.07  E-value=4.7e-10  Score=131.70  Aligned_cols=153  Identities=12%  Similarity=0.111  Sum_probs=109.1

Q ss_pred             HHHHHHHHHHhhcc----------CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHH
Q 003038          212 NEDVMYVIENLMSK----------RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEV  281 (854)
Q Consensus       212 ~~ei~~v~~~L~r~----------~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~  281 (854)
                      .+.++..++.+..+          ....++|+||||+|||.+++++|..          .+.+|++++.+.+.++|.||.
T Consensus       251 k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~----------~~~~fi~v~~~~l~sk~vGes  320 (494)
T COG0464         251 KEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALE----------SRSRFISVKGSELLSKWVGES  320 (494)
T ss_pred             HHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhh----------CCCeEEEeeCHHHhccccchH
Confidence            34455555554433          3336899999999999999999974          467999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-CCCCceEEEEEecCHHHHH
Q 003038          282 EQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGENARFWLMGIATFQSYM  359 (854)
Q Consensus       282 E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~g~l~lIgatT~~ey~  359 (854)
                      |++++++|..+++.  .|+||||||++.+ ..+.....+      ..++.+..+...+.. ... ..+.+||||+.... 
T Consensus       321 ek~ir~~F~~A~~~--~p~iiFiDEiDs~~~~r~~~~~~------~~~r~~~~lL~~~d~~e~~-~~v~vi~aTN~p~~-  390 (494)
T COG0464         321 EKNIRELFEKARKL--APSIIFIDEIDSLASGRGPSEDG------SGRRVVGQLLTELDGIEKA-EGVLVIAATNRPDD-  390 (494)
T ss_pred             HHHHHHHHHHHHcC--CCcEEEEEchhhhhccCCCCCch------HHHHHHHHHHHHhcCCCcc-CceEEEecCCCccc-
Confidence            99999999999976  7999999999999 544322111      112455555555532 222 25999999998773 


Q ss_pred             HhhccCCchhhhhcc-CCCCCCCchHHHHh
Q 003038          360 RCKSGHPSLETLWSL-HPLTIPAGSLSLSL  388 (854)
Q Consensus       360 k~~~~~pale~~~~~-~~v~i~~~sl~~al  388 (854)
                          .||++-|--|| -.+.|+.|+....+
T Consensus       391 ----ld~a~lR~gRfd~~i~v~~pd~~~r~  416 (494)
T COG0464         391 ----LDPALLRPGRFDRLIYVPLPDLEERL  416 (494)
T ss_pred             ----cCHhhcccCccceEeecCCCCHHHHH
Confidence                58888774344 34556666665544

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.06  E-value=7.5e-10  Score=130.50  Aligned_cols=135  Identities=14%  Similarity=0.145  Sum_probs=85.6

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +.|+||++++..|.+++...|.                 ...+||+||+|+|||++|+.||+.++..... ....|..+.
T Consensus        16 ~dIiGQe~v~~~L~~ai~~~ri-----------------~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~-~~~pCg~C~   77 (624)
T PRK14959         16 AEVAGQETVKAILSRAAQENRV-----------------APAYLFSGTRGVGKTTIARIFAKALNCETAP-TGEPCNTCE   77 (624)
T ss_pred             HHhcCCHHHHHHHHHHHHcCCC-----------------CceEEEECCCCCCHHHHHHHHHHhccccCCC-CCCCCcccH
Confidence            4578999999999988875322                 3589999999999999999999999753110 000111111


Q ss_pred             CcCCCcccccc-ccccCCCC-CCchHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDSR-NKRSRDEQ-SCSYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~~-~~rl~~~~-g~g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .+.......|. +.. +.+. ..+..+  .|.+.+..    ..++||||||+|+++...++.|+++||+-          
T Consensus        78 sC~~i~~g~hpDv~e-Id~a~~~~Id~iR~L~~~~~~~p~~g~~kVIIIDEad~Lt~~a~naLLk~LEEP----------  146 (624)
T PRK14959         78 QCRKVTQGMHVDVVE-IDGASNRGIDDAKRLKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEEP----------  146 (624)
T ss_pred             HHHHHhcCCCCceEE-EecccccCHHHHHHHHHHHHhhhhcCCceEEEEEChHhCCHHHHHHHHHHhhcc----------
Confidence            00000001110 100 1111 113333  45555554    45789999999999999999999999962          


Q ss_pred             ecCCeEEEEecCC
Q 003038          770 SLGDAIVILSCES  782 (854)
Q Consensus       770 ~~~~aIiIlTsn~  782 (854)
                       -.+++|||+|+.
T Consensus       147 -~~~~ifILaTt~  158 (624)
T PRK14959        147 -PARVTFVLATTE  158 (624)
T ss_pred             -CCCEEEEEecCC
Confidence             246788998864

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=99.06  E-value=7.1e-10  Score=131.59  Aligned_cols=139  Identities=17%  Similarity=0.156  Sum_probs=89.4

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCce---EEEcc-
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNF---VSIAL-  693 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~---i~id~-  693 (854)
                      ..|+||+.++..|.+++...                 |....+||+||+|+|||++|+.||+.|+.....-   -.+++ 
T Consensus        24 ~dliGq~~~v~~L~~~~~~g-----------------ri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~c   86 (598)
T PRK09111         24 DDLIGQEAMVRTLTNAFETG-----------------RIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLC   86 (598)
T ss_pred             HHhcCcHHHHHHHHHHHHcC-----------------CCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccC
Confidence            46899999999999988753                 2345899999999999999999999997532110   00111 


Q ss_pred             ccccCcCCCccccccccccCCCCCC-chHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCC
Q 003038          694 SSFSSTRADSTEDSRNKRSRDEQSC-SYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSG  766 (854)
Q Consensus       694 s~~~~~~~~s~e~~~~~rl~~~~g~-g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G  766 (854)
                      ..+..+.......|.--..+.+... |..+  .+.+.++..|    ++||+|||+|+++...+|.|+++||+        
T Consensus        87 g~c~~C~~i~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~~a~naLLKtLEe--------  158 (598)
T PRK09111         87 GVGEHCQAIMEGRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEE--------  158 (598)
T ss_pred             cccHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCCHHHHHHHHHHHHh--------
Confidence            1110000000011110000112222 5544  5666666555    78999999999999999999999996        


Q ss_pred             ceeecCCeEEEEecCCCC
Q 003038          767 DEVSLGDAIVILSCESFS  784 (854)
Q Consensus       767 ~~v~~~~aIiIlTsn~f~  784 (854)
                         .-.+++|||+|+..+
T Consensus       159 ---Pp~~~~fIl~tte~~  173 (598)
T PRK09111        159 ---PPPHVKFIFATTEIR  173 (598)
T ss_pred             ---CCCCeEEEEEeCChh
Confidence               224677899886543

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=99.06  E-value=5.3e-10  Score=115.91  Aligned_cols=140  Identities=14%  Similarity=0.156  Sum_probs=102.8

Q ss_pred             CCCCCCC-cHHHHHHHHHHhhcc----------CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccc
Q 003038          204 RVSLDPI-RNEDVMYVIENLMSK----------RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISS  272 (854)
Q Consensus       204 ~g~ldpv-r~~ei~~v~~~L~r~----------~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~  272 (854)
                      +-.+|-| ..||.++--.++++-          -.+|++++||||+|||.++++||..          .++.++.+....
T Consensus       117 ~it~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane----------~kvp~l~vkat~  186 (368)
T COG1223         117 DITLDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANE----------AKVPLLLVKATE  186 (368)
T ss_pred             cccHhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcc----------cCCceEEechHH
Confidence            3456666 777776655554432          5679999999999999999999965          456799999999


Q ss_pred             ccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc--cccccccccccccchhhhHHHHHHHh-hcc-cC--CCCce
Q 003038          273 FRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA--EFRASSSEQVRGYYCSIEHIIMEIGK-LVC-GI--GENAR  346 (854)
Q Consensus       273 l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l--~~~~~~~~~~~~~~~~~~~~~~~~~~-ll~-~~--~g~g~  346 (854)
                      |+.-+.|+-.+|+.++.+.+++.  .|||+||||++.+  +.+-..          ...-|.++-| ||- ..  ..+..
T Consensus       187 liGehVGdgar~Ihely~rA~~~--aPcivFiDE~DAiaLdRryQe----------lRGDVsEiVNALLTelDgi~eneG  254 (368)
T COG1223         187 LIGEHVGDGARRIHELYERARKA--APCIVFIDELDAIALDRRYQE----------LRGDVSEIVNALLTELDGIKENEG  254 (368)
T ss_pred             HHHHHhhhHHHHHHHHHHHHHhc--CCeEEEehhhhhhhhhhhHHH----------hcccHHHHHHHHHHhccCcccCCc
Confidence            99999999999999999999986  7999999999999  433110          1112333333 331 11  11225


Q ss_pred             EEEEEecCHHHHHHhhccCCchhh
Q 003038          347 FWLMGIATFQSYMRCKSGHPSLET  370 (854)
Q Consensus       347 l~lIgatT~~ey~k~~~~~pale~  370 (854)
                      +..|+||+--+.     .|||+.+
T Consensus       255 VvtIaaTN~p~~-----LD~aiRs  273 (368)
T COG1223         255 VVTIAATNRPEL-----LDPAIRS  273 (368)
T ss_pred             eEEEeecCChhh-----cCHHHHh
Confidence            999999997773     5888888

>CHL00181 cbbX CbbX; Provisional

Probab=99.05  E-value=5.1e-10  Score=122.03  Aligned_cols=139  Identities=11%  Similarity=0.086  Sum_probs=96.8

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHc-CCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEK-GDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~-~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..|++|+||||||||++|+.+|..... |-    +.+.+++.++...|.+.|.|+.+.+..++++.+.     +-|||||
T Consensus        59 ~~~ill~G~pGtGKT~lAr~la~~~~~~g~----~~~~~~~~v~~~~l~~~~~g~~~~~~~~~l~~a~-----ggVLfID  129 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALKMADILYKLGY----IKKGHLLTVTRDDLVGQYIGHTAPKTKEVLKKAM-----GGVLFID  129 (287)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHcCC----CCCCceEEecHHHHHHHHhccchHHHHHHHHHcc-----CCEEEEE
Confidence            446899999999999999999987543 32    3344689999888888899998888877777643     3499999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccC-CCCCCCch
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLH-PLTIPAGS  383 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~-~v~i~~~s  383 (854)
                      |+|.+ ..+...+      +.  ......+-.++..  .++.+.+|+|++.+.-.+++..+|+|.+  ||. .|.+++.+
T Consensus       130 E~~~l~~~~~~~~------~~--~e~~~~L~~~me~--~~~~~~vI~ag~~~~~~~~~~~np~L~s--R~~~~i~F~~~t  197 (287)
T CHL00181        130 EAYYLYKPDNERD------YG--SEAIEILLQVMEN--QRDDLVVIFAGYKDRMDKFYESNPGLSS--RIANHVDFPDYT  197 (287)
T ss_pred             ccchhccCCCccc------hH--HHHHHHHHHHHhc--CCCCEEEEEeCCcHHHHHHHhcCHHHHH--hCCceEEcCCcC
Confidence            99999 5322110      00  0122233333322  2236999999987776677788999999  774 56777666


Q ss_pred             HHH
Q 003038          384 LSL  386 (854)
Q Consensus       384 l~~  386 (854)
                      ...
T Consensus       198 ~~e  200 (287)
T CHL00181        198 PEE  200 (287)
T ss_pred             HHH
Confidence            443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.05  E-value=1.2e-09  Score=128.47  Aligned_cols=134  Identities=14%  Similarity=0.158  Sum_probs=85.3

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..+.+++...                 +....+||+||+|+|||++|+.||+.++.... ...-.|..+.
T Consensus        16 ~divGq~~v~~~L~~~i~~~-----------------~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~-~~~~pcg~C~   77 (527)
T PRK14969         16 SELVGQEHVVRALTNALEQQ-----------------RLHHAYLFTGTRGVGKTTLARILAKSLNCETG-VTATPCGVCS   77 (527)
T ss_pred             HHhcCcHHHHHHHHHHHHcC-----------------CCCEEEEEECCCCCCHHHHHHHHHHHhcCCCC-CCCCCCCCCH
Confidence            45799999999999988753                 23457899999999999999999999975321 0000111111


Q ss_pred             CcCCCccccccccccC--CCCCC-chHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCce
Q 003038          698 STRADSTEDSRNKRSR--DEQSC-SYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDE  768 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~--~~~g~-g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~  768 (854)
                      .+.......|  ..++  .+... +.++  .+.+.+...|    ++||+|||+|+++...+|.|++.||+-         
T Consensus        78 ~C~~i~~~~~--~d~~ei~~~~~~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls~~a~naLLK~LEep---------  146 (527)
T PRK14969         78 ACLEIDSGRF--VDLIEVDAASNTQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLSKSAFNAMLKTLEEP---------  146 (527)
T ss_pred             HHHHHhcCCC--CceeEeeccccCCHHHHHHHHHHHhhCcccCCceEEEEcCcccCCHHHHHHHHHHHhCC---------
Confidence            0000000001  0111  11111 3433  4555555544    689999999999999999999999972         


Q ss_pred             eecCCeEEEEecCC
Q 003038          769 VSLGDAIVILSCES  782 (854)
Q Consensus       769 v~~~~aIiIlTsn~  782 (854)
                        -.+++|||+|+.
T Consensus       147 --p~~~~fIL~t~d  158 (527)
T PRK14969        147 --PEHVKFILATTD  158 (527)
T ss_pred             --CCCEEEEEEeCC
Confidence              246778887754

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.05  E-value=4.7e-10  Score=119.34  Aligned_cols=156  Identities=13%  Similarity=0.203  Sum_probs=103.7

Q ss_pred             HHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceE
Q 003038          610 TSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFV  689 (854)
Q Consensus       610 ~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i  689 (854)
                      +.+.+.|...||||+.|.+.++=+|..+-.-+.......   --.=.-..+|+.||||+|||.||+.||+.|   +-+|.
T Consensus        53 ~eik~~Ld~YVIGQe~AKKvLsVAVYNHYKRl~~~~~~~---dvEL~KSNILLiGPTGsGKTlLAqTLAk~L---nVPFa  126 (408)
T COG1219          53 KEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNNKEDND---DVELSKSNILLIGPTGSGKTLLAQTLAKIL---NVPFA  126 (408)
T ss_pred             HHHHHHhhhheecchhhhceeeeeehhHHHHHhccCCCC---ceeeeeccEEEECCCCCcHHHHHHHHHHHh---CCCee
Confidence            588899999999999999999988865532222110000   000011378999999999999999999999   56777


Q ss_pred             EEccccccCcCCCccccccccccCCCCCC-chH-H-HHHHHHH-------cCCCEEEEEecCCCCC--------------
Q 003038          690 SIALSSFSSTRADSTEDSRNKRSRDEQSC-SYI-E-RFAEAVS-------NNPHRVFLIEDVEQAD--------------  745 (854)
Q Consensus       690 ~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~~-e-~L~eav~-------~~p~~ViliDEieka~--------------  745 (854)
                      --|.+..++                 .|| |-+ | -|...+.       +..+.||+||||||..              
T Consensus       127 iADATtLTE-----------------AGYVGEDVENillkLlqaadydV~rAerGIIyIDEIDKIarkSeN~SITRDVSG  189 (408)
T COG1219         127 IADATTLTE-----------------AGYVGEDVENILLKLLQAADYDVERAERGIIYIDEIDKIARKSENPSITRDVSG  189 (408)
T ss_pred             eccccchhh-----------------ccccchhHHHHHHHHHHHcccCHHHHhCCeEEEechhhhhccCCCCCcccccCc
Confidence            777665552                 244 322 2 2333333       3446799999999974              


Q ss_pred             HHHHHHHHHhhhcCeEec---CCCc--------eeecCCeEEEEecCCCCCCCCCC
Q 003038          746 YCSQKGFKRAIESGRIVT---SSGD--------EVSLGDAIVILSCESFSSRSRAC  790 (854)
Q Consensus       746 ~~v~~~Ll~~le~G~l~d---~~G~--------~v~~~~aIiIlTsn~f~~~s~~~  790 (854)
                      ..||.+||++|| |.+..   ..||        .||.+|-.||+ -..|+-.....
T Consensus       190 EGVQQALLKiiE-GTvasVPPqGGRKHP~Qe~iqvDT~NILFIc-gGAF~GlekiI  243 (408)
T COG1219         190 EGVQQALLKIIE-GTVASVPPQGGRKHPQQEFIQVDTSNILFIC-GGAFAGLEKII  243 (408)
T ss_pred             hHHHHHHHHHHc-CceeccCCCCCCCCCccceEEEcccceeEEe-ccccccHHHHH
Confidence            359999999997 44432   2344        46777877776 44676655443

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=99.04  E-value=1.3e-09  Score=120.30  Aligned_cols=137  Identities=16%  Similarity=0.212  Sum_probs=94.2

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC-------------
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH-------------  685 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~-------------  685 (854)
                      .++|+++++..+...+....                +-...+||+||+|+|||.+|.+||+.+|+..             
T Consensus         2 ~~~~~~~~~~~l~~~~~~~~----------------~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~   65 (325)
T COG0470           2 ELVPWQEAVKRLLVQALESG----------------RLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSC   65 (325)
T ss_pred             CcccchhHHHHHHHHHHhcC----------------CCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhh
Confidence            35677777777776666421                1122599999999999999999999999765             


Q ss_pred             --------CceEEEccccccCcCCCccccccccccCCCCCCc-hHH---HHHHHHHc----CCCEEEEEecCCCCCHHHH
Q 003038          686 --------NNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCS-YIE---RFAEAVSN----NPHRVFLIEDVEQADYCSQ  749 (854)
Q Consensus       686 --------~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g-~~e---~L~eav~~----~p~~ViliDEieka~~~v~  749 (854)
                              ..++.++.+.-.                   +.. ..+   .+.+....    .++.||+|||+|+++++.+
T Consensus        66 ~~~~~~~~~d~lel~~s~~~-------------------~~~i~~~~vr~~~~~~~~~~~~~~~kviiidead~mt~~A~  126 (325)
T COG0470          66 KLIPAGNHPDFLELNPSDLR-------------------KIDIIVEQVRELAEFLSESPLEGGYKVVIIDEADKLTEDAA  126 (325)
T ss_pred             hHHhhcCCCceEEecccccC-------------------CCcchHHHHHHHHHHhccCCCCCCceEEEeCcHHHHhHHHH
Confidence                    233333322111                   000 112   23333322    4589999999999999999


Q ss_pred             HHHHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCCCCCCCCccCCCCCchhhcccccCCCCCceeeeccC
Q 003038          750 KGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRACSPPTKQKSDGCEEEKGAAMEGTSPSVSLDLNI  822 (854)
Q Consensus       750 ~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~~sp~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  822 (854)
                      |+|++.+|+           .-.++.|||+||   .+++..+|.                  .|+|+.+.+..
T Consensus       127 nallk~lEe-----------p~~~~~~il~~n---~~~~il~tI------------------~SRc~~i~f~~  167 (325)
T COG0470         127 NALLKTLEE-----------PPKNTRFILITN---DPSKILPTI------------------RSRCQRIRFKP  167 (325)
T ss_pred             HHHHHHhcc-----------CCCCeEEEEEcC---Chhhccchh------------------hhcceeeecCC
Confidence            999999995           457889999998   344444566                  78888887764

>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=99.04  E-value=1.6e-10  Score=111.92  Aligned_cols=114  Identities=17%  Similarity=0.241  Sum_probs=75.2

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccC--CCCCCchHH-HHHHHHHcCCCEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSR--DEQSCSYIE-RFAEAVSNNPHRV  735 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~--~~~g~g~~e-~L~eav~~~p~~V  735 (854)
                      .+++.||+|+|||++|+.||+.+   ..+++.+.++..++       ...+...+  .+....+.+ .+..+++  ...|
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~---~~~~~~i~~~~~~~-------~~dl~g~~~~~~~~~~~~~~~l~~a~~--~~~i   68 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALL---GRPVIRINCSSDTT-------EEDLIGSYDPSNGQFEFKDGPLVRAMR--KGGI   68 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH---TCEEEEEE-TTTST-------HHHHHCEEET-TTTTCEEE-CCCTTHH--EEEE
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh---hcceEEEEeccccc-------cccceeeeeeccccccccccccccccc--ceeE
Confidence            37899999999999999999999   56888888886652       11111100  000001111 2333333  4579


Q ss_pred             EEEecCCCCCHHHHHHHHHhhhcCeEecCC-CceeecCC-------eEEEEecCCCC
Q 003038          736 FLIEDVEQADYCSQKGFKRAIESGRIVTSS-GDEVSLGD-------AIVILSCESFS  784 (854)
Q Consensus       736 iliDEieka~~~v~~~Ll~~le~G~l~d~~-G~~v~~~~-------aIiIlTsn~f~  784 (854)
                      ++||||+++++.++..|+.+++++++.-.. ++.+...+       .+||+|+|.-+
T Consensus        69 l~lDEin~a~~~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~  125 (139)
T PF07728_consen   69 LVLDEINRAPPEVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRD  125 (139)
T ss_dssp             EEESSCGG--HHHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST
T ss_pred             EEECCcccCCHHHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCC
Confidence            999999999999999999999999888433 34454443       89999999655

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.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.04  E-value=1.4e-09  Score=124.22  Aligned_cols=137  Identities=20%  Similarity=0.233  Sum_probs=85.1

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc----eE---E
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN----FV---S  690 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~----~i---~  690 (854)
                      ..|+||+.++..|.+++...+                 -...+||+||+|+|||++|+++|+.+++....    ..   .
T Consensus        16 ~eiiGq~~~~~~L~~~~~~~~-----------------~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~   78 (397)
T PRK14955         16 ADITAQEHITRTIQNSLRMGR-----------------VGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVT   78 (397)
T ss_pred             hhccChHHHHHHHHHHHHhCC-----------------cceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCC
Confidence            468999999998888776532                 24579999999999999999999999763200    00   0


Q ss_pred             EccccccCcCCCccccc-cccccCCCCC-CchHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          691 IALSSFSSTRADSTEDS-RNKRSRDEQS-CSYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~-~~~rl~~~~g-~g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                      --|..+..+...-...| .+.. +.+.. .+..+  .+.+.+...|    ++||+|||+|+++...++.|+++|++.   
T Consensus        79 ~~c~~c~~c~~~~~~~~~n~~~-~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEep---  154 (397)
T PRK14955         79 EPCGECESCRDFDAGTSLNISE-FDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEP---  154 (397)
T ss_pred             CCCCCCHHHHHHhcCCCCCeEe-ecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhcC---
Confidence            00111110000000000 0000 11111 13443  4556665444    689999999999999999999999962   


Q ss_pred             cCCCceeecCCeEEEEecCCC
Q 003038          763 TSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       763 d~~G~~v~~~~aIiIlTsn~f  783 (854)
                              -..++|||+++..
T Consensus       155 --------~~~t~~Il~t~~~  167 (397)
T PRK14955        155 --------PPHAIFIFATTEL  167 (397)
T ss_pred             --------CCCeEEEEEeCCh
Confidence                    2366788877543

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=99.04  E-value=7.2e-10  Score=124.58  Aligned_cols=137  Identities=12%  Similarity=0.139  Sum_probs=85.8

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC-ceE-------
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN-NFV-------  689 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~-~~i-------  689 (854)
                      ..|+||++++..+.+++.+.|                 -.+.+||+||+|+||+.+|..+|+.++.... .-.       
T Consensus        19 ~~iiGq~~~~~~L~~~~~~~r-----------------l~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~   81 (365)
T PRK07471         19 TALFGHAAAEAALLDAYRSGR-----------------LHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPT   81 (365)
T ss_pred             hhccChHHHHHHHHHHHHcCC-----------------CCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccc
Confidence            468999999999999988643                 2457999999999999999999999986431 000       


Q ss_pred             EEc-cccccCcCCCccccc----cccccCCCCC------CchHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHH
Q 003038          690 SIA-LSSFSSTRADSTEDS----RNKRSRDEQS------CSYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGF  752 (854)
Q Consensus       690 ~id-~s~~~~~~~~s~e~~----~~~rl~~~~g------~g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~L  752 (854)
                      .++ +..+..++......|    .+.......+      .+.++  .+.+.+..    ..++||+|||+|++++..+|.|
T Consensus        82 ~l~~~~~c~~c~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~m~~~aanaL  161 (365)
T PRK07471         82 SLAIDPDHPVARRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTAAEGGWRVVIVDTADEMNANAANAL  161 (365)
T ss_pred             cccCCCCChHHHHHHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcCcccCCCEEEEEechHhcCHHHHHHH
Confidence            000 000100000000011    1111000111      12333  34444443    4468999999999999999999


Q ss_pred             HHhhhcCeEecCCCceeecCCeEEEEecCC
Q 003038          753 KRAIESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       753 l~~le~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      ++.+|+-.           .+++|||+|+.
T Consensus       162 LK~LEepp-----------~~~~~IL~t~~  180 (365)
T PRK07471        162 LKVLEEPP-----------ARSLFLLVSHA  180 (365)
T ss_pred             HHHHhcCC-----------CCeEEEEEECC
Confidence            99999731           46778888864

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.04  E-value=1.3e-09  Score=126.84  Aligned_cols=136  Identities=17%  Similarity=0.171  Sum_probs=84.4

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc---eEEEccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN---FVSIALS  694 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~---~i~id~s  694 (854)
                      ..++||++++..+.+++...                 +..+.+||+||+|+|||++|++||+.+......   ....-|.
T Consensus        21 ~dliGq~~vv~~L~~ai~~~-----------------ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~   83 (507)
T PRK06645         21 AELQGQEVLVKVLSYTILND-----------------RLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCE   83 (507)
T ss_pred             HHhcCcHHHHHHHHHHHHcC-----------------CCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCC
Confidence            34699999999998887753                 234689999999999999999999999642110   0000000


Q ss_pred             cccCcCCCccccc-cccccCCCCC-CchHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCC
Q 003038          695 SFSSTRADSTEDS-RNKRSRDEQS-CSYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSG  766 (854)
Q Consensus       695 ~~~~~~~~s~e~~-~~~rl~~~~g-~g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G  766 (854)
                      .+..+.......| .+.. ++... .|..+  .+.+.+...|    ++||+|||+|.++...++.|++.|++.       
T Consensus        84 ~C~~C~~i~~~~h~Dv~e-idaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEep-------  155 (507)
T PRK06645         84 QCTNCISFNNHNHPDIIE-IDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEP-------  155 (507)
T ss_pred             CChHHHHHhcCCCCcEEE-eeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhhc-------
Confidence            0000000000000 0000 11111 13333  4555555544    789999999999999999999999962       


Q ss_pred             ceeecCCeEEEEecCC
Q 003038          767 DEVSLGDAIVILSCES  782 (854)
Q Consensus       767 ~~v~~~~aIiIlTsn~  782 (854)
                          -.+++|||.++.
T Consensus       156 ----p~~~vfI~aTte  167 (507)
T PRK06645        156 ----PPHIIFIFATTE  167 (507)
T ss_pred             ----CCCEEEEEEeCC
Confidence                346778887754

>CHL00176 ftsH cell division protein; Validated

Probab=99.03  E-value=9.2e-10  Score=131.53  Aligned_cols=152  Identities=12%  Similarity=0.102  Sum_probs=105.1

Q ss_pred             HHHHHHHHHHhhccC---------cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHH
Q 003038          212 NEDVMYVIENLMSKR---------KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVE  282 (854)
Q Consensus       212 ~~ei~~v~~~L~r~~---------k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E  282 (854)
                      .++++.+++.|....         .++++|+||||+|||.+++++|...          ++.++.++.+.|...+.|...
T Consensus       192 k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~----------~~p~i~is~s~f~~~~~g~~~  261 (638)
T CHL00176        192 KEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEA----------EVPFFSISGSEFVEMFVGVGA  261 (638)
T ss_pred             HHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHh----------CCCeeeccHHHHHHHhhhhhH
Confidence            466777776665432         3589999999999999999999763          568999999988888888888


Q ss_pred             HHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc---CCCCceEEEEEecCHHHH
Q 003038          283 QRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG---IGENARFWLMGIATFQSY  358 (854)
Q Consensus       283 ~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~---~~g~g~l~lIgatT~~ey  358 (854)
                      .++++++..++..  .|+||||||||.+ ..+..+..+ .+  ...+.   -+..||..   ..++..+.+||+|+..+.
T Consensus       262 ~~vr~lF~~A~~~--~P~ILfIDEID~l~~~r~~~~~~-~~--~e~~~---~L~~LL~~~dg~~~~~~ViVIaaTN~~~~  333 (638)
T CHL00176        262 ARVRDLFKKAKEN--SPCIVFIDEIDAVGRQRGAGIGG-GN--DEREQ---TLNQLLTEMDGFKGNKGVIVIAATNRVDI  333 (638)
T ss_pred             HHHHHHHHHHhcC--CCcEEEEecchhhhhcccCCCCC-Cc--HHHHH---HHHHHHhhhccccCCCCeeEEEecCchHh
Confidence            9999999999875  7999999999999 443221000 00  01112   23344421   122236999999987653


Q ss_pred             HHhhccCCchhhhhcc-CCCCCCCchHHH
Q 003038          359 MRCKSGHPSLETLWSL-HPLTIPAGSLSL  386 (854)
Q Consensus       359 ~k~~~~~pale~~~~~-~~v~i~~~sl~~  386 (854)
                           .||+|-|.-|| ..|.|+.|++..
T Consensus       334 -----LD~ALlRpGRFd~~I~v~lPd~~~  357 (638)
T CHL00176        334 -----LDAALLRPGRFDRQITVSLPDREG  357 (638)
T ss_pred             -----hhhhhhccccCceEEEECCCCHHH
Confidence                 57888774345 346666666544

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=99.02  E-value=1.5e-08  Score=119.02  Aligned_cols=127  Identities=11%  Similarity=0.144  Sum_probs=85.7

Q ss_pred             HHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCC
Q 003038          219 IENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGR  298 (854)
Q Consensus       219 ~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~  298 (854)
                      .+.+.....+.++++|+||+|||.++++++..           +...+.++.....+++.|+.+.++..++..++..  .
T Consensus        10 ~~~~~~~~~~~v~~~g~~~~~~t~~~~~~a~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~--~   76 (494)
T COG0464          10 FKKLGIEPPKGVLLHGPPGTGKTLLARALANE-----------GAEFLSINGPEILSKYVGESELRLRELFEEAEKL--A   76 (494)
T ss_pred             HHHhCCCCCCCceeeCCCCCchhHHHHHHHhc-----------cCcccccCcchhhhhhhhHHHHHHHHHHHHHHHh--C
Confidence            34445567889999999999999999999976           2233555556667779999999999999999986  5


Q ss_pred             CeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhh
Q 003038          299 GIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLET  370 (854)
Q Consensus       299 ~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~  370 (854)
                      +.|+|+||++.+ .........      .....+..+..++.... ++.+.++|+|...     ...+|++.+
T Consensus        77 ~~ii~~d~~~~~~~~~~~~~~~------~~~~v~~~l~~~~d~~~-~~~v~~~~~~~~~-----~~~~~a~~~  137 (494)
T COG0464          77 PSIIFIDEIDALAPKRSSDQGE------VERRVVAQLLALMDGLK-RGQVIVIGATNRP-----DGLDPAKRR  137 (494)
T ss_pred             CCeEeechhhhcccCccccccc------hhhHHHHHHHHhccccc-CCceEEEeecCCc-----cccChhHhC
Confidence            689999999999 654431000      11234444444443212 3346666644332     345666655

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.02  E-value=8.8e-10  Score=120.14  Aligned_cols=138  Identities=10%  Similarity=0.067  Sum_probs=96.2

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGD  306 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfide  306 (854)
                      ..+++|+||||||||++|+++|+.+..-.   .+....++.++...+...+.|+.+.++.++++.+.     +.||||||
T Consensus        58 ~~~vll~G~pGTGKT~lA~~ia~~l~~~g---~~~~~~~v~v~~~~l~~~~~g~~~~~~~~~~~~a~-----~gvL~iDE  129 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVALRMAQILHRLG---YVRKGHLVSVTRDDLVGQYIGHTAPKTKEILKRAM-----GGVLFIDE  129 (284)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHHHHHcC---CcccceEEEecHHHHhHhhcccchHHHHHHHHHcc-----CcEEEEec
Confidence            44789999999999999999998876421   22334688888888888888888888877777653     35899999


Q ss_pred             cccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCchH
Q 003038          307 LEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGSL  384 (854)
Q Consensus       307 l~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~sl  384 (854)
                      ++.+ ..+....      +  .......+..++..  +++++++|++++.+.-..+...+|+|.+  || +.|.+|+.+.
T Consensus       130 i~~L~~~~~~~~------~--~~~~~~~Ll~~le~--~~~~~~vI~a~~~~~~~~~~~~np~L~s--R~~~~i~fp~l~~  197 (284)
T TIGR02880       130 AYYLYRPDNERD------Y--GQEAIEILLQVMEN--QRDDLVVILAGYKDRMDSFFESNPGFSS--RVAHHVDFPDYSE  197 (284)
T ss_pred             hhhhccCCCccc------h--HHHHHHHHHHHHhc--CCCCEEEEEeCCcHHHHHHHhhCHHHHh--hCCcEEEeCCcCH
Confidence            9999 4322110      0  01122333344432  2236999999998766666778999999  77 4577777653

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.

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=99.01  E-value=1.3e-09  Score=121.43  Aligned_cols=139  Identities=19%  Similarity=0.180  Sum_probs=98.7

Q ss_pred             HHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc
Q 003038          608 NLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN  687 (854)
Q Consensus       608 ~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~  687 (854)
                      .+..+...+.+.++|+++++..+..++..                    .+.+||.||+|+|||.+|+.+|+.+.   .+
T Consensus        14 ~~~~~~~~~~~~~~g~~~~~~~~l~a~~~--------------------~~~vll~G~PG~gKT~la~~lA~~l~---~~   70 (329)
T COG0714          14 ILGKIRSELEKVVVGDEEVIELALLALLA--------------------GGHVLLEGPPGVGKTLLARALARALG---LP   70 (329)
T ss_pred             HHHHHHhhcCCeeeccHHHHHHHHHHHHc--------------------CCCEEEECCCCccHHHHHHHHHHHhC---CC
Confidence            45677888888999999888887777664                    24689999999999999999999993   68


Q ss_pred             eEEEccccccCcCCCccc----c----ccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcC
Q 003038          688 FVSIALSSFSSTRADSTE----D----SRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESG  759 (854)
Q Consensus       688 ~i~id~s~~~~~~~~s~e----~----~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G  759 (854)
                      |+++.++......+.-+.    .    ....++..+|       ++.+++    .|+|+|||.+++|.+|+.|+++|+++
T Consensus        71 ~~~i~~t~~l~p~d~~G~~~~~~~~~~~~~~~~~~gp-------l~~~~~----~ill~DEInra~p~~q~aLl~~l~e~  139 (329)
T COG0714          71 FVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVPGP-------LFAAVR----VILLLDEINRAPPEVQNALLEALEER  139 (329)
T ss_pred             eEEEecCCCCCHHHhcCchhHhhhhccCCeEEEecCC-------cccccc----eEEEEeccccCCHHHHHHHHHHHhCc
Confidence            999998866531111100    0    0111111111       222222    69999999999999999999999999


Q ss_pred             eEecCCCce-eecCCeEE-EEecC
Q 003038          760 RIVTSSGDE-VSLGDAIV-ILSCE  781 (854)
Q Consensus       760 ~l~d~~G~~-v~~~~aIi-IlTsn  781 (854)
                      +++.. |.. +.+....+ |.|+|
T Consensus       140 ~vtv~-~~~~~~~~~~f~viaT~N  162 (329)
T COG0714         140 QVTVP-GLTTIRLPPPFIVIATQN  162 (329)
T ss_pred             EEEEC-CcCCcCCCCCCEEEEccC
Confidence            99964 333 66765544 45667

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.01  E-value=1.7e-09  Score=128.48  Aligned_cols=137  Identities=20%  Similarity=0.239  Sum_probs=86.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC---c-eEE---
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN---N-FVS---  690 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~---~-~i~---  690 (854)
                      +.|+||+.++..|.+++...+.                 ...+||+||+|+|||++|+.||+.++....   + +.+   
T Consensus        16 ~eivGQe~i~~~L~~~i~~~ri-----------------~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~   78 (620)
T PRK14954         16 ADITAQEHITHTIQNSLRMDRV-----------------GHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVT   78 (620)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCC-----------------CeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccC
Confidence            4679999999998888765322                 357999999999999999999999976320   0 000   


Q ss_pred             EccccccCcCCCccccc-cccccCCCCCC-chHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          691 IALSSFSSTRADSTEDS-RNKRSRDEQSC-SYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~-~~~rl~~~~g~-g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                      -.|..+..+...-...| .+.. +.+... +.++  .+.+.+...|    ++||+|||+|+++...+|.|+++||+-   
T Consensus        79 ~~Cg~C~sC~~~~~g~~~n~~~-~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEeP---  154 (620)
T PRK14954         79 EPCGECESCRDFDAGTSLNISE-FDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEEP---  154 (620)
T ss_pred             CCCccCHHHHHHhccCCCCeEE-ecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhCC---
Confidence            01111110000000001 1111 111111 3443  4556665444    689999999999999999999999972   


Q ss_pred             cCCCceeecCCeEEEEecCCC
Q 003038          763 TSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       763 d~~G~~v~~~~aIiIlTsn~f  783 (854)
                              -.+++|||+++..
T Consensus       155 --------p~~tv~IL~t~~~  167 (620)
T PRK14954        155 --------PPHAIFIFATTEL  167 (620)
T ss_pred             --------CCCeEEEEEeCCh
Confidence                    2457788877644

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.01  E-value=2.4e-09  Score=125.11  Aligned_cols=134  Identities=16%  Similarity=0.111  Sum_probs=85.0

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .|+||++++..|.+.+...                 +..+.+||+||+|+|||++|++||+.++......  ..|..+..
T Consensus        15 dvvGq~~v~~~L~~~i~~~-----------------~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~--~~cg~C~s   75 (504)
T PRK14963         15 EVVGQEHVKEVLLAALRQG-----------------RLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDP--KPCGECES   75 (504)
T ss_pred             HhcChHHHHHHHHHHHHcC-----------------CCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCC--CCCCcChh
Confidence            5899999999998887753                 2235789999999999999999999996422110  01111111


Q ss_pred             cCCCccccccccccCCCCC-CchHH--HHHHHHHcC----CCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeec
Q 003038          699 TRADSTEDSRNKRSRDEQS-CSYIE--RFAEAVSNN----PHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSL  771 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~g-~g~~e--~L~eav~~~----p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~  771 (854)
                      +.......|..-..+.+.+ .+..+  .+.+.+...    .++||+|||++.++...++.|++.|++.           -
T Consensus        76 c~~i~~~~h~dv~el~~~~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep-----------~  144 (504)
T PRK14963         76 CLAVRRGAHPDVLEIDAASNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEP-----------P  144 (504)
T ss_pred             hHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhC-----------C
Confidence            1000000111000111111 14333  455555543    4689999999999999999999999962           2


Q ss_pred             CCeEEEEecCC
Q 003038          772 GDAIVILSCES  782 (854)
Q Consensus       772 ~~aIiIlTsn~  782 (854)
                      .+++|||+++.
T Consensus       145 ~~t~~Il~t~~  155 (504)
T PRK14963        145 EHVIFILATTE  155 (504)
T ss_pred             CCEEEEEEcCC
Confidence            46778888864

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=99.00  E-value=1.4e-09  Score=125.65  Aligned_cols=131  Identities=15%  Similarity=0.164  Sum_probs=86.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCce------EEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNF------VSI  691 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~------i~i  691 (854)
                      ..|+||+.++..+.+.+...+                 ....+||+||+|+|||++|+.+|+.+++....-      .+.
T Consensus        17 ~diiGq~~~v~~L~~~i~~~~-----------------i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~   79 (451)
T PRK06305         17 SEILGQDAVVAVLKNALRFNR-----------------AAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCA   79 (451)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----------------CceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccH
Confidence            468999999999888887532                 245799999999999999999999998642110      001


Q ss_pred             ccccccCcCCCccccc-cccccCCCCCC-chHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEec
Q 003038          692 ALSSFSSTRADSTEDS-RNKRSRDEQSC-SYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVT  763 (854)
Q Consensus       692 d~s~~~~~~~~s~e~~-~~~rl~~~~g~-g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d  763 (854)
                      +|..+..      ..+ .+..+ .+... |..+  .+.+.+..    .+++||+|||+|+++...++.|+++||+.    
T Consensus        80 ~C~~i~~------~~~~d~~~i-~g~~~~gid~ir~i~~~l~~~~~~~~~kvvIIdead~lt~~~~n~LLk~lEep----  148 (451)
T PRK06305         80 SCKEISS------GTSLDVLEI-DGASHRGIEDIRQINETVLFTPSKSRYKIYIIDEVHMLTKEAFNSLLKTLEEP----  148 (451)
T ss_pred             HHHHHhc------CCCCceEEe-eccccCCHHHHHHHHHHHHhhhhcCCCEEEEEecHHhhCHHHHHHHHHHhhcC----
Confidence            1111110      000 01111 11112 4443  45555543    46899999999999999999999999972    


Q ss_pred             CCCceeecCCeEEEEecCCC
Q 003038          764 SSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       764 ~~G~~v~~~~aIiIlTsn~f  783 (854)
                             -.+++|||+|+..
T Consensus       149 -------~~~~~~Il~t~~~  161 (451)
T PRK06305        149 -------PQHVKFFLATTEI  161 (451)
T ss_pred             -------CCCceEEEEeCCh
Confidence                   1366788888643

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.00  E-value=1.5e-09  Score=133.16  Aligned_cols=140  Identities=11%  Similarity=0.103  Sum_probs=100.1

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEe
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      +..++++|+||||||||++++++|...          +..|+.++.+.+.+.|.|+.|+.+++++..++..  .|+||||
T Consensus       485 ~~~~giLL~GppGtGKT~lakalA~e~----------~~~fi~v~~~~l~~~~vGese~~i~~~f~~A~~~--~p~iifi  552 (733)
T TIGR01243       485 RPPKGVLLFGPPGTGKTLLAKAVATES----------GANFIAVRGPEILSKWVGESEKAIREIFRKARQA--APAIIFF  552 (733)
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHhc----------CCCEEEEehHHHhhcccCcHHHHHHHHHHHHHhc--CCEEEEE
Confidence            355678999999999999999999863          5689999999999999999999999999999986  7999999


Q ss_pred             Cccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCc
Q 003038          305 GDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAG  382 (854)
Q Consensus       305 del~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~  382 (854)
                      ||++.+ ..++....     ....+..+..+-..+.+-...+.+.+||||+..+     ..||++-|--|| +.|.|+-|
T Consensus       553 DEid~l~~~r~~~~~-----~~~~~~~~~~lL~~ldg~~~~~~v~vI~aTn~~~-----~ld~allRpgRfd~~i~v~~P  622 (733)
T TIGR01243       553 DEIDAIAPARGARFD-----TSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPD-----ILDPALLRPGRFDRLILVPPP  622 (733)
T ss_pred             EChhhhhccCCCCCC-----ccHHHHHHHHHHHHhhcccCCCCEEEEEeCCChh-----hCCHhhcCCCccceEEEeCCc
Confidence            999999 54432110     1112233333333332211122699999998765     468998763345 34566666


Q ss_pred             hHHH
Q 003038          383 SLSL  386 (854)
Q Consensus       383 sl~~  386 (854)
                      +...
T Consensus       623 d~~~  626 (733)
T TIGR01243       623 DEEA  626 (733)
T ss_pred             CHHH
Confidence            5443

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.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.99  E-value=2.2e-09  Score=124.46  Aligned_cols=134  Identities=17%  Similarity=0.174  Sum_probs=81.9

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..|..++...                 +....+||+||+|+|||++|+++|+.++....... ..|..+.
T Consensus        14 ~divGq~~i~~~L~~~i~~~-----------------~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~-~pc~~c~   75 (472)
T PRK14962         14 SEVVGQDHVKKLIINALKKN-----------------SISHAYIFAGPRGTGKTTVARILAKSLNCENRKGV-EPCNECR   75 (472)
T ss_pred             HHccCcHHHHHHHHHHHHcC-----------------CCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCC-CCCcccH
Confidence            45899999988888776642                 23457899999999999999999999965321100 0000000


Q ss_pred             CcCCCccccc-cccccCCCC-CCchHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDS-RNKRSRDEQ-SCSYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~-~~~rl~~~~-g~g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .+.......+ .+-. +.+. ..|..+  .+.+.++..|    +.||+|||+|.++...++.|+..|++.          
T Consensus        76 ~c~~i~~g~~~dv~e-l~aa~~~gid~iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p----------  144 (472)
T PRK14962         76 ACRSIDEGTFMDVIE-LDAASNRGIDEIRKIRDAVGYRPMEGKYKVYIIDEVHMLTKEAFNALLKTLEEP----------  144 (472)
T ss_pred             HHHHHhcCCCCccEE-EeCcccCCHHHHHHHHHHHhhChhcCCeEEEEEEChHHhHHHHHHHHHHHHHhC----------
Confidence            0000000000 0000 1111 113333  4555555444    689999999999999999999999961          


Q ss_pred             ecCCeEEEEecC
Q 003038          770 SLGDAIVILSCE  781 (854)
Q Consensus       770 ~~~~aIiIlTsn  781 (854)
                       -.+++||++|+
T Consensus       145 -~~~vv~Ilatt  155 (472)
T PRK14962        145 -PSHVVFVLATT  155 (472)
T ss_pred             -CCcEEEEEEeC
Confidence             13567787765

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=98.99  E-value=1.6e-09  Score=119.59  Aligned_cols=133  Identities=13%  Similarity=0.116  Sum_probs=87.2

Q ss_pred             cCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC--ceEEEccc
Q 003038          617 EKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN--NFVSIALS  694 (854)
Q Consensus       617 ~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~--~~i~id~s  694 (854)
                      ...|+||++++..+..++...|.                 .+.+||+||.|+||+.+|+++|+.+++...  ...+-.+.
T Consensus         3 f~~iiGq~~~~~~L~~~i~~~rl-----------------~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~   65 (314)
T PRK07399          3 FANLIGQPLAIELLTAAIKQNRI-----------------APAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLE   65 (314)
T ss_pred             HHHhCCHHHHHHHHHHHHHhCCC-----------------CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccc
Confidence            35789999999999999887433                 358999999999999999999999987541  00000000


Q ss_pred             cccCcCCCcccccccc-------ccC-------------CCCCCchHH--HHHHHHHcCC----CEEEEEecCCCCCHHH
Q 003038          695 SFSSTRADSTEDSRNK-------RSR-------------DEQSCSYIE--RFAEAVSNNP----HRVFLIEDVEQADYCS  748 (854)
Q Consensus       695 ~~~~~~~~s~e~~~~~-------rl~-------------~~~g~g~~e--~L~eav~~~p----~~ViliDEieka~~~v  748 (854)
                      ...  +.   +-+.+.       +.+             ..+..+.++  .+.+.+...|    ++||+||++|+++...
T Consensus        66 ~~~--hP---Dl~~i~p~~~~~g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m~~~a  140 (314)
T PRK07399         66 EGN--HP---DLLWVEPTYQHQGKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETMNEAA  140 (314)
T ss_pred             cCC--CC---CEEEEeccccccccccchhhhhhccccccccccCcHHHHHHHHHHHccCcccCCceEEEEEchhhcCHHH
Confidence            000  00   000000       000             000012222  4666666544    7899999999999999


Q ss_pred             HHHHHHhhhcCeEecCCCceeecCCeEEEEecCCC
Q 003038          749 QKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       749 ~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                      +|+||+.||+-          .  +++|||+|+..
T Consensus       141 aNaLLK~LEEP----------p--~~~fILi~~~~  163 (314)
T PRK07399        141 ANALLKTLEEP----------G--NGTLILIAPSP  163 (314)
T ss_pred             HHHHHHHHhCC----------C--CCeEEEEECCh
Confidence            99999999972          2  56788888644

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=98.99  E-value=3.1e-09  Score=114.46  Aligned_cols=114  Identities=12%  Similarity=0.156  Sum_probs=76.8

Q ss_pred             cccccHHHHHHHHHHHHH-------hhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhC----CCCc
Q 003038          619 KVPWQKDTVYDIANTVLK-------CRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFG----SHNN  687 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~-------~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg----~~~~  687 (854)
                      .++|++++...|...+..       .+.|+..+          .....++|+||+|+|||++|+.+|+.++.    +...
T Consensus         7 ~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~----------~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~   76 (261)
T TIGR02881         7 RMVGLDEVKALIKEIYAWIQINEKRKEEGLKTS----------KQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGH   76 (261)
T ss_pred             HhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCC----------CCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCc
Confidence            379999888777654432       23455432          23358999999999999999999998853    2234


Q ss_pred             eEEEccccccCcCCCccccccccccCCCCCCchH-HHHHHHHHcCCCEEEEEecCCCCC--------HHHHHHHHHhhhc
Q 003038          688 FVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYI-ERFAEAVSNNPHRVFLIEDVEQAD--------YCSQKGFKRAIES  758 (854)
Q Consensus       688 ~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~-e~L~eav~~~p~~ViliDEieka~--------~~v~~~Ll~~le~  758 (854)
                      ++.++++.+.       .     ..+     |.. ..+.+.+.+....||||||||.+.        .+.++.|++.|++
T Consensus        77 ~v~~~~~~l~-------~-----~~~-----g~~~~~~~~~~~~a~~~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~  139 (261)
T TIGR02881        77 LIEVERADLV-------G-----EYI-----GHTAQKTREVIKKALGGVLFIDEAYSLARGGEKDFGKEAIDTLVKGMED  139 (261)
T ss_pred             eEEecHHHhh-------h-----hhc-----cchHHHHHHHHHhccCCEEEEechhhhccCCccchHHHHHHHHHHHHhc
Confidence            5555544332       0     001     221 245566666667899999999865        4688999999987


Q ss_pred             C
Q 003038          759 G  759 (854)
Q Consensus       759 G  759 (854)
                      +
T Consensus       140 ~  140 (261)
T TIGR02881       140 N  140 (261)
T ss_pred             c
Confidence            4

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.

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=98.99  E-value=3.4e-09  Score=123.61  Aligned_cols=135  Identities=13%  Similarity=0.122  Sum_probs=83.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..+...+...+                 -...+||+||+|+|||++|+.||+.+++....=. --|..+.
T Consensus        14 deiiGqe~v~~~L~~~I~~gr-----------------l~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~-~pC~~C~   75 (535)
T PRK08451         14 DELIGQESVSKTLSLALDNNR-----------------LAHAYLFSGLRGSGKTSSARIFARALVCEQGPSS-TPCDTCI   75 (535)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-----------------CCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCC-CCCcccH
Confidence            458999999999998886432                 2357899999999999999999999975321100 0000000


Q ss_pred             CcCCCcccccc-ccccCCCCC-CchHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDSR-NKRSRDEQS-CSYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~~-~~rl~~~~g-~g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .+.......|. +.. +.+.. .|..+  .+.+.+..    .+++||+|||+|+++.+.+|+|++.||+-          
T Consensus        76 ~C~~~~~~~h~dv~e-ldaas~~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt~~A~NALLK~LEEp----------  144 (535)
T PRK08451         76 QCQSALENRHIDIIE-MDAASNRGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEP----------  144 (535)
T ss_pred             HHHHHhhcCCCeEEE-eccccccCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHHhhc----------
Confidence            00000000000 000 01111 13333  23333333    34789999999999999999999999972          


Q ss_pred             ecCCeEEEEecCC
Q 003038          770 SLGDAIVILSCES  782 (854)
Q Consensus       770 ~~~~aIiIlTsn~  782 (854)
                       -.+++|||+|+.
T Consensus       145 -p~~t~FIL~ttd  156 (535)
T PRK08451        145 -PSYVKFILATTD  156 (535)
T ss_pred             -CCceEEEEEECC
Confidence             246778998864

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.98  E-value=1.9e-09  Score=119.22  Aligned_cols=125  Identities=21%  Similarity=0.307  Sum_probs=85.0

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||+.++..+...+...                 +-...+||+||.|+||+++|+.+|+.+++....-.+.|+..+.
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~-----------------~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~   66 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKN-----------------RFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFK   66 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcC-----------------CCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEec
Confidence            46899999999998887542                 2345889999999999999999999997642110001111110


Q ss_pred             CcCCCccccccccccCCCCCCchHH--HHHHHHHcC----CCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeec
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIE--RFAEAVSNN----PHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSL  771 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e--~L~eav~~~----p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~  771 (854)
                                   . ..+...+.++  .+.+.+...    .++||+||++|+++...+|.|++.||+           .-
T Consensus        67 -------------~-~~~~~i~v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m~~~a~naLLK~LEe-----------pp  121 (313)
T PRK05564         67 -------------P-INKKSIGVDDIRNIIEEVNKKPYEGDKKVIIIYNSEKMTEQAQNAFLKTIEE-----------PP  121 (313)
T ss_pred             -------------c-ccCCCCCHHHHHHHHHHHhcCcccCCceEEEEechhhcCHHHHHHHHHHhcC-----------CC
Confidence                         0 0111123333  344444344    468999999999999999999999996           22


Q ss_pred             CCeEEEEecCCCC
Q 003038          772 GDAIVILSCESFS  784 (854)
Q Consensus       772 ~~aIiIlTsn~f~  784 (854)
                      .+++|||+|+..+
T Consensus       122 ~~t~~il~~~~~~  134 (313)
T PRK05564        122 KGVFIILLCENLE  134 (313)
T ss_pred             CCeEEEEEeCChH
Confidence            5778898885433

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.97  E-value=3.2e-09  Score=115.03  Aligned_cols=146  Identities=14%  Similarity=0.187  Sum_probs=106.1

Q ss_pred             cccccHHHHHHHHHHHH--------HhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEE
Q 003038          619 KVPWQKDTVYDIANTVL--------KCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVS  690 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~--------~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~  690 (854)
                      .|-|-++-+++|.++|.        -.+.|+..|+             =+|++||||+|||.|||++|...   ...||+
T Consensus       152 dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPK-------------GVLLYGPPGTGKTLLAkAVA~~T---~AtFIr  215 (406)
T COG1222         152 DIGGLDEQIQEIREVVELPLKNPELFEELGIDPPK-------------GVLLYGPPGTGKTLLAKAVANQT---DATFIR  215 (406)
T ss_pred             hccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCC-------------ceEeeCCCCCcHHHHHHHHHhcc---CceEEE
Confidence            35666777777877773        2356665442             36889999999999999999965   678999


Q ss_pred             EccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCC-----------CCHHHHHHHHHhhhcC
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQ-----------ADYCSQKGFKRAIESG  759 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEiek-----------a~~~v~~~Ll~~le~G  759 (854)
                      +..|++.       +++     + +-|.-....+++..+++..+||||||||-           .+.+||..+++.|-+=
T Consensus       216 vvgSElV-------qKY-----i-GEGaRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~ql  282 (406)
T COG1222         216 VVGSELV-------QKY-----I-GEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQL  282 (406)
T ss_pred             eccHHHH-------HHH-----h-ccchHHHHHHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhc
Confidence            9999887       443     2 11112223688888999999999999994           4789999999999751


Q ss_pred             eEecCCCceeecCCeEEEEecCCCCCCCCCCCCCcc--CCCC
Q 003038          760 RIVTSSGDEVSLGDAIVILSCESFSSRSRACSPPTK--QKSD  799 (854)
Q Consensus       760 ~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~~sp~~~--~~~~  799 (854)
                      -=-|.      ..|.-|||.||-+|..-++.=.|=|  +++.
T Consensus       283 DGFD~------~~nvKVI~ATNR~D~LDPALLRPGR~DRkIE  318 (406)
T COG1222         283 DGFDP------RGNVKVIMATNRPDILDPALLRPGRFDRKIE  318 (406)
T ss_pred             cCCCC------CCCeEEEEecCCccccChhhcCCCcccceee
Confidence            11111      3578899999999988888655544  4444

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=98.97  E-value=2.2e-09  Score=121.96  Aligned_cols=141  Identities=12%  Similarity=0.113  Sum_probs=97.4

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..++++|+||||+|||++++++|...          +..++.+..+.+...|.|+.+..+++++..++..  .|+|||||
T Consensus       178 ~pkgvLL~GppGTGKT~LAkalA~~l----------~~~fi~i~~s~l~~k~~ge~~~~lr~lf~~A~~~--~P~ILfID  245 (398)
T PTZ00454        178 PPRGVLLYGPPGTGKTMLAKAVAHHT----------TATFIRVVGSEFVQKYLGEGPRMVRDVFRLAREN--APSIIFID  245 (398)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHhc----------CCCEEEEehHHHHHHhcchhHHHHHHHHHHHHhc--CCeEEEEE
Confidence            46789999999999999999999763          5678888888888889999999999999999875  79999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCch
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGS  383 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~s  383 (854)
                      |++.+ ..+.....+   ....+.+..+++-+.+....+.+.+.+|+||+..+     ..||+|-|--|| +.|.|+.|+
T Consensus       246 EID~i~~~r~~~~~~---~d~~~~r~l~~LL~~ld~~~~~~~v~VI~aTN~~d-----~LDpAllR~GRfd~~I~~~~P~  317 (398)
T PTZ00454        246 EVDSIATKRFDAQTG---ADREVQRILLELLNQMDGFDQTTNVKVIMATNRAD-----TLDPALLRPGRLDRKIEFPLPD  317 (398)
T ss_pred             CHhhhccccccccCC---ccHHHHHHHHHHHHHhhccCCCCCEEEEEecCCch-----hCCHHHcCCCcccEEEEeCCcC
Confidence            99999 543211001   01112234444434342211223599999998654     578888763344 335666555


Q ss_pred             HHH
Q 003038          384 LSL  386 (854)
Q Consensus       384 l~~  386 (854)
                      ...
T Consensus       318 ~~~  320 (398)
T PTZ00454        318 RRQ  320 (398)
T ss_pred             HHH
Confidence            433

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=98.97  E-value=3.8e-09  Score=126.26  Aligned_cols=145  Identities=19%  Similarity=0.192  Sum_probs=92.1

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..+..++...                 +..+.+||+||+|+|||++|++||+.+++.......-.|..+.
T Consensus        18 ~dIiGQe~~v~~L~~aI~~~-----------------rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~   80 (725)
T PRK07133         18 DDIVGQDHIVQTLKNIIKSN-----------------KISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECI   80 (725)
T ss_pred             HHhcCcHHHHHHHHHHHHcC-----------------CCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHH
Confidence            45799999999999988753                 2345789999999999999999999997643211000111111


Q ss_pred             CcCCCccccccccccCCCCCC-chHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceee
Q 003038          698 STRADSTEDSRNKRSRDEQSC-SYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVS  770 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~-g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~  770 (854)
                      .   +. +.+.---.+.+.+. |..+  .|.+.+...|    ++|++|||+|.++...++.|++.||+.           
T Consensus        81 ~---~~-~~~~Dvieidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~~A~NALLKtLEEP-----------  145 (725)
T PRK07133         81 E---NV-NNSLDIIEMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLSKSAFNALLKTLEEP-----------  145 (725)
T ss_pred             H---hh-cCCCcEEEEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCCHHHHHHHHHHhhcC-----------
Confidence            0   00 00000000111121 4443  5667776654    689999999999999999999999963           


Q ss_pred             cCCeEEEEecCCCCCCC-CCCCCCc
Q 003038          771 LGDAIVILSCESFSSRS-RACSPPT  794 (854)
Q Consensus       771 ~~~aIiIlTsn~f~~~s-~~~sp~~  794 (854)
                      -.+++|||+|+..+... +..|.|+
T Consensus       146 P~~tifILaTte~~KLl~TI~SRcq  170 (725)
T PRK07133        146 PKHVIFILATTEVHKIPLTILSRVQ  170 (725)
T ss_pred             CCceEEEEEcCChhhhhHHHHhhce
Confidence            24667888776543332 2244443

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.96  E-value=3.1e-09  Score=126.91  Aligned_cols=135  Identities=20%  Similarity=0.183  Sum_probs=84.1

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..|...+...                 +-...+||+||+|+|||++|+.+|+.++.....----.|..+.
T Consensus        17 ~~viGq~~~~~~L~~~i~~~-----------------~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~   79 (614)
T PRK14971         17 ESVVGQEALTTTLKNAIATN-----------------KLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECE   79 (614)
T ss_pred             HHhcCcHHHHHHHHHHHHcC-----------------CCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcch
Confidence            46899999999998888753                 2245799999999999999999999996421100000011110


Q ss_pred             CcCCCccccc-cccccCCCCCC-chHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDS-RNKRSRDEQSC-SYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~-~~~rl~~~~g~-g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      ++.......+ .+.. +.+.+. +..+  .+.+.++..|    ++||+|||+|+++...++.|+++||+-          
T Consensus        80 sC~~~~~~~~~n~~~-ld~~~~~~vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls~~a~naLLK~LEep----------  148 (614)
T PRK14971         80 SCVAFNEQRSYNIHE-LDAASNNSVDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLSQAAFNAFLKTLEEP----------  148 (614)
T ss_pred             HHHHHhcCCCCceEE-ecccccCCHHHHHHHHHHHhhCcccCCcEEEEEECcccCCHHHHHHHHHHHhCC----------
Confidence            0000000001 0101 111111 2222  3344445444    789999999999999999999999962          


Q ss_pred             ecCCeEEEEecC
Q 003038          770 SLGDAIVILSCE  781 (854)
Q Consensus       770 ~~~~aIiIlTsn  781 (854)
                       -.+++|||+|+
T Consensus       149 -p~~tifIL~tt  159 (614)
T PRK14971        149 -PSYAIFILATT  159 (614)
T ss_pred             -CCCeEEEEEeC
Confidence             24678999875

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=98.96  E-value=2.1e-09  Score=118.56  Aligned_cols=146  Identities=13%  Similarity=0.163  Sum_probs=93.5

Q ss_pred             ccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc
Q 003038          620 VPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST  699 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~  699 (854)
                      .|||..+...+.+++.+.|.                 .+.+||.||+|+||+.+|+.+|+.++.....- .-.|..+.++
T Consensus         4 yPW~~~~~~~l~~~~~~~rl-----------------~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~-~~~Cg~C~sC   65 (325)
T PRK06871          4 YPWLQPTYQQITQAFQQGLG-----------------HHALLFKADSGLGTEQLIRALAQWLMCQTPQG-DQPCGQCHSC   65 (325)
T ss_pred             CcchHHHHHHHHHHHHcCCc-----------------ceeEEeECCCCCCHHHHHHHHHHHHcCCCCCC-CCCCCCCHHH
Confidence            59999999999999886432                 46899999999999999999999997643210 0012211111


Q ss_pred             CCCccccccccccCCC-CC--CchHH--HHHHHHHcC----CCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceee
Q 003038          700 RADSTEDSRNKRSRDE-QS--CSYIE--RFAEAVSNN----PHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVS  770 (854)
Q Consensus       700 ~~~s~e~~~~~rl~~~-~g--~g~~e--~L~eav~~~----p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~  770 (854)
                      +......|.--..+.| .+  .+.++  .+.+.+...    +++|++||++|+|+...+|+||+.||+           .
T Consensus        66 ~~~~~g~HPD~~~i~p~~~~~I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLLKtLEE-----------P  134 (325)
T PRK06871         66 HLFQAGNHPDFHILEPIDNKDIGVDQVREINEKVSQHAQQGGNKVVYIQGAERLTEAAANALLKTLEE-----------P  134 (325)
T ss_pred             HHHhcCCCCCEEEEccccCCCCCHHHHHHHHHHHhhccccCCceEEEEechhhhCHHHHHHHHHHhcC-----------C
Confidence            0000011110111112 12  25544  455565544    468999999999999999999999997           3


Q ss_pred             cCCeEEEEecCCCCC-CCCCCCCCc
Q 003038          771 LGDAIVILSCESFSS-RSRACSPPT  794 (854)
Q Consensus       771 ~~~aIiIlTsn~f~~-~s~~~sp~~  794 (854)
                      -.+++|||+|+.-+. .++.-|.|+
T Consensus       135 p~~~~fiL~t~~~~~llpTI~SRC~  159 (325)
T PRK06871        135 RPNTYFLLQADLSAALLPTIYSRCQ  159 (325)
T ss_pred             CCCeEEEEEECChHhCchHHHhhce
Confidence            367889998865333 334345443

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=98.96  E-value=2.1e-09  Score=120.22  Aligned_cols=137  Identities=16%  Similarity=0.186  Sum_probs=85.6

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc---eEEE--c
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN---FVSI--A  692 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~---~i~i--d  692 (854)
                      .+|+||++++..+..++...|                 -.+.+||.||.|+|||++|+.+|+.++.....   -..+  .
T Consensus        23 ~~l~Gh~~a~~~L~~a~~~gr-----------------l~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~~~~~   85 (351)
T PRK09112         23 TRLFGHEEAEAFLAQAYREGK-----------------LHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPETLADP   85 (351)
T ss_pred             hhccCcHHHHHHHHHHHHcCC-----------------CCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccccCCC
Confidence            568999999999999987643                 24578999999999999999999999763211   0011  0


Q ss_pred             cccccCcCCCccccc-c---ccccCCCC------CCchHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhh
Q 003038          693 LSSFSSTRADSTEDS-R---NKRSRDEQ------SCSYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAI  756 (854)
Q Consensus       693 ~s~~~~~~~~s~e~~-~---~~rl~~~~------g~g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~l  756 (854)
                      +.....++-.....| .   +.+.....      ..+.++  .+.+.+..    ..++||+|||+|++++..+|.|++.+
T Consensus        86 ~~~c~~c~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~L  165 (351)
T PRK09112         86 DPASPVWRQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTL  165 (351)
T ss_pred             CCCCHHHHHHHcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHH
Confidence            000000000000011 0   11110010      112333  45555543    46799999999999999999999999


Q ss_pred             hcCeEecCCCceeecCCeEEEEecCC
Q 003038          757 ESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       757 e~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      |+..           .+++|||.|+.
T Consensus       166 EEpp-----------~~~~fiLit~~  180 (351)
T PRK09112        166 EEPP-----------ARALFILISHS  180 (351)
T ss_pred             hcCC-----------CCceEEEEECC
Confidence            9731           46678887743

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=98.95  E-value=4.6e-09  Score=123.32  Aligned_cols=140  Identities=17%  Similarity=0.171  Sum_probs=87.5

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..+.+++...+                 ....+||+||+|+|||++|+++|+.++.....-.. -|..+.
T Consensus        16 ~dIIGQe~iv~~L~~aI~~~r-----------------l~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~-~Cg~C~   77 (605)
T PRK05896         16 KQIIGQELIKKILVNAILNNK-----------------LTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGD-CCNSCS   77 (605)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----------------CCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCC-CCcccH
Confidence            357899999999988876532                 23579999999999999999999999753211000 011110


Q ss_pred             CcCCCccccccccccCCCCC-CchHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceee
Q 003038          698 STRADSTEDSRNKRSRDEQS-CSYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVS  770 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g-~g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~  770 (854)
                      .+.......|.--..+.+.+ .|..+  .+.+.+...|    ++||+|||+|.++...++.|+..||+.           
T Consensus        78 sCr~i~~~~h~DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~~A~NaLLKtLEEP-----------  146 (605)
T PRK05896         78 VCESINTNQSVDIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEEP-----------  146 (605)
T ss_pred             HHHHHHcCCCCceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCHHHHHHHHHHHHhC-----------
Confidence            00000000000000011111 24433  4555555544    689999999999999999999999962           


Q ss_pred             cCCeEEEEecCCCCCC
Q 003038          771 LGDAIVILSCESFSSR  786 (854)
Q Consensus       771 ~~~aIiIlTsn~f~~~  786 (854)
                      -.+++|||+|+.....
T Consensus       147 p~~tvfIL~Tt~~~KL  162 (605)
T PRK05896        147 PKHVVFIFATTEFQKI  162 (605)
T ss_pred             CCcEEEEEECCChHhh
Confidence            2467899888654433

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=98.95  E-value=2e-09  Score=127.58  Aligned_cols=153  Identities=12%  Similarity=0.103  Sum_probs=113.3

Q ss_pred             cHHHHHHHHHHhhcc---------CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHH
Q 003038          211 RNEDVMYVIENLMSK---------RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEV  281 (854)
Q Consensus       211 r~~ei~~v~~~L~r~---------~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~  281 (854)
                      =.+||+.++..|.-.         -.+.++|+||||||||-+|+++|-.          .|+.|++++.+.|+.++.|--
T Consensus       319 AK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGE----------AgVPF~svSGSEFvE~~~g~~  388 (774)
T KOG0731|consen  319 AKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGE----------AGVPFFSVSGSEFVEMFVGVG  388 (774)
T ss_pred             HHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcc----------cCCceeeechHHHHHHhcccc
Confidence            357888888887532         4567999999999999999999965          789999999999999988888


Q ss_pred             HHHHHHHHHHHHhhhCCCeEEEeCccccc-ccccc-ccccccccchhhhHHHHHHHhhc-cc--CCCCceEEEEEecCHH
Q 003038          282 EQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRAS-SSEQVRGYYCSIEHIIMEIGKLV-CG--IGENARFWLMGIATFQ  356 (854)
Q Consensus       282 E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~-~~~~~~~~~~~~~~~~~~~~~ll-~~--~~g~g~l~lIgatT~~  356 (854)
                      ..|+++|+..++..  .|+|+|||||+.+ ..+.+ ...+ .+ .    ---..+.+|| ..  ....+.+.+|++|+-.
T Consensus       389 asrvr~lf~~ar~~--aP~iifideida~~~~r~G~~~~~-~~-~----e~e~tlnQll~emDgf~~~~~vi~~a~tnr~  460 (774)
T KOG0731|consen  389 ASRVRDLFPLARKN--APSIIFIDEIDAVGRKRGGKGTGG-GQ-D----EREQTLNQLLVEMDGFETSKGVIVLAATNRP  460 (774)
T ss_pred             hHHHHHHHHHhhcc--CCeEEEecccccccccccccccCC-CC-h----HHHHHHHHHHHHhcCCcCCCcEEEEeccCCc
Confidence            99999999999986  7999999999999 54421 1000 00 0    0123455666 22  1222469999999865


Q ss_pred             HHHHhhccCCchhhhhcc-CCCCCCCchHHH
Q 003038          357 SYMRCKSGHPSLETLWSL-HPLTIPAGSLSL  386 (854)
Q Consensus       357 ey~k~~~~~pale~~~~~-~~v~i~~~sl~~  386 (854)
                      .     ..||||-|-=|| ..|.|.-|.+.-
T Consensus       461 d-----~ld~allrpGRfdr~i~i~~p~~~~  486 (774)
T KOG0731|consen  461 D-----ILDPALLRPGRFDRQIQIDLPDVKG  486 (774)
T ss_pred             c-----ccCHHhcCCCccccceeccCCchhh
Confidence            5     579999886666 556777776543

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=98.94  E-value=3.7e-09  Score=116.40  Aligned_cols=165  Identities=14%  Similarity=0.198  Sum_probs=107.0

Q ss_pred             HHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCC---------------------ccc---------CCC---c-CC--
Q 003038          608 NLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTM---------------------RRK---------GKF---K-DH--  651 (854)
Q Consensus       608 ~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~---------------------~~~---------~~~---~-~~--  651 (854)
                      --|.+|+.|.+.|+||+.|.+.++=+|.++..-+.                     +|.         +..   + ..  
T Consensus       135 ~PkeI~~~Ldk~VVGQe~AKKvLsVAVYnHYkRI~hn~~s~~~~~a~~s~~~~~~~~P~~~~~~~~~a~~~~~~r~~~~~  214 (564)
T KOG0745|consen  135 TPKEICEYLDKFVVGQEKAKKVLSVAVYNHYKRIYHNEPSRQKELAEASKSAKDRDNPIELEISESNAQWPNNQRQIAKA  214 (564)
T ss_pred             ChHHHHHHhhhheechhhhhheeeehhhHHHHHHhcchHHHHHHHhhhhhcccCCCCcccccccccccccccccchhccc
Confidence            35799999999999999999999888854311000                     000         000   0 00  


Q ss_pred             cccCc------ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCC-chH-H-
Q 003038          652 SEVKE------ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSC-SYI-E-  722 (854)
Q Consensus       652 ~~~kp------~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~~-e-  722 (854)
                      -....      -..+|++||+|+|||.||+.||+.|   .-+|.-.||+..+++                 || |-+ | 
T Consensus       215 ld~~~~dv~LeKSNvLllGPtGsGKTllaqTLAr~l---dVPfaIcDcTtLTQA-----------------GYVGeDVEs  274 (564)
T KOG0745|consen  215 LDEDDEDVELEKSNVLLLGPTGSGKTLLAQTLARVL---DVPFAICDCTTLTQA-----------------GYVGEDVES  274 (564)
T ss_pred             ccccccceeeecccEEEECCCCCchhHHHHHHHHHh---CCCeEEecccchhhc-----------------ccccccHHH
Confidence            00000      0268999999999999999999999   578888898877632                 23 211 1 


Q ss_pred             HHHHH-------HHcCCCEEEEEecCCCCC--------------HHHHHHHHHhhhcCeE--------ecCCCc--eeec
Q 003038          723 RFAEA-------VSNNPHRVFLIEDVEQAD--------------YCSQKGFKRAIESGRI--------VTSSGD--EVSL  771 (854)
Q Consensus       723 ~L~ea-------v~~~p~~ViliDEieka~--------------~~v~~~Ll~~le~G~l--------~d~~G~--~v~~  771 (854)
                      .|...       |.+....|||||||||..              ..||.+||+.+|--.+        +...|+  .||.
T Consensus       275 vi~KLl~~A~~nVekAQqGIVflDEvDKi~~~~~~i~~~RDVsGEGVQQaLLKllEGtvVnVpeK~~~~~~rgd~vqiDT  354 (564)
T KOG0745|consen  275 VIQKLLQEAEYNVEKAQQGIVFLDEVDKITKKAESIHTSRDVSGEGVQQALLKLLEGTVVNVPEKGSRRKPRGDTVQIDT  354 (564)
T ss_pred             HHHHHHHHccCCHHHHhcCeEEEehhhhhcccCccccccccccchhHHHHHHHHhcccEEcccCCCCCCCCCCCeEEEec
Confidence            12221       334567899999999975              3599999999973222        233454  4577


Q ss_pred             CCeEEEEecCCCCCCCCCCCCC
Q 003038          772 GDAIVILSCESFSSRSRACSPP  793 (854)
Q Consensus       772 ~~aIiIlTsn~f~~~s~~~sp~  793 (854)
                      +|-.||. +..|.-.-+..+.+
T Consensus       355 tnILFia-sGAF~~Ldk~I~rR  375 (564)
T KOG0745|consen  355 TNILFIA-SGAFVGLDKIISRR  375 (564)
T ss_pred             cceEEEe-cccccchHHHHHHh
Confidence            8877777 56676665554444

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

Probab=98.94  E-value=2.8e-09  Score=123.37  Aligned_cols=157  Identities=14%  Similarity=0.208  Sum_probs=109.7

Q ss_pred             HHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC
Q 003038          606 SENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH  685 (854)
Q Consensus       606 ~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~  685 (854)
                      .-.|..-...|.+.=.|-+++.+.|.+.|.-++.  ...          -.--.+.|+||||||||.+||.||+.|   +
T Consensus       399 n~dl~~Ak~iLdeDHYgm~dVKeRILEfiAV~kL--rgs----------~qGkIlCf~GPPGVGKTSI~kSIA~AL---n  463 (906)
T KOG2004|consen  399 NLDLARAKEILDEDHYGMEDVKERILEFIAVGKL--RGS----------VQGKILCFVGPPGVGKTSIAKSIARAL---N  463 (906)
T ss_pred             hhhHHHHHHhhcccccchHHHHHHHHHHHHHHhh--ccc----------CCCcEEEEeCCCCCCcccHHHHHHHHh---C
Confidence            3456677788888889999999999988876643  110          111379999999999999999999999   4


Q ss_pred             CceEEEccccccCcCCCccccccccccCCCCCC-chH-HHHHHHHHcC--CCEEEEEecCCCCCHHH----HHHHHHhhh
Q 003038          686 NNFVSIALSSFSSTRADSTEDSRNKRSRDEQSC-SYI-ERFAEAVSNN--PHRVFLIEDVEQADYCS----QKGFKRAIE  757 (854)
Q Consensus       686 ~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~~-e~L~eav~~~--p~~ViliDEieka~~~v----~~~Ll~~le  757 (854)
                      ..|.|+......+       .-.++.-+  .-| |.. .++.+++++.  .+.|||||||||.-...    -.+||..+|
T Consensus       464 RkFfRfSvGG~tD-------vAeIkGHR--RTYVGAMPGkiIq~LK~v~t~NPliLiDEvDKlG~g~qGDPasALLElLD  534 (906)
T KOG2004|consen  464 RKFFRFSVGGMTD-------VAEIKGHR--RTYVGAMPGKIIQCLKKVKTENPLILIDEVDKLGSGHQGDPASALLELLD  534 (906)
T ss_pred             CceEEEecccccc-------HHhhcccc--eeeeccCChHHHHHHHhhCCCCceEEeehhhhhCCCCCCChHHHHHHhcC
Confidence            6788888776652       11111100  011 111 2567777652  23499999999986533    358888887


Q ss_pred             ---cCeEecCC-CceeecCCeEEEEecCCCCCC
Q 003038          758 ---SGRIVTSS-GDEVSLGDAIVILSCESFSSR  786 (854)
Q Consensus       758 ---~G~l~d~~-G~~v~~~~aIiIlTsn~f~~~  786 (854)
                         +-.|.|.. .-.+|++.+.||+|.|..+..
T Consensus       535 PEQNanFlDHYLdVp~DLSkVLFicTAN~idtI  567 (906)
T KOG2004|consen  535 PEQNANFLDHYLDVPVDLSKVLFICTANVIDTI  567 (906)
T ss_pred             hhhccchhhhccccccchhheEEEEeccccccC
Confidence               45666643 467999999999999987655

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=98.93  E-value=5.7e-09  Score=112.53  Aligned_cols=109  Identities=14%  Similarity=0.172  Sum_probs=75.5

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCC-CCC-------------------
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDE-QSC-------------------  718 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~-~g~-------------------  718 (854)
                      .+||.||+|+|||++|++||+.+   ..+|+.++++.-...          +.+++. .++                   
T Consensus        23 ~vLL~G~~GtGKT~lA~~la~~l---g~~~~~i~~~~~~~~----------~dllg~~~~~~~~~~~~~~~~~~~~~~~~   89 (262)
T TIGR02640        23 PVHLRGPAGTGKTTLAMHVARKR---DRPVMLINGDAELTT----------SDLVGSYAGYTRKKVHDQFIHNVVKLEDI   89 (262)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHh---CCCEEEEeCCccCCH----------HHHhhhhcccchhhHHHHHHHHhhhhhcc
Confidence            57899999999999999999966   357888888753310          011100 000                   


Q ss_pred             ---chHH-HHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCC----Cceeec-CCeEEEEecCC
Q 003038          719 ---SYIE-RFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSS----GDEVSL-GDAIVILSCES  782 (854)
Q Consensus       719 ---g~~e-~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~----G~~v~~-~~aIiIlTsn~  782 (854)
                         .|.+ .|..+.++  ..+++||||+++++++|+.|+++|++|.++-.+    ++.+.. .+..||+|+|.
T Consensus        90 ~~~~~~~g~l~~A~~~--g~~lllDEi~r~~~~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~  160 (262)
T TIGR02640        90 VRQNWVDNRLTLAVRE--GFTLVYDEFTRSKPETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNP  160 (262)
T ss_pred             cceeecCchHHHHHHc--CCEEEEcchhhCCHHHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCC
Confidence               0111 35555543  359999999999999999999999999987543    233322 46679999984

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).

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=98.93  E-value=2e-09  Score=119.80  Aligned_cols=136  Identities=16%  Similarity=0.195  Sum_probs=85.8

Q ss_pred             Ccccc-cHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          618 KKVPW-QKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       618 ~~V~G-Q~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      .+|+| |+.++..+...+...                 +-...+||+||+|+||+++|+.+|+.++.....= ..-|..+
T Consensus         5 ~~i~~~q~~~~~~L~~~~~~~-----------------~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~-~~~cg~C   66 (329)
T PRK08058          5 EQLTALQPVVVKMLQNSIAKN-----------------RLSHAYLFEGAKGTGKKATALWLAKSLFCLERNG-VEPCGTC   66 (329)
T ss_pred             HHHHhhHHHHHHHHHHHHHcC-----------------CCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCC-CCCCCcC
Confidence            45777 999999998887653                 3346889999999999999999999998643100 0001111


Q ss_pred             cCcCCCccccccccccCCCCC--CchHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCce
Q 003038          697 SSTRADSTEDSRNKRSRDEQS--CSYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDE  768 (854)
Q Consensus       697 ~~~~~~s~e~~~~~rl~~~~g--~g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~  768 (854)
                      ..+.......|.--..+.+.+  .+.++  .+.+.+..    .+++||+|||+|+++...+|.|++.||+-         
T Consensus        67 ~~c~~~~~~~hpD~~~i~~~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEP---------  137 (329)
T PRK08058         67 TNCKRIDSGNHPDVHLVAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEP---------  137 (329)
T ss_pred             HHHHHHhcCCCCCEEEeccccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCC---------
Confidence            100000001111001111112  13333  34455543    34789999999999999999999999972         


Q ss_pred             eecCCeEEEEecCC
Q 003038          769 VSLGDAIVILSCES  782 (854)
Q Consensus       769 v~~~~aIiIlTsn~  782 (854)
                        -.+++|||+|+.
T Consensus       138 --p~~~~~Il~t~~  149 (329)
T PRK08058        138 --SGGTTAILLTEN  149 (329)
T ss_pred             --CCCceEEEEeCC
Confidence              257789998863

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=98.93  E-value=2.9e-09  Score=117.27  Aligned_cols=132  Identities=12%  Similarity=0.157  Sum_probs=86.2

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      -.+||..+...+..++.+.|.                 .+.+||.||.|+||+.+|+.+|+.++.....    .+..+..
T Consensus         5 ~yPW~~~~~~~l~~~~~~~rl-----------------~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~----~~~~c~~   63 (319)
T PRK08769          5 FSPWQQRAYDQTVAALDAGRL-----------------GHGLLICGPEGLGKRAVALALAEHVLASGPD----PAAAQRT   63 (319)
T ss_pred             ccccHHHHHHHHHHHHHcCCc-----------------ceeEeeECCCCCCHHHHHHHHHHHHhCCCCC----CCCcchH
Confidence            359999999999998876432                 4589999999999999999999999864311    0100000


Q ss_pred             cCCCccccccccccC--CCC--C------CchHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          699 TRADSTEDSRNKRSR--DEQ--S------CSYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~--~~~--g------~g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                      +.-.....|.--..+  .|.  +      .+.++  .+.+.+...|    ++||+||++|+++....|+||+.||+    
T Consensus        64 c~~~~~g~HPD~~~i~~~p~~~~~k~~~~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEE----  139 (319)
T PRK08769         64 RQLIAAGTHPDLQLVSFIPNRTGDKLRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEE----  139 (319)
T ss_pred             HHHHhcCCCCCEEEEecCCCcccccccccccHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHHhhC----
Confidence            000000111100111  111  1      12323  4555555555    58999999999999999999999997    


Q ss_pred             cCCCceeecCCeEEEEecCC
Q 003038          763 TSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       763 d~~G~~v~~~~aIiIlTsn~  782 (854)
                             .-.+++|||+|+.
T Consensus       140 -------Pp~~~~fiL~~~~  152 (319)
T PRK08769        140 -------PSPGRYLWLISAQ  152 (319)
T ss_pred             -------CCCCCeEEEEECC
Confidence                   2357889998864

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=98.93  E-value=3.6e-09  Score=121.11  Aligned_cols=141  Identities=9%  Similarity=0.061  Sum_probs=95.6

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..++++|+||||||||++|+++|..+          +..++.+..+.|...|.|+.+..+++++..++..  .|+|||||
T Consensus       216 ~p~gVLL~GPPGTGKT~LAraIA~el----------~~~fi~V~~seL~~k~~Ge~~~~vr~lF~~A~~~--~P~ILfID  283 (438)
T PTZ00361        216 PPKGVILYGPPGTGKTLLAKAVANET----------SATFLRVVGSELIQKYLGDGPKLVRELFRVAEEN--APSIVFID  283 (438)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhh----------CCCEEEEecchhhhhhcchHHHHHHHHHHHHHhC--CCcEEeHH
Confidence            45689999999999999999999874          3467888888888889999999999999999875  79999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCch
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGS  383 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~s  383 (854)
                      ||+.+ ..+.....+.   ...+....+++-+.+......+.+.+|+||+.-+.     .||+|-|-.|| ..|.|+.|+
T Consensus       284 EID~l~~kR~~~~sgg---~~e~qr~ll~LL~~Ldg~~~~~~V~VI~ATNr~d~-----LDpaLlRpGRfd~~I~~~~Pd  355 (438)
T PTZ00361        284 EIDAIGTKRYDATSGG---EKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIES-----LDPALIRPGRIDRKIEFPNPD  355 (438)
T ss_pred             HHHHHhccCCCCCCcc---cHHHHHHHHHHHHHHhhhcccCCeEEEEecCChHH-----hhHHhccCCeeEEEEEeCCCC
Confidence            99999 5432211110   01111222333333321111235999999986442     47888764444 456777666


Q ss_pred             HHH
Q 003038          384 LSL  386 (854)
Q Consensus       384 l~~  386 (854)
                      ...
T Consensus       356 ~~~  358 (438)
T PTZ00361        356 EKT  358 (438)
T ss_pred             HHH
Confidence            443

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.93  E-value=6.7e-09  Score=120.94  Aligned_cols=132  Identities=18%  Similarity=0.177  Sum_probs=86.6

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc----e-EEEc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN----F-VSIA  692 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~----~-i~id  692 (854)
                      ..|+||++++..+.+++...                 +..+.+||+||+|+|||++|+.+|+.+++....    + .+.+
T Consensus        16 ~diiGq~~i~~~L~~~i~~~-----------------~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~n   78 (486)
T PRK14953         16 KEVIGQEIVVRILKNAVKLQ-----------------RVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCEN   78 (486)
T ss_pred             HHccChHHHHHHHHHHHHcC-----------------CCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHH
Confidence            45799999999998888653                 234578999999999999999999999742110    0 0011


Q ss_pred             cccccCcCCCccccc-cccccCCC-CCCchHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecC
Q 003038          693 LSSFSSTRADSTEDS-RNKRSRDE-QSCSYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTS  764 (854)
Q Consensus       693 ~s~~~~~~~~s~e~~-~~~rl~~~-~g~g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~  764 (854)
                      |..+..      ..+ .+.. +.+ ...|..+  .+.+.+...|    +.||+|||+|+++...++.|++.|++.     
T Consensus        79 c~~i~~------g~~~d~~e-idaas~~gvd~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~~a~naLLk~LEep-----  146 (486)
T PRK14953         79 CVEIDK------GSFPDLIE-IDAASNRGIDDIRALRDAVSYTPIKGKYKVYIIDEAHMLTKEAFNALLKTLEEP-----  146 (486)
T ss_pred             HHHHhc------CCCCcEEE-EeCccCCCHHHHHHHHHHHHhCcccCCeeEEEEEChhhcCHHHHHHHHHHHhcC-----
Confidence            111110      000 0000 111 1124443  5667776655    579999999999999999999999963     


Q ss_pred             CCceeecCCeEEEEecCCCC
Q 003038          765 SGDEVSLGDAIVILSCESFS  784 (854)
Q Consensus       765 ~G~~v~~~~aIiIlTsn~f~  784 (854)
                            -.+++|||+++..+
T Consensus       147 ------p~~~v~Il~tt~~~  160 (486)
T PRK14953        147 ------PPRTIFILCTTEYD  160 (486)
T ss_pred             ------CCCeEEEEEECCHH
Confidence                  23567888776443

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=98.92  E-value=6.8e-09  Score=122.46  Aligned_cols=121  Identities=12%  Similarity=0.146  Sum_probs=80.1

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHH-------hCCCCceEEE
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLV-------FGSHNNFVSI  691 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~l-------fg~~~~~i~i  691 (854)
                      .++||++++..+..++..       +          . ...+||+||+|+|||.+|+++.+..       |.....|+.+
T Consensus        66 ~iiGqs~~i~~l~~al~~-------~----------~-~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~~~~~~~fi~i  127 (531)
T TIGR02902        66 EIIGQEEGIKALKAALCG-------P----------N-PQHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAAFVEI  127 (531)
T ss_pred             HeeCcHHHHHHHHHHHhC-------C----------C-CceEEEECCCCCCHHHHHHHHHHHhhhccCCCcCCCCCEEEE
Confidence            489999999888765321       1          1 2367999999999999999998753       3335689999


Q ss_pred             ccccccCcCCCccccccccccCC---CC--------CC-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcC
Q 003038          692 ALSSFSSTRADSTEDSRNKRSRD---EQ--------SC-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESG  759 (854)
Q Consensus       692 d~s~~~~~~~~s~e~~~~~rl~~---~~--------g~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G  759 (854)
                      |++.....     ++.....++.   .+        +. |+.+...+++.+....++|||||+++++..|+.|+++|+++
T Consensus       128 d~~~~~~~-----~~~~~~~li~~~~~p~~~~~~~~g~~g~~~~~~G~l~~a~gG~L~IdEI~~L~~~~q~~LL~~Le~~  202 (531)
T TIGR02902       128 DATTARFD-----ERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKPGAVTRAHGGVLFIDEIGELHPVQMNKLLKVLEDR  202 (531)
T ss_pred             ccccccCC-----ccccchhhcCCcccchhccccccccCCcccccCchhhccCCcEEEEechhhCCHHHHHHHHHHHHhC
Confidence            98632100     1000000110   00        00 11111233556677899999999999999999999999998


Q ss_pred             eEe
Q 003038          760 RIV  762 (854)
Q Consensus       760 ~l~  762 (854)
                      ++.
T Consensus       203 ~~~  205 (531)
T TIGR02902       203 KVF  205 (531)
T ss_pred             eee
Confidence            764

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.

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=98.92  E-value=6.9e-09  Score=122.68  Aligned_cols=136  Identities=17%  Similarity=0.184  Sum_probs=85.5

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..+...+...                 +....+||+||+|+|||++|++||+.+++.... -..-|..+.
T Consensus        16 ~diiGqe~iv~~L~~~i~~~-----------------~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~-~~~pC~~C~   77 (563)
T PRK06647         16 NSLEGQDFVVETLKHSIESN-----------------KIANAYIFSGPRGVGKTSSARAFARCLNCVNGP-TPMPCGECS   77 (563)
T ss_pred             HHccCcHHHHHHHHHHHHcC-----------------CCCeEEEEECCCCCCHHHHHHHHHHhhccccCC-CCCCCccch
Confidence            46899999999998888753                 224579999999999999999999999753210 000011111


Q ss_pred             CcCCCccccc-cccccCCCCC-CchHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDS-RNKRSRDEQS-CSYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~-~~~rl~~~~g-~g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .+.......+ .+.. +.+.. .+..+  .+.+.+..    .+++||+|||+|+++...+|.|++.+|+.          
T Consensus        78 ~C~~i~~~~~~dv~~-idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEep----------  146 (563)
T PRK06647         78 SCKSIDNDNSLDVIE-IDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEEP----------  146 (563)
T ss_pred             HHHHHHcCCCCCeEE-ecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCHHHHHHHHHhhccC----------
Confidence            0000000000 0000 11111 13332  34333333    45789999999999999999999999962          


Q ss_pred             ecCCeEEEEecCCC
Q 003038          770 SLGDAIVILSCESF  783 (854)
Q Consensus       770 ~~~~aIiIlTsn~f  783 (854)
                       -.+++|||+|+..
T Consensus       147 -p~~~vfI~~tte~  159 (563)
T PRK06647        147 -PPYIVFIFATTEV  159 (563)
T ss_pred             -CCCEEEEEecCCh
Confidence             2477899987654

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=98.91  E-value=3.8e-09  Score=116.30  Aligned_cols=147  Identities=11%  Similarity=0.116  Sum_probs=95.1

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      -.|||..+...+..++.+.|                 -.+.+||.||.|+||+.+|+.+|+.++.....-  -.|..+.+
T Consensus         4 ~yPWl~~~~~~l~~~~~~~r-----------------l~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~--~~Cg~C~s   64 (319)
T PRK06090          4 DYPWLVPVWQNWKAGLDAGR-----------------IPGALLLQSDEGLGVESLVELFSRALLCQNYQS--EACGFCHS   64 (319)
T ss_pred             CcccHHHHHHHHHHHHHcCC-----------------cceeEeeECCCCCCHHHHHHHHHHHHcCCCCCC--CCCCCCHH
Confidence            45999999999998887643                 356899999999999999999999997643210  11222211


Q ss_pred             cCCCccccccccccCCCC--CC--chHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCce
Q 003038          699 TRADSTEDSRNKRSRDEQ--SC--SYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDE  768 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~--g~--g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~  768 (854)
                      ++......|.--..+.|.  +.  +.++  .+.+.+...|    ++|++||++|+++...+|+||+.+|+          
T Consensus        65 C~~~~~g~HPD~~~i~p~~~~~~I~vdqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEE----------  134 (319)
T PRK06090         65 CELMQSGNHPDLHVIKPEKEGKSITVEQIRQCNRLAQESSQLNGYRLFVIEPADAMNESASNALLKTLEE----------  134 (319)
T ss_pred             HHHHHcCCCCCEEEEecCcCCCcCCHHHHHHHHHHHhhCcccCCceEEEecchhhhCHHHHHHHHHHhcC----------
Confidence            110000112111112121  11  4433  4555554444    79999999999999999999999997          


Q ss_pred             eecCCeEEEEecCCCC-CCCCCCCCCcc
Q 003038          769 VSLGDAIVILSCESFS-SRSRACSPPTK  795 (854)
Q Consensus       769 v~~~~aIiIlTsn~f~-~~s~~~sp~~~  795 (854)
                       .-.+++|||+|+.-+ -..+.-|.|++
T Consensus       135 -Pp~~t~fiL~t~~~~~lLpTI~SRCq~  161 (319)
T PRK06090        135 -PAPNCLFLLVTHNQKRLLPTIVSRCQQ  161 (319)
T ss_pred             -CCCCeEEEEEECChhhChHHHHhccee
Confidence             336788999886533 33444566644

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=98.91  E-value=7.1e-09  Score=117.10  Aligned_cols=155  Identities=12%  Similarity=0.097  Sum_probs=104.5

Q ss_pred             cHHHHHHHHHHhhcc-------------CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccc
Q 003038          211 RNEDVMYVIENLMSK-------------RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMN  277 (854)
Q Consensus       211 r~~ei~~v~~~L~r~-------------~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~  277 (854)
                      .++.++++.+.+...             ..++++|+||||||||++|+++|...          +..++.+..+.+...|
T Consensus       127 l~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l----------~~~~~~v~~~~l~~~~  196 (364)
T TIGR01242       127 LEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHET----------NATFIRVVGSELVRKY  196 (364)
T ss_pred             hHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhC----------CCCEEecchHHHHHHh
Confidence            677777777665321             24569999999999999999999874          3467777777777778


Q ss_pred             hHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcc---cCCCCceEEEEEec
Q 003038          278 RVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVC---GIGENARFWLMGIA  353 (854)
Q Consensus       278 rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~---~~~g~g~l~lIgat  353 (854)
                      .|+.+..++.++..++..  .|+||||||++.+ ..+.....+.   . +  .....+..++.   .....+.+.+|++|
T Consensus       197 ~g~~~~~i~~~f~~a~~~--~p~il~iDEiD~l~~~~~~~~~~~---~-~--~~~~~l~~ll~~ld~~~~~~~v~vI~tt  268 (364)
T TIGR01242       197 IGEGARLVREIFELAKEK--APSIIFIDEIDAIAAKRTDSGTSG---D-R--EVQRTLMQLLAELDGFDPRGNVKVIAAT  268 (364)
T ss_pred             hhHHHHHHHHHHHHHHhc--CCcEEEhhhhhhhccccccCCCCc---c-H--HHHHHHHHHHHHhhCCCCCCCEEEEEec
Confidence            999999999999988865  6899999999999 4332110000   0 0  11223334441   11112369999999


Q ss_pred             CHHHHHHhhccCCchhhhhccC-CCCCCCchHHHHh
Q 003038          354 TFQSYMRCKSGHPSLETLWSLH-PLTIPAGSLSLSL  388 (854)
Q Consensus       354 T~~ey~k~~~~~pale~~~~~~-~v~i~~~sl~~al  388 (854)
                      +..+     ..+|++-|.+||. .|.|+.|+.....
T Consensus       269 n~~~-----~ld~al~r~grfd~~i~v~~P~~~~r~  299 (364)
T TIGR01242       269 NRPD-----ILDPALLRPGRFDRIIEVPLPDFEGRL  299 (364)
T ss_pred             CChh-----hCChhhcCcccCceEEEeCCcCHHHHH
Confidence            8654     3688887766663 4667766655433

Many proteins may score above the trusted cutoff because an internal

>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=98.91  E-value=6.7e-10  Score=114.85  Aligned_cols=86  Identities=13%  Similarity=0.176  Sum_probs=52.0

Q ss_pred             CCCC-cHHHHHHHHHHhhcc---C---cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchH
Q 003038          207 LDPI-RNEDVMYVIENLMSK---R---KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRV  279 (854)
Q Consensus       207 ldpv-r~~ei~~v~~~L~r~---~---k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rg  279 (854)
                      ||-+ .++++..-+.++.+.   +   -.+++|+||||+|||++++-+|..+          ++.|..++...+.     
T Consensus        23 L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~----------~~~~~~~sg~~i~-----   87 (233)
T PF05496_consen   23 LDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANEL----------GVNFKITSGPAIE-----   87 (233)
T ss_dssp             CCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHC----------T--EEEEECCC-------
T ss_pred             HHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhcc----------CCCeEeccchhhh-----
Confidence            4444 777777777776442   1   1368999999999999999999874          4566665543332     


Q ss_pred             HHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cc
Q 003038          280 EVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EF  312 (854)
Q Consensus       280 e~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~  312 (854)
                          +..++...+.+. +.+.||||||||.+ ..
T Consensus        88 ----k~~dl~~il~~l-~~~~ILFIDEIHRlnk~  116 (233)
T PF05496_consen   88 ----KAGDLAAILTNL-KEGDILFIDEIHRLNKA  116 (233)
T ss_dssp             ----SCHHHHHHHHT---TT-EEEECTCCC--HH
T ss_pred             ----hHHHHHHHHHhc-CCCcEEEEechhhccHH
Confidence                122233333333 45789999999999 54

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.

>TIGR01817 nifA Nif-specific regulatory protein

Probab=98.91  E-value=5.5e-09  Score=123.87  Aligned_cols=143  Identities=13%  Similarity=0.184  Sum_probs=100.5

Q ss_pred             cCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          617 EKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       617 ~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      ...++|++.++..+...+.+..                +...++|+.|++|+||+.+|++|.+.......+|+.+||..+
T Consensus       195 ~~~liG~s~~~~~~~~~~~~~a----------------~~~~pvli~Ge~GtGK~~lA~~ih~~s~r~~~pfv~i~c~~~  258 (534)
T TIGR01817       195 EDGIIGKSPAMRQVVDQARVVA----------------RSNSTVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAAL  258 (534)
T ss_pred             cCceEECCHHHHHHHHHHHHHh----------------CcCCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeecCCC
Confidence            4578999999999888888753                223578999999999999999999988777889999999987


Q ss_pred             cCcCCCccccccccccCC-CCC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCC
Q 003038          697 SSTRADSTEDSRNKRSRD-EQS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGD  773 (854)
Q Consensus       697 ~~~~~~s~e~~~~~rl~~-~~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~  773 (854)
                      .       +....+.+.+ ..| + |....-.+.+......++|||||+++++.+|..|+++|++|.++...|...--.+
T Consensus       259 ~-------~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~GtL~ldei~~L~~~~Q~~Ll~~l~~~~~~~~~~~~~~~~~  331 (534)
T TIGR01817       259 S-------ETLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVD  331 (534)
T ss_pred             C-------HHHHHHHHcCCCCCccCCCCcCCCCcccccCCCeEEEechhhCCHHHHHHHHHHHhcCcEEECCCCceEeec
Confidence            6       2211111111 000 0 1000000112233467999999999999999999999999998764443333346


Q ss_pred             eEEEEecCC
Q 003038          774 AIVILSCES  782 (854)
Q Consensus       774 aIiIlTsn~  782 (854)
                      +.||+||+.
T Consensus       332 ~riI~~s~~  340 (534)
T TIGR01817       332 VRLVAATNR  340 (534)
T ss_pred             EEEEEeCCC
Confidence            788888763

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.

>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=98.90  E-value=3.7e-09  Score=100.28  Aligned_cols=109  Identities=17%  Similarity=0.277  Sum_probs=63.5

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc-ccCcCCCcc-----ccccccccCCCCCCchHHHHHHHHHcCC
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS-FSSTRADST-----EDSRNKRSRDEQSCSYIERFAEAVSNNP  732 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~-~~~~~~~s~-----e~~~~~rl~~~~g~g~~e~L~eav~~~p  732 (854)
                      ++|+.|++|+|||.+|++||+.+-   ..|.||.++. ... .+..+     .+....++..+|.+              
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~~---~~f~RIq~tpdllP-sDi~G~~v~~~~~~~f~~~~GPif--------------   62 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSLG---LSFKRIQFTPDLLP-SDILGFPVYDQETGEFEFRPGPIF--------------   62 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHTT-----EEEEE--TT--H-HHHHEEEEEETTTTEEEEEE-TT---------------
T ss_pred             CEeeECCCccHHHHHHHHHHHHcC---CceeEEEecCCCCc-ccceeeeeeccCCCeeEeecChhh--------------
Confidence            479999999999999999999983   4677887652 210 00000     00000000111111              


Q ss_pred             CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEE-ecCCCCCC
Q 003038          733 HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVIL-SCESFSSR  786 (854)
Q Consensus       733 ~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIl-Tsn~f~~~  786 (854)
                      ..|+|+|||.+++|.+|.+|+++|++++++. .|.+..+.+..+|+ |-|..+..
T Consensus        63 ~~ill~DEiNrappktQsAlLeam~Er~Vt~-~g~~~~lp~pf~ViATqNp~e~~  116 (131)
T PF07726_consen   63 TNILLADEINRAPPKTQSALLEAMEERQVTI-DGQTYPLPDPFFVIATQNPVEQE  116 (131)
T ss_dssp             SSEEEEETGGGS-HHHHHHHHHHHHHSEEEE-TTEEEE--SS-EEEEEE-TT--S
T ss_pred             hceeeecccccCCHHHHHHHHHHHHcCeEEe-CCEEEECCCcEEEEEecCccccC
Confidence            3599999999999999999999999999995 57889998866655 66865443

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.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=98.90  E-value=3.1e-09  Score=118.15  Aligned_cols=148  Identities=10%  Similarity=0.109  Sum_probs=95.8

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      -.|||..+...+...+.+.|                 -.+.+||.||+|+||+.+|+++|+.++.....- .-.|..+.+
T Consensus         3 ~yPWl~~~~~~l~~~~~~~r-----------------l~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~-~~~Cg~C~s   64 (334)
T PRK07993          3 WYPWLRPDYEQLVGSYQAGR-----------------GHHALLIQALPGMGDDALIYALSRWLMCQQPQG-HKSCGHCRG   64 (334)
T ss_pred             CCCCChHHHHHHHHHHHcCC-----------------cceEEeeECCCCCCHHHHHHHHHHHHcCCCCCC-CCCCCCCHH
Confidence            35999999999998887643                 356899999999999999999999998642110 001222211


Q ss_pred             cCCCccccccccccCCCC----CCchHH--HHHHHHHcC----CCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCce
Q 003038          699 TRADSTEDSRNKRSRDEQ----SCSYIE--RFAEAVSNN----PHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDE  768 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~----g~g~~e--~L~eav~~~----p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~  768 (854)
                      +.......|.--..+.|.    ..+.++  .+.+.+...    .++|++||++|+|+....|+||+.||+-         
T Consensus        65 C~~~~~g~HPD~~~i~p~~~~~~I~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEP---------  135 (334)
T PRK07993         65 CQLMQAGTHPDYYTLTPEKGKSSLGVDAVREVTEKLYEHARLGGAKVVWLPDAALLTDAAANALLKTLEEP---------  135 (334)
T ss_pred             HHHHHcCCCCCEEEEecccccccCCHHHHHHHHHHHhhccccCCceEEEEcchHhhCHHHHHHHHHHhcCC---------
Confidence            100000111111112121    124444  456655544    4789999999999999999999999972         


Q ss_pred             eecCCeEEEEecCCCCC-CCCCCCCCcc
Q 003038          769 VSLGDAIVILSCESFSS-RSRACSPPTK  795 (854)
Q Consensus       769 v~~~~aIiIlTsn~f~~-~s~~~sp~~~  795 (854)
                        -.+++|||+|+.-+. .++..|.|+.
T Consensus       136 --p~~t~fiL~t~~~~~lLpTIrSRCq~  161 (334)
T PRK07993        136 --PENTWFFLACREPARLLATLRSRCRL  161 (334)
T ss_pred             --CCCeEEEEEECChhhChHHHHhcccc
Confidence              357889998865433 3344666654

>CHL00206 ycf2 Ycf2; Provisional

Probab=98.89  E-value=3.4e-09  Score=134.00  Aligned_cols=128  Identities=9%  Similarity=0.033  Sum_probs=88.9

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccc---------------------------
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMN---------------------------  277 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~---------------------------  277 (854)
                      +-.+.++|+||||||||.+|++||..          .++.|++++++.|+.++                           
T Consensus      1628 ~pPKGILLiGPPGTGKTlLAKALA~e----------s~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~~ 1697 (2281)
T CHL00206       1628 SPSRGILVIGSIGTGRSYLVKYLATN----------SYVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRDL 1697 (2281)
T ss_pred             CCCCceEEECCCCCCHHHHHHHHHHh----------cCCceEEEEHHHHhhccccccccccccccccccccccccccccc
Confidence            46779999999999999999999976          47789999988887532                           


Q ss_pred             --------------hHHHH--HHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc
Q 003038          278 --------------RVEVE--QRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG  340 (854)
Q Consensus       278 --------------rge~E--~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~  340 (854)
                                    .|+-+  .|++.+++.|++.  .||||||||||.+ ......            .....+.+.|..
T Consensus      1698 ~~e~~e~~n~~~~~m~~~e~~~rIr~lFelARk~--SPCIIFIDEIDaL~~~ds~~------------ltL~qLLneLDg 1763 (2281)
T CHL00206       1698 DTELLTMMNALTMDMMPKIDRFYITLQFELAKAM--SPCIIWIPNIHDLNVNESNY------------LSLGLLVNSLSR 1763 (2281)
T ss_pred             chhhhhhcchhhhhhhhhhhHHHHHHHHHHHHHC--CCeEEEEEchhhcCCCccce------------ehHHHHHHHhcc
Confidence                          11222  3589999999986  7999999999999 432110            012222233321


Q ss_pred             C---CCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCC
Q 003038          341 I---GENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPA  381 (854)
Q Consensus       341 ~---~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~  381 (854)
                      .   .....|.|||||+...     ..||||-|-=|| +.|.|+-
T Consensus      1764 ~~~~~s~~~VIVIAATNRPD-----~LDPALLRPGRFDR~I~Ir~ 1803 (2281)
T CHL00206       1764 DCERCSTRNILVIASTHIPQ-----KVDPALIAPNKLNTCIKIRR 1803 (2281)
T ss_pred             ccccCCCCCEEEEEeCCCcc-----cCCHhHcCCCCCCeEEEeCC
Confidence            1   1122599999999765     589999885556 3444543

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.89  E-value=9.6e-09  Score=122.70  Aligned_cols=140  Identities=19%  Similarity=0.185  Sum_probs=86.5

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..|.+++...+                 -...+||+||+|+|||++|+.||+.++.....-.--.|..+.
T Consensus        16 ~eiiGq~~~~~~L~~~i~~~~-----------------i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~~c~   78 (585)
T PRK14950         16 AELVGQEHVVQTLRNAIAEGR-----------------VAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGTCE   78 (585)
T ss_pred             HHhcCCHHHHHHHHHHHHhCC-----------------CceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccCH
Confidence            468999999999988887532                 234789999999999999999999996422100000011110


Q ss_pred             CcCCCcccccc-ccccCCCCC-CchHH--HHHHHHHcC----CCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDSR-NKRSRDEQS-CSYIE--RFAEAVSNN----PHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~~-~~rl~~~~g-~g~~e--~L~eav~~~----p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .+.......|. +-. +.+.. .+..+  .+.+.+...    .++||+|||+|+++...++.|+++|++.          
T Consensus        79 ~c~~i~~~~~~d~~~-i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEep----------  147 (585)
T PRK14950         79 MCRAIAEGSAVDVIE-MDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEP----------  147 (585)
T ss_pred             HHHHHhcCCCCeEEE-EeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcC----------
Confidence            00000000000 000 11111 23333  455555544    4689999999999999999999999973          


Q ss_pred             ecCCeEEEEecCCCCCC
Q 003038          770 SLGDAIVILSCESFSSR  786 (854)
Q Consensus       770 ~~~~aIiIlTsn~f~~~  786 (854)
                       -.+++|||+++..+..
T Consensus       148 -p~~tv~Il~t~~~~kl  163 (585)
T PRK14950        148 -PPHAIFILATTEVHKV  163 (585)
T ss_pred             -CCCeEEEEEeCChhhh
Confidence             1467888888765433

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=98.88  E-value=1.5e-08  Score=113.68  Aligned_cols=136  Identities=16%  Similarity=0.180  Sum_probs=84.5

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..+...+...                 +....+||+||+|+|||++|+.||+.+++....- .-.+..+.
T Consensus        14 ~~iig~~~~~~~l~~~~~~~-----------------~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~-~~~c~~c~   75 (355)
T TIGR02397        14 EDVIGQEHIVQTLKNAIKNG-----------------RIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPD-GEPCNECE   75 (355)
T ss_pred             hhccCcHHHHHHHHHHHHcC-----------------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCC-CCCCCCCH
Confidence            46799999999999887642                 2345899999999999999999999997542100 00111110


Q ss_pred             CcCCCccccc-cccccCCCCCC-chH--HHHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          698 STRADSTEDS-RNKRSRDEQSC-SYI--ERFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~-~~~rl~~~~g~-g~~--e~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      ++.......+ .+.. +.+.+. +..  ..+.+.+...|    ++||+|||+|+++...++.|++.+++.          
T Consensus        76 ~c~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~p~~~~~~vviidea~~l~~~~~~~Ll~~le~~----------  144 (355)
T TIGR02397        76 SCKEINSGSSLDVIE-IDAASNNGVDDIREILDNVKYAPSSGKYKVYIIDEVHMLSKSAFNALLKTLEEP----------  144 (355)
T ss_pred             HHHHHhcCCCCCEEE-eeccccCCHHHHHHHHHHHhcCcccCCceEEEEeChhhcCHHHHHHHHHHHhCC----------
Confidence            0000000000 0000 111111 221  24555555544    689999999999999999999999862          


Q ss_pred             ecCCeEEEEecCCC
Q 003038          770 SLGDAIVILSCESF  783 (854)
Q Consensus       770 ~~~~aIiIlTsn~f  783 (854)
                       -.+++||++++..
T Consensus       145 -~~~~~lIl~~~~~  157 (355)
T TIGR02397       145 -PEHVVFILATTEP  157 (355)
T ss_pred             -ccceeEEEEeCCH
Confidence             2467788887653

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.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=98.88  E-value=6e-09  Score=115.93  Aligned_cols=139  Identities=14%  Similarity=0.171  Sum_probs=97.5

Q ss_pred             ccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc
Q 003038          620 VPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST  699 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~  699 (854)
                      ++|+..++..+...+.+.-.                ...++|+.|++|+||+.+|++|...-.....+|+.+||+...+ 
T Consensus         1 liG~S~~m~~~~~~~~~~a~----------------~~~pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~~~~~-   63 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLAP----------------LDRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSE-   63 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHhC----------------CCCCEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCCCCCh-
Confidence            57899888888888877532                2347899999999999999999887766678999999997652 


Q ss_pred             CCCccccccccccCC-CCC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEE
Q 003038          700 RADSTEDSRNKRSRD-EQS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIV  776 (854)
Q Consensus       700 ~~~s~e~~~~~rl~~-~~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIi  776 (854)
                            ...-+.+.+ ..| + |....-.+.+......++|||||+.+++.+|..|+++|++|.+..-.|...--.++.|
T Consensus        64 ------~~l~~~lfG~~~g~~~ga~~~~~G~~~~a~gGtL~Ldei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~Ri  137 (329)
T TIGR02974        64 ------NLLDSELFGHEAGAFTGAQKRHQGRFERADGGTLFLDELATASLLVQEKLLRVIEYGEFERVGGSQTLQVDVRL  137 (329)
T ss_pred             ------HHHHHHHhccccccccCcccccCCchhhCCCCEEEeCChHhCCHHHHHHHHHHHHcCcEEecCCCceeccceEE
Confidence                  111111111 000 0 1100011123344578999999999999999999999999998754444444467889


Q ss_pred             EEecC
Q 003038          777 ILSCE  781 (854)
Q Consensus       777 IlTsn  781 (854)
                      |++|+
T Consensus       138 I~at~  142 (329)
T TIGR02974       138 VCATN  142 (329)
T ss_pred             EEech
Confidence            99886

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

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=98.88  E-value=3.8e-09  Score=115.06  Aligned_cols=113  Identities=10%  Similarity=0.158  Sum_probs=86.9

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      .-++++|+||||+|||-+++++|.+          .++.|+.++++.+.+.+.||.++-++.+|..+.+-  .|+|+|||
T Consensus       126 p~kGiLL~GPpG~GKTmlAKA~Ake----------aga~fInv~~s~lt~KWfgE~eKlv~AvFslAsKl--~P~iIFID  193 (386)
T KOG0737|consen  126 PPKGILLYGPPGTGKTMLAKAIAKE----------AGANFINVSVSNLTSKWFGEAQKLVKAVFSLASKL--QPSIIFID  193 (386)
T ss_pred             CCccceecCCCCchHHHHHHHHHHH----------cCCCcceeeccccchhhHHHHHHHHHHHHhhhhhc--Ccceeehh
Confidence            6789999999999999999999987          68899999999999998899999999999999987  79999999


Q ss_pred             ccccc-cccccccccccccchh-hhHHHHHHHhhcccCCCCceEEEEEecCH
Q 003038          306 DLEWA-EFRASSSEQVRGYYCS-IEHIIMEIGKLVCGIGENARFWLMGIATF  355 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~-~~~~~~~~~~ll~~~~g~g~l~lIgatT~  355 (854)
                      |+..+ +.+++..+.    .|. |..-.|-...-|.. .++-+|-++|||+.
T Consensus       194 Evds~L~~R~s~dHE----a~a~mK~eFM~~WDGl~s-~~~~rVlVlgATNR  240 (386)
T KOG0737|consen  194 EVDSFLGQRRSTDHE----ATAMMKNEFMALWDGLSS-KDSERVLVLGATNR  240 (386)
T ss_pred             hHHHHHhhcccchHH----HHHHHHHHHHHHhccccC-CCCceEEEEeCCCC
Confidence            99999 777433221    222 11222222333321 12226999999973

>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=98.87  E-value=7e-09  Score=98.60  Aligned_cols=101  Identities=19%  Similarity=0.225  Sum_probs=70.7

Q ss_pred             EEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCC-CEEEEE
Q 003038          660 LFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNP-HRVFLI  738 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p-~~Vili  738 (854)
                      +||+||+|+|||++|+.+|+.+   ..+++.+++++...       ...      .........+...+.... .+||+|
T Consensus         1 ill~G~~G~GKT~l~~~la~~l---~~~~~~i~~~~~~~-------~~~------~~~~~~i~~~~~~~~~~~~~~vl~i   64 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYL---GFPFIEIDGSELIS-------SYA------GDSEQKIRDFFKKAKKSAKPCVLFI   64 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHT---TSEEEEEETTHHHT-------SST------THHHHHHHHHHHHHHHTSTSEEEEE
T ss_pred             CEEECcCCCCeeHHHHHHHhhc---cccccccccccccc-------ccc------cccccccccccccccccccceeeee
Confidence            5899999999999999999998   46789999886651       100      000011123444444454 699999


Q ss_pred             ecCCCCCHHH-----------HHHHHHhhhcCeEecCCCceeecCCeEEEEecCCCC
Q 003038          739 EDVEQADYCS-----------QKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFS  784 (854)
Q Consensus       739 DEieka~~~v-----------~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~  784 (854)
                      ||+|++-+..           .+.|+..|++..-.        -++.+||+|||..+
T Consensus        65 De~d~l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~--------~~~~~vI~ttn~~~  113 (132)
T PF00004_consen   65 DEIDKLFPKSQPSSSSFEQRLLNQLLSLLDNPSSK--------NSRVIVIATTNSPD  113 (132)
T ss_dssp             ETGGGTSHHCSTSSSHHHHHHHHHHHHHHHTTTTT--------SSSEEEEEEESSGG
T ss_pred             ccchhcccccccccccccccccceeeecccccccc--------cccceeEEeeCChh
Confidence            9999998776           88888888853211        35689999998643

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 ....

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=98.87  E-value=5.2e-09  Score=116.14  Aligned_cols=132  Identities=16%  Similarity=0.211  Sum_probs=81.9

Q ss_pred             ccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc
Q 003038          620 VPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST  699 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~  699 (854)
                      .|||......+...   .                 |-.+.+||+||+|+||+.+|+.+|+.++..... ---.|..+.++
T Consensus         5 yPWl~~~~~~~~~~---~-----------------r~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~-~~~~Cg~C~sC   63 (328)
T PRK05707          5 YPWQQSLWQQLAGR---G-----------------RHPHAYLLHGPAGIGKRALAERLAAALLCEAPQ-GGGACGSCKGC   63 (328)
T ss_pred             CCCcHHHHHHHHHC---C-----------------CcceeeeeECCCCCCHHHHHHHHHHHHcCCCCC-CCCCCCCCHHH
Confidence            58999777776432   1                 335689999999999999999999999754211 00011111111


Q ss_pred             CCCccccccccccCCCC----CCchHH--HHHHHHHcC----CCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          700 RADSTEDSRNKRSRDEQ----SCSYIE--RFAEAVSNN----PHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       700 ~~~s~e~~~~~rl~~~~----g~g~~e--~L~eav~~~----p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      +......|.--..+.+.    ..+.++  .+.+.+...    +++|++||++|+++...+|.|++.||+-          
T Consensus        64 ~~~~~g~HPD~~~i~~~~~~~~i~id~iR~l~~~~~~~~~~~~~kv~iI~~a~~m~~~aaNaLLK~LEEP----------  133 (328)
T PRK05707         64 QLLRAGSHPDNFVLEPEEADKTIKVDQVRELVSFVVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLEEP----------  133 (328)
T ss_pred             HHHhcCCCCCEEEEeccCCCCCCCHHHHHHHHHHHhhccccCCCeEEEECChhhCCHHHHHHHHHHHhCC----------
Confidence            00000111100111111    124443  455555544    4789999999999999999999999972          


Q ss_pred             ecCCeEEEEecCCC
Q 003038          770 SLGDAIVILSCESF  783 (854)
Q Consensus       770 ~~~~aIiIlTsn~f  783 (854)
                       -.+++|||+|+.-
T Consensus       134 -p~~~~fiL~t~~~  146 (328)
T PRK05707        134 -SGDTVLLLISHQP  146 (328)
T ss_pred             -CCCeEEEEEECCh
Confidence             2577899988654

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.87  E-value=1.4e-08  Score=121.39  Aligned_cols=137  Identities=12%  Similarity=0.128  Sum_probs=84.6

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceE-EEccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFV-SIALSSF  696 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i-~id~s~~  696 (854)
                      ..|+||++++..|..++...|.                 ...+||+||+|+|||.+|++||+.+++....-. .-.|..+
T Consensus        16 ~~liGq~~i~~~L~~~l~~~rl-----------------~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg~C   78 (620)
T PRK14948         16 DELVGQEAIATTLKNALISNRI-----------------APAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCGKC   78 (620)
T ss_pred             hhccChHHHHHHHHHHHHcCCC-----------------CceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCccc
Confidence            4689999999999888875321                 247999999999999999999999976321000 0001110


Q ss_pred             cCcCCCcccccc-ccccCCCCCCchHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          697 SSTRADSTEDSR-NKRSRDEQSCSYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       697 ~~~~~~s~e~~~-~~rl~~~~g~g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      ..+.......|. +-.+-.....+..+  .+.+.+..    .+++||+|||+|+++...++.|++.||+-          
T Consensus        79 ~~C~~i~~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEeP----------  148 (620)
T PRK14948         79 ELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEEP----------  148 (620)
T ss_pred             HHHHHHhcCCCccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhcC----------
Confidence            000000000010 00000111113332  34444443    45789999999999999999999999952          


Q ss_pred             ecCCeEEEEecCC
Q 003038          770 SLGDAIVILSCES  782 (854)
Q Consensus       770 ~~~~aIiIlTsn~  782 (854)
                       -.+++|||+|+.
T Consensus       149 -p~~tvfIL~t~~  160 (620)
T PRK14948        149 -PPRVVFVLATTD  160 (620)
T ss_pred             -CcCeEEEEEeCC
Confidence             246788988764

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=98.83  E-value=9.8e-09  Score=106.64  Aligned_cols=117  Identities=9%  Similarity=0.064  Sum_probs=79.9

Q ss_pred             HhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcc
Q 003038          614 NALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIAL  693 (854)
Q Consensus       614 ~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~  693 (854)
                      +.-...|+||++|...- +.|...   +.+|.+..     ...+-.+||+||+|+|||.|||+||...   ..+|+.+..
T Consensus       117 ~it~ddViGqEeAK~kc-rli~~y---LenPe~Fg-----~WAPknVLFyGppGTGKTm~Akalane~---kvp~l~vka  184 (368)
T COG1223         117 DITLDDVIGQEEAKRKC-RLIMEY---LENPERFG-----DWAPKNVLFYGPPGTGKTMMAKALANEA---KVPLLLVKA  184 (368)
T ss_pred             cccHhhhhchHHHHHHH-HHHHHH---hhChHHhc-----ccCcceeEEECCCCccHHHHHHHHhccc---CCceEEech
Confidence            33346799999997653 333332   22332211     1223478999999999999999999866   567888876


Q ss_pred             ccccCcCCCccccccccccCCCCCCchHH--HHHHHHHcCCCEEEEEecCCCCC------------HHHHHHHHHhhh
Q 003038          694 SSFSSTRADSTEDSRNKRSRDEQSCSYIE--RFAEAVSNNPHRVFLIEDVEQAD------------YCSQKGFKRAIE  757 (854)
Q Consensus       694 s~~~~~~~~s~e~~~~~rl~~~~g~g~~e--~L~eav~~~p~~ViliDEieka~------------~~v~~~Ll~~le  757 (854)
                      .+..       ++|-        |-|...  +|++..++...|||||||+|-.-            .++-|+||.-||
T Consensus       185 t~li-------GehV--------Gdgar~Ihely~rA~~~aPcivFiDE~DAiaLdRryQelRGDVsEiVNALLTelD  247 (368)
T COG1223         185 TELI-------GEHV--------GDGARRIHELYERARKAAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELD  247 (368)
T ss_pred             HHHH-------HHHh--------hhHHHHHHHHHHHHHhcCCeEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhcc
Confidence            6554       3331        113333  78888899889999999999652            247788888876

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=98.83  E-value=1.9e-08  Score=114.46  Aligned_cols=135  Identities=11%  Similarity=0.168  Sum_probs=90.4

Q ss_pred             cccccHHHHHHHHHHHHHh--------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEE
Q 003038          619 KVPWQKDTVYDIANTVLKC--------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVS  690 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~--------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~  690 (854)
                      .|.|.++.+..|...|...        ..|+.             +...+||+||+|+|||.+|+++|..+   ...|+.
T Consensus       132 di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~-------------~p~gvLL~GppGtGKT~lAkaia~~~---~~~~i~  195 (389)
T PRK03992        132 DIGGLEEQIREVREAVELPLKKPELFEEVGIE-------------PPKGVLLYGPPGTGKTLLAKAVAHET---NATFIR  195 (389)
T ss_pred             HhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCC-------------CCCceEEECCCCCChHHHHHHHHHHh---CCCEEE
Confidence            4688888888888887542        12222             23468999999999999999999987   356888


Q ss_pred             EccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCC-----------CHHHHHHHHHhhhcC
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQA-----------DYCSQKGFKRAIESG  759 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka-----------~~~v~~~Ll~~le~G  759 (854)
                      ++++++.       ..+     + +.+......+.+..+.+..+||||||||.+           ++.++..|.+.+..-
T Consensus       196 v~~~~l~-------~~~-----~-g~~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~l  262 (389)
T PRK03992        196 VVGSELV-------QKF-----I-GEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEM  262 (389)
T ss_pred             eehHHHh-------Hhh-----c-cchHHHHHHHHHHHHhcCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhc
Confidence            8877654       111     0 000012234566666777799999999986           567788888877541


Q ss_pred             eEecCCCceeecCCeEEEEecCCCCCCCC
Q 003038          760 RIVTSSGDEVSLGDAIVILSCESFSSRSR  788 (854)
Q Consensus       760 ~l~d~~G~~v~~~~aIiIlTsn~f~~~s~  788 (854)
                      .-.      .+..+.+||+|||..+....
T Consensus       263 d~~------~~~~~v~VI~aTn~~~~ld~  285 (389)
T PRK03992        263 DGF------DPRGNVKIIAATNRIDILDP  285 (389)
T ss_pred             ccc------CCCCCEEEEEecCChhhCCH
Confidence            111      12247789999997654433

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.82  E-value=3e-08  Score=110.27  Aligned_cols=135  Identities=21%  Similarity=0.283  Sum_probs=84.4

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC--CceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH--NNFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~--~~~i~id~s~  695 (854)
                      ..++||++++..+..++...                 + ..+++|+||+|+|||++|+++++.+++..  .+++.++++.
T Consensus        15 ~~~~g~~~~~~~L~~~~~~~-----------------~-~~~lll~Gp~GtGKT~la~~~~~~l~~~~~~~~~~~i~~~~   76 (337)
T PRK12402         15 EDILGQDEVVERLSRAVDSP-----------------N-LPHLLVQGPPGSGKTAAVRALARELYGDPWENNFTEFNVAD   76 (337)
T ss_pred             HHhcCCHHHHHHHHHHHhCC-----------------C-CceEEEECCCCCCHHHHHHHHHHHhcCcccccceEEechhh
Confidence            34689999998888776521                 1 23689999999999999999999998653  4678888876


Q ss_pred             ccCcC-CCccccccccccCCCC---CCchHHHHHHHH----Hc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEec
Q 003038          696 FSSTR-ADSTEDSRNKRSRDEQ---SCSYIERFAEAV----SN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVT  763 (854)
Q Consensus       696 ~~~~~-~~s~e~~~~~rl~~~~---g~g~~e~L~eav----~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d  763 (854)
                      +.... ..-.+.....+.....   +....+.+.+.+    +.    .+++||+|||++.+++..++.|+..|++..   
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~~~~~~L~~~le~~~---  153 (337)
T PRK12402         77 FFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALREDAQQALRRIMEQYS---  153 (337)
T ss_pred             hhhcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCHHHHHHHHHHHHhcc---
Confidence            54100 0000000000001000   000112222222    22    346899999999999999999999998531   


Q ss_pred             CCCceeecCCeEEEEecC
Q 003038          764 SSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       764 ~~G~~v~~~~aIiIlTsn  781 (854)
                              .++.||++++
T Consensus       154 --------~~~~~Il~~~  163 (337)
T PRK12402        154 --------RTCRFIIATR  163 (337)
T ss_pred             --------CCCeEEEEeC
Confidence                    2456777775

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=98.82  E-value=1.9e-08  Score=106.20  Aligned_cols=107  Identities=13%  Similarity=0.142  Sum_probs=77.7

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ...+||+++.+.+.-.|...+.    +         ....-++||+||||.|||+||..+|..+ |.  ++.....    
T Consensus        26 ~efiGQ~~vk~~L~ifI~AAk~----r---------~e~lDHvLl~GPPGlGKTTLA~IIA~Em-gv--n~k~tsG----   85 (332)
T COG2255          26 DEFIGQEKVKEQLQIFIKAAKK----R---------GEALDHVLLFGPPGLGKTTLAHIIANEL-GV--NLKITSG----   85 (332)
T ss_pred             HHhcChHHHHHHHHHHHHHHHh----c---------CCCcCeEEeeCCCCCcHHHHHHHHHHHh-cC--CeEeccc----
Confidence            3469999999999888877654    1         1345689999999999999999999999 32  2211111    


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHH-cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVS-NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~-~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                              +.     +..+|     .|...+. -.|+.|+||||||++.+.+...|..+||+.++-
T Consensus        86 --------p~-----leK~g-----DlaaiLt~Le~~DVLFIDEIHrl~~~vEE~LYpaMEDf~lD  133 (332)
T COG2255          86 --------PA-----LEKPG-----DLAAILTNLEEGDVLFIDEIHRLSPAVEEVLYPAMEDFRLD  133 (332)
T ss_pred             --------cc-----ccChh-----hHHHHHhcCCcCCeEEEehhhhcChhHHHHhhhhhhheeEE
Confidence                    00     00111     2333332 367899999999999999999999999997765

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=98.82  E-value=9.6e-09  Score=119.96  Aligned_cols=152  Identities=13%  Similarity=0.129  Sum_probs=112.0

Q ss_pred             HHHHHHHHHHhhc---------cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHH
Q 003038          212 NEDVMYVIENLMS---------KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVE  282 (854)
Q Consensus       212 ~~ei~~v~~~L~r---------~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E  282 (854)
                      .+|+..+++-|.-         +-.+.++|+||||+|||.+++++|-.          .++.|++.+.++|+-+|.|==-
T Consensus       159 keel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgE----------A~VPFf~iSGS~FVemfVGvGA  228 (596)
T COG0465         159 KEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGE----------AGVPFFSISGSDFVEMFVGVGA  228 (596)
T ss_pred             HHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcc----------cCCCceeccchhhhhhhcCCCc
Confidence            4667777777652         34567999999999999999999854          5788999999999999888778


Q ss_pred             HHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhc-cc--CCCCceEEEEEecCHHHH
Q 003038          283 QRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CG--IGENARFWLMGIATFQSY  358 (854)
Q Consensus       283 ~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~--~~g~g~l~lIgatT~~ey  358 (854)
                      .|.++++..+++.  .|||+|||||+.+ ..++.+ .|.++  .--|+   -+..|| ..  ..++..+.+|+||+..+ 
T Consensus       229 sRVRdLF~qAkk~--aP~IIFIDEiDAvGr~Rg~g-~Gggn--derEQ---TLNQlLvEmDGF~~~~gviviaaTNRpd-  299 (596)
T COG0465         229 SRVRDLFEQAKKN--APCIIFIDEIDAVGRQRGAG-LGGGN--DEREQ---TLNQLLVEMDGFGGNEGVIVIAATNRPD-  299 (596)
T ss_pred             HHHHHHHHHhhcc--CCCeEEEehhhhcccccCCC-CCCCc--hHHHH---HHHHHHhhhccCCCCCceEEEecCCCcc-
Confidence            9999999999986  7899999999999 444322 11111  00111   344566 32  23334699999999887 


Q ss_pred             HHhhccCCchhhhhcc-CCCCCCCchHHH
Q 003038          359 MRCKSGHPSLETLWSL-HPLTIPAGSLSL  386 (854)
Q Consensus       359 ~k~~~~~pale~~~~~-~~v~i~~~sl~~  386 (854)
                          .-||||-|--|| ..|.|+-|.+..
T Consensus       300 ----VlD~ALlRpgRFDRqI~V~~PDi~g  324 (596)
T COG0465         300 ----VLDPALLRPGRFDRQILVELPDIKG  324 (596)
T ss_pred             ----cchHhhcCCCCcceeeecCCcchhh
Confidence                469999885455 677887777543

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=98.81  E-value=2.8e-08  Score=102.72  Aligned_cols=113  Identities=15%  Similarity=0.201  Sum_probs=83.0

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLI  738 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vili  738 (854)
                      -+|++||+|+|||.|||++|..-   ...||++..|+|.       .++-      +.|......++...++|..+||||
T Consensus       191 gvllygppg~gktml~kava~~t---~a~firvvgsefv-------qkyl------gegprmvrdvfrlakenapsiifi  254 (408)
T KOG0727|consen  191 GVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFV-------QKYL------GEGPRMVRDVFRLAKENAPSIIFI  254 (408)
T ss_pred             ceEEeCCCCCcHHHHHHHHhhcc---chheeeeccHHHH-------HHHh------ccCcHHHHHHHHHHhccCCcEEEe
Confidence            35778999999999999999864   6789999999987       4432      111123345677778999999999


Q ss_pred             ecCCC-----------CCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCCCCCCCC
Q 003038          739 EDVEQ-----------ADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRACSPP  793 (854)
Q Consensus       739 DEiek-----------a~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~~sp~  793 (854)
                      ||||.           ++.+||..|+..+..-   |+...   -.|.-+||.+|--|....+.=.|
T Consensus       255 deidaiatkrfdaqtgadrevqril~ellnqm---dgfdq---~~nvkvimatnradtldpallrp  314 (408)
T KOG0727|consen  255 DEIDAIATKRFDAQTGADREVQRILIELLNQM---DGFDQ---TTNVKVIMATNRADTLDPALLRP  314 (408)
T ss_pred             ehhhhHhhhhccccccccHHHHHHHHHHHHhc---cCcCc---ccceEEEEecCcccccCHhhcCC
Confidence            99994           6889999999988641   11111   24777999999877776664433

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=98.81  E-value=2.1e-08  Score=121.02  Aligned_cols=136  Identities=11%  Similarity=0.116  Sum_probs=94.9

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      -+++++|+||||+|||++++.++...          ++.++.++.+.+...+.|..+.++++++..++..  .|+|||||
T Consensus       184 ~~~gill~G~~G~GKt~~~~~~a~~~----------~~~f~~is~~~~~~~~~g~~~~~~~~~f~~a~~~--~P~IifID  251 (644)
T PRK10733        184 IPKGVLMVGPPGTGKTLLAKAIAGEA----------KVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKA--APCIIFID  251 (644)
T ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHc----------CCCEEEEehHHhHHhhhcccHHHHHHHHHHHHhc--CCcEEEeh
Confidence            36689999999999999999998763          5689999999888889999999999999999875  79999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhc---ccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCC
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV---CGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIP  380 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll---~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~  380 (854)
                      |++.+ ..+..+..+.   ....+.   -+..+|   ....++..+.+||||+..+     ..||+|-|-=|| ..|.|+
T Consensus       252 EiD~l~~~r~~~~~g~---~~~~~~---~ln~lL~~mdg~~~~~~vivIaaTN~p~-----~lD~Al~RpgRfdr~i~v~  320 (644)
T PRK10733        252 EIDAVGRQRGAGLGGG---HDEREQ---TLNQMLVEMDGFEGNEGIIVIAATNRPD-----VLDPALLRPGRFDRQVVVG  320 (644)
T ss_pred             hHhhhhhccCCCCCCC---chHHHH---HHHHHHHhhhcccCCCCeeEEEecCChh-----hcCHHHhCCcccceEEEcC
Confidence            99999 4433211110   011112   233444   2112233599999999766     468888763234 344455


Q ss_pred             CchH
Q 003038          381 AGSL  384 (854)
Q Consensus       381 ~~sl  384 (854)
                      -|+.
T Consensus       321 ~Pd~  324 (644)
T PRK10733        321 LPDV  324 (644)
T ss_pred             CCCH
Confidence            4443

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.80  E-value=3.2e-08  Score=111.89  Aligned_cols=117  Identities=20%  Similarity=0.236  Sum_probs=80.5

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC-------ceEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN-------NFVS  690 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~-------~~i~  690 (854)
                      +.|+||+.++..+.+.+...                 +....+||+||+|+|||++|+++|+.+++...       ++..
T Consensus        17 ~~iig~~~~~~~l~~~i~~~-----------------~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~   79 (367)
T PRK14970         17 DDVVGQSHITNTLLNAIENN-----------------HLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNI   79 (367)
T ss_pred             HhcCCcHHHHHHHHHHHHcC-----------------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcce
Confidence            45799999999988888642                 22358999999999999999999999975210       1111


Q ss_pred             EccccccCcCCCccccccccccCCCCCCchHH--HHHHHHHcC----CCEEEEEecCCCCCHHHHHHHHHhhhcCeEecC
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSCSYIE--RFAEAVSNN----PHRVFLIEDVEQADYCSQKGFKRAIESGRIVTS  764 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e--~L~eav~~~----p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~  764 (854)
                      +++.                   .....+..+  .+.+.++..    +++||+|||+++++...++.|++.+++.     
T Consensus        80 ~~l~-------------------~~~~~~~~~i~~l~~~~~~~p~~~~~kiviIDE~~~l~~~~~~~ll~~le~~-----  135 (367)
T PRK14970         80 FELD-------------------AASNNSVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLSSAAFNAFLKTLEEP-----  135 (367)
T ss_pred             EEec-------------------cccCCCHHHHHHHHHHHhhccccCCcEEEEEeChhhcCHHHHHHHHHHHhCC-----
Confidence            1110                   000012222  344444433    4689999999999999999999999851     


Q ss_pred             CCceeecCCeEEEEecC
Q 003038          765 SGDEVSLGDAIVILSCE  781 (854)
Q Consensus       765 ~G~~v~~~~aIiIlTsn  781 (854)
                            -.+++||++|+
T Consensus       136 ------~~~~~~Il~~~  146 (367)
T PRK14970        136 ------PAHAIFILATT  146 (367)
T ss_pred             ------CCceEEEEEeC
Confidence                  23678888875

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.78  E-value=2.4e-08  Score=114.73  Aligned_cols=106  Identities=14%  Similarity=0.198  Sum_probs=72.5

Q ss_pred             cccccHHHHHH---HHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          619 KVPWQKDTVYD---IANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       619 ~V~GQ~~av~~---Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      .++||++++..   +...+..                  +...+++|+||+|+|||++|+.||+.+   ...|+.++.+.
T Consensus        13 d~vGq~~~v~~~~~L~~~i~~------------------~~~~~ilL~GppGtGKTtLA~~ia~~~---~~~~~~l~a~~   71 (413)
T PRK13342         13 EVVGQEHLLGPGKPLRRMIEA------------------GRLSSMILWGPPGTGKTTLARIIAGAT---DAPFEALSAVT   71 (413)
T ss_pred             HhcCcHHHhCcchHHHHHHHc------------------CCCceEEEECCCCCCHHHHHHHHHHHh---CCCEEEEeccc
Confidence            47999999876   6666542                  123478999999999999999999977   34677766542


Q ss_pred             ccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeE
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRI  761 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l  761 (854)
                      ..        ...+.        ...+..........+.||||||||++....|+.|+..+++|.+
T Consensus        72 ~~--------~~~ir--------~ii~~~~~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le~~~i  121 (413)
T PRK13342         72 SG--------VKDLR--------EVIEEARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVEDGTI  121 (413)
T ss_pred             cc--------HHHHH--------HHHHHHHHhhhcCCceEEEEechhhhCHHHHHHHHHHhhcCcE
Confidence            11        00000        0111111112234678999999999999999999999997654

>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=98.78  E-value=4.8e-08  Score=93.20  Aligned_cols=129  Identities=13%  Similarity=0.146  Sum_probs=85.4

Q ss_pred             cccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcC
Q 003038          621 PWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTR  700 (854)
Q Consensus       621 ~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~  700 (854)
                      +|++.++..|...+..                  ....+++++||+|+|||.+++.+++.++.....++.++++.+..  
T Consensus         1 ~~~~~~~~~i~~~~~~------------------~~~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~~~~~--   60 (151)
T cd00009           1 VGQEEAIEALREALEL------------------PPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLE--   60 (151)
T ss_pred             CchHHHHHHHHHHHhC------------------CCCCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehhhhhh--
Confidence            4677777777666543                  12347899999999999999999999976667788888775541  


Q ss_pred             CCccccccccccCCCCCCch--HHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEE
Q 003038          701 ADSTEDSRNKRSRDEQSCSY--IERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVIL  778 (854)
Q Consensus       701 ~~s~e~~~~~rl~~~~g~g~--~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIl  778 (854)
                           ........     .+  ..............+|+|||++.+.+.....+++.|+......     ....++.||+
T Consensus        61 -----~~~~~~~~-----~~~~~~~~~~~~~~~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~-----~~~~~~~ii~  125 (151)
T cd00009          61 -----GLVVAELF-----GHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLR-----IDRENVRVIG  125 (151)
T ss_pred             -----hhHHHHHh-----hhhhHhHHHHhhccCCCeEEEEeChhhhhHHHHHHHHHHHHhcCcee-----ccCCCeEEEE
Confidence                 11100000     00  0011122234456899999999999999999999998743321     2346778889


Q ss_pred             ecCCCC
Q 003038          779 SCESFS  784 (854)
Q Consensus       779 Tsn~f~  784 (854)
                      ++|...
T Consensus       126 ~~~~~~  131 (151)
T cd00009         126 ATNRPL  131 (151)
T ss_pred             ecCccc
Confidence            887533

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.

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=98.77  E-value=3.1e-08  Score=116.71  Aligned_cols=142  Identities=11%  Similarity=0.116  Sum_probs=99.5

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++|+..++..+...+.+.-.                ...++|+.|++|+||+.+|++|.........+|+.+||..+.
T Consensus       187 ~~iig~s~~~~~~~~~i~~~a~----------------~~~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~p~v~v~c~~~~  250 (509)
T PRK05022        187 GEMIGQSPAMQQLKKEIEVVAA----------------SDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALP  250 (509)
T ss_pred             CceeecCHHHHHHHHHHHHHhC----------------CCCcEEEECCCCccHHHHHHHHHHhCCcCCCCeEEEEcccCC
Confidence            3699999999999999888522                234789999999999999999999876677899999999886


Q ss_pred             CcCCCccccccccccCCC-CC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCe
Q 003038          698 STRADSTEDSRNKRSRDE-QS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDA  774 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~-~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~a  774 (854)
                      +       ...-+.+.+. .| + |....-...+.......+|||||+.+++.+|..|+++|++|.+.--.|....-.++
T Consensus       251 ~-------~~~e~~lfG~~~g~~~ga~~~~~g~~~~a~gGtL~ldeI~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~  323 (509)
T PRK05022        251 E-------SLAESELFGHVKGAFTGAISNRSGKFELADGGTLFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDV  323 (509)
T ss_pred             h-------HHHHHHhcCccccccCCCcccCCcchhhcCCCEEEecChhhCCHHHHHHHHHHHhcCCEeeCCCCcceecce
Confidence            2       1111111110 00 0 11110011123344678999999999999999999999999886543333333577


Q ss_pred             EEEEecCC
Q 003038          775 IVILSCES  782 (854)
Q Consensus       775 IiIlTsn~  782 (854)
                      .||++|+.
T Consensus       324 RiI~~t~~  331 (509)
T PRK05022        324 RVIAATNR  331 (509)
T ss_pred             EEEEecCC
Confidence            88888863

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=98.77  E-value=1.6e-08  Score=113.83  Aligned_cols=127  Identities=12%  Similarity=0.111  Sum_probs=92.7

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      --+..+|.||||+|||.+++++|-.          .++.|+.+..++|.+.|.||.|.-++.|+.-++..  .|-|+|||
T Consensus       185 p~rglLLfGPpgtGKtmL~~aiAsE----------~~atff~iSassLtsK~~Ge~eK~vralf~vAr~~--qPsvifid  252 (428)
T KOG0740|consen  185 PVRGLLLFGPPGTGKTMLAKAIATE----------SGATFFNISASSLTSKYVGESEKLVRALFKVARSL--QPSVIFID  252 (428)
T ss_pred             ccchhheecCCCCchHHHHHHHHhh----------hcceEeeccHHHhhhhccChHHHHHHHHHHHHHhc--CCeEEEec
Confidence            4456789999999999999999976          47899999999999999999999999999999975  89999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHH-Hhhc-ccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccCCC
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEI-GKLV-CGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPL  377 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~-~~ll-~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v  377 (854)
                      |++.+ ..+....+.    +  ....-++. .... +...+++++.+||||+...     +.|-++.|  |||.+
T Consensus       253 Eidslls~Rs~~e~e----~--srr~ktefLiq~~~~~s~~~drvlvigaTN~P~-----e~Dea~~R--rf~kr  314 (428)
T KOG0740|consen  253 EIDSLLSKRSDNEHE----S--SRRLKTEFLLQFDGKNSAPDDRVLVIGATNRPW-----ELDEAARR--RFVKR  314 (428)
T ss_pred             hhHHHHhhcCCcccc----c--chhhhhHHHhhhccccCCCCCeEEEEecCCCch-----HHHHHHHH--Hhhce
Confidence            99999 655321110    1  11122221 1111 2223456899999998533     46677777  77653

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=98.77  E-value=1.6e-08  Score=104.49  Aligned_cols=143  Identities=13%  Similarity=0.144  Sum_probs=102.2

Q ss_pred             CCCCCCcHHHHHHHHHH------hhc----cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc
Q 003038          205 VSLDPIRNEDVMYVIEN------LMS----KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR  274 (854)
Q Consensus       205 g~ldpvr~~ei~~v~~~------L~r----~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~  274 (854)
                      |.+|- -..||+..++.      |-+    .-.+.++|+||||||||.+|+++|..          ..+.|+.+..+.|+
T Consensus       158 ggld~-qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~----------t~a~firvvgsefv  226 (408)
T KOG0727|consen  158 GGLDV-QKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH----------TTAAFIRVVGSEFV  226 (408)
T ss_pred             ccchh-hHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhc----------cchheeeeccHHHH
Confidence            44443 45566666554      221    35788999999999999999999975          34678999899999


Q ss_pred             ccchHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEE
Q 003038          275 HMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMG  351 (854)
Q Consensus       275 ~~~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIg  351 (854)
                      ..|.||-..-++++|..+++.  .|.|+|||||+.+ -.+-.+   .++..--+.+..+++-|-+.+  ...  .+.+|-
T Consensus       227 qkylgegprmvrdvfrlaken--apsiifideidaiatkrfda---qtgadrevqril~ellnqmdgfdq~~--nvkvim  299 (408)
T KOG0727|consen  227 QKYLGEGPRMVRDVFRLAKEN--APSIIFIDEIDAIATKRFDA---QTGADREVQRILIELLNQMDGFDQTT--NVKVIM  299 (408)
T ss_pred             HHHhccCcHHHHHHHHHHhcc--CCcEEEeehhhhHhhhhccc---cccccHHHHHHHHHHHHhccCcCccc--ceEEEE
Confidence            999999999999999999986  7999999999999 222110   011122244555665555532  223  599999


Q ss_pred             ecCHHHHHHhhccCCchhh
Q 003038          352 IATFQSYMRCKSGHPSLET  370 (854)
Q Consensus       352 atT~~ey~k~~~~~pale~  370 (854)
                      ||+...     ..||||-|
T Consensus       300 atnrad-----tldpallr  313 (408)
T KOG0727|consen  300 ATNRAD-----TLDPALLR  313 (408)
T ss_pred             ecCccc-----ccCHhhcC
Confidence            998765     46899887

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=98.77  E-value=1.7e-08  Score=115.00  Aligned_cols=139  Identities=10%  Similarity=0.178  Sum_probs=105.3

Q ss_pred             hcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          616 LEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       616 L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      ....++|+..++..|-..|.+.-                .....+|+.|++|+||..+||+|-+.--....+||.+||..
T Consensus       139 ~~~~liG~S~am~~l~~~i~kvA----------------~s~a~VLI~GESGtGKElvAr~IH~~S~R~~~PFVavNcaA  202 (464)
T COG2204         139 LGGELVGESPAMQQLRRLIAKVA----------------PSDASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAA  202 (464)
T ss_pred             ccCCceecCHHHHHHHHHHHHHh----------------CCCCCEEEECCCCCcHHHHHHHHHhhCcccCCCceeeeccc
Confidence            45689999999999999988752                23457899999999999999999987666678999999998


Q ss_pred             ccCcCCCccccccccccCCCCCCchHH-HHHHHHH-------cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCc
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIE-RFAEAVS-------NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGD  767 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e-~L~eav~-------~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~  767 (854)
                      +..       .---+.|.     ||.. .++++..       ......+|||||..++.++|..||+++++|.++--.|.
T Consensus       203 ip~-------~l~ESELF-----GhekGAFTGA~~~r~G~fE~A~GGTLfLDEI~~mpl~~Q~kLLRvLqe~~~~rvG~~  270 (464)
T COG2204         203 IPE-------NLLESELF-----GHEKGAFTGAITRRIGRFEQANGGTLFLDEIGEMPLELQVKLLRVLQEREFERVGGN  270 (464)
T ss_pred             CCH-------HHHHHHhh-----cccccCcCCcccccCcceeEcCCceEEeeccccCCHHHHHHHHHHHHcCeeEecCCC
Confidence            872       22112222     2221 2344433       34567899999999999999999999999999975554


Q ss_pred             eeecCCeEEEEecCC
Q 003038          768 EVSLGDAIVILSCES  782 (854)
Q Consensus       768 ~v~~~~aIiIlTsn~  782 (854)
                      +--=-|+.||.+||.
T Consensus       271 ~~i~vdvRiIaaT~~  285 (464)
T COG2204         271 KPIKVDVRIIAATNR  285 (464)
T ss_pred             cccceeeEEEeecCc
Confidence            444447889999873

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=98.76  E-value=3e-08  Score=102.87  Aligned_cols=143  Identities=12%  Similarity=0.121  Sum_probs=103.4

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEe
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      +-.+.++++||||+|||-++++.|..          .++.|+.|-...|+-+|.|+-.+-+++.|..++..  .|+|+||
T Consensus       203 ~pPKGvLmYGPPGTGKTlmARAcAaq----------T~aTFLKLAgPQLVQMfIGdGAkLVRDAFaLAKEk--aP~IIFI  270 (424)
T KOG0652|consen  203 RPPKGVLMYGPPGTGKTLMARACAAQ----------TNATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEK--APTIIFI  270 (424)
T ss_pred             CCCCceEeeCCCCCcHHHHHHHHHHh----------ccchHHHhcchHHHhhhhcchHHHHHHHHHHhhcc--CCeEEEE
Confidence            35567899999999999999998865          35567777777778889999999999999999985  7999999


Q ss_pred             CccccccccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCch
Q 003038          305 GDLEWAEFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGS  383 (854)
Q Consensus       305 del~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~s  383 (854)
                      |||+.+|...-.++..+  .--|.+...++-|-|.+.....++.+|+||+.-.     ..||||-|--|| ..+..|-|.
T Consensus       271 DElDAIGtKRfDSek~G--DREVQRTMLELLNQLDGFss~~~vKviAATNRvD-----iLDPALlRSGRLDRKIEfP~Pn  343 (424)
T KOG0652|consen  271 DELDAIGTKRFDSEKAG--DREVQRTMLELLNQLDGFSSDDRVKVIAATNRVD-----ILDPALLRSGRLDRKIEFPHPN  343 (424)
T ss_pred             echhhhccccccccccc--cHHHHHHHHHHHHhhcCCCCccceEEEeeccccc-----ccCHHHhhcccccccccCCCCC
Confidence            99999943322212111  1224456667777674433345899999998655     468999875455 456666665


Q ss_pred             HHH
Q 003038          384 LSL  386 (854)
Q Consensus       384 l~~  386 (854)
                      -..
T Consensus       344 e~a  346 (424)
T KOG0652|consen  344 EEA  346 (424)
T ss_pred             hHH
Confidence            443

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=98.76  E-value=2e-08  Score=111.62  Aligned_cols=145  Identities=12%  Similarity=0.128  Sum_probs=86.4

Q ss_pred             ccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc
Q 003038          620 VPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST  699 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~  699 (854)
                      .|||..+...+...  +.                 |-.+.+||+||+|+||+.+|+.+|+.+......-..--|..+..+
T Consensus         3 yPW~~~~~~~l~~~--~~-----------------rl~ha~Lf~Gp~G~GK~~lA~~~A~~LlC~~~~~~~~~Cg~C~~C   63 (342)
T PRK06964          3 YPWQTDDWNRLQAL--RA-----------------RLPHALLLHGQAGIGKLDFAQHLAQGLLCETPQPDGEPCGTCAAC   63 (342)
T ss_pred             CcccHHHHHHHHHh--cC-----------------CcceEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCHHH
Confidence            48999988887773  11                 334689999999999999999999999653210000011111100


Q ss_pred             CCCccccccccccCCC------------------------------CCCchHH--HHHHHHHcC----CCEEEEEecCCC
Q 003038          700 RADSTEDSRNKRSRDE------------------------------QSCSYIE--RFAEAVSNN----PHRVFLIEDVEQ  743 (854)
Q Consensus       700 ~~~s~e~~~~~rl~~~------------------------------~g~g~~e--~L~eav~~~----p~~ViliDEiek  743 (854)
                      .......|.--..+.|                              ...+.++  .|.+.+...    .++|++||++|+
T Consensus        64 ~~~~~~~HPD~~~i~p~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~I~idqiR~l~~~~~~~~~~~~~kV~iI~~ae~  143 (342)
T PRK06964         64 NWFAQGNHPDYRIVRPEALAAEAPGAADEAKEADADEGGKKTKAPSKEIKIEQVRALLDFCGVGTHRGGARVVVLYPAEA  143 (342)
T ss_pred             HHHHcCCCCCEEEEecccccccccccccccccchhhcccccccccccccCHHHHHHHHHHhccCCccCCceEEEEechhh
Confidence            0000001100000000                              0113333  455555444    478999999999


Q ss_pred             CCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCCCCC-CCCCCCCc
Q 003038          744 ADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSR-SRACSPPT  794 (854)
Q Consensus       744 a~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~-s~~~sp~~  794 (854)
                      ++....|.||+.+|+           .-.+++|||+|+.-+.. ++.-|.|+
T Consensus       144 m~~~AaNaLLKtLEE-----------Pp~~t~fiL~t~~~~~LLpTI~SRcq  184 (342)
T PRK06964        144 LNVAAANALLKTLEE-----------PPPGTVFLLVSARIDRLLPTILSRCR  184 (342)
T ss_pred             cCHHHHHHHHHHhcC-----------CCcCcEEEEEECChhhCcHHHHhcCE
Confidence            999999999999996           23678899988653333 33345543

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]

Probab=98.75  E-value=3.2e-08  Score=111.45  Aligned_cols=135  Identities=15%  Similarity=0.233  Sum_probs=106.8

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .||||..|+..+...|..--                +....+|++|.|||||.-+||+|-++---..++||.+||..+. 
T Consensus       224 ~iIG~S~am~~ll~~i~~VA----------------~Sd~tVLi~GETGtGKElvAraIH~~S~R~~kPfV~~NCAAlP-  286 (550)
T COG3604         224 GIIGRSPAMRQLLKEIEVVA----------------KSDSTVLIRGETGTGKELVARAIHQLSPRRDKPFVKLNCAALP-  286 (550)
T ss_pred             cceecCHHHHHHHHHHHHHh----------------cCCCeEEEecCCCccHHHHHHHHHhhCcccCCCceeeeccccc-
Confidence            68999999999998887631                2345789999999999999999999887788999999999887 


Q ss_pred             cCCCccccccccccCCCCCCchHH-HHHHHHHcCCC-------EEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceee
Q 003038          699 TRADSTEDSRNKRSRDEQSCSYIE-RFAEAVSNNPH-------RVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVS  770 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~g~g~~e-~L~eav~~~p~-------~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~  770 (854)
                            +.---+.|.     ||.. .++.|++.++.       .-+|+|||--++..+|-.||+++++|.|.-=.|...-
T Consensus       287 ------esLlESELF-----GHeKGAFTGA~~~r~GrFElAdGGTLFLDEIGelPL~lQaKLLRvLQegEieRvG~~r~i  355 (550)
T COG3604         287 ------ESLLESELF-----GHEKGAFTGAINTRRGRFELADGGTLFLDEIGELPLALQAKLLRVLQEGEIERVGGDRTI  355 (550)
T ss_pred             ------hHHHHHHHh-----cccccccccchhccCcceeecCCCeEechhhccCCHHHHHHHHHHHhhcceeecCCCcee
Confidence                  222222222     4443 57888887764       4699999999999999999999999999864443333


Q ss_pred             cCCeEEEEecC
Q 003038          771 LGDAIVILSCE  781 (854)
Q Consensus       771 ~~~aIiIlTsn  781 (854)
                      --|+.||..||
T Consensus       356 kVDVRiIAATN  366 (550)
T COG3604         356 KVDVRVIAATN  366 (550)
T ss_pred             EEEEEEEeccc
Confidence            33678999998

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

Probab=98.74  E-value=1.5e-08  Score=109.36  Aligned_cols=121  Identities=17%  Similarity=0.190  Sum_probs=74.7

Q ss_pred             ccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc-ccchHHHHHHHHHHHHHHHhhhCCCeEE
Q 003038          224 SKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR-HMNRVEVEQRVEEIKNLVRSCLGRGIVL  302 (854)
Q Consensus       224 r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~-~~~rge~E~rl~~l~~~~~~~~~~~~IL  302 (854)
                      ..+-+..||.||||||||++++-++.--.+       ...+|++++...-. ...|+-||+--++. .+    .++..||
T Consensus       159 q~~ipSmIlWGppG~GKTtlArlia~tsk~-------~SyrfvelSAt~a~t~dvR~ife~aq~~~-~l----~krkTil  226 (554)
T KOG2028|consen  159 QNRIPSMILWGPPGTGKTTLARLIASTSKK-------HSYRFVELSATNAKTNDVRDIFEQAQNEK-SL----TKRKTIL  226 (554)
T ss_pred             cCCCCceEEecCCCCchHHHHHHHHhhcCC-------CceEEEEEeccccchHHHHHHHHHHHHHH-hh----hcceeEE
Confidence            367888999999999999999988854222       23567777644221 12455554332211 11    1467999


Q ss_pred             EeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhh---hhccCCCC
Q 003038          303 NLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLET---LWSLHPLT  378 (854)
Q Consensus       303 fidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~---~~~~~~v~  378 (854)
                      ||||||.+ .....                    .+|+. -.+|.|.+|||||.+.-.   ..+.+|-.   +|-|.+++
T Consensus       227 FiDEiHRFNksQQD--------------------~fLP~-VE~G~I~lIGATTENPSF---qln~aLlSRC~VfvLekL~  282 (554)
T KOG2028|consen  227 FIDEIHRFNKSQQD--------------------TFLPH-VENGDITLIGATTENPSF---QLNAALLSRCRVFVLEKLP  282 (554)
T ss_pred             EeHHhhhhhhhhhh--------------------cccce-eccCceEEEecccCCCcc---chhHHHHhccceeEeccCC
Confidence            99999999 55431                    24433 334579999999987643   34555543   23344444


Q ss_pred             CC
Q 003038          379 IP  380 (854)
Q Consensus       379 i~  380 (854)
                      +.
T Consensus       283 ~n  284 (554)
T KOG2028|consen  283 VN  284 (554)
T ss_pred             HH
Confidence            43

>CHL00195 ycf46 Ycf46; Provisional

Probab=98.74  E-value=5e-08  Score=113.40  Aligned_cols=102  Identities=13%  Similarity=0.137  Sum_probs=68.2

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLI  738 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vili  738 (854)
                      -+||+||+|||||.+|+++|..+   ..+|++++++.+.       ...     .+. ......++....+....+||||
T Consensus       261 GILL~GPpGTGKTllAkaiA~e~---~~~~~~l~~~~l~-------~~~-----vGe-se~~l~~~f~~A~~~~P~IL~I  324 (489)
T CHL00195        261 GLLLVGIQGTGKSLTAKAIANDW---QLPLLRLDVGKLF-------GGI-----VGE-SESRMRQMIRIAEALSPCILWI  324 (489)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHh---CCCEEEEEhHHhc-------ccc-----cCh-HHHHHHHHHHHHHhcCCcEEEe
Confidence            57899999999999999999987   4689999987554       110     000 0011124555556667799999


Q ss_pred             ecCCCCCH------------HHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCC
Q 003038          739 EDVEQADY------------CSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRS  787 (854)
Q Consensus       739 DEieka~~------------~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s  787 (854)
                      ||||++-.            .+.+.|+..|++.           -++.+||.|||..+...
T Consensus       325 DEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~-----------~~~V~vIaTTN~~~~Ld  374 (489)
T CHL00195        325 DEIDKAFSNSESKGDSGTTNRVLATFITWLSEK-----------KSPVFVVATANNIDLLP  374 (489)
T ss_pred             hhhhhhhccccCCCCchHHHHHHHHHHHHHhcC-----------CCceEEEEecCChhhCC
Confidence            99997633            2445566666531           13567889999765543

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=98.74  E-value=3.5e-08  Score=109.75  Aligned_cols=141  Identities=13%  Similarity=0.179  Sum_probs=96.7

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++|++.++..+...+.+.-                +...++|+.|++|+||+.+|++|...-.....+|+.+||..+.
T Consensus         6 ~~liG~S~~~~~~~~~i~~~a----------------~~~~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~~~   69 (326)
T PRK11608          6 DNLLGEANSFLEVLEQVSRLA----------------PLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALN   69 (326)
T ss_pred             CccEECCHHHHHHHHHHHHHh----------------CCCCCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCCCC
Confidence            458999999998888888752                1234789999999999999999987665556899999999775


Q ss_pred             CcCCCccccccccccCC-CCC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCe
Q 003038          698 STRADSTEDSRNKRSRD-EQS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDA  774 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~-~~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~a  774 (854)
                      +       ......+.+ ..+ + |....-...+.......+|||||+.+++.+|..|+++|++|.+.-..|...--.++
T Consensus        70 ~-------~~~~~~lfg~~~~~~~g~~~~~~g~l~~a~gGtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~  142 (326)
T PRK11608         70 E-------NLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNV  142 (326)
T ss_pred             H-------HHHHHHHccccccccCCcccccCCchhccCCCeEEeCChhhCCHHHHHHHHHHHhcCcEEeCCCCceeeccE
Confidence            1       110011111 000 0 11111112233445678999999999999999999999999887543332222478


Q ss_pred             EEEEecC
Q 003038          775 IVILSCE  781 (854)
Q Consensus       775 IiIlTsn  781 (854)
                      .||+||+
T Consensus       143 RiI~~s~  149 (326)
T PRK11608        143 RLVCATN  149 (326)
T ss_pred             EEEEeCc
Confidence            8888875

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=98.73  E-value=3e-08  Score=116.37  Aligned_cols=135  Identities=16%  Similarity=0.195  Sum_probs=96.6

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHH--------hCCCCceEE
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLV--------FGSHNNFVS  690 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~l--------fg~~~~~i~  690 (854)
                      .++|+..++..+...+.+.-                +...++|+.|++|+||+.+|++|-..+        .....+|+.
T Consensus       220 ~iiG~S~~m~~~~~~i~~~A----------------~s~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~  283 (538)
T PRK15424        220 DLLGQSPQMEQVRQTILLYA----------------RSSAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVA  283 (538)
T ss_pred             heeeCCHHHHHHHHHHHHHh----------------CCCCcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEE
Confidence            48999999999998888752                223578999999999999999999873        335679999


Q ss_pred             EccccccCcCCCccccccccccCCCCCCchHH-HHHH--------HHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeE
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSCSYIE-RFAE--------AVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRI  761 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e-~L~e--------av~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l  761 (854)
                      +||+.+.       +...-+.+.     ||.+ .++.        .+.......+|||||+.+++.+|..|+++|+++.+
T Consensus       284 inCaal~-------e~lleseLF-----G~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp~~~Q~kLl~~L~e~~~  351 (538)
T PRK15424        284 VNCGAIA-------ESLLEAELF-----GYEEGAFTGSRRGGRAGLFEIAHGGTLFLDEIGEMPLPLQTRLLRVLEEKEV  351 (538)
T ss_pred             eecccCC-------hhhHHHHhc-----CCccccccCccccccCCchhccCCCEEEEcChHhCCHHHHHHHHhhhhcCeE
Confidence            9999876       211111111     1111 1111        22344567999999999999999999999999998


Q ss_pred             ecCCCceeecCCeEEEEecC
Q 003038          762 VTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       762 ~d~~G~~v~~~~aIiIlTsn  781 (854)
                      +--.|...---|+.||++||
T Consensus       352 ~r~G~~~~~~~dvRiIaat~  371 (538)
T PRK15424        352 TRVGGHQPVPVDVRVISATH  371 (538)
T ss_pred             EecCCCceeccceEEEEecC
Confidence            75444333234677888775

>PHA02244 ATPase-like protein

Probab=98.73  E-value=1.5e-07  Score=104.42  Aligned_cols=110  Identities=18%  Similarity=0.212  Sum_probs=77.8

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHH-HHHHHHHcCCCEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIE-RFAEAVSNNPHRVFL  737 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e-~L~eav~~~p~~Vil  737 (854)
                      .+||.||+|||||.+|++||..+   ..+|++++.  ..       +...+...+...+ .+.+ .|+.++++  ..+++
T Consensus       121 PVLL~GppGtGKTtLA~aLA~~l---g~pfv~In~--l~-------d~~~L~G~i~~~g-~~~dgpLl~A~~~--GgvLi  185 (383)
T PHA02244        121 PVFLKGGAGSGKNHIAEQIAEAL---DLDFYFMNA--IM-------DEFELKGFIDANG-KFHETPFYEAFKK--GGLFF  185 (383)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh---CCCEEEEec--Ch-------HHHhhcccccccc-cccchHHHHHhhc--CCEEE
Confidence            57889999999999999999986   356887762  22       1111111111111 2222 57777654  57999


Q ss_pred             EecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCC
Q 003038          738 IEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       738 iDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                      ||||+.++++++..|..+++++.+.-..++...-.+..||+|+|..
T Consensus       186 LDEId~a~p~vq~~L~~lLd~r~l~l~g~~i~~h~~FRlIATsN~~  231 (383)
T PHA02244        186 IDEIDASIPEALIIINSAIANKFFDFADERVTAHEDFRVISAGNTL  231 (383)
T ss_pred             EeCcCcCCHHHHHHHHHHhccCeEEecCcEEecCCCEEEEEeeCCC
Confidence            9999999999999999999998777554443344788999999963

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=98.72  E-value=9.5e-08  Score=98.72  Aligned_cols=143  Identities=13%  Similarity=0.116  Sum_probs=109.9

Q ss_pred             hhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeE
Q 003038          222 LMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIV  301 (854)
Q Consensus       222 L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~I  301 (854)
                      |.-...+.++|+||||+|||-+++++|..          ..+.|+.++.+.|+-.|.||--.-+++||--++.+  .|.|
T Consensus       176 LGIaQPKGvlLygppgtGktLlaraVahh----------t~c~firvsgselvqk~igegsrmvrelfvmareh--apsi  243 (404)
T KOG0728|consen  176 LGIAQPKGVLLYGPPGTGKTLLARAVAHH----------TDCTFIRVSGSELVQKYIGEGSRMVRELFVMAREH--APSI  243 (404)
T ss_pred             cCCCCCcceEEecCCCCchhHHHHHHHhh----------cceEEEEechHHHHHHHhhhhHHHHHHHHHHHHhc--CCce
Confidence            44447788999999999999999999975          57899999999999999999999999999999998  7999


Q ss_pred             EEeCccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCC
Q 003038          302 LNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPL  377 (854)
Q Consensus       302 Lfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v  377 (854)
                      +|+|||+.+ ..+..++.   +..+-+.+...++-|-|..  +..  .+.+|-||+.=.     ..||||-|--|. ..+
T Consensus       244 ifmdeidsigs~r~e~~~---ggdsevqrtmlellnqldgfeatk--nikvimatnrid-----ild~allrpgridrki  313 (404)
T KOG0728|consen  244 IFMDEIDSIGSSRVESGS---GGDSEVQRTMLELLNQLDGFEATK--NIKVIMATNRID-----ILDPALLRPGRIDRKI  313 (404)
T ss_pred             EeeecccccccccccCCC---CccHHHHHHHHHHHHhcccccccc--ceEEEEeccccc-----cccHhhcCCCcccccc
Confidence            999999999 44432211   1234456677777777743  333  599999997533     468998874444 567


Q ss_pred             CCCCchHHH
Q 003038          378 TIPAGSLSL  386 (854)
Q Consensus       378 ~i~~~sl~~  386 (854)
                      ..|+|+.++
T Consensus       314 efp~p~e~a  322 (404)
T KOG0728|consen  314 EFPPPNEEA  322 (404)
T ss_pred             cCCCCCHHH
Confidence            777776554

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.72  E-value=9.9e-08  Score=104.94  Aligned_cols=106  Identities=13%  Similarity=0.124  Sum_probs=72.7

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +.++||++++..|...+...+..             .++..+++|+||+|+|||.+|+++|+.+-   ..+..++.+...
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~~-------------~~~~~~~ll~Gp~G~GKT~la~~ia~~~~---~~~~~~~~~~~~   67 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKMR-------------QEALDHLLLYGPPGLGKTTLAHIIANEMG---VNLKITSGPALE   67 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHhc-------------CCCCCeEEEECCCCCCHHHHHHHHHHHhC---CCEEEeccchhc
Confidence            35799999999988887654321             12234789999999999999999999872   123222221111


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHc-CCCEEEEEecCCCCCHHHHHHHHHhhhcCeE
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSN-NPHRVFLIEDVEQADYCSQKGFKRAIESGRI  761 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~-~p~~ViliDEieka~~~v~~~Ll~~le~G~l  761 (854)
                                       ..  +   .+.+.+.. ....|+|||||+++++..++.|+.+|++++.
T Consensus        68 -----------------~~--~---~l~~~l~~~~~~~vl~iDEi~~l~~~~~e~l~~~~~~~~~  110 (305)
T TIGR00635        68 -----------------KP--G---DLAAILTNLEEGDVLFIDEIHRLSPAVEELLYPAMEDFRL  110 (305)
T ss_pred             -----------------Cc--h---hHHHHHHhcccCCEEEEehHhhhCHHHHHHhhHHHhhhhe
Confidence                             00  1   12222222 3457999999999999999999999998764

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=98.72  E-value=1.1e-07  Score=105.80  Aligned_cols=128  Identities=12%  Similarity=0.123  Sum_probs=83.7

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++||++++..+...+...+..             ..+...++|+||+|+|||++|+.+|+.+ +  ..+..++.+.+.
T Consensus        25 ~~~vG~~~~~~~l~~~l~~~~~~-------------~~~~~~~ll~GppG~GKT~la~~ia~~l-~--~~~~~~~~~~~~   88 (328)
T PRK00080         25 DEFIGQEKVKENLKIFIEAAKKR-------------GEALDHVLLYGPPGLGKTTLANIIANEM-G--VNIRITSGPALE   88 (328)
T ss_pred             HHhcCcHHHHHHHHHHHHHHHhc-------------CCCCCcEEEECCCCccHHHHHHHHHHHh-C--CCeEEEeccccc
Confidence            34799999999988888665331             1344588999999999999999999988 2  233333322111


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEec--CCC---cee--e
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVT--SSG---DEV--S  770 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d--~~G---~~v--~  770 (854)
                                       ..  +....+...+  .+..||||||||++++..++.|+.+|++.++..  ..|   +.+  .
T Consensus        89 -----------------~~--~~l~~~l~~l--~~~~vl~IDEi~~l~~~~~e~l~~~~e~~~~~~~l~~~~~~~~~~~~  147 (328)
T PRK00080         89 -----------------KP--GDLAAILTNL--EEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAARSIRLD  147 (328)
T ss_pred             -----------------Ch--HHHHHHHHhc--ccCCEEEEecHhhcchHHHHHHHHHHHhcceeeeeccCccccceeec
Confidence                             00  1111122222  356899999999999999999999999876431  111   222  2


Q ss_pred             cCCeEEEEecCC
Q 003038          771 LGDAIVILSCES  782 (854)
Q Consensus       771 ~~~aIiIlTsn~  782 (854)
                      ....++|+++|.
T Consensus       148 l~~~~li~at~~  159 (328)
T PRK00080        148 LPPFTLIGATTR  159 (328)
T ss_pred             CCCceEEeecCC
Confidence            345667777764

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=98.70  E-value=3.1e-08  Score=119.93  Aligned_cols=142  Identities=10%  Similarity=0.098  Sum_probs=96.9

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++|++.++..+...+.+.-                +...++||.|++|+||+.+|++|.........+|+.+||..+.
T Consensus       325 ~~l~g~s~~~~~~~~~~~~~a----------------~~~~pvli~Ge~GtGK~~~A~~ih~~s~r~~~pfv~vnc~~~~  388 (638)
T PRK11388        325 DHMPQDSPQMRRLIHFGRQAA----------------KSSFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYP  388 (638)
T ss_pred             cceEECCHHHHHHHHHHHHHh----------------CcCCCEEEECCCCcCHHHHHHHHHHhCCccCCCeEEEECCCCC
Confidence            468999988887777766642                1234689999999999999999999877677899999999876


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEE
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVI  777 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiI  777 (854)
                             +....+.+.+....+........+.......+|||||+.+++.+|..|+++|++|.++...|...---++.||
T Consensus       389 -------~~~~~~elfg~~~~~~~~~~~g~~~~a~~GtL~ldei~~l~~~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI  461 (638)
T PRK11388        389 -------DEALAEEFLGSDRTDSENGRLSKFELAHGGTLFLEKVEYLSPELQSALLQVLKTGVITRLDSRRLIPVDVRVI  461 (638)
T ss_pred             -------hHHHHHHhcCCCCcCccCCCCCceeECCCCEEEEcChhhCCHHHHHHHHHHHhcCcEEeCCCCceEEeeEEEE
Confidence                   2111111221000000000011233445789999999999999999999999999988543322222256788


Q ss_pred             EecCC
Q 003038          778 LSCES  782 (854)
Q Consensus       778 lTsn~  782 (854)
                      +||+.
T Consensus       462 ~~t~~  466 (638)
T PRK11388        462 ATTTA  466 (638)
T ss_pred             EeccC
Confidence            88763

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=98.70  E-value=8.9e-08  Score=105.13  Aligned_cols=121  Identities=11%  Similarity=0.124  Sum_probs=82.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCC-CchHH-HHHHHHHcCCCEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQS-CSYIE-RFAEAVSNNPHRVF  736 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g-~g~~e-~L~eav~~~p~~Vi  736 (854)
                      .+||.||+|+|||++|+.||+.+   ..++++++++......+.-+ .... .+..+.. ..|.+ .|..+.++  ..++
T Consensus        66 ~ilL~G~pGtGKTtla~~lA~~l---~~~~~rV~~~~~l~~~DliG-~~~~-~l~~g~~~~~f~~GpL~~A~~~--g~il  138 (327)
T TIGR01650        66 RVMVQGYHGTGKSTHIEQIAARL---NWPCVRVNLDSHVSRIDLVG-KDAI-VLKDGKQITEFRDGILPWALQH--NVAL  138 (327)
T ss_pred             cEEEEeCCCChHHHHHHHHHHHH---CCCeEEEEecCCCChhhcCC-Ccee-eccCCcceeEEecCcchhHHhC--CeEE
Confidence            58999999999999999999999   46889999886552111110 0000 0000000 01111 35555543  3689


Q ss_pred             EEecCCCCCHHHHHHHHHhhh-cCeEec-CCCceeecC-CeEEEEecCCCCCC
Q 003038          737 LIEDVEQADYCSQKGFKRAIE-SGRIVT-SSGDEVSLG-DAIVILSCESFSSR  786 (854)
Q Consensus       737 liDEieka~~~v~~~Ll~~le-~G~l~d-~~G~~v~~~-~aIiIlTsn~f~~~  786 (854)
                      |||||+.++|++++.|..++| +|.++- ..|+.+.-. +-.+|.|.|..++.
T Consensus       139 llDEin~a~p~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~g~G  191 (327)
T TIGR01650       139 CFDEYDAGRPDVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANTIGLG  191 (327)
T ss_pred             EechhhccCHHHHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCCCCcC
Confidence            999999999999999999999 567775 456777554 77899999976543

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.

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]

Probab=98.69  E-value=2.5e-08  Score=104.99  Aligned_cols=127  Identities=13%  Similarity=0.117  Sum_probs=95.3

Q ss_pred             hccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEE
Q 003038          223 MSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVL  302 (854)
Q Consensus       223 ~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~IL  302 (854)
                      .-+-.+.++|+|+||+|||-+++++|..          -.+.|+.+--+.|+-.|.|+-.+-+++||.-+..+  .|.|+
T Consensus       215 GikpPKGVIlyG~PGTGKTLLAKAVANq----------TSATFlRvvGseLiQkylGdGpklvRqlF~vA~e~--apSIv  282 (440)
T KOG0726|consen  215 GIKPPKGVILYGEPGTGKTLLAKAVANQ----------TSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEH--APSIV  282 (440)
T ss_pred             CCCCCCeeEEeCCCCCchhHHHHHHhcc----------cchhhhhhhhHHHHHHHhccchHHHHHHHHHHHhc--CCceE
Confidence            3356778999999999999999999965          34577777777788889999999999999999987  79999


Q ss_pred             EeCccccc-ccc-ccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhh
Q 003038          303 NLGDLEWA-EFR-ASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLET  370 (854)
Q Consensus       303 fidel~~l-~~~-~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~  370 (854)
                      |||||+.+ ..+ .+.++|..    -+.+...++-|-|...-.||++.+|-||+-=+     ..||||-|
T Consensus       283 FiDEIdAiGtKRyds~Sgger----EiQrtmLELLNQldGFdsrgDvKvimATnrie-----~LDPaLiR  343 (440)
T KOG0726|consen  283 FIDEIDAIGTKRYDSNSGGER----EIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-----TLDPALIR  343 (440)
T ss_pred             EeehhhhhccccccCCCccHH----HHHHHHHHHHHhccCccccCCeEEEEeccccc-----ccCHhhcC
Confidence            99999999 322 22222211    23355567666664422245799999998544     46888887

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=98.68  E-value=1.7e-08  Score=106.59  Aligned_cols=121  Identities=15%  Similarity=0.146  Sum_probs=76.9

Q ss_pred             CcHHHHHHHHHHhhccCc-C-----CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHH
Q 003038          210 IRNEDVMYVIENLMSKRK-R-----NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQ  283 (854)
Q Consensus       210 vr~~ei~~v~~~L~r~~k-~-----n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~  283 (854)
                      +.++.++.-+++.-+-.| |     +++|+||||.|||+++.-+|..+          |+.+...         .|-.=+
T Consensus        29 iGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Em----------gvn~k~t---------sGp~le   89 (332)
T COG2255          29 IGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANEL----------GVNLKIT---------SGPALE   89 (332)
T ss_pred             cChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHh----------cCCeEec---------cccccc
Confidence            367888888888754422 2     48999999999999999999875          2333332         233334


Q ss_pred             HHHHHHHHHHhhhCCCeEEEeCccccc-ccccccccccccc-chhhhHHHHHHHhhccc-CCCC----ceEEEEEecCHH
Q 003038          284 RVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGY-YCSIEHIIMEIGKLVCG-IGEN----ARFWLMGIATFQ  356 (854)
Q Consensus       284 rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~-~~~~~~~~~~~~~ll~~-~~g~----g~l~lIgatT~~  356 (854)
                      |-.+|...+... ..+.||||||||.+ ..       ..+. |.+||.-..|+----+| ++.-    ..|++|||||-.
T Consensus        90 K~gDlaaiLt~L-e~~DVLFIDEIHrl~~~-------vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLppFTLIGATTr~  161 (332)
T COG2255          90 KPGDLAAILTNL-EEGDVLFIDEIHRLSPA-------VEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPPFTLIGATTRA  161 (332)
T ss_pred             ChhhHHHHHhcC-CcCCeEEEehhhhcChh-------HHHHhhhhhhheeEEEEEccCCccceEeccCCCeeEeeecccc
Confidence            555566666554 56889999999999 43       1232 66666654442111122 2110    259999999954


Q ss_pred             H
Q 003038          357 S  357 (854)
Q Consensus       357 e  357 (854)
                      -
T Consensus       162 G  162 (332)
T COG2255         162 G  162 (332)
T ss_pred             c
Confidence            3

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=98.68  E-value=1.3e-07  Score=104.57  Aligned_cols=116  Identities=15%  Similarity=0.149  Sum_probs=80.4

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..+...+...                 +....+||+||+|+|||++|+++++.+ +  ..++.++++. .
T Consensus        21 ~~~~~~~~~~~~l~~~~~~~-----------------~~~~~lll~G~~G~GKT~la~~l~~~~-~--~~~~~i~~~~-~   79 (316)
T PHA02544         21 DECILPAADKETFKSIVKKG-----------------RIPNMLLHSPSPGTGKTTVAKALCNEV-G--AEVLFVNGSD-C   79 (316)
T ss_pred             HHhcCcHHHHHHHHHHHhcC-----------------CCCeEEEeeCcCCCCHHHHHHHHHHHh-C--ccceEeccCc-c
Confidence            35799999999888777631                 223577889999999999999999987 2  3566666543 1


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHc----CCCEEEEEecCCCC-CHHHHHHHHHhhhcCeEecCCCceeecC
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSN----NPHRVFLIEDVEQA-DYCSQKGFKRAIESGRIVTSSGDEVSLG  772 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~----~p~~ViliDEieka-~~~v~~~Ll~~le~G~l~d~~G~~v~~~  772 (854)
                             .   ..        ...+.+.+....    .+++||+|||+|++ ..+.++.|+..+++.           -+
T Consensus        80 -------~---~~--------~i~~~l~~~~~~~~~~~~~~vliiDe~d~l~~~~~~~~L~~~le~~-----------~~  130 (316)
T PHA02544         80 -------R---ID--------FVRNRLTRFASTVSLTGGGKVIIIDEFDRLGLADAQRHLRSFMEAY-----------SK  130 (316)
T ss_pred             -------c---HH--------HHHHHHHHHHHhhcccCCCeEEEEECcccccCHHHHHHHHHHHHhc-----------CC
Confidence                   0   00        000112222221    35789999999999 778899999889852           14


Q ss_pred             CeEEEEecCCC
Q 003038          773 DAIVILSCESF  783 (854)
Q Consensus       773 ~aIiIlTsn~f  783 (854)
                      ++.||+|||..
T Consensus       131 ~~~~Ilt~n~~  141 (316)
T PHA02544        131 NCSFIITANNK  141 (316)
T ss_pred             CceEEEEcCCh
Confidence            67899999854

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

Probab=98.68  E-value=2.6e-08  Score=107.60  Aligned_cols=90  Identities=17%  Similarity=0.262  Sum_probs=61.2

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHH-HHHHHHHcCCCEE
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIE-RFAEAVSNNPHRV  735 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e-~L~eav~~~p~~V  735 (854)
                      +.+++|+||+|+|||+|||.||..--...-.||.+....-.           ....+     +..+ .-.+...-+...|
T Consensus       162 ipSmIlWGppG~GKTtlArlia~tsk~~SyrfvelSAt~a~-----------t~dvR-----~ife~aq~~~~l~krkTi  225 (554)
T KOG2028|consen  162 IPSMILWGPPGTGKTTLARLIASTSKKHSYRFVELSATNAK-----------TNDVR-----DIFEQAQNEKSLTKRKTI  225 (554)
T ss_pred             CCceEEecCCCCchHHHHHHHHhhcCCCceEEEEEeccccc-----------hHHHH-----HHHHHHHHHHhhhcceeE
Confidence            56899999999999999999998653333346655433111           00000     1111 1111112244689


Q ss_pred             EEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          736 FLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       736 iliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                      +|||||++.....|+.||..+|+|.++
T Consensus       226 lFiDEiHRFNksQQD~fLP~VE~G~I~  252 (554)
T KOG2028|consen  226 LFIDEIHRFNKSQQDTFLPHVENGDIT  252 (554)
T ss_pred             EEeHHhhhhhhhhhhcccceeccCceE
Confidence            999999999999999999999999887

>PRK04195 replication factor C large subunit; Provisional

Probab=98.67  E-value=1.6e-07  Score=110.10  Aligned_cols=117  Identities=16%  Similarity=0.193  Sum_probs=81.2

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .|+||++++..|...+.....|              ++...+||+||+|+|||++|++||+.+ |  -.++.++.+.+. 
T Consensus        15 dlvg~~~~~~~l~~~l~~~~~g--------------~~~~~lLL~GppG~GKTtla~ala~el-~--~~~ielnasd~r-   76 (482)
T PRK04195         15 DVVGNEKAKEQLREWIESWLKG--------------KPKKALLLYGPPGVGKTSLAHALANDY-G--WEVIELNASDQR-   76 (482)
T ss_pred             HhcCCHHHHHHHHHHHHHHhcC--------------CCCCeEEEECCCCCCHHHHHHHHHHHc-C--CCEEEEcccccc-
Confidence            3799999999999988765432              234589999999999999999999988 2  457777776543 


Q ss_pred             cCCCccccccccccCCCCCCchHHHHHHHHH-----cCCCEEEEEecCCCCCH----HHHHHHHHhhhcCeEecCCCcee
Q 003038          699 TRADSTEDSRNKRSRDEQSCSYIERFAEAVS-----NNPHRVFLIEDVEQADY----CSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~-----~~p~~ViliDEieka~~----~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                            ....+.+.           +.++..     ..++.||+|||+|.++.    ..++.|++.+++.          
T Consensus        77 ------~~~~i~~~-----------i~~~~~~~sl~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~~~----------  129 (482)
T PRK04195         77 ------TADVIERV-----------AGEAATSGSLFGARRKLILLDEVDGIHGNEDRGGARAILELIKKA----------  129 (482)
T ss_pred             ------cHHHHHHH-----------HHHhhccCcccCCCCeEEEEecCcccccccchhHHHHHHHHHHcC----------
Confidence                  11111111           111111     13678999999999876    6788899999853          


Q ss_pred             ecCCeEEEEecCCC
Q 003038          770 SLGDAIVILSCESF  783 (854)
Q Consensus       770 ~~~~aIiIlTsn~f  783 (854)
                         +.-|||+||..
T Consensus       130 ---~~~iIli~n~~  140 (482)
T PRK04195        130 ---KQPIILTANDP  140 (482)
T ss_pred             ---CCCEEEeccCc
Confidence               22377778753

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=98.67  E-value=5.4e-08  Score=114.28  Aligned_cols=135  Identities=16%  Similarity=0.202  Sum_probs=96.9

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .++|+..++..+...+.+.-                +...++|+.|++|+||+.+|+.|...-.....+|+.+||..+. 
T Consensus       213 ~iiG~S~~m~~~~~~i~~~A----------------~~~~pVLI~GE~GTGKe~lA~~IH~~S~r~~~pfv~inC~~l~-  275 (526)
T TIGR02329       213 DLLGASAPMEQVRALVRLYA----------------RSDATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIA-  275 (526)
T ss_pred             heeeCCHHHHHHHHHHHHHh----------------CCCCcEEEECCCCcCHHHHHHHHHHhcCcCCCCEEEeccccCC-
Confidence            48999999999888887652                2235789999999999999999988766677899999999876 


Q ss_pred             cCCCccccccccccCCCCCCchHH-HHH--------HHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          699 TRADSTEDSRNKRSRDEQSCSYIE-RFA--------EAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~g~g~~e-~L~--------eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                            +...-+.+.     ||.+ .++        ..+.......+|||||+.+++.+|..|+++|+++.++.-.|...
T Consensus       276 ------e~lleseLF-----G~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp~~~Q~~Ll~~L~~~~~~r~g~~~~  344 (526)
T TIGR02329       276 ------ESLLEAELF-----GYEEGAFTGARRGGRTGLIEAAHRGTLFLDEIGEMPLPLQTRLLRVLEEREVVRVGGTEP  344 (526)
T ss_pred             ------hhHHHHHhc-----CCcccccccccccccccchhhcCCceEEecChHhCCHHHHHHHHHHHhcCcEEecCCCce
Confidence                  211111111     1111 111        11223446789999999999999999999999998875444333


Q ss_pred             ecCCeEEEEecC
Q 003038          770 SLGDAIVILSCE  781 (854)
Q Consensus       770 ~~~~aIiIlTsn  781 (854)
                      ---|+.||++|+
T Consensus       345 ~~~dvRiIaat~  356 (526)
T TIGR02329       345 VPVDVRVVAATH  356 (526)
T ss_pred             eeecceEEeccC
Confidence            334677888775

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=98.67  E-value=1.6e-07  Score=114.76  Aligned_cols=141  Identities=11%  Similarity=0.148  Sum_probs=98.9

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .++|+..++..+...+.+.-.                ...++|+.|++|+|||.+|++|...-.....+|+.+||..+..
T Consensus       377 ~liG~S~~~~~~~~~~~~~a~----------------~~~pVLI~GE~GTGK~~lA~~ih~~s~r~~~~~v~i~c~~~~~  440 (686)
T PRK15429        377 EIIGRSEAMYSVLKQVEMVAQ----------------SDSTVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPA  440 (686)
T ss_pred             ceeecCHHHHHHHHHHHHHhC----------------CCCCEEEECCCCcCHHHHHHHHHHhcCCCCCCeEEEecccCCh
Confidence            699999999888888776421                2347899999999999999999987766678999999987651


Q ss_pred             cCCCccccccccccCC-CCC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeE
Q 003038          699 TRADSTEDSRNKRSRD-EQS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAI  775 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~-~~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aI  775 (854)
                             ....+.+.+ ..+ + |....-...+.....+++|||||+.+++++|..|+++|++|.+....+...-..++.
T Consensus       441 -------~~~~~~lfg~~~~~~~g~~~~~~g~le~a~~GtL~Ldei~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~R  513 (686)
T PRK15429        441 -------GLLESDLFGHERGAFTGASAQRIGRFELADKSSLFLDEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVR  513 (686)
T ss_pred             -------hHhhhhhcCcccccccccccchhhHHHhcCCCeEEEechhhCCHHHHHHHHHHHHhCCEEeCCCCCcccceEE
Confidence                   110111111 000 1 111111122334456899999999999999999999999998876444444446788


Q ss_pred             EEEecCC
Q 003038          776 VILSCES  782 (854)
Q Consensus       776 iIlTsn~  782 (854)
                      ||+||+.
T Consensus       514 iI~~t~~  520 (686)
T PRK15429        514 LIAATNR  520 (686)
T ss_pred             EEEeCCC
Confidence            9998863

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.67  E-value=6.7e-08  Score=100.60  Aligned_cols=138  Identities=12%  Similarity=0.089  Sum_probs=102.0

Q ss_pred             cHHHHHHHHHHhh-------------ccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccc
Q 003038          211 RNEDVMYVIENLM-------------SKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMN  277 (854)
Q Consensus       211 r~~ei~~v~~~L~-------------r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~  277 (854)
                      ..++|.++-++..             -.-.+.++|+||||+|||-.++++|.|          .++-|+.+=-+.|+..|
T Consensus       182 ckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanr----------tdacfirvigselvqky  251 (435)
T KOG0729|consen  182 CKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANR----------TDACFIRVIGSELVQKY  251 (435)
T ss_pred             hHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcc----------cCceEEeehhHHHHHHH
Confidence            5666666655522             124567999999999999999999988          46788888788888889


Q ss_pred             hHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecC
Q 003038          278 RVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIAT  354 (854)
Q Consensus       278 rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT  354 (854)
                      .||-..-+++||+-++..  +-||+|+|||+.+ |++-..  |.+ ...-+.+...++-+-|..  .||  .+.++-||+
T Consensus       252 vgegarmvrelf~martk--kaciiffdeidaiggarfdd--g~g-gdnevqrtmleli~qldgfdprg--nikvlmatn  324 (435)
T KOG0729|consen  252 VGEGARMVRELFEMARTK--KACIIFFDEIDAIGGARFDD--GAG-GDNEVQRTMLELINQLDGFDPRG--NIKVLMATN  324 (435)
T ss_pred             hhhhHHHHHHHHHHhccc--ceEEEEeeccccccCccccC--CCC-CcHHHHHHHHHHHHhccCCCCCC--CeEEEeecC
Confidence            999999999999999874  7899999999999 765321  111 122345566676666643  456  599998887


Q ss_pred             HHHHHHhhccCCchhh
Q 003038          355 FQSYMRCKSGHPSLET  370 (854)
Q Consensus       355 ~~ey~k~~~~~pale~  370 (854)
                      ...     ..||||-|
T Consensus       325 rpd-----tldpallr  335 (435)
T KOG0729|consen  325 RPD-----TLDPALLR  335 (435)
T ss_pred             CCC-----CcCHhhcC
Confidence            433     36888877

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=98.67  E-value=5.8e-08  Score=114.55  Aligned_cols=142  Identities=12%  Similarity=0.088  Sum_probs=96.1

Q ss_pred             cCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          617 EKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       617 ~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      ...++|+..++..+...+.+.-.                ...++|++|++|+||+.+|+++...-.....+|+.+||+.+
T Consensus       203 f~~~ig~s~~~~~~~~~~~~~A~----------------~~~pvlI~GE~GtGK~~lA~aiH~~s~r~~~pfv~inca~~  266 (520)
T PRK10820        203 FSQIVAVSPKMRQVVEQARKLAM----------------LDAPLLITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASI  266 (520)
T ss_pred             ccceeECCHHHHHHHHHHHHHhC----------------CCCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeccccC
Confidence            34789999888877777665421                13368999999999999999998877667789999999987


Q ss_pred             cCcCCCccccccccccCC-CCC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCC
Q 003038          697 SSTRADSTEDSRNKRSRD-EQS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGD  773 (854)
Q Consensus       697 ~~~~~~s~e~~~~~rl~~-~~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~  773 (854)
                      .       +...-+.+.+ .+| + |..+.-...+.......+|||||+.+++.+|..|+++|++|.++...+...--.+
T Consensus       267 ~-------~~~~e~elFG~~~~~~~~~~~~~~g~~e~a~~GtL~LdeI~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~  339 (520)
T PRK10820        267 P-------DDVVESELFGHAPGAYPNALEGKKGFFEQANGGSVLLDEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVD  339 (520)
T ss_pred             C-------HHHHHHHhcCCCCCCcCCcccCCCChhhhcCCCEEEEeChhhCCHHHHHHHHHHHhcCCcccCCCCcceeee
Confidence            6       2111111111 010 0 1101001122334467899999999999999999999999988754433333346


Q ss_pred             eEEEEecC
Q 003038          774 AIVILSCE  781 (854)
Q Consensus       774 aIiIlTsn  781 (854)
                      +.||+||+
T Consensus       340 vRiI~st~  347 (520)
T PRK10820        340 VRVICATQ  347 (520)
T ss_pred             eEEEEecC
Confidence            77888775

>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes

Probab=98.66  E-value=4.5e-08  Score=78.77  Aligned_cols=52  Identities=27%  Similarity=0.397  Sum_probs=47.4

Q ss_pred             HHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHh
Q 003038           23 AMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVAL   77 (854)
Q Consensus        23 A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L   77 (854)
                      |+++|++++|.+|+++|||++|+.++++.+.++|+++|+++   +.++..++..+
T Consensus         1 A~~~A~~~~~~~i~~eHlL~all~~~~~~~~~il~~~~id~---~~l~~~i~~~l   52 (53)
T PF02861_consen    1 AQELARERGHQYISPEHLLLALLEDPDSIAARILKKLGIDP---EQLKAAIEKAL   52 (53)
T ss_dssp             HHHHHHHTTBSSE-HHHHHHHHHHHTTSHHHHHHHHTTCHH---HHHHHHHHHHH
T ss_pred             CHHHHHHcCCCcccHHHHHHHHHhhhhHHHHHHHHHcCCCH---HHHHHHHHHHh
Confidence            78999999999999999999999999999999999999986   78888888765

The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.65  E-value=1.3e-07  Score=96.77  Aligned_cols=116  Identities=19%  Similarity=0.198  Sum_probs=68.7

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCC--CCchHH--HHHHHHHc-
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQ--SCSYIE--RFAEAVSN-  730 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~--g~g~~e--~L~eav~~-  730 (854)
                      ....+||+||+|+|||++|+.+|+.+++....-. ..+..+..+.......|.--..+.+.  ..+..+  .+.+.+.. 
T Consensus        13 ~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~-~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i~~i~~~~~~~   91 (188)
T TIGR00678        13 LAHAYLFAGPEGVGKELLALALAKALLCEQPGGG-EPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQVRELVEFLSRT   91 (188)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCC-CCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHHHHHHHHHccC
Confidence            3468999999999999999999999986421000 00000000000000000000001111  113333  34555554 


Q ss_pred             ---CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCC
Q 003038          731 ---NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       731 ---~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                         .+++||+|||+|+++...++.|+..||+.           -.+++|||+++..
T Consensus        92 ~~~~~~kviiide~~~l~~~~~~~Ll~~le~~-----------~~~~~~il~~~~~  136 (188)
T TIGR00678        92 PQESGRRVVIIEDAERMNEAAANALLKTLEEP-----------PPNTLFILITPSP  136 (188)
T ss_pred             cccCCeEEEEEechhhhCHHHHHHHHHHhcCC-----------CCCeEEEEEECCh
Confidence               45789999999999999999999999862           1467888888643

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.

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=98.65  E-value=1.3e-07  Score=107.64  Aligned_cols=134  Identities=13%  Similarity=0.130  Sum_probs=85.2

Q ss_pred             cccccHHHHHHHHHHHHHh--------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEE
Q 003038          619 KVPWQKDTVYDIANTVLKC--------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVS  690 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~--------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~  690 (854)
                      .|.|.+..+..|..+|...        +.|+.             |...+||+||+|+|||.+|+++|..+   ...|++
T Consensus       146 digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~-------------~pkgvLL~GppGTGKT~LAkalA~~l---~~~fi~  209 (398)
T PTZ00454        146 DIGGLDIQKQEIREAVELPLTCPELYEQIGID-------------PPRGVLLYGPPGTGKTMLAKAVAHHT---TATFIR  209 (398)
T ss_pred             HcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCC-------------CCceEEEECCCCCCHHHHHHHHHHhc---CCCEEE
Confidence            4789999999988888532        22332             23367889999999999999999987   356788


Q ss_pred             EccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCC-----------CHHHHHHHHHhhhcC
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQA-----------DYCSQKGFKRAIESG  759 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka-----------~~~v~~~Ll~~le~G  759 (854)
                      +..+++.       .++     + +.+......+....+.+..+||||||||.+           +..++..+.+.+..-
T Consensus       210 i~~s~l~-------~k~-----~-ge~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~l  276 (398)
T PTZ00454        210 VVGSEFV-------QKY-----L-GEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQM  276 (398)
T ss_pred             EehHHHH-------HHh-----c-chhHHHHHHHHHHHHhcCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHh
Confidence            8766543       111     1 000012234555666667799999999965           345666666665431


Q ss_pred             eEecCCCceeecCCeEEEEecCCCCCCC
Q 003038          760 RIVTSSGDEVSLGDAIVILSCESFSSRS  787 (854)
Q Consensus       760 ~l~d~~G~~v~~~~aIiIlTsn~f~~~s  787 (854)
                         |..   -.-.+.+||+|||..+...
T Consensus       277 ---d~~---~~~~~v~VI~aTN~~d~LD  298 (398)
T PTZ00454        277 ---DGF---DQTTNVKVIMATNRADTLD  298 (398)
T ss_pred             ---hcc---CCCCCEEEEEecCCchhCC
Confidence               000   0124678999998655443

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=98.64  E-value=5.1e-08  Score=108.17  Aligned_cols=134  Identities=13%  Similarity=0.133  Sum_probs=81.5

Q ss_pred             ccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc
Q 003038          620 VPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST  699 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~  699 (854)
                      .|||..+...+...  .   |              |-.+.+||.||+|+||+.+|+.+|+.+......--...|..+.++
T Consensus         3 yPW~~~~w~~l~~~--~---~--------------r~~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C   63 (325)
T PRK08699          3 YPWHQEQWRQIAEH--W---E--------------RRPNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSC   63 (325)
T ss_pred             CCccHHHHHHHHHh--c---C--------------CcceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHH
Confidence            48999888887765  1   1              234689999999999999999999998642210000011111110


Q ss_pred             CCCccccccccccCCC------CC-----CchHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          700 RADSTEDSRNKRSRDE------QS-----CSYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       700 ~~~s~e~~~~~rl~~~------~g-----~g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                      .......|.--..+.|      .|     .+.++  .+.+.+...|    ++||++|+++.+++..++.|++.||+..  
T Consensus        64 ~~~~~~~HpD~~~~~p~~~~~~~g~~~~~I~id~iR~l~~~~~~~p~~~~~kV~iiEp~~~Ld~~a~naLLk~LEep~--  141 (325)
T PRK08699         64 HLFGQGSHPDFYEITPLSDEPENGRKLLQIKIDAVREIIDNVYLTSVRGGLRVILIHPAESMNLQAANSLLKVLEEPP--  141 (325)
T ss_pred             HHHhcCCCCCEEEEecccccccccccCCCcCHHHHHHHHHHHhhCcccCCceEEEEechhhCCHHHHHHHHHHHHhCc--
Confidence            0000011110001111      11     13433  5666666544    6899999999999999999999999741  


Q ss_pred             cCCCceeecCCeEEEEecCCC
Q 003038          763 TSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       763 d~~G~~v~~~~aIiIlTsn~f  783 (854)
                               .+++||++|...
T Consensus       142 ---------~~~~~Ilvth~~  153 (325)
T PRK08699        142 ---------PQVVFLLVSHAA  153 (325)
T ss_pred             ---------CCCEEEEEeCCh
Confidence                     246677777543

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

Probab=98.63  E-value=1.7e-07  Score=106.58  Aligned_cols=142  Identities=15%  Similarity=0.226  Sum_probs=93.3

Q ss_pred             hhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          615 ALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       615 ~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      .+. .+++-++.++.+..++..                    ...++|+||+|+|||++|+.||..+.+. ..+.++++-
T Consensus       173 ~l~-d~~i~e~~le~l~~~L~~--------------------~~~iil~GppGtGKT~lA~~la~~l~~~-~~~~~v~~V  230 (459)
T PRK11331        173 ALN-DLFIPETTIETILKRLTI--------------------KKNIILQGPPGVGKTFVARRLAYLLTGE-KAPQRVNMV  230 (459)
T ss_pred             Hhh-cccCCHHHHHHHHHHHhc--------------------CCCEEEECCCCCCHHHHHHHHHHHhcCC-cccceeeEE
Confidence            344 367777777777666552                    1268899999999999999999998764 455667766


Q ss_pred             cccCcCCCccccccccccCC--CCCC-chH------HHHHHHHHcCC--CEEEEEecCCCCCHH-HHHHHHHhhhcCe--
Q 003038          695 SFSSTRADSTEDSRNKRSRD--EQSC-SYI------ERFAEAVSNNP--HRVFLIEDVEQADYC-SQKGFKRAIESGR--  760 (854)
Q Consensus       695 ~~~~~~~~s~e~~~~~rl~~--~~g~-g~~------e~L~eav~~~p--~~ViliDEieka~~~-v~~~Ll~~le~G~--  760 (854)
                      .|.       ..++...++.  .|++ ||.      -++....+++|  ..||+||||++++.. ++..+++.||.+.  
T Consensus       231 tFH-------psySYeDFI~G~rP~~vgy~~~~G~f~~~~~~A~~~p~~~~vliIDEINRani~kiFGel~~lLE~~~rg  303 (459)
T PRK11331        231 QFH-------QSYSYEDFIQGYRPNGVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINRANLSKVFGEVMMLMEHDKRG  303 (459)
T ss_pred             eec-------ccccHHHHhcccCCCCCCeEecCchHHHHHHHHHhcccCCcEEEEehhhccCHHHhhhhhhhhccccccc
Confidence            665       3333333331  1222 332      13444555555  579999999999965 7999999999641  


Q ss_pred             ----E--e--cCCCceee-cCCeEEEEecCCCCC
Q 003038          761 ----I--V--TSSGDEVS-LGDAIVILSCESFSS  785 (854)
Q Consensus       761 ----l--~--d~~G~~v~-~~~aIiIlTsn~f~~  785 (854)
                          +  .  ...++.+. -.|..||.|.|.-|.
T Consensus       304 ~~~~v~l~y~e~d~e~f~iP~Nl~IIgTMNt~Dr  337 (459)
T PRK11331        304 ENWSVPLTYSENDEERFYVPENVYIIGLMNTADR  337 (459)
T ss_pred             cccceeeeccccccccccCCCCeEEEEecCcccc
Confidence                1  1  11122232 479999999998763

>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=98.62  E-value=9.8e-08  Score=98.16  Aligned_cols=141  Identities=13%  Similarity=0.218  Sum_probs=80.8

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||+.++..+--+..    |                .+.+||.||+|+|||.+|+.|+..|=    .+..-.+-+..
T Consensus         3 ~dI~GQe~aKrAL~iAAa----G----------------~h~lLl~GppGtGKTmlA~~l~~lLP----~l~~~e~le~~   58 (206)
T PF01078_consen    3 SDIVGQEEAKRALEIAAA----G----------------GHHLLLIGPPGTGKTMLARRLPSLLP----PLTEEEALEVS   58 (206)
T ss_dssp             CCSSSTHHHHHHHHHHHH----C----------------C--EEEES-CCCTHHHHHHHHHHCS------CCEECCESS-
T ss_pred             hhhcCcHHHHHHHHHHHc----C----------------CCCeEEECCCCCCHHHHHHHHHHhCC----CCchHHHhhhc
Confidence            579999988887665544    2                24799999999999999999998772    22222222211


Q ss_pred             CcCCCcc--ccccc--cccC-CCCCCchHHHH--------HHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecC
Q 003038          698 STRADST--EDSRN--KRSR-DEQSCSYIERF--------AEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTS  764 (854)
Q Consensus       698 ~~~~~s~--e~~~~--~rl~-~~~g~g~~e~L--------~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~  764 (854)
                      .-.+...  .....  .+.. .+...-....|        ...|....+.|+||||+-..++.+.+.|++.+++|+++-.
T Consensus        59 ~i~s~~~~~~~~~~~~~~Pfr~phhs~s~~~liGgg~~~~PGeislAh~GVLflDE~~ef~~~vld~Lr~ple~g~v~i~  138 (206)
T PF01078_consen   59 KIYSVAGLGPDEGLIRQRPFRAPHHSASEAALIGGGRPPRPGEISLAHRGVLFLDELNEFDRSVLDALRQPLEDGEVTIS  138 (206)
T ss_dssp             -S-TT---S---EEEE---EEEE-TT--HHHHHEEGGGEEE-CGGGGTTSEEEECETTTS-HHHHHHHHHHHHHSBEEEE
T ss_pred             cccccccCCCCCceecCCCcccCCCCcCHHHHhCCCcCCCcCHHHHhcCCEEEechhhhcCHHHHHHHHHHHHCCeEEEE
Confidence            1000000  00000  0000 01100000111        1124445678999999999999999999999999999864


Q ss_pred             -CCceeec-CCeEEEEecCC
Q 003038          765 -SGDEVSL-GDAIVILSCES  782 (854)
Q Consensus       765 -~G~~v~~-~~aIiIlTsn~  782 (854)
                       .|..+.| .+-++|.|.|.
T Consensus       139 R~~~~~~~Pa~f~lv~a~NP  158 (206)
T PF01078_consen  139 RAGGSVTYPARFLLVAAMNP  158 (206)
T ss_dssp             ETTEEEEEB--EEEEEEE-S
T ss_pred             ECCceEEEecccEEEEEecc
Confidence             4566665 58899999985

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.

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.62  E-value=6.2e-08  Score=108.77  Aligned_cols=137  Identities=11%  Similarity=0.164  Sum_probs=96.0

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhC-CCCceEEEccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFG-SHNNFVSIALSSF  696 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg-~~~~~i~id~s~~  696 (854)
                      ..+||.+.....+.+.|.+.    . |           -.-.+|+.|++|+||+.+|++|...--. ...+||++||..|
T Consensus        78 ~~LIG~~~~~~~~~eqik~~----a-p-----------~~~~vLi~GetGtGKel~A~~iH~~s~r~~~~PFI~~NCa~~  141 (403)
T COG1221          78 DDLIGESPSLQELREQIKAY----A-P-----------SGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAY  141 (403)
T ss_pred             hhhhccCHHHHHHHHHHHhh----C-C-----------CCCcEEEecCCCccHHHHHHHHHHhhhcccCCCEEEEEHHHh
Confidence            45799997777777766651    1 1           1236899999999999999999943323 3679999999999


Q ss_pred             cCcCCCccccccccccCCCCCCchHH-HHHH-------HHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCce
Q 003038          697 SSTRADSTEDSRNKRSRDEQSCSYIE-RFAE-------AVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDE  768 (854)
Q Consensus       697 ~~~~~~s~e~~~~~rl~~~~g~g~~e-~L~e-------av~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~  768 (854)
                      ++       ....+.+.     ||.+ .++.       .+.......+|+|||..+++..|..|+++||+|.++-=.|..
T Consensus       142 ~e-------n~~~~eLF-----G~~kGaftGa~~~k~Glfe~A~GGtLfLDEI~~LP~~~Q~kLl~~le~g~~~rvG~~~  209 (403)
T COG1221         142 SE-------NLQEAELF-----GHEKGAFTGAQGGKAGLFEQANGGTLFLDEIHRLPPEGQEKLLRVLEEGEYRRVGGSQ  209 (403)
T ss_pred             Cc-------CHHHHHHh-----ccccceeecccCCcCchheecCCCEEehhhhhhCCHhHHHHHHHHHHcCceEecCCCC
Confidence            83       22222221     2221 1222       233344679999999999999999999999999999544444


Q ss_pred             eecCCeEEEEecCC
Q 003038          769 VSLGDAIVILSCES  782 (854)
Q Consensus       769 v~~~~aIiIlTsn~  782 (854)
                      +--.|+.+|+.++.
T Consensus       210 ~~~~dVRli~AT~~  223 (403)
T COG1221         210 PRPVDVRLICATTE  223 (403)
T ss_pred             CcCCCceeeecccc
Confidence            55567788887763

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=98.62  E-value=2.7e-07  Score=101.70  Aligned_cols=115  Identities=21%  Similarity=0.335  Sum_probs=78.8

Q ss_pred             ccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC--ceEEEcccccc
Q 003038          620 VPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN--NFVSIALSSFS  697 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~--~~i~id~s~~~  697 (854)
                      ++||++++..+...+...                 + ...++|+||+|+|||.+++.+++.+++...  .++.++.+...
T Consensus        19 ~~g~~~~~~~l~~~i~~~-----------------~-~~~~ll~G~~G~GKt~~~~~l~~~l~~~~~~~~~i~~~~~~~~   80 (319)
T PRK00440         19 IVGQEEIVERLKSYVKEK-----------------N-MPHLLFAGPPGTGKTTAALALARELYGEDWRENFLELNASDER   80 (319)
T ss_pred             hcCcHHHHHHHHHHHhCC-----------------C-CCeEEEECCCCCCHHHHHHHHHHHHcCCccccceEEecccccc
Confidence            679999999888877531                 1 124799999999999999999999987542  23333322111


Q ss_pred             CcCCCccccccccccCCCCCCch-HHHHHHHHHc-----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeec
Q 003038          698 STRADSTEDSRNKRSRDEQSCSY-IERFAEAVSN-----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSL  771 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~-~e~L~eav~~-----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~  771 (854)
                                         +... .+.+.+..+.     .+++||+|||+|.++.+.++.|+++++...           
T Consensus        81 -------------------~~~~~~~~i~~~~~~~~~~~~~~~vviiDe~~~l~~~~~~~L~~~le~~~-----------  130 (319)
T PRK00440         81 -------------------GIDVIRNKIKEFARTAPVGGAPFKIIFLDEADNLTSDAQQALRRTMEMYS-----------  130 (319)
T ss_pred             -------------------chHHHHHHHHHHHhcCCCCCCCceEEEEeCcccCCHHHHHHHHHHHhcCC-----------
Confidence                               0111 1233333332     346799999999999999999999998531           


Q ss_pred             CCeEEEEecCC
Q 003038          772 GDAIVILSCES  782 (854)
Q Consensus       772 ~~aIiIlTsn~  782 (854)
                      .+++|||+||.
T Consensus       131 ~~~~lIl~~~~  141 (319)
T PRK00440        131 QNTRFILSCNY  141 (319)
T ss_pred             CCCeEEEEeCC
Confidence            34678888864

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=98.62  E-value=1.7e-07  Score=101.58  Aligned_cols=118  Identities=15%  Similarity=0.187  Sum_probs=76.1

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCC----CchHH--HHHHHHHc
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQS----CSYIE--RFAEAVSN  730 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g----~g~~e--~L~eav~~  730 (854)
                      .+.+||.||+|+||+.+|.++|+.++.....-   .+..+..      ..|.--..+.|.+    .+.++  .+.+.+..
T Consensus        19 ~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~---~c~~~~~------~~HPD~~~i~p~~~~~~I~idqiR~l~~~~~~   89 (290)
T PRK05917         19 PSAIILHGQDLSNLSARAYELASLILKETSPE---AAYKISQ------KIHPDIHEFSPQGKGRLHSIETPRAIKKQIWI   89 (290)
T ss_pred             CeeEeeECCCCCcHHHHHHHHHHHHhCCCCcc---HHHHHhc------CCCCCEEEEecCCCCCcCcHHHHHHHHHHHhh
Confidence            56899999999999999999999998643220   1110100      1111000111211    13333  45555555


Q ss_pred             CC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCCCCC-CCCCCCCc
Q 003038          731 NP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSR-SRACSPPT  794 (854)
Q Consensus       731 ~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~-s~~~sp~~  794 (854)
                      .|    ++|++||++|+++.+.+|+||+.||+           .-.+++|||.|+.-+.. ++..|.|+
T Consensus        90 ~p~e~~~kv~ii~~ad~mt~~AaNaLLK~LEE-----------Pp~~~~fiL~~~~~~~ll~TI~SRcq  147 (290)
T PRK05917         90 HPYESPYKIYIIHEADRMTLDAISAFLKVLED-----------PPQHGVIILTSAKPQRLPPTIRSRSL  147 (290)
T ss_pred             CccCCCceEEEEechhhcCHHHHHHHHHHhhc-----------CCCCeEEEEEeCChhhCcHHHHhcce
Confidence            44    69999999999999999999999997           34678899988653333 34445553

>KOG0651 consensus 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones]

Probab=98.61  E-value=1.1e-07  Score=101.29  Aligned_cols=121  Identities=15%  Similarity=0.107  Sum_probs=94.7

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCccc
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLE  308 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfidel~  308 (854)
                      -++|+||||+|||-+++.+|..+          |+.++.+..+.|.++|-||...-+++.+..++.+  .|||||+|||+
T Consensus       168 g~ll~GppGtGKTlla~~Vaa~m----------g~nfl~v~ss~lv~kyiGEsaRlIRemf~yA~~~--~pciifmdeiD  235 (388)
T KOG0651|consen  168 GLLLYGPPGTGKTLLARAVAATM----------GVNFLKVVSSALVDKYIGESARLIRDMFRYAREV--IPCIIFMDEID  235 (388)
T ss_pred             eeEEeCCCCCchhHHHHHHHHhc----------CCceEEeeHhhhhhhhcccHHHHHHHHHHHHhhh--CceEEeehhhh
Confidence            46899999999999999999875          7889999999999999999999999999999998  78999999999


Q ss_pred             cc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecCHHHHHHhhccCCchhhh
Q 003038          309 WA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIATFQSYMRCKSGHPSLETL  371 (854)
Q Consensus       309 ~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT~~ey~k~~~~~pale~~  371 (854)
                      .+ |..-+  + .+...--+...-|++.+-+-.  ..+  ++-+|-||+--.     .-||+|-|-
T Consensus       236 AigGRr~s--e-~Ts~dreiqrTLMeLlnqmdgfd~l~--rVk~ImatNrpd-----tLdpaLlRp  291 (388)
T KOG0651|consen  236 AIGGRRFS--E-GTSSDREIQRTLMELLNQMDGFDTLH--RVKTIMATNRPD-----TLDPALLRP  291 (388)
T ss_pred             hhccEEec--c-ccchhHHHHHHHHHHHHhhccchhcc--cccEEEecCCcc-----ccchhhcCC
Confidence            99 66532  1 122222345677777776632  333  699999997432     257888763

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=98.59  E-value=1.5e-07  Score=106.43  Aligned_cols=142  Identities=11%  Similarity=0.109  Sum_probs=85.4

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|.|.++.+..|...|.....   ++....  ...-.+...+||+||+|+|||.+|+++|..+.   ..|+++..+++.
T Consensus       122 ~di~Gl~~~~~~l~~~i~~~~~---~~~~~~--~~g~~~p~gvLL~GppGtGKT~lakaia~~l~---~~~~~v~~~~l~  193 (364)
T TIGR01242       122 EDIGGLEEQIREIREAVELPLK---HPELFE--EVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN---ATFIRVVGSELV  193 (364)
T ss_pred             HHhCChHHHHHHHHHHHHHHhc---CHHHHH--hcCCCCCceEEEECCCCCCHHHHHHHHHHhCC---CCEEecchHHHH
Confidence            3578999999999888864311   100000  00001223588999999999999999999873   457776654332


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCC-----------CHHHHHHHHHhhhcCeEecCCC
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQA-----------DYCSQKGFKRAIESGRIVTSSG  766 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka-----------~~~v~~~Ll~~le~G~l~d~~G  766 (854)
                             ..+     + +.+......+.+..+.+..+||||||||.+           ++.++..|.+.+..-.-.    
T Consensus       194 -------~~~-----~-g~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~----  256 (364)
T TIGR01242       194 -------RKY-----I-GEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGF----  256 (364)
T ss_pred             -------HHh-----h-hHHHHHHHHHHHHHHhcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCC----
Confidence                   110     0 000012224555556666689999999986           456777777777531000    


Q ss_pred             ceeecCCeEEEEecCCCCCC
Q 003038          767 DEVSLGDAIVILSCESFSSR  786 (854)
Q Consensus       767 ~~v~~~~aIiIlTsn~f~~~  786 (854)
                        ....+.+||+|||..+..
T Consensus       257 --~~~~~v~vI~ttn~~~~l  274 (364)
T TIGR01242       257 --DPRGNVKVIAATNRPDIL  274 (364)
T ss_pred             --CCCCCEEEEEecCChhhC
Confidence              112477899999865443

Many proteins may score above the trusted cutoff because an internal

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

Probab=98.59  E-value=1.3e-07  Score=96.96  Aligned_cols=119  Identities=15%  Similarity=0.263  Sum_probs=83.9

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC--CCceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS--HNNFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~--~~~~i~id~s~  695 (854)
                      ..|+|.++.|..+.-....                  .-...++|.||||+|||+.+.+||+.|.|.  .+.++.+|.|.
T Consensus        27 ~dIVGNe~tv~rl~via~~------------------gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASd   88 (333)
T KOG0991|consen   27 QDIVGNEDTVERLSVIAKE------------------GNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASD   88 (333)
T ss_pred             HHhhCCHHHHHHHHHHHHc------------------CCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCcc
Confidence            3479999888876544332                  223489999999999999999999999984  34555555542


Q ss_pred             ccCcCCCccccccccccCCCCCCchHH-HHHHH----HH--cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCce
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIE-RFAEA----VS--NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDE  768 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e-~L~ea----v~--~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~  768 (854)
                      --                   |-.... ++.-.    |.  ...|.||++||.|.|....|.+|.+.||           
T Consensus        89 eR-------------------GIDvVRn~IK~FAQ~kv~lp~grhKIiILDEADSMT~gAQQAlRRtME-----------  138 (333)
T KOG0991|consen   89 ER-------------------GIDVVRNKIKMFAQKKVTLPPGRHKIIILDEADSMTAGAQQALRRTME-----------  138 (333)
T ss_pred             cc-------------------ccHHHHHHHHHHHHhhccCCCCceeEEEeeccchhhhHHHHHHHHHHH-----------
Confidence            11                   111111 11111    11  1347899999999999999999999998           


Q ss_pred             eecCCeEEEEecCCCC
Q 003038          769 VSLGDAIVILSCESFS  784 (854)
Q Consensus       769 v~~~~aIiIlTsn~f~  784 (854)
                      +.-+.+.|+|.||.+.
T Consensus       139 iyS~ttRFalaCN~s~  154 (333)
T KOG0991|consen  139 IYSNTTRFALACNQSE  154 (333)
T ss_pred             HHcccchhhhhhcchh
Confidence            5667788999999764

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=98.59  E-value=1.1e-07  Score=111.72  Aligned_cols=138  Identities=16%  Similarity=0.118  Sum_probs=82.8

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .|+|++++...+...+...+........      ..++...+||+||+|+|||.+|++||...   ..+|+.++.+++. 
T Consensus        56 di~g~~~~k~~l~~~~~~l~~~~~~~~~------g~~~~~giLL~GppGtGKT~la~alA~~~---~~~~~~i~~~~~~-  125 (495)
T TIGR01241        56 DVAGIDEAKEELMEIVDFLKNPSKFTKL------GAKIPKGVLLVGPPGTGKTLLAKAVAGEA---GVPFFSISGSDFV-  125 (495)
T ss_pred             HhCCHHHHHHHHHHHHHHHHCHHHHHhc------CCCCCCcEEEECCCCCCHHHHHHHHHHHc---CCCeeeccHHHHH-
Confidence            4688888888777766543211000000      01223358999999999999999999976   4578888877654 


Q ss_pred             cCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCH--------------HHHHHHHHhhhcCeEecC
Q 003038          699 TRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADY--------------CSQKGFKRAIESGRIVTS  764 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~--------------~v~~~Ll~~le~G~l~d~  764 (854)
                            +.+.      +.+......+.+..+.+..+||||||||.+.+              .+.+.|+..|+.  +.  
T Consensus       126 ------~~~~------g~~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~--~~--  189 (495)
T TIGR01241       126 ------EMFV------GVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDG--FG--  189 (495)
T ss_pred             ------HHHh------cccHHHHHHHHHHHHhcCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhcc--cc--
Confidence                  1110      00101222455556666668999999988632              244555555542  11  


Q ss_pred             CCceeecCCeEEEEecCCCCCCC
Q 003038          765 SGDEVSLGDAIVILSCESFSSRS  787 (854)
Q Consensus       765 ~G~~v~~~~aIiIlTsn~f~~~s  787 (854)
                           +-.+.+||.|||..+...
T Consensus       190 -----~~~~v~vI~aTn~~~~ld  207 (495)
T TIGR01241       190 -----TNTGVIVIAATNRPDVLD  207 (495)
T ss_pred             -----CCCCeEEEEecCChhhcC
Confidence                 113468888998755443

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.

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=98.54  E-value=1.9e-07  Score=108.90  Aligned_cols=140  Identities=11%  Similarity=0.157  Sum_probs=97.6

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .++|...++..+...+.+..                +....+++.|++|+||+.+|++|.+..+....+|+.+||+.+. 
T Consensus       139 ~lig~s~~~~~l~~~~~~~~----------------~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~i~i~c~~~~-  201 (469)
T PRK10923        139 DIIGEAPAMQDVFRIIGRLS----------------RSSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIP-  201 (469)
T ss_pred             cceecCHHHHHHHHHHHHHh----------------ccCCeEEEEeCCCCcHHHHHHHHHhcCCCCCCCeEeeeCCCCC-
Confidence            57888877777777665421                2234789999999999999999999887778899999999775 


Q ss_pred             cCCCccccccccccCC-CCC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeE
Q 003038          699 TRADSTEDSRNKRSRD-EQS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAI  775 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~-~~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aI  775 (854)
                            +......+.+ ..| + |....-...+.......+|||||+.+++.+|..|+++|++|.++...|......|+.
T Consensus       202 ------~~~~~~~lfg~~~g~~~~~~~~~~g~~~~a~~Gtl~l~~i~~l~~~~q~~L~~~l~~~~~~~~~~~~~~~~~~r  275 (469)
T PRK10923        202 ------KDLIESELFGHEKGAFTGANTIRQGRFEQADGGTLFLDEIGDMPLDVQTRLLRVLADGQFYRVGGYAPVKVDVR  275 (469)
T ss_pred             ------HHHHHHHhcCCCCCCCCCCCcCCCCCeeECCCCEEEEeccccCCHHHHHHHHHHHhcCcEEeCCCCCeEEeeEE
Confidence                  2211111111 001 1 111000111223445688999999999999999999999999987555444456889


Q ss_pred             EEEecC
Q 003038          776 VILSCE  781 (854)
Q Consensus       776 iIlTsn  781 (854)
                      ||+||+
T Consensus       276 ii~~~~  281 (469)
T PRK10923        276 IIAATH  281 (469)
T ss_pred             EEEeCC
Confidence            999886

>smart00763 AAA_PrkA PrkA AAA domain

Probab=98.53  E-value=5.9e-07  Score=99.75  Aligned_cols=51  Identities=16%  Similarity=0.186  Sum_probs=43.8

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHH
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .|+|+++++..+.+.+.....|...+            .-.++|+||+|+|||++|++||+.+
T Consensus        52 ~~~G~~~~i~~lv~~l~~~a~g~~~~------------r~il~L~GPPGsGKStla~~La~~l  102 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQGLEER------------KQILYLLGPVGGGKSSLVECLKRGL  102 (361)
T ss_pred             hccCcHHHHHHHHHHHHHHHhcCCCC------------CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            79999999999999998877665432            2368999999999999999999987

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

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.53  E-value=3.9e-07  Score=104.76  Aligned_cols=124  Identities=15%  Similarity=0.132  Sum_probs=80.9

Q ss_pred             HHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhh-
Q 003038          218 VIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCL-  296 (854)
Q Consensus       218 v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~-  296 (854)
                      +...+..++..+++|+||||||||++++.++...          +..++.++....   .    ...++++++.+.... 
T Consensus        27 L~~~i~~~~~~~ilL~GppGtGKTtLA~~ia~~~----------~~~~~~l~a~~~---~----~~~ir~ii~~~~~~~~   89 (413)
T PRK13342         27 LRRMIEAGRLSSMILWGPPGTGKTTLARIIAGAT----------DAPFEALSAVTS---G----VKDLREVIEEARQRRS   89 (413)
T ss_pred             HHHHHHcCCCceEEEECCCCCCHHHHHHHHHHHh----------CCCEEEEecccc---c----HHHHHHHHHHHHHhhh
Confidence            4444556677799999999999999999999864          345666654321   1    123344444443211 


Q ss_pred             -CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-CCCCceEEEEEecCHHHHHHhhccCCchhhhhc
Q 003038          297 -GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGENARFWLMGIATFQSYMRCKSGHPSLETLWS  373 (854)
Q Consensus       297 -~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~  373 (854)
                       +++.||||||+|.+ .....                    .|++. ..+  .+.+||+||...+.+   .+|+|.+  |
T Consensus        90 ~g~~~vL~IDEi~~l~~~~q~--------------------~LL~~le~~--~iilI~att~n~~~~---l~~aL~S--R  142 (413)
T PRK13342         90 AGRRTILFIDEIHRFNKAQQD--------------------ALLPHVEDG--TITLIGATTENPSFE---VNPALLS--R  142 (413)
T ss_pred             cCCceEEEEechhhhCHHHHH--------------------HHHHHhhcC--cEEEEEeCCCChhhh---ccHHHhc--c
Confidence             46789999999999 43210                    13322 223  699999999877643   5788888  6


Q ss_pred             cCCCCCCCchHH
Q 003038          374 LHPLTIPAGSLS  385 (854)
Q Consensus       374 ~~~v~i~~~sl~  385 (854)
                      ++.+.++..+..
T Consensus       143 ~~~~~~~~ls~e  154 (413)
T PRK13342        143 AQVFELKPLSEE  154 (413)
T ss_pred             ceeeEeCCCCHH
Confidence            677777665533

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=98.53  E-value=3.8e-07  Score=99.18  Aligned_cols=142  Identities=15%  Similarity=0.130  Sum_probs=87.7

Q ss_pred             ccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCC
Q 003038          622 WQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRA  701 (854)
Q Consensus       622 GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~  701 (854)
                      +|..++..+..++.+.|                 -.+.+||.||  +||+.+|+.+|+.++.....-. -.|..+..++.
T Consensus         6 ~q~~~~~~L~~~~~~~r-----------------l~hAyLf~G~--~G~~~~A~~~A~~llC~~~~~~-~~Cg~C~~C~~   65 (290)
T PRK07276          6 KQPKVFQRFQTILEQDR-----------------LNHAYLFSGD--FASFEMALFLAQSLFCEQKEGV-LPCGHCRSCRL   65 (290)
T ss_pred             HHHHHHHHHHHHHHcCC-----------------cceeeeeeCC--ccHHHHHHHHHHHHcCCCCCCC-CCCCCCHHHHH
Confidence            58888888888887643                 3568999996  6899999999999986432100 01111111100


Q ss_pred             CccccccccccCCCCCC--chHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCC
Q 003038          702 DSTEDSRNKRSRDEQSC--SYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGD  773 (854)
Q Consensus       702 ~s~e~~~~~rl~~~~g~--g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~  773 (854)
                      .....|.--..+.|.|.  +.++  .+.+.+..    .+++||+||++|+++....|+||+.+|+           .-.+
T Consensus        66 i~~~~HPD~~~i~p~~~~I~idqIR~l~~~~~~~p~~~~~kV~II~~ad~m~~~AaNaLLKtLEE-----------Pp~~  134 (290)
T PRK07276         66 IEQGEFSDVTVIEPQGQVIKTDTIRELVKNFSQSGYEGKQQVFIIKDADKMHVNAANSLLKVIEE-----------PQSE  134 (290)
T ss_pred             HhcCCCCCeeeecCCCCcCCHHHHHHHHHHHhhCcccCCcEEEEeehhhhcCHHHHHHHHHHhcC-----------CCCC
Confidence            00011211111223332  3433  45555544    4479999999999999999999999997           2357


Q ss_pred             eEEEEecCCC-CCCCCCCCCCc
Q 003038          774 AIVILSCESF-SSRSRACSPPT  794 (854)
Q Consensus       774 aIiIlTsn~f-~~~s~~~sp~~  794 (854)
                      ++|||+|+.- .-.++.-|.|+
T Consensus       135 t~~iL~t~~~~~lLpTI~SRcq  156 (290)
T PRK07276        135 IYIFLLTNDENKVLPTIKSRTQ  156 (290)
T ss_pred             eEEEEEECChhhCchHHHHcce
Confidence            8899988543 34444455554

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=98.52  E-value=2.4e-07  Score=102.91  Aligned_cols=143  Identities=14%  Similarity=0.077  Sum_probs=81.6

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHh------CCCCceEEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVF------GSHNNFVSI  691 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lf------g~~~~~i~i  691 (854)
                      ..|+||++++..+.-+....                  ..+.+||.|++|+|||++||+||..|-      +.+-.+.++
T Consensus         8 ~~i~Gq~~~~~~l~~~~~~~------------------~~~~vLl~G~pG~gKT~lar~la~llP~~~~~e~~~~~~~~~   69 (334)
T PRK13407          8 SAIVGQEEMKQAMVLTAIDP------------------GIGGVLVFGDRGTGKSTAVRALAALLPLIKAVEGCPVNSARP   69 (334)
T ss_pred             HHhCCHHHHHHHHHHHHhcc------------------CCCcEEEEcCCCCCHHHHHHHHHHHCCCcchhcccccccCcc
Confidence            35799999998777654321                  135799999999999999999999982      111112222


Q ss_pred             ccccccCcCCCccccccccc---cCC-CCC------CchHHHHHHH------------HHcCCCEEEEEecCCCCCHHHH
Q 003038          692 ALSSFSSTRADSTEDSRNKR---SRD-EQS------CSYIERFAEA------------VSNNPHRVFLIEDVEQADYCSQ  749 (854)
Q Consensus       692 d~s~~~~~~~~s~e~~~~~r---l~~-~~g------~g~~e~L~ea------------v~~~p~~ViliDEieka~~~v~  749 (854)
                      .+.  ......+... ...+   ++. |.+      .|.. .+...            +.+....++++|||+.+++.+|
T Consensus        70 ~~~--~~~~~~~~~~-~~~~~~p~~~~p~~~t~~~l~G~~-d~~~~l~~g~~~~~~G~l~~A~~GiL~lDEInrl~~~~q  145 (334)
T PRK13407         70 EDC--PEWAHVSSTT-MIERPTPVVDLPLGVTEDRVVGAL-DIERALTRGEKAFEPGLLARANRGYLYIDEVNLLEDHIV  145 (334)
T ss_pred             cCC--cccccccCCc-ccccCCccccCCCCCCcceeecch-hhhhhhhcCCeeecCCceEEcCCCeEEecChHhCCHHHH
Confidence            110  0000000000 0000   000 000      0110 11111            1122346999999999999999


Q ss_pred             HHHHHhhhcCeEec-CCCceeecC-CeEEEEecCC
Q 003038          750 KGFKRAIESGRIVT-SSGDEVSLG-DAIVILSCES  782 (854)
Q Consensus       750 ~~Ll~~le~G~l~d-~~G~~v~~~-~aIiIlTsn~  782 (854)
                      +.|+++|++|.++- ..|....+. ..++|.|.|.
T Consensus       146 ~~Lle~mee~~v~v~r~G~~~~~p~rfiviAt~NP  180 (334)
T PRK13407        146 DLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNP  180 (334)
T ss_pred             HHHHHHHHcCCeEEEECCeEEecCCCEEEEecCCc
Confidence            99999999998542 345455553 4566667664

>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=98.52  E-value=7.1e-07  Score=85.07  Aligned_cols=91  Identities=15%  Similarity=0.124  Sum_probs=63.4

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHH---HHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQR---VEE  287 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~r---l~~  287 (854)
                      ++..+..+...+.+...++++|+||||+|||++++.++..+..       .+..++.++...............   ...
T Consensus         3 ~~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~~-------~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~   75 (151)
T cd00009           3 QEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFR-------PGAPFLYLNASDLLEGLVVAELFGHFLVRL   75 (151)
T ss_pred             hHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhhc-------CCCCeEEEehhhhhhhhHHHHHhhhhhHhH
Confidence            6778888888888777889999999999999999999988752       356777777766655422221111   111


Q ss_pred             HHHHHHhhhCCCeEEEeCccccc
Q 003038          288 IKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       288 l~~~~~~~~~~~~ILfidel~~l  310 (854)
                      .......  ..+.+|+|||++.+
T Consensus        76 ~~~~~~~--~~~~~lilDe~~~~   96 (151)
T cd00009          76 LFELAEK--AKPGVLFIDEIDSL   96 (151)
T ss_pred             HHHhhcc--CCCeEEEEeChhhh
Confidence            1111222  35789999999887

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.

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=98.52  E-value=3.8e-07  Score=110.71  Aligned_cols=107  Identities=17%  Similarity=0.239  Sum_probs=69.5

Q ss_pred             cccccHHHHHH---HHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          619 KVPWQKDTVYD---IANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       619 ~V~GQ~~av~~---Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      .++||++++..   +...+..                  +...+++|+||+|+|||++|+++|+.+   ...|+.++.+.
T Consensus        29 d~vGQe~ii~~~~~L~~~i~~------------------~~~~slLL~GPpGtGKTTLA~aIA~~~---~~~f~~lna~~   87 (725)
T PRK13341         29 EFVGQDHILGEGRLLRRAIKA------------------DRVGSLILYGPPGVGKTTLARIIANHT---RAHFSSLNAVL   87 (725)
T ss_pred             HhcCcHHHhhhhHHHHHHHhc------------------CCCceEEEECCCCCCHHHHHHHHHHHh---cCcceeehhhh
Confidence            47899998853   3333321                  224589999999999999999999876   24566665431


Q ss_pred             ccCcCCCccccccccccCCCCCCchHHHHHHHHH-cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVS-NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~-~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                      ..           ++.+.     ...+...+.+. ...+.|+||||||.++...|+.|+..+++|.+.
T Consensus        88 ~~-----------i~dir-----~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~~qQdaLL~~lE~g~Ii  139 (725)
T PRK13341         88 AG-----------VKDLR-----AEVDRAKERLERHGKRTILFIDEVHRFNKAQQDALLPWVENGTIT  139 (725)
T ss_pred             hh-----------hHHHH-----HHHHHHHHHhhhcCCceEEEEeChhhCCHHHHHHHHHHhcCceEE
Confidence            11           00000     00011111121 234679999999999999999999999987543

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=98.51  E-value=1.2e-07  Score=115.62  Aligned_cols=128  Identities=13%  Similarity=0.167  Sum_probs=92.5

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..|.++++||||+|||.++++||....+|.     +..-|+.-+.....+.+.||.|+.|+-++++++..  .|.|+|+|
T Consensus       298 pPrgvL~~GppGTGkTl~araLa~~~s~~~-----~kisffmrkgaD~lskwvgEaERqlrllFeeA~k~--qPSIIffd  370 (1080)
T KOG0732|consen  298 PPRGVLFHGPPGTGKTLMARALAAACSRGN-----RKISFFMRKGADCLSKWVGEAERQLRLLFEEAQKT--QPSIIFFD  370 (1080)
T ss_pred             CCcceeecCCCCCchhHHHHhhhhhhcccc-----cccchhhhcCchhhccccCcHHHHHHHHHHHHhcc--CceEEecc
Confidence            356699999999999999999998876653     55566666666777789999999999999999987  89999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhh
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETL  371 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~  371 (854)
                      ||.=| ..+++--++.-      ...+..+-.|+-+--++|.+.+||||....|     .||+|.|-
T Consensus       371 eIdGlapvrSskqEqih------~SIvSTLLaLmdGldsRgqVvvigATnRpda-----~dpaLRRP  426 (1080)
T KOG0732|consen  371 EIDGLAPVRSSKQEQIH------ASIVSTLLALMDGLDSRGQVVVIGATNRPDA-----IDPALRRP  426 (1080)
T ss_pred             ccccccccccchHHHhh------hhHHHHHHHhccCCCCCCceEEEcccCCccc-----cchhhcCC
Confidence            99876 44432101100      0123333334422112347999999998886     47999874

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.51  E-value=6.8e-07  Score=107.00  Aligned_cols=154  Identities=12%  Similarity=0.088  Sum_probs=93.6

Q ss_pred             cHHHHHHHHHHhhcc----CcCCc-eeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc---c-----
Q 003038          211 RNEDVMYVIENLMSK----RKRNF-VVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM---N-----  277 (854)
Q Consensus       211 r~~ei~~v~~~L~r~----~k~n~-vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~---~-----  277 (854)
                      ||+|+++|...|..-    ..+|+ .|+|+||+|||++|+.+++.+...---..+..+.++.++...+...   |     
T Consensus       760 REeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sIYqvI~q  839 (1164)
T PTZ00112        760 REKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAAYQVLYK  839 (1164)
T ss_pred             hHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHHHHHHHH
Confidence            999999999887642    33455 4899999999999999998875321011233467777776433211   1     


Q ss_pred             --------hH-HHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcc-cCCCCce
Q 003038          278 --------RV-EVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVC-GIGENAR  346 (854)
Q Consensus       278 --------rg-e~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~-~~~g~g~  346 (854)
                              +| ...+.+..++..+.......+||+|||||.| ....              ..   +-+|+. +....++
T Consensus       840 qL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~Q--------------DV---LYnLFR~~~~s~SK  902 (1164)
T PTZ00112        840 QLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQ--------------KV---LFTLFDWPTKINSK  902 (1164)
T ss_pred             HHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCccHH--------------HH---HHHHHHHhhccCCe
Confidence                    11 2234566666666432133569999999999 6422              12   223332 1111236


Q ss_pred             EEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCch
Q 003038          347 FWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGS  383 (854)
Q Consensus       347 l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~s  383 (854)
                      |.+||+++.-.+..  ..+|.+..++++..|..++.+
T Consensus       903 LiLIGISNdlDLpe--rLdPRLRSRLg~eeIvF~PYT  937 (1164)
T PTZ00112        903 LVLIAISNTMDLPE--RLIPRCRSRLAFGRLVFSPYK  937 (1164)
T ss_pred             EEEEEecCchhcch--hhhhhhhhccccccccCCCCC
Confidence            99999998666544  236777773333446665544

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=98.51  E-value=2.2e-07  Score=106.14  Aligned_cols=137  Identities=14%  Similarity=0.221  Sum_probs=102.9

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+|...++..+...+.+.                .+....+|+.|.+|+||..+|+++-+.--..+.+||+|||....
T Consensus       245 ~~Iig~S~~m~~~~~~akr~----------------A~tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiP  308 (560)
T COG3829         245 DDIIGESPAMLRVLELAKRI----------------AKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAIP  308 (560)
T ss_pred             hhhccCCHHHHHHHHHHHhh----------------cCCCCcEEEecCCCccHHHHHHHHHhcCcccCCCeEEEecccCC
Confidence            46899987666655555443                13456889999999999999999998776668999999999877


Q ss_pred             CcCCCccccccccccCCCCCCchHH-HHHHHHHc-CC-------CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCce
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIE-RFAEAVSN-NP-------HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDE  768 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e-~L~eav~~-~p-------~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~  768 (854)
                             +.---+.|.     ||.. .++.|.+. +|       +.-+|+|||--++...|..||++++++.+.-=.|.+
T Consensus       309 -------e~LlESELF-----Gye~GAFTGA~~~GK~GlfE~A~gGTLFLDEIgempl~LQaKLLRVLQEkei~rvG~t~  376 (560)
T COG3829         309 -------ETLLESELF-----GYEKGAFTGASKGGKPGLFELANGGTLFLDEIGEMPLPLQAKLLRVLQEKEIERVGGTK  376 (560)
T ss_pred             -------HHHHHHHHh-----CcCCccccccccCCCCcceeeccCCeEEehhhccCCHHHHHHHHHHHhhceEEecCCCC
Confidence                   322222222     4443 46777765 33       456999999999999999999999999998655555


Q ss_pred             eecCCeEEEEecCC
Q 003038          769 VSLGDAIVILSCES  782 (854)
Q Consensus       769 v~~~~aIiIlTsn~  782 (854)
                      .--.|..||-++|.
T Consensus       377 ~~~vDVRIIAATN~  390 (560)
T COG3829         377 PIPVDVRIIAATNR  390 (560)
T ss_pred             ceeeEEEEEeccCc
Confidence            55567789999984

>TIGR03689 pup_AAA proteasome ATPase

Probab=98.50  E-value=5.2e-07  Score=105.04  Aligned_cols=132  Identities=13%  Similarity=0.095  Sum_probs=78.0

Q ss_pred             cccccHHHHHHHHHHHHHh--------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC------
Q 003038          619 KVPWQKDTVYDIANTVLKC--------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS------  684 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~--------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~------  684 (854)
                      .|.|.+..+..|..+|..-        +.|+.             |..-+||+||||+|||.+|+++|..+...      
T Consensus       183 dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~-------------~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~  249 (512)
T TIGR03689       183 DIGGLDSQIEQIRDAVELPFLHPELYREYDLK-------------PPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETG  249 (512)
T ss_pred             HcCChHHHHHHHHHHHHHHhhCHHHHHhccCC-------------CCcceEEECCCCCcHHHHHHHHHHhhccccccccC
Confidence            3568888888888887531        22332             23358999999999999999999987321      


Q ss_pred             -CCceEEEccccccCcCCCccccccccccCCCCCCchHH----HHHHHHHc----CCCEEEEEecCCCCC--------H-
Q 003038          685 -HNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIE----RFAEAVSN----NPHRVFLIEDVEQAD--------Y-  746 (854)
Q Consensus       685 -~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e----~L~eav~~----~p~~ViliDEieka~--------~-  746 (854)
                       ...|+.+..+++.            ....     |-.+    .+++..++    +..+||||||||..-        . 
T Consensus       250 ~~~~fl~v~~~eLl------------~kyv-----Gete~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s~d  312 (512)
T TIGR03689       250 DKSYFLNIKGPELL------------NKYV-----GETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVSSD  312 (512)
T ss_pred             CceeEEeccchhhc------------cccc-----chHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCccch
Confidence             1223333322211            0000     2111    33344433    356899999999752        1 


Q ss_pred             ---HHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCCCC
Q 003038          747 ---CSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRA  789 (854)
Q Consensus       747 ---~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~  789 (854)
                         .+.+.|+..|+.  +       -+..+.+||+|||..+....+
T Consensus       313 ~e~~il~~LL~~LDg--l-------~~~~~ViVI~ATN~~d~LDpA  349 (512)
T TIGR03689       313 VETTVVPQLLSELDG--V-------ESLDNVIVIGASNREDMIDPA  349 (512)
T ss_pred             HHHHHHHHHHHHhcc--c-------ccCCceEEEeccCChhhCCHh
Confidence               234566666652  1       123578999999975544333

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.49  E-value=7.4e-07  Score=101.55  Aligned_cols=152  Identities=14%  Similarity=0.206  Sum_probs=93.3

Q ss_pred             cHHHHHHHHHHhhcc----CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc-----------
Q 003038          211 RNEDVMYVIENLMSK----RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH-----------  275 (854)
Q Consensus       211 r~~ei~~v~~~L~r~----~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~-----------  275 (854)
                      |++|++++...|..-    ..+|++|+|+||+|||++++.++..+....     .+..++.++......           
T Consensus        35 Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~-----~~~~~v~in~~~~~~~~~~~~~i~~~  109 (394)
T PRK00411         35 REEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIA-----VKVVYVYINCQIDRTRYAIFSEIARQ  109 (394)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhc-----CCcEEEEEECCcCCCHHHHHHHHHHH
Confidence            999999999998432    446899999999999999999998875532     245666666532211           


Q ss_pred             --c----chH-HHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceE
Q 003038          276 --M----NRV-EVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARF  347 (854)
Q Consensus       276 --~----~rg-e~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l  347 (854)
                        +    .+| .+++-+..+.+.+... +.++||+|||++.+ .....             .....+.+++....+. .+
T Consensus       110 l~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~viviDE~d~l~~~~~~-------------~~l~~l~~~~~~~~~~-~v  174 (394)
T PRK00411        110 LFGHPPPSSGLSFDELFDKIAEYLDER-DRVLIVALDDINYLFEKEGN-------------DVLYSLLRAHEEYPGA-RI  174 (394)
T ss_pred             hcCCCCCCCCCCHHHHHHHHHHHHHhc-CCEEEEEECCHhHhhccCCc-------------hHHHHHHHhhhccCCC-eE
Confidence              0    111 2344445555555543 56799999999999 43221             1222333333211121 58


Q ss_pred             EEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchH
Q 003038          348 WLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSL  384 (854)
Q Consensus       348 ~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl  384 (854)
                      .+|++++.......  .+|.+.+.++.+.|.+++.+.
T Consensus       175 ~vI~i~~~~~~~~~--l~~~~~s~~~~~~i~f~py~~  209 (394)
T PRK00411        175 GVIGISSDLTFLYI--LDPRVKSVFRPEEIYFPPYTA  209 (394)
T ss_pred             EEEEEECCcchhhh--cCHHHHhcCCcceeecCCCCH
Confidence            89999886655543  466666633334556665443

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=98.49  E-value=3.4e-07  Score=105.03  Aligned_cols=136  Identities=15%  Similarity=0.174  Sum_probs=84.9

Q ss_pred             cccccHHHHHHHHHHHHHh--------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEE
Q 003038          619 KVPWQKDTVYDIANTVLKC--------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVS  690 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~--------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~  690 (854)
                      .|.|.+..+..|..++..-        ..|+.             +...+||+||+|+|||.+|+++|..+   ...|++
T Consensus       184 DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~-------------~p~gVLL~GPPGTGKT~LAraIA~el---~~~fi~  247 (438)
T PTZ00361        184 DIGGLEQQIQEIKEAVELPLTHPELYDDIGIK-------------PPKGVILYGPPGTGKTLLAKAVANET---SATFLR  247 (438)
T ss_pred             HhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCC-------------CCcEEEEECCCCCCHHHHHHHHHHhh---CCCEEE
Confidence            3588899999998888532        12322             22357889999999999999999987   346888


Q ss_pred             EccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCC-----------CHHHHHHHHHhhhcC
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQA-----------DYCSQKGFKRAIESG  759 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka-----------~~~v~~~Ll~~le~G  759 (854)
                      +..+++.       ..+     + +.+......+++..+.+..+||||||||..           +.+++..+++.+..=
T Consensus       248 V~~seL~-------~k~-----~-Ge~~~~vr~lF~~A~~~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~L  314 (438)
T PTZ00361        248 VVGSELI-------QKY-----L-GDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQL  314 (438)
T ss_pred             Eecchhh-------hhh-----c-chHHHHHHHHHHHHHhCCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHH
Confidence            8776554       111     1 000011224555556666789999999864           234556666555420


Q ss_pred             eEecCCCceeecCCeEEEEecCCCCCCCCC
Q 003038          760 RIVTSSGDEVSLGDAIVILSCESFSSRSRA  789 (854)
Q Consensus       760 ~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~  789 (854)
                         |+.   -.-.+.+||++||..+....+
T Consensus       315 ---dg~---~~~~~V~VI~ATNr~d~LDpa  338 (438)
T PTZ00361        315 ---DGF---DSRGDVKVIMATNRIESLDPA  338 (438)
T ss_pred             ---hhh---cccCCeEEEEecCChHHhhHH
Confidence               000   012367899999976555443

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=98.47  E-value=3.9e-07  Score=109.95  Aligned_cols=129  Identities=17%  Similarity=0.175  Sum_probs=81.4

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHh----------CCC--
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVF----------GSH--  685 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lf----------g~~--  685 (854)
                      ..|+||++++..+.-+...       +           ..+.+||.|++|+|||.+|++|+..+-          ++.  
T Consensus         4 ~~ivGq~~~~~al~~~av~-------~-----------~~g~vli~G~~GtgKs~lar~l~~~lp~~~~~~~~~~~c~p~   65 (633)
T TIGR02442         4 TAIVGQEDLKLALLLNAVD-------P-----------RIGGVLIRGEKGTAKSTAARGLAALLPPIDVVAGCPFSCDPD   65 (633)
T ss_pred             chhcChHHHHHHHHHHhhC-------C-----------CCCeEEEEcCCCCcHHHHHHHHHHhCCCceeccCCcCCCCCC
Confidence            4689999988766544332       1           246799999999999999999999882          210  


Q ss_pred             --------------------CceEEEccccccCcCCCccccccccccCCCCCCchHHHHHH------------HHHcCCC
Q 003038          686 --------------------NNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAE------------AVSNNPH  733 (854)
Q Consensus       686 --------------------~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~e------------av~~~p~  733 (854)
                                          .+|+.+.++..            ..+++     |.. .+..            .+.....
T Consensus        66 ~~~~~~~~~~~~~~~~~~~~~pfv~~p~~~t------------~~~l~-----G~~-d~~~~l~~g~~~~~~G~L~~A~~  127 (633)
T TIGR02442        66 DPEEWCEECRRKYRPSEQRPVPFVNLPLGAT------------EDRVV-----GSL-DIERALREGEKAFQPGLLAEAHR  127 (633)
T ss_pred             CccccChhhhhcccccccCCCCeeeCCCCCc------------HHHcC-----Ccc-cHHHHhhcCCeeecCcceeecCC
Confidence                                11111111100            00111     111 0111            1223345


Q ss_pred             EEEEEecCCCCCHHHHHHHHHhhhcCeEec-CCCceeec-CCeEEEEecCC
Q 003038          734 RVFLIEDVEQADYCSQKGFKRAIESGRIVT-SSGDEVSL-GDAIVILSCES  782 (854)
Q Consensus       734 ~ViliDEieka~~~v~~~Ll~~le~G~l~d-~~G~~v~~-~~aIiIlTsn~  782 (854)
                      .|+|||||+++++.+|+.|+++|++|.++- ..|....+ .+.++|.|+|.
T Consensus       128 GiL~lDEi~~l~~~~q~~Ll~~le~g~~~v~r~g~~~~~~~~~~lIat~np  178 (633)
T TIGR02442       128 GILYIDEVNLLDDHLVDVLLDAAAMGVNRVEREGLSVSHPARFVLIGTMNP  178 (633)
T ss_pred             CeEEeChhhhCCHHHHHHHHHHHhcCCEEEEECCceeeecCCeEEEEecCC
Confidence            799999999999999999999999996542 23444444 46778888773

A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.

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

Probab=98.46  E-value=5.5e-07  Score=110.59  Aligned_cols=111  Identities=15%  Similarity=0.253  Sum_probs=76.3

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC-------CCceEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS-------HNNFVS  690 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-------~~~~i~  690 (854)
                      ..|+||++.+..+...+.+.                  ....++|+||+|||||.+++.||+.+...       ...++.
T Consensus       182 ~~~igr~~ei~~~~~~L~~~------------------~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~  243 (731)
T TIGR02639       182 DPLIGREDELERTIQVLCRR------------------KKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYS  243 (731)
T ss_pred             CcccCcHHHHHHHHHHHhcC------------------CCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEE
Confidence            35799998888777555331                  12367899999999999999999987432       245666


Q ss_pred             EccccccCcCCCccccccccccCCCCCC--chHHHHHHH---HHcCCCEEEEEecCCCCC---------HHHHHHHHHhh
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSC--SYIERFAEA---VSNNPHRVFLIEDVEQAD---------YCSQKGFKRAI  756 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~--g~~e~L~ea---v~~~p~~ViliDEieka~---------~~v~~~Ll~~l  756 (854)
                      +|++...                .+..|  .+.++|...   +++++..|+||||||.+-         .++++.|+..+
T Consensus       244 ~~~~~l~----------------a~~~~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l  307 (731)
T TIGR02639       244 LDMGSLL----------------AGTKYRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAGATSGGSMDASNLLKPAL  307 (731)
T ss_pred             ecHHHHh----------------hhccccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccCCCCCccHHHHHHHHHHH
Confidence            6655332                11112  233344444   345667899999999663         56899999999


Q ss_pred             hcCeEe
Q 003038          757 ESGRIV  762 (854)
Q Consensus       757 e~G~l~  762 (854)
                      ++|.++
T Consensus       308 ~~g~i~  313 (731)
T TIGR02639       308 SSGKLR  313 (731)
T ss_pred             hCCCeE
Confidence            988776

>CHL00176 ftsH cell division protein; Validated

Probab=98.46  E-value=5.7e-07  Score=107.86  Aligned_cols=136  Identities=13%  Similarity=0.113  Sum_probs=81.9

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .|+|.+++...+...+...+..-.... .     -.++...+||+||+|+|||.+|++||...   ..+|+.+++++|. 
T Consensus       184 dv~G~~~~k~~l~eiv~~lk~~~~~~~-~-----g~~~p~gVLL~GPpGTGKT~LAralA~e~---~~p~i~is~s~f~-  253 (638)
T CHL00176        184 DIAGIEEAKEEFEEVVSFLKKPERFTA-V-----GAKIPKGVLLVGPPGTGKTLLAKAIAGEA---EVPFFSISGSEFV-  253 (638)
T ss_pred             hccChHHHHHHHHHHHHHHhCHHHHhh-c-----cCCCCceEEEECCCCCCHHHHHHHHHHHh---CCCeeeccHHHHH-
Confidence            477888888777776644322111000 0     01223358999999999999999999976   4678888888765 


Q ss_pred             cCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCC-----------HH---HHHHHHHhhhcCeEecC
Q 003038          699 TRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQAD-----------YC---SQKGFKRAIESGRIVTS  764 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~-----------~~---v~~~Ll~~le~G~l~d~  764 (854)
                            +.+.      +.+......+.+..+.+..+||||||||.+.           ..   +.+.|+..|+. . .  
T Consensus       254 ------~~~~------g~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg-~-~--  317 (638)
T CHL00176        254 ------EMFV------GVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDG-F-K--  317 (638)
T ss_pred             ------HHhh------hhhHHHHHHHHHHHhcCCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhcc-c-c--
Confidence                  2111      0011112245555666677999999999773           33   34444444442 1 1  


Q ss_pred             CCceeecCCeEEEEecCCCCC
Q 003038          765 SGDEVSLGDAIVILSCESFSS  785 (854)
Q Consensus       765 ~G~~v~~~~aIiIlTsn~f~~  785 (854)
                           .-.+.+||.+||..+.
T Consensus       318 -----~~~~ViVIaaTN~~~~  333 (638)
T CHL00176        318 -----GNKGVIVIAATNRVDI  333 (638)
T ss_pred             -----CCCCeeEEEecCchHh
Confidence                 1135788889986443

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.44  E-value=1.9e-06  Score=97.18  Aligned_cols=153  Identities=13%  Similarity=0.227  Sum_probs=92.3

Q ss_pred             cHHHHHHHHHHhhc----cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc-----------
Q 003038          211 RNEDVMYVIENLMS----KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH-----------  275 (854)
Q Consensus       211 r~~ei~~v~~~L~r----~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~-----------  275 (854)
                      |++|++.+...|..    .+.+|++|+||||+|||++++.++..+.... +..=....++.++......           
T Consensus        20 Re~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~-~~~~~~~~~v~in~~~~~~~~~~~~~i~~~   98 (365)
T TIGR02928        20 RDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAA-EDRDVRVVTVYVNCQILDTLYQVLVELANQ   98 (365)
T ss_pred             cHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHh-hccCCceEEEEEECCCCCCHHHHHHHHHHH
Confidence            99999999998863    3557899999999999999999998765310 1000014566666432211           


Q ss_pred             ----c----chH-HHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-CCCC
Q 003038          276 ----M----NRV-EVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGEN  344 (854)
Q Consensus       276 ----~----~rg-e~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~  344 (854)
                          +    .+| .+++.++.+++.+... +.++||+|||++.+ +....              ....+.++... ....
T Consensus        99 l~~~~~~~~~~~~~~~~~~~~l~~~l~~~-~~~~vlvIDE~d~L~~~~~~--------------~L~~l~~~~~~~~~~~  163 (365)
T TIGR02928        99 LRGSGEEVPTTGLSTSEVFRRLYKELNER-GDSLIIVLDEIDYLVGDDDD--------------LLYQLSRARSNGDLDN  163 (365)
T ss_pred             HhhcCCCCCCCCCCHHHHHHHHHHHHHhc-CCeEEEEECchhhhccCCcH--------------HHHhHhccccccCCCC
Confidence                0    011 1344456666666544 56899999999999 54321              22233333111 1111


Q ss_pred             ceEEEEEecCHHHHHHhhccCCchhhhhcc--CCCCCCCch
Q 003038          345 ARFWLMGIATFQSYMRCKSGHPSLETLWSL--HPLTIPAGS  383 (854)
Q Consensus       345 g~l~lIgatT~~ey~k~~~~~pale~~~~~--~~v~i~~~s  383 (854)
                      ..+.+|++++.-.+..  .-+|.+.+  +|  +.|.+++.+
T Consensus       164 ~~v~lI~i~n~~~~~~--~l~~~~~s--~~~~~~i~f~p~~  200 (365)
T TIGR02928       164 AKVGVIGISNDLKFRE--NLDPRVKS--SLCEEEIIFPPYD  200 (365)
T ss_pred             CeEEEEEEECCcchHh--hcCHHHhc--cCCcceeeeCCCC
Confidence            3699999997655543  23566655  45  345666554

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.

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=98.44  E-value=6.6e-07  Score=103.94  Aligned_cols=140  Identities=11%  Similarity=0.133  Sum_probs=95.2

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .++|+..++..+...+.+...                ....+++.|++|+||+.+|+.+.........+|+.+||..+.+
T Consensus       144 ~ii~~S~~~~~~~~~~~~~a~----------------~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~~~i~c~~~~~  207 (457)
T PRK11361        144 HILTNSPAMMDICKDTAKIAL----------------SQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPE  207 (457)
T ss_pred             ceecccHHHhHHHHHHHHHcC----------------CCcEEEEEcCCCccHHHHHHHHHHhCCCCCCCeEEEECCCCCH
Confidence            488888888777776665422                2347899999999999999999887766778999999997752


Q ss_pred             cCCCccccccccccCCC-CC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeE
Q 003038          699 TRADSTEDSRNKRSRDE-QS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAI  775 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~-~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aI  775 (854)
                             ....+.+.+. .+ + |-...-...+......+||||||+++++.+|..|+++|+++.+.--.|...--.|+.
T Consensus       208 -------~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ld~i~~l~~~~q~~L~~~l~~~~~~~~~~~~~~~~~~r  280 (457)
T PRK11361        208 -------SLLESELFGHEKGAFTGAQTLRQGLFERANEGTLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIR  280 (457)
T ss_pred             -------HHHHHHhcCCCCCCCCCCCCCCCCceEECCCCEEEEechhhCCHHHHHHHHHHHhcCcEEeCCCCceeeeceE
Confidence                   1111111110 00 0 000000112233456799999999999999999999999998775434333345778


Q ss_pred             EEEecC
Q 003038          776 VILSCE  781 (854)
Q Consensus       776 iIlTsn  781 (854)
                      ||+||+
T Consensus       281 ii~~t~  286 (457)
T PRK11361        281 IIAATN  286 (457)
T ss_pred             EEEeCC
Confidence            999886

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=98.44  E-value=4.8e-07  Score=96.26  Aligned_cols=126  Identities=10%  Similarity=0.029  Sum_probs=79.5

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCC--CchHH--HHHHHHHc-
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQS--CSYIE--RFAEAVSN-  730 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g--~g~~e--~L~eav~~-  730 (854)
                      +.+.+||+||.|+||..+|.++|+.++.....   -.|..+.++.......|.--..+.|.+  .+.++  .+.+.+.. 
T Consensus         6 ~~HA~Lf~G~~G~G~~~lA~~~A~~llC~~~~---~~Cg~C~sC~~i~~~~HPDl~~i~p~~~~I~id~ir~l~~~l~~~   82 (261)
T PRK05818          6 KTHPLLLIERKGSFLKPFLYEYLTSIVCTKAN---GFCKTCESCLKILNGKYNDFYLIFDQKNPIKKEDALSIINKLNRP   82 (261)
T ss_pred             CCcceeeeCCCCCcHHHHHHHHHHHHcCCCCC---CCCCCCHHHHHHhcCCCCCEEEecCCcccCCHHHHHHHHHHHccC
Confidence            45689999999999999999999999865321   012222211111111121111111221  24443  45554433 


Q ss_pred             ----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCC-CCCCCCCCCCcc
Q 003038          731 ----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESF-SSRSRACSPPTK  795 (854)
Q Consensus       731 ----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f-~~~s~~~sp~~~  795 (854)
                          .+++|++|+++|+++....|+||+.+|+           .-.+++|||+|+.- .-.++..|+|++
T Consensus        83 s~e~~~~KV~II~~ae~m~~~AaNaLLK~LEE-----------Pp~~t~fiLit~~~~~lLpTI~SRCq~  141 (261)
T PRK05818         83 SVESNGKKIYIIYGIEKLNKQSANSLLKLIEE-----------PPKNTYGIFTTRNENNILNTILSRCVQ  141 (261)
T ss_pred             chhcCCCEEEEeccHhhhCHHHHHHHHHhhcC-----------CCCCeEEEEEECChHhCchHhhhheee
Confidence                3579999999999999999999999997           34688899988654 444445566543

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.44  E-value=5.8e-07  Score=94.19  Aligned_cols=79  Identities=11%  Similarity=0.213  Sum_probs=58.8

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEE
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVF  736 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vi  736 (854)
                      ..+++|+||+|||||.+|+.+++..+.....++.++++.+.       ...              ..+.+.+.  .+.+|
T Consensus        38 ~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~~~~~~-------~~~--------------~~~~~~~~--~~~lL   94 (226)
T TIGR03420        38 DRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAELA-------QAD--------------PEVLEGLE--QADLV   94 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEeHHHHH-------HhH--------------HHHHhhcc--cCCEE
Confidence            35899999999999999999999987666678888887664       110              11222222  24699


Q ss_pred             EEecCCCCCHHH--HHHHHHhhhc
Q 003038          737 LIEDVEQADYCS--QKGFKRAIES  758 (854)
Q Consensus       737 liDEieka~~~v--~~~Ll~~le~  758 (854)
                      +|||++.++...  ++.|...++.
T Consensus        95 vIDdi~~l~~~~~~~~~L~~~l~~  118 (226)
T TIGR03420        95 CLDDVEAIAGQPEWQEALFHLYNR  118 (226)
T ss_pred             EEeChhhhcCChHHHHHHHHHHHH
Confidence            999999998744  8888888864

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.

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.42  E-value=6.5e-07  Score=84.38  Aligned_cols=115  Identities=12%  Similarity=0.084  Sum_probs=72.3

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCcccccccc----ccC--CCCCCchH--HHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNK----RSR--DEQSCSYI--ERFAEAVS  729 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~----rl~--~~~g~g~~--e~L~eav~  729 (854)
                      ..++|.||+|+|||++++.||..++.....++.++++....       .....    ...  .....+..  +.+.+.++
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   75 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILE-------EVLDQLLLIIVGGKKASGSGELRLRLALALAR   75 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEccc-------cCHHHHHhhhhhccCCCCCHHHHHHHHHHHHH
Confidence            37899999999999999999999976554688888775541       11100    000  01111222  25666667


Q ss_pred             cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCC
Q 003038          730 NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       730 ~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      +.++.||+|||++++..............   ....-......+..+|+++|.
T Consensus        76 ~~~~~viiiDei~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~i~~~~~  125 (148)
T smart00382       76 KLKPDVLILDEITSLLDAEQEALLLLLEE---LRLLLLLKSEKNLTVILTTND  125 (148)
T ss_pred             hcCCCEEEEECCcccCCHHHHHHHHhhhh---hHHHHHHHhcCCCEEEEEeCC
Confidence            77789999999999988776665543211   000011233456678888874

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.

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.40  E-value=1.6e-06  Score=104.15  Aligned_cols=120  Identities=12%  Similarity=0.104  Sum_probs=77.3

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHh-------CCCCceEEE
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVF-------GSHNNFVSI  691 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lf-------g~~~~~i~i  691 (854)
                      .++||+.++..+...+..       +          .+ ..++|+||+|+|||++|+.+++...       .....|+.+
T Consensus       155 ~iiGqs~~~~~l~~~ia~-------~----------~~-~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i  216 (615)
T TIGR02903       155 EIVGQERAIKALLAKVAS-------P----------FP-QHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEV  216 (615)
T ss_pred             hceeCcHHHHHHHHHHhc-------C----------CC-CeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEE
Confidence            489999999877655421       1          12 3689999999999999999988763       134678999


Q ss_pred             ccccccCcCCCcccccccc-ccCCC---CCC-chHHH---------HHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhh
Q 003038          692 ALSSFSSTRADSTEDSRNK-RSRDE---QSC-SYIER---------FAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIE  757 (854)
Q Consensus       692 d~s~~~~~~~~s~e~~~~~-rl~~~---~g~-g~~e~---------L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le  757 (854)
                      +++.+..      +...+. .+++.   +.+ +....         ....+......|+||||++.+++..|+.|+++|+
T Consensus       217 ~~~~l~~------d~~~i~~~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~~~Q~~Ll~~Le  290 (615)
T TIGR02903       217 DGTTLRW------DPREVTNPLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLKVLE  290 (615)
T ss_pred             echhccC------CHHHHhHHhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCHHHHHHHHHHHh
Confidence            9876531      000000 00100   000 00000         1112223446799999999999999999999999


Q ss_pred             cCeEe
Q 003038          758 SGRIV  762 (854)
Q Consensus       758 ~G~l~  762 (854)
                      ++++.
T Consensus       291 ~~~v~  295 (615)
T TIGR02903       291 DKRVE  295 (615)
T ss_pred             hCeEE
Confidence            98754

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.

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=98.40  E-value=1.1e-06  Score=97.22  Aligned_cols=111  Identities=10%  Similarity=0.076  Sum_probs=71.8

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHH----HHHHHHH-
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIE----RFAEAVS-  729 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e----~L~eav~-  729 (854)
                      +++.-++|+||+|||||.+|+++|..+   .-+|+.+++++..+       ++     .     |-.+    ++++..+ 
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~el---g~~~i~vsa~eL~s-------k~-----v-----GEsEk~IR~~F~~A~~  205 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKM---GIEPIVMSAGELES-------EN-----A-----GEPGKLIRQRYREAAD  205 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHc---CCCeEEEEHHHhhc-------Cc-----C-----CcHHHHHHHHHHHHHH
Confidence            445578999999999999999999998   45789998886651       11     1     3222    2232222 


Q ss_pred             ----cCCCEEEEEecCCCCCHH------------HHHHHHHhhhc-------CeEecCCCceeecCCeEEEEecCCCCCC
Q 003038          730 ----NNPHRVFLIEDVEQADYC------------SQKGFKRAIES-------GRIVTSSGDEVSLGDAIVILSCESFSSR  786 (854)
Q Consensus       730 ----~~p~~ViliDEieka~~~------------v~~~Ll~~le~-------G~l~d~~G~~v~~~~aIiIlTsn~f~~~  786 (854)
                          +...+||||||||..-+.            +...|+..+|.       |..++    .-..++++||.|+|.++..
T Consensus       206 ~a~~~~aPcVLFIDEIDA~~g~r~~~~~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~----~~~~~~V~VIaTTNrpd~L  281 (413)
T PLN00020        206 IIKKKGKMSCLFINDLDAGAGRFGTTQYTVNNQMVNGTLMNIADNPTNVSLGGDWRE----KEEIPRVPIIVTGNDFSTL  281 (413)
T ss_pred             HhhccCCCeEEEEehhhhcCCCCCCCCcchHHHHHHHHHHHHhcCCccccccccccc----cccCCCceEEEeCCCcccC
Confidence                334599999999965321            22456777763       21110    1134578899999987766


Q ss_pred             CCC
Q 003038          787 SRA  789 (854)
Q Consensus       787 s~~  789 (854)
                      ..+
T Consensus       282 DpA  284 (413)
T PLN00020        282 YAP  284 (413)
T ss_pred             CHh
Confidence            444

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=98.40  E-value=7.5e-07  Score=103.22  Aligned_cols=140  Identities=14%  Similarity=0.152  Sum_probs=94.6

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .++|+...+..+...+...-                ....++++.|++|+||+.+|+.+.........+|+.+||..+. 
T Consensus       140 ~lig~s~~~~~l~~~i~~~a----------------~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~v~v~c~~~~-  202 (445)
T TIGR02915       140 GLITSSPGMQKICRTIEKIA----------------PSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIP-  202 (445)
T ss_pred             ceeecCHHHHHHHHHHHHHh----------------CCCCCEEEECCCCcCHHHHHHHHHHhCCcCCCCeEEEECCCCC-
Confidence            47888888877777666431                1234677899999999999999998876667889999999775 


Q ss_pred             cCCCccccccccccCCC-CC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeE
Q 003038          699 TRADSTEDSRNKRSRDE-QS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAI  775 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~-~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aI  775 (854)
                            +..--+.+.+. .| + |......+.+......++|||||+.+++.+|..|+++|++|.+.--.|....-.++.
T Consensus       203 ------~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~~~q~~l~~~l~~~~~~~~~~~~~~~~~~r  276 (445)
T TIGR02915       203 ------ENLLESELFGYEKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVR  276 (445)
T ss_pred             ------hHHHHHHhcCCCCCCcCCCccCCCCceeECCCCEEEEechhhCCHHHHHHHHHHHhhCeEEeCCCCceeeeceE
Confidence                  21111111110 00 0 111111122334456899999999999999999999999998875444333234778


Q ss_pred             EEEecC
Q 003038          776 VILSCE  781 (854)
Q Consensus       776 iIlTsn  781 (854)
                      ||+||+
T Consensus       277 ii~~~~  282 (445)
T TIGR02915       277 IVCATN  282 (445)
T ss_pred             EEEecC
Confidence            888886

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=98.40  E-value=6.7e-07  Score=86.89  Aligned_cols=108  Identities=12%  Similarity=0.181  Sum_probs=76.3

Q ss_pred             cccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcC
Q 003038          621 PWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTR  700 (854)
Q Consensus       621 ~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~  700 (854)
                      +|+..++..+.+.+.+...                ....+++.|++|+||+.+|+.|...-......|+.+++....   
T Consensus         1 vG~S~~~~~l~~~l~~~a~----------------~~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~~~~~~~---   61 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAK----------------SSSPVLITGEPGTGKSLLARALHRYSGRANGPFIVIDCASLP---   61 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHC----------------SSS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCCCHHCTC---
T ss_pred             CCCCHHHHHHHHHHHHHhC----------------CCCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEechhhCc---
Confidence            5788888888888887642                224689999999999999999998765555566665554321   


Q ss_pred             CCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEec
Q 003038          701 ADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSC  780 (854)
Q Consensus       701 ~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTs  780 (854)
                                              .+.+.+.....++|+|||.++++.|..|++.|+...          -.++.+|+||
T Consensus        62 ------------------------~~~l~~a~~gtL~l~~i~~L~~~~Q~~L~~~l~~~~----------~~~~RlI~ss  107 (138)
T PF14532_consen   62 ------------------------AELLEQAKGGTLYLKNIDRLSPEAQRRLLDLLKRQE----------RSNVRLIASS  107 (138)
T ss_dssp             ------------------------HHHHHHCTTSEEEEECGCCS-HHHHHHHHHHHHHCT----------TTTSEEEEEE
T ss_pred             ------------------------HHHHHHcCCCEEEECChHHCCHHHHHHHHHHHHhcC----------CCCeEEEEEe
Confidence                                    122333466789999999999999999999998732          2345788887


Q ss_pred             C
Q 003038          781 E  781 (854)
Q Consensus       781 n  781 (854)
                      +
T Consensus       108 ~  108 (138)
T PF14532_consen  108 S  108 (138)
T ss_dssp             C
T ss_pred             C
Confidence            4

>PRK04132 replication factor C small subunit; Provisional

Probab=98.39  E-value=7.5e-07  Score=108.83  Aligned_cols=96  Identities=21%  Similarity=0.301  Sum_probs=70.4

Q ss_pred             eEEEec--CCCchHHHHHHHHHHHHhCC--CCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHc----
Q 003038          659 WLFFQG--VDADAKEKIAKELARLVFGS--HNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSN----  730 (854)
Q Consensus       659 ~lLf~G--p~GvGKt~lAr~LA~~lfg~--~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~----  730 (854)
                      .-++.|  |.+.|||++|++||+.+||.  ..+++.+|.|...       ....+           .+.+.++...    
T Consensus       566 ~~~~~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNASd~r-------gid~I-----------R~iIk~~a~~~~~~  627 (846)
T PRK04132        566 HNFIGGNLPTVLHNTTAALALARELFGENWRHNFLELNASDER-------GINVI-----------REKVKEFARTKPIG  627 (846)
T ss_pred             hhhhcCCCCCcccHHHHHHHHHHhhhcccccCeEEEEeCCCcc-------cHHHH-----------HHHHHHHHhcCCcC
Confidence            456678  99999999999999999986  4578999888543       00011           0122232222    


Q ss_pred             -CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCC
Q 003038          731 -NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       731 -~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                       .++.||+|||+|+++++.|++|++.||+           .-.+++|||+||..
T Consensus       628 ~~~~KVvIIDEaD~Lt~~AQnALLk~lEe-----------p~~~~~FILi~N~~  670 (846)
T PRK04132        628 GASFKIIFLDEADALTQDAQQALRRTMEM-----------FSSNVRFILSCNYS  670 (846)
T ss_pred             CCCCEEEEEECcccCCHHHHHHHHHHhhC-----------CCCCeEEEEEeCCh
Confidence             2468999999999999999999999996           12467799999854

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=98.37  E-value=1.6e-06  Score=94.98  Aligned_cols=124  Identities=12%  Similarity=0.163  Sum_probs=83.6

Q ss_pred             ccccHHHHHHHHHHHHH------hhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcc
Q 003038          620 VPWQKDTVYDIANTVLK------CRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIAL  693 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~------~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~  693 (854)
                      |.|-.+|++-|-++|..      .-.|+.            +|---+|++||||+|||.|||++|-.-   ..-|..+..
T Consensus       214 Iagl~~AK~lL~EAVvlPi~mPe~F~Gir------------rPWkgvLm~GPPGTGKTlLAKAvATEc---~tTFFNVSs  278 (491)
T KOG0738|consen  214 IAGLHEAKKLLKEAVVLPIWMPEFFKGIR------------RPWKGVLMVGPPGTGKTLLAKAVATEC---GTTFFNVSS  278 (491)
T ss_pred             hcchHHHHHHHHHHHhhhhhhHHHHhhcc------------cccceeeeeCCCCCcHHHHHHHHHHhh---cCeEEEech
Confidence            67788899988888853      334554            345568899999999999999999864   233433333


Q ss_pred             ccccCcCCCccccccccccCCCCCCchHH----HHHHHHHcCCCEEEEEecCCC------------CCHHHHHHHHHhhh
Q 003038          694 SSFSSTRADSTEDSRNKRSRDEQSCSYIE----RFAEAVSNNPHRVFLIEDVEQ------------ADYCSQKGFKRAIE  757 (854)
Q Consensus       694 s~~~~~~~~s~e~~~~~rl~~~~g~g~~e----~L~eav~~~p~~ViliDEiek------------a~~~v~~~Ll~~le  757 (854)
                      +...       .+.     +     |-.|    -|++..|....++|||||||-            ++..|.+-||.-||
T Consensus       279 stlt-------SKw-----R-----GeSEKlvRlLFemARfyAPStIFiDEIDslcs~RG~s~EHEaSRRvKsELLvQmD  341 (491)
T KOG0738|consen  279 STLT-------SKW-----R-----GESEKLVRLLFEMARFYAPSTIFIDEIDSLCSQRGGSSEHEASRRVKSELLVQMD  341 (491)
T ss_pred             hhhh-------hhh-----c-----cchHHHHHHHHHHHHHhCCceeehhhHHHHHhcCCCccchhHHHHHHHHHHHHhh
Confidence            3222       111     1     4334    478888888889999999995            45678899999887


Q ss_pred             cCeEecCCCceeecCCeEEEEecC
Q 003038          758 SGRIVTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       758 ~G~l~d~~G~~v~~~~aIiIlTsn  781 (854)
                      -      -+....-+..+|||.+.
T Consensus       342 G------~~~t~e~~k~VmVLAAT  359 (491)
T KOG0738|consen  342 G------VQGTLENSKVVMVLAAT  359 (491)
T ss_pred             c------cccccccceeEEEEecc
Confidence            2      12222235667777553

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=98.37  E-value=1.5e-06  Score=96.95  Aligned_cols=141  Identities=13%  Similarity=0.135  Sum_probs=81.3

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC----CceEEEcc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH----NNFVSIAL  693 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~----~~~i~id~  693 (854)
                      ..|+||++++..+..++..       |           ..+-+||.|++|+|||++||.+++++....    .+|.    
T Consensus        17 ~~ivGq~~~k~al~~~~~~-------p-----------~~~~vli~G~~GtGKs~~ar~~~~~l~~~~~~~~~pf~----   74 (350)
T CHL00081         17 TAIVGQEEMKLALILNVID-------P-----------KIGGVMIMGDRGTGKSTTIRALVDLLPEIEVVKDDPFN----   74 (350)
T ss_pred             HHHhChHHHHHHHHHhccC-------C-----------CCCeEEEEcCCCCCHHHHHHHHHHHHhhcCccCCCCCC----
Confidence            4589999988877666543       2           245688999999999999999999885311    1221    


Q ss_pred             ccccCcCCCccc--c---------ccccc---cCC-CCCCchHHH------HHHH------------HHcCCCEEEEEec
Q 003038          694 SSFSSTRADSTE--D---------SRNKR---SRD-EQSCSYIER------FAEA------------VSNNPHRVFLIED  740 (854)
Q Consensus       694 s~~~~~~~~s~e--~---------~~~~r---l~~-~~g~g~~e~------L~ea------------v~~~p~~ViliDE  740 (854)
                       .|........+  .         ....+   .+. |.+-. .++      +..+            +.+....|+++||
T Consensus        75 -~~p~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~~t-ed~l~G~iD~~~al~~g~~~~~~GlL~~A~~GiL~lDE  152 (350)
T CHL00081         75 -SHPSDPELMSDEVREAIQNGETIETEKIKIPMVDLPLGAT-EDRVCGTIDIEKALTEGVKAFEPGLLAKANRGILYVDE  152 (350)
T ss_pred             -CCCCChhhhchhhhhhhcccccccceeccccceecCCCCc-hhhccCcccHHHHhhcCcccccCCeeeecCCCEEEecC
Confidence             11100000000  0         00000   000 11100 011      1112            2233357999999


Q ss_pred             CCCCCHHHHHHHHHhhhcCeEec-CCCceeecC-CeEEEEecCC
Q 003038          741 VEQADYCSQKGFKRAIESGRIVT-SSGDEVSLG-DAIVILSCES  782 (854)
Q Consensus       741 ieka~~~v~~~Ll~~le~G~l~d-~~G~~v~~~-~aIiIlTsn~  782 (854)
                      |+.+++.+|..|+++|++|..+- ..|....+. +.|+|.|.|.
T Consensus       153 InrL~~~~Q~~LLeam~e~~~~ier~G~s~~~p~rfiviaT~np  196 (350)
T CHL00081        153 VNLLDDHLVDILLDSAASGWNTVEREGISIRHPARFVLVGSGNP  196 (350)
T ss_pred             hHhCCHHHHHHHHHHHHhCCeEEeeCCeeeecCCCEEEEeccCc
Confidence            99999999999999999986553 235544443 4555555553

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=98.36  E-value=8e-07  Score=98.93  Aligned_cols=145  Identities=12%  Similarity=0.119  Sum_probs=81.0

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHH----------hCC---
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLV----------FGS---  684 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~l----------fg~---  684 (854)
                      ..|+||++++..+..++..       |           ..+++++.|++|+|||+++++|+..+          |++   
T Consensus         4 ~~ivgq~~~~~al~~~~~~-------~-----------~~g~vli~G~~G~gKttl~r~~~~~~~~~~~~~~~~~~~~~~   65 (337)
T TIGR02030         4 TAIVGQDEMKLALLLNVID-------P-----------KIGGVMVMGDRGTGKSTAVRALAALLPEIKAVAGCPFNSSPS   65 (337)
T ss_pred             cccccHHHHHHHHHHHhcC-------C-----------CCCeEEEEcCCCCCHHHHHHHHHHhhcccccccCCCCCCCCC
Confidence            4689999998887666542       1           25689999999999999999999988          221   


Q ss_pred             CCceEEEccccccCc-CCCcccc--ccccccCC----CCCCchHHHHHH------------HHHcCCCEEEEEecCCCCC
Q 003038          685 HNNFVSIALSSFSST-RADSTED--SRNKRSRD----EQSCSYIERFAE------------AVSNNPHRVFLIEDVEQAD  745 (854)
Q Consensus       685 ~~~~i~id~s~~~~~-~~~s~e~--~~~~rl~~----~~g~g~~e~L~e------------av~~~p~~ViliDEieka~  745 (854)
                      ...++..++...... ...+...  ..+-++..    ..-.|.. .+..            .+.+....++|+|||+.++
T Consensus        66 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~lP~~~t~d~l~G~~-d~~~~l~~g~~~~~~GlL~~A~~GvL~lDEi~~L~  144 (337)
T TIGR02030        66 DPEMMCEEVRIRVDSQEPLSIIKKPVPVVDLPLGATEDRVCGTL-DIERALTEGVKAFEPGLLARANRGILYIDEVNLLE  144 (337)
T ss_pred             CccccChHHhhhhhcccccccccCCCCcCCCCCCCcccceecch-hHhhHhhcCCEEeecCcceeccCCEEEecChHhCC
Confidence            111111111100000 0000000  00001110    0001211 1111            1222334799999999999


Q ss_pred             HHHHHHHHHhhhcCeEec-CCCceeecC-CeEEEEecC
Q 003038          746 YCSQKGFKRAIESGRIVT-SSGDEVSLG-DAIVILSCE  781 (854)
Q Consensus       746 ~~v~~~Ll~~le~G~l~d-~~G~~v~~~-~aIiIlTsn  781 (854)
                      +.+|..|+++|++|.++- ..|....+. +.++|.|.|
T Consensus       145 ~~~Q~~Ll~~l~~g~~~v~r~G~~~~~~~r~iviat~n  182 (337)
T TIGR02030       145 DHLVDVLLDVAASGWNVVEREGISIRHPARFVLVGSGN  182 (337)
T ss_pred             HHHHHHHHHHHHhCCeEEEECCEEEEcCCCEEEEeccc
Confidence            999999999999996432 235444443 445555555

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.

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=98.35  E-value=2.3e-06  Score=104.06  Aligned_cols=127  Identities=13%  Similarity=0.144  Sum_probs=75.1

Q ss_pred             HHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhh
Q 003038          217 YVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCL  296 (854)
Q Consensus       217 ~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~  296 (854)
                      .+...+...+-.+++|+||||||||++++.++..+          +.+++.++..  ..+. .++.+.+..+....... 
T Consensus        42 ~L~~~i~~~~~~slLL~GPpGtGKTTLA~aIA~~~----------~~~f~~lna~--~~~i-~dir~~i~~a~~~l~~~-  107 (725)
T PRK13341         42 LLRRAIKADRVGSLILYGPPGVGKTTLARIIANHT----------RAHFSSLNAV--LAGV-KDLRAEVDRAKERLERH-  107 (725)
T ss_pred             HHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHh----------cCcceeehhh--hhhh-HHHHHHHHHHHHHhhhc-
Confidence            34444555566799999999999999999999764          2345555432  1111 12222222222222222 


Q ss_pred             CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccC
Q 003038          297 GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLH  375 (854)
Q Consensus       297 ~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~  375 (854)
                      +.+.||||||+|.+ ....                 .   .|++. ..+|.+.+||+||...|.+   .+++|.+  |.+
T Consensus       108 ~~~~IL~IDEIh~Ln~~qQ-----------------d---aLL~~-lE~g~IiLI~aTTenp~~~---l~~aL~S--R~~  161 (725)
T PRK13341        108 GKRTILFIDEVHRFNKAQQ-----------------D---ALLPW-VENGTITLIGATTENPYFE---VNKALVS--RSR  161 (725)
T ss_pred             CCceEEEEeChhhCCHHHH-----------------H---HHHHH-hcCceEEEEEecCCChHhh---hhhHhhc--ccc
Confidence            45689999999999 4321                 1   13322 1223699999999987764   3567765  444


Q ss_pred             CCCCCCch
Q 003038          376 PLTIPAGS  383 (854)
Q Consensus       376 ~v~i~~~s  383 (854)
                      .+.++..+
T Consensus       162 v~~l~pLs  169 (725)
T PRK13341        162 LFRLKSLS  169 (725)
T ss_pred             ceecCCCC
Confidence            55555443

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=98.35  E-value=2.7e-06  Score=103.71  Aligned_cols=159  Identities=13%  Similarity=0.163  Sum_probs=101.3

Q ss_pred             HHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCccc--CCCcCC----cccCcceeEEEecCCCchHHHHHHHHHHH
Q 003038          607 ENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRK--GKFKDH----SEVKEETWLFFQGVDADAKEKIAKELARL  680 (854)
Q Consensus       607 e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~--~~~~~~----~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~  680 (854)
                      .-+..|.+.+.-.|+|+++++..|+-.+..   |..+..  +....+    .+-|...++|+.|++|+||+.+|+.+++.
T Consensus       439 ~i~~~L~~SiaP~I~G~e~vK~ailL~L~g---G~~k~~~~~~~~dg~~~~~~iRgdihVLLvGDPGTGKSqLAr~Ih~l  515 (915)
T PTZ00111        439 MIYRILLDSFAPSIKARNNVKIGLLCQLFS---GNKNSSDFNKSPDACYKVDNFRGIINVLLCGDPGTAKSQLLHYTHLL  515 (915)
T ss_pred             HHHHHHHHHhCCeEECCHHHHHHHHHHHhc---CCccccccccccccccccccccCCceEEEeCCCCccHHHHHHHHHHh
Confidence            446778888899999999999888655543   332100  000000    01245569999999999999999999985


Q ss_pred             Hh----CCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhh
Q 003038          681 VF----GSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAI  756 (854)
Q Consensus       681 lf----g~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~l  756 (854)
                      -.    -+...++.++++.+...      ...      ..| .+. .-.+++......+++|||++++++..|..|+++|
T Consensus       516 spR~~ytsG~~~s~vgLTa~~~~------~d~------~tG-~~~-le~GaLvlAdgGtL~IDEidkms~~~Q~aLlEaM  581 (915)
T PTZ00111        516 SPRSIYTSGKSSSSVGLTASIKF------NES------DNG-RAM-IQPGAVVLANGGVCCIDELDKCHNESRLSLYEVM  581 (915)
T ss_pred             CCccccCCCCCCccccccchhhh------ccc------ccC-ccc-ccCCcEEEcCCCeEEecchhhCCHHHHHHHHHHH
Confidence            32    22244444444432200      000      000 000 0011233444579999999999999999999999


Q ss_pred             hcCeEecC-CCceeec-CCeEEEEecCC
Q 003038          757 ESGRIVTS-SGDEVSL-GDAIVILSCES  782 (854)
Q Consensus       757 e~G~l~d~-~G~~v~~-~~aIiIlTsn~  782 (854)
                      +++.++-. .|-...+ .++.||.++|.
T Consensus       582 EqqtIsI~KaGi~~tL~ar~rVIAAaNP  609 (915)
T PTZ00111        582 EQQTVTIAKAGIVATLKAETAILASCNP  609 (915)
T ss_pred             hCCEEEEecCCcceecCCCeEEEEEcCC
Confidence            99998744 4655555 48889999986

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=98.35  E-value=1.2e-06  Score=102.03  Aligned_cols=140  Identities=11%  Similarity=0.186  Sum_probs=97.4

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .++|...+...+...+.+..                +...++++.|.+|+||+.+|+++.+.......+|+.+||..+.+
T Consensus       135 ~lig~s~~~~~v~~~i~~~a----------------~~~~~vli~Ge~GtGK~~~A~~ih~~~~~~~~~~~~~~c~~~~~  198 (463)
T TIGR01818       135 ELIGEAPAMQEVFRAIGRLS----------------RSDITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPK  198 (463)
T ss_pred             ceeecCHHHHHHHHHHHHHh----------------CcCCeEEEECCCCCCHHHHHHHHHHhCCCCCCCeEEEeCCCCCH
Confidence            47888888888887776532                12246789999999999999999998877788999999987751


Q ss_pred             cCCCccccccccccCC-CCC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeE
Q 003038          699 TRADSTEDSRNKRSRD-EQS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAI  775 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~-~~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aI  775 (854)
                             ....+.+.+ ..+ + |....-.+.+.......+|||||+.+++.+|..|+++|++|.++..+|....-.++.
T Consensus       199 -------~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~ei~~l~~~~q~~ll~~l~~~~~~~~~~~~~~~~~~r  271 (463)
T TIGR01818       199 -------DLIESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVR  271 (463)
T ss_pred             -------HHHHHHhcCCCCCCCCCcccCCCCcEEECCCCeEEEEchhhCCHHHHHHHHHHHhcCcEEECCCCceeeeeeE
Confidence                   111111111 000 1 111111112234446789999999999999999999999999886555544445778


Q ss_pred             EEEecC
Q 003038          776 VILSCE  781 (854)
Q Consensus       776 iIlTsn  781 (854)
                      ||+||+
T Consensus       272 ii~~~~  277 (463)
T TIGR01818       272 IVAATH  277 (463)
T ss_pred             EEEeCC
Confidence            888886

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.34  E-value=2e-06  Score=106.69  Aligned_cols=111  Identities=14%  Similarity=0.214  Sum_probs=74.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC-------CCceEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS-------HNNFVS  690 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-------~~~~i~  690 (854)
                      ..|+||++.+..+...+.+.                  ...+.+|+||+|||||.+++.||+.+-..       ...++.
T Consensus       187 d~~iGr~~ei~~~i~~l~r~------------------~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~  248 (852)
T TIGR03345       187 DPVLGRDDEIRQMIDILLRR------------------RQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLS  248 (852)
T ss_pred             CcccCCHHHHHHHHHHHhcC------------------CcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEE
Confidence            35799998877777765432                  12266899999999999999999987322       234566


Q ss_pred             EccccccCcCCCccccccccccCCCCCC--chHHHH---HHHHHc-CCCEEEEEecCCCCCH--------HHHHHHHHhh
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSC--SYIERF---AEAVSN-NPHRVFLIEDVEQADY--------CSQKGFKRAI  756 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~--g~~e~L---~eav~~-~p~~ViliDEieka~~--------~v~~~Ll~~l  756 (854)
                      ++++.+.                ++..|  .+.++|   .+.+++ ....|+|||||+.+..        ++-|.|+.++
T Consensus       249 l~l~~l~----------------ag~~~~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l  312 (852)
T TIGR03345       249 LDLGLLQ----------------AGASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQAGQGDAANLLKPAL  312 (852)
T ss_pred             eehhhhh----------------cccccchHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCCccccccHHHHhhHHh
Confidence            6665432                11122  233343   333333 3467999999998742        4556899999


Q ss_pred             hcCeEe
Q 003038          757 ESGRIV  762 (854)
Q Consensus       757 e~G~l~  762 (854)
                      +.|.++
T Consensus       313 ~~G~l~  318 (852)
T TIGR03345       313 ARGELR  318 (852)
T ss_pred             hCCCeE
Confidence            998887

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.

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

Probab=98.33  E-value=1.1e-06  Score=100.19  Aligned_cols=95  Identities=13%  Similarity=0.150  Sum_probs=61.3

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcc----cccccccchHH---HH-
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLS----ISSFRHMNRVE---VE-  282 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~----~~~l~~~~rge---~E-  282 (854)
                      .++++..++..|.  .+.|++|+|+||+|||.+|+.||..+.....+.   .+..+.++    ...++.|++-.   ++ 
T Consensus       180 ~e~~le~l~~~L~--~~~~iil~GppGtGKT~lA~~la~~l~~~~~~~---~v~~VtFHpsySYeDFI~G~rP~~vgy~~  254 (459)
T PRK11331        180 PETTIETILKRLT--IKKNIILQGPPGVGKTFVARRLAYLLTGEKAPQ---RVNMVQFHQSYSYEDFIQGYRPNGVGFRR  254 (459)
T ss_pred             CHHHHHHHHHHHh--cCCCEEEECCCCCCHHHHHHHHHHHhcCCcccc---eeeEEeecccccHHHHhcccCCCCCCeEe
Confidence            7888999998887  478999999999999999999998875332222   23333333    22344332100   10 


Q ss_pred             --HHHHHHHHHHHhhhCCCeEEEeCccccc
Q 003038          283 --QRVEEIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       283 --~rl~~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                        --+.++...++.....+.|||||||...
T Consensus       255 ~~G~f~~~~~~A~~~p~~~~vliIDEINRa  284 (459)
T PRK11331        255 KDGIFYNFCQQAKEQPEKKYVFIIDEINRA  284 (459)
T ss_pred             cCchHHHHHHHHHhcccCCcEEEEehhhcc
Confidence              1234444555543135899999999776

>PRK10865 protein disaggregation chaperone; Provisional

Probab=98.31  E-value=1.6e-06  Score=107.83  Aligned_cols=110  Identities=11%  Similarity=0.199  Sum_probs=75.0

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC-------CCceEEE
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS-------HNNFVSI  691 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-------~~~~i~i  691 (854)
                      .|+||++-+..+...+.+.                  ....++|+||+|||||.+|+.||..+...       ...++.+
T Consensus       179 ~vigr~~ei~~~i~iL~r~------------------~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~l  240 (857)
T PRK10865        179 PVIGRDEEIRRTIQVLQRR------------------TKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLAL  240 (857)
T ss_pred             cCCCCHHHHHHHHHHHhcC------------------CcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEEE
Confidence            4799998777776665442                  12367899999999999999999987532       2456666


Q ss_pred             ccccccCcCCCccccccccccCCCCCC--chHHHHHHH---H-HcCCCEEEEEecCCCCC--------HHHHHHHHHhhh
Q 003038          692 ALSSFSSTRADSTEDSRNKRSRDEQSC--SYIERFAEA---V-SNNPHRVFLIEDVEQAD--------YCSQKGFKRAIE  757 (854)
Q Consensus       692 d~s~~~~~~~~s~e~~~~~rl~~~~g~--g~~e~L~ea---v-~~~p~~ViliDEieka~--------~~v~~~Ll~~le  757 (854)
                      +++...                .+..|  .+.++|...   + +.....|+||||||.+.        -+.++.|+.+++
T Consensus       241 ~l~~l~----------------ag~~~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~~~~~d~~~~lkp~l~  304 (857)
T PRK10865        241 DMGALV----------------AGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALA  304 (857)
T ss_pred             ehhhhh----------------hccchhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCCCccchhHHHHhcchhh
Confidence            665332                11122  233333333   3 23456899999999874        247999999999


Q ss_pred             cCeEe
Q 003038          758 SGRIV  762 (854)
Q Consensus       758 ~G~l~  762 (854)
                      .|.++
T Consensus       305 ~g~l~  309 (857)
T PRK10865        305 RGELH  309 (857)
T ss_pred             cCCCe
Confidence            98777

>PRK15115 response regulator GlrR; Provisional

Probab=98.29  E-value=2e-06  Score=99.68  Aligned_cols=117  Identities=9%  Similarity=0.106  Sum_probs=79.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCC-CCC-C-chHHHHHHHHHcCCCE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRD-EQS-C-SYIERFAEAVSNNPHR  734 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~-~~g-~-g~~e~L~eav~~~p~~  734 (854)
                      .++++.|++|+||+.+|+.+.+.......+|+.+||..+..       ....+.+.+ ..| + |....-...+......
T Consensus       158 ~~vli~Ge~GtGk~~lA~~ih~~s~r~~~~f~~i~c~~~~~-------~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~g  230 (444)
T PRK15115        158 VSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALPE-------QLLESELFGHARGAFTGAVSNREGLFQAAEGG  230 (444)
T ss_pred             CeEEEEcCCcchHHHHHHHHHHhcCCCCCCeEEEeCCCCCH-------HHHHHHhcCCCcCCCCCCccCCCCcEEECCCC
Confidence            47899999999999999999998766678999999997752       111011110 000 0 1100001112334457


Q ss_pred             EEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecC
Q 003038          735 VFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       735 ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn  781 (854)
                      .+|||||+.+++..|..|+++|++|.++--.+....-.++.||+||+
T Consensus       231 tl~l~~i~~l~~~~q~~L~~~l~~~~~~~~g~~~~~~~~~rii~~~~  277 (444)
T PRK15115        231 TLFLDEIGDMPAPLQVKLLRVLQERKVRPLGSNRDIDIDVRIISATH  277 (444)
T ss_pred             EEEEEccccCCHHHHHHHHHHHhhCCEEeCCCCceeeeeEEEEEeCC
Confidence            99999999999999999999999998864333332334788999886

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=98.28  E-value=2.9e-06  Score=91.59  Aligned_cols=136  Identities=11%  Similarity=0.017  Sum_probs=78.0

Q ss_pred             HHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccc------ccccccchHHH-----
Q 003038          213 EDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSI------SSFRHMNRVEV-----  281 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~------~~l~~~~rge~-----  281 (854)
                      +-+++++..+.  ..++++|.||||||||++|+.+|..+          |..++.++.      +.++..+.|.-     
T Consensus         9 ~l~~~~l~~l~--~g~~vLL~G~~GtGKT~lA~~la~~l----------g~~~~~i~~~~~~~~~dllg~~~~~~~~~~~   76 (262)
T TIGR02640         9 RVTSRALRYLK--SGYPVHLRGPAGTGKTTLAMHVARKR----------DRPVMLINGDAELTTSDLVGSYAGYTRKKVH   76 (262)
T ss_pred             HHHHHHHHHHh--cCCeEEEEcCCCCCHHHHHHHHHHHh----------CCCEEEEeCCccCCHHHHhhhhcccchhhHH
Confidence            33455666555  46799999999999999999999753          345555533      23333222111     


Q ss_pred             HHHHH----------------HHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcc-----
Q 003038          282 EQRVE----------------EIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVC-----  339 (854)
Q Consensus       282 E~rl~----------------~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~-----  339 (854)
                      .+-+.                -+...++    .|-+|+||||+.+ ..-                 ...+..+|.     
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~g~l~~A~~----~g~~lllDEi~r~~~~~-----------------q~~Ll~~Le~~~~~  135 (262)
T TIGR02640        77 DQFIHNVVKLEDIVRQNWVDNRLTLAVR----EGFTLVYDEFTRSKPET-----------------NNVLLSVFEEGVLE  135 (262)
T ss_pred             HHHHHHhhhhhcccceeecCchHHHHHH----cCCEEEEcchhhCCHHH-----------------HHHHHHHhcCCeEE
Confidence            11000                1112222    3458999999988 321                 112333331     


Q ss_pred             -cCCC--------CceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCch
Q 003038          340 -GIGE--------NARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGS  383 (854)
Q Consensus       340 -~~~g--------~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~s  383 (854)
                       +..+        ...+++|+++++..|.-..+..++|.+  ||-.+.|+-|+
T Consensus       136 i~~~~~~~~~i~~~~~frvIaTsN~~~~~g~~~l~~aL~~--R~~~i~i~~P~  186 (262)
T TIGR02640       136 LPGKRGTSRYVDVHPEFRVIFTSNPVEYAGVHETQDALLD--RLITIFMDYPD  186 (262)
T ss_pred             ccCCCCCCceEecCCCCEEEEeeCCccccceecccHHHHh--hcEEEECCCCC
Confidence             1111        025899999998887655566788888  55444444443

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).

>TIGR00368 Mg chelatase-related protein

Probab=98.28  E-value=4.7e-06  Score=97.47  Aligned_cols=140  Identities=12%  Similarity=0.129  Sum_probs=85.5

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||..++..+.-++.                    ....++|.||+|+|||++|+.|+..+...... +.++.+...
T Consensus       192 ~dv~Gq~~~~~al~~aa~--------------------~g~~vlliG~pGsGKTtlar~l~~llp~~~~~-~~le~~~i~  250 (499)
T TIGR00368       192 KDIKGQQHAKRALEIAAA--------------------GGHNLLLFGPPGSGKTMLASRLQGILPPLTNE-EAIETARIW  250 (499)
T ss_pred             HHhcCcHHHHhhhhhhcc--------------------CCCEEEEEecCCCCHHHHHHHHhcccCCCCCc-EEEeccccc
Confidence            457999988766554432                    12478999999999999999999987543211 222222211


Q ss_pred             CcCC-C------cc----c-ccccc--ccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEec
Q 003038          698 STRA-D------ST----E-DSRNK--RSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVT  763 (854)
Q Consensus       698 ~~~~-~------s~----e-~~~~~--rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d  763 (854)
                      +... .      ..    . .|+.+  .++++   |.. .-.+.+......|+|||||+++++.+|+.|++.||+|.++-
T Consensus       251 s~~g~~~~~~~~~~~Pf~~p~~s~s~~~~~gg---g~~-~~pG~i~lA~~GvLfLDEi~e~~~~~~~~L~~~LE~~~v~i  326 (499)
T TIGR00368       251 SLVGKLIDRKQIKQRPFRSPHHSASKPALVGG---GPI-PLPGEISLAHNGVLFLDELPEFKRSVLDALREPIEDGSISI  326 (499)
T ss_pred             cchhhhccccccccCCccccccccchhhhhCC---ccc-cchhhhhccCCCeEecCChhhCCHHHHHHHHHHHHcCcEEE
Confidence            1000 0      00    0 00000  01110   100 01223455567899999999999999999999999999763


Q ss_pred             -CCCceeec-CCeEEEEecCC
Q 003038          764 -SSGDEVSL-GDAIVILSCES  782 (854)
Q Consensus       764 -~~G~~v~~-~~aIiIlTsn~  782 (854)
                       ..|..+.+ .+..+|.++|.
T Consensus       327 ~r~g~~~~~pa~frlIaa~Np  347 (499)
T TIGR00368       327 SRASAKIFYPARFQLVAAMNP  347 (499)
T ss_pred             EecCcceeccCCeEEEEecCC
Confidence             23444444 58889998884

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>smart00350 MCM minichromosome maintenance proteins

Probab=98.28  E-value=3.8e-06  Score=99.06  Aligned_cols=157  Identities=14%  Similarity=0.183  Sum_probs=96.9

Q ss_pred             HHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC
Q 003038          607 ENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN  686 (854)
Q Consensus       607 e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~  686 (854)
                      ..+..|.+.+...|+||+.+...|.-++...   ..+...   ++..-+...++|+.|++|+|||.+||.+++..-.  .
T Consensus       192 ~~~~~l~~si~p~i~G~~~~k~~l~l~l~gg---~~~~~~---~~~~~r~~~~vLL~G~pGtGKs~lar~l~~~~~r--~  263 (509)
T smart00350      192 DIYERLSRSLAPSIYGHEDIKKAILLLLFGG---VHKNLP---DGMKIRGDINILLLGDPGTAKSQLLKYVEKTAPR--A  263 (509)
T ss_pred             HHHHHHHHhhCccccCcHHHHHHHHHHHhCC---CccccC---CCccccccceEEEeCCCChhHHHHHHHHHHHcCc--c
Confidence            3456788899999999998877766555432   111000   0001133458999999999999999999997632  2


Q ss_pred             ceEEEccc---cccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEec
Q 003038          687 NFVSIALS---SFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVT  763 (854)
Q Consensus       687 ~~i~id~s---~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d  763 (854)
                      .|+....+   .+..        ...   ..+.+.++. .-.+++......+++|||++++++..|..|+++|+++.++-
T Consensus       264 ~~~~~~~~~~~~l~~--------~~~---~~~~~g~~~-~~~G~l~~A~~Gil~iDEi~~l~~~~q~~L~e~me~~~i~i  331 (509)
T smart00350      264 VYTTGKGSSAVGLTA--------AVT---RDPETREFT-LEGGALVLADNGVCCIDEFDKMDDSDRTAIHEAMEQQTISI  331 (509)
T ss_pred             eEcCCCCCCcCCccc--------cce---EccCcceEE-ecCccEEecCCCEEEEechhhCCHHHHHHHHHHHhcCEEEE
Confidence            23321111   1110        000   000000000 00112233446799999999999999999999999999875


Q ss_pred             C-CCceeec-CCeEEEEecCCC
Q 003038          764 S-SGDEVSL-GDAIVILSCESF  783 (854)
Q Consensus       764 ~-~G~~v~~-~~aIiIlTsn~f  783 (854)
                      . .|....+ .++.||.|+|..
T Consensus       332 ~k~G~~~~l~~~~~viAa~NP~  353 (509)
T smart00350      332 AKAGITTTLNARCSVLAAANPI  353 (509)
T ss_pred             EeCCEEEEecCCcEEEEEeCCC
Confidence            4 4655555 478889999853

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=98.27  E-value=2.2e-06  Score=102.33  Aligned_cols=142  Identities=16%  Similarity=0.132  Sum_probs=93.5

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +.|-|.++|..+|-+.|.-.+....+.+ ..     .|.+.=.|++||||||||.|||++|-.-   .-+|+.+..|+|.
T Consensus       311 kDVAG~deAK~El~E~V~fLKNP~~Y~~-lG-----AKiPkGvLL~GPPGTGKTLLAKAiAGEA---gVPF~svSGSEFv  381 (774)
T KOG0731|consen  311 KDVAGVDEAKEELMEFVKFLKNPEQYQE-LG-----AKIPKGVLLVGPPGTGKTLLAKAIAGEA---GVPFFSVSGSEFV  381 (774)
T ss_pred             ccccCcHHHHHHHHHHHHHhcCHHHHHH-cC-----CcCcCceEEECCCCCcHHHHHHHHhccc---CCceeeechHHHH
Confidence            6789999999999999865433222111 00     1233345788999999999999999754   5799999999998


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCH---------------HHHHHHHHhhhcCeEe
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADY---------------CSQKGFKRAIESGRIV  762 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~---------------~v~~~Ll~~le~G~l~  762 (854)
                             |-+-      +.|..-...|+...|.+-.+|||+||||-...               ..+|.|+--|| |   
T Consensus       382 -------E~~~------g~~asrvr~lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emD-g---  444 (774)
T KOG0731|consen  382 -------EMFV------GVGASRVRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMD-G---  444 (774)
T ss_pred             -------HHhc------ccchHHHHHHHHHhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhc-C---
Confidence                   3221      11111223677778888889999999995422               23344444443 2   


Q ss_pred             cCCCceeecCCeEEEEecCCCCCCCCCC
Q 003038          763 TSSGDEVSLGDAIVILSCESFSSRSRAC  790 (854)
Q Consensus       763 d~~G~~v~~~~aIiIlTsn~f~~~s~~~  790 (854)
                          -..+ .++||+.+||-.|..-.+.
T Consensus       445 ----f~~~-~~vi~~a~tnr~d~ld~al  467 (774)
T KOG0731|consen  445 ----FETS-KGVIVLAATNRPDILDPAL  467 (774)
T ss_pred             ----CcCC-CcEEEEeccCCccccCHHh
Confidence                2223 6788899999766655553

>TIGR00763 lon ATP-dependent protease La

Probab=98.26  E-value=2e-06  Score=106.36  Aligned_cols=126  Identities=7%  Similarity=0.039  Sum_probs=80.1

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc---------ccchHHHHHHHHHHHHHHHhhhC
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR---------HMNRVEVEQRVEEIKNLVRSCLG  297 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~---------~~~rge~E~rl~~l~~~~~~~~~  297 (854)
                      ..+++|+||||||||++++.+|..+          +..++.++++.+.         ..|.|....++.+.+..+...  
T Consensus       347 ~~~lll~GppG~GKT~lAk~iA~~l----------~~~~~~i~~~~~~~~~~i~g~~~~~~g~~~g~i~~~l~~~~~~--  414 (775)
T TIGR00763       347 GPILCLVGPPGVGKTSLGKSIAKAL----------NRKFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQGLKKAKTK--  414 (775)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHh----------cCCeEEEeCCCcccHHHHcCCCCceeCCCCchHHHHHHHhCcC--
Confidence            3468999999999999999999875          3456666544321         236677777777776665543  


Q ss_pred             CCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc---------CCC----CceEEEEEecCHHHHHHhhc
Q 003038          298 RGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG---------IGE----NARFWLMGIATFQSYMRCKS  363 (854)
Q Consensus       298 ~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~---------~~g----~g~l~lIgatT~~ey~k~~~  363 (854)
                      .+ |+|||||+.+ ....+.         +    ..-+-.+|.+         ..+    -+.+.+|+||+.-.     .
T Consensus       415 ~~-villDEidk~~~~~~~~---------~----~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~~I~TtN~~~-----~  475 (775)
T TIGR00763       415 NP-LFLLDEIDKIGSSFRGD---------P----ASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIATANSID-----T  475 (775)
T ss_pred             CC-EEEEechhhcCCccCCC---------H----HHHHHHhcCHHhcCccccccCCceeccCCEEEEEecCCch-----h
Confidence            34 7899999999 422111         1    1112222221         000    02588888887632     4


Q ss_pred             cCCchhhhhccCCCCCCCchHH
Q 003038          364 GHPSLETLWSLHPLTIPAGSLS  385 (854)
Q Consensus       364 ~~pale~~~~~~~v~i~~~sl~  385 (854)
                      -+|+|-+  ||+.|.++..+..
T Consensus       476 i~~~L~~--R~~vi~~~~~~~~  495 (775)
T TIGR00763       476 IPRPLLD--RMEVIELSGYTEE  495 (775)
T ss_pred             CCHHHhC--CeeEEecCCCCHH
Confidence            5899998  8888888876643

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.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=98.26  E-value=3.5e-06  Score=88.69  Aligned_cols=74  Identities=12%  Similarity=0.145  Sum_probs=58.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      .+++|+||+|+|||.+|+++++.++.....++.+++....       +..                  .  ......+|+
T Consensus        43 ~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~~~~~-------~~~------------------~--~~~~~~~li   95 (227)
T PRK08903         43 RFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAASPL-------LAF------------------D--FDPEAELYA   95 (227)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEehHHhH-------HHH------------------h--hcccCCEEE
Confidence            4789999999999999999999988777788888776443       110                  0  011256999


Q ss_pred             EecCCCCCHHHHHHHHHhhhc
Q 003038          738 IEDVEQADYCSQKGFKRAIES  758 (854)
Q Consensus       738 iDEieka~~~v~~~Ll~~le~  758 (854)
                      |||||.+++..+..|+.+++.
T Consensus        96 iDdi~~l~~~~~~~L~~~~~~  116 (227)
T PRK08903         96 VDDVERLDDAQQIALFNLFNR  116 (227)
T ss_pred             EeChhhcCchHHHHHHHHHHH
Confidence            999999999999999999974

>PRK06893 DNA replication initiation factor; Validated

Probab=98.25  E-value=3.5e-06  Score=89.18  Aligned_cols=93  Identities=11%  Similarity=0.204  Sum_probs=59.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      .+++|+||+|+|||.|++++|..+.......+.+.+....                     .+...+.+.+  ....+++
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~~~~~---------------------~~~~~~~~~~--~~~dlLi   96 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLSKSQ---------------------YFSPAVLENL--EQQDLVC   96 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeHHHhh---------------------hhhHHHHhhc--ccCCEEE
Confidence            4799999999999999999999886554455555543221                     0001122222  2357999


Q ss_pred             EecCCCCC--HHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCC
Q 003038          738 IEDVEQAD--YCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       738 iDEieka~--~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      ||||+...  +..+..|+..|+.-+  +       -+..++|+|+|.
T Consensus        97 lDDi~~~~~~~~~~~~l~~l~n~~~--~-------~~~~illits~~  134 (229)
T PRK06893         97 LDDLQAVIGNEEWELAIFDLFNRIK--E-------QGKTLLLISADC  134 (229)
T ss_pred             EeChhhhcCChHHHHHHHHHHHHHH--H-------cCCcEEEEeCCC
Confidence            99999864  555667777776421  1       123457787763

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.23  E-value=3.6e-06  Score=104.67  Aligned_cols=111  Identities=14%  Similarity=0.203  Sum_probs=77.8

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC-------CCceEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS-------HNNFVS  690 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-------~~~~i~  690 (854)
                      ..|+|.+..+..+...+.+.                  ....++|+||+|||||.+|+.||..+-..       ...++.
T Consensus       179 ~~~igr~~ei~~~~~~L~r~------------------~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~  240 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRR------------------TKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVIT  240 (821)
T ss_pred             CCCCCcHHHHHHHHHHHccc------------------ccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEE
Confidence            45899998888888876542                  11256899999999999999999987421       246677


Q ss_pred             EccccccCcCCCccccccccccCCCCCC-c-hHHH---HHHHHHcCCCEEEEEecCCCCC--------HHHHHHHHHhhh
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSC-S-YIER---FAEAVSNNPHRVFLIEDVEQAD--------YCSQKGFKRAIE  757 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~-g-~~e~---L~eav~~~p~~ViliDEieka~--------~~v~~~Ll~~le  757 (854)
                      +|++...                ++..| | +.++   +.+.+...+..|+||||||...        .++.+.|+.++.
T Consensus       241 l~~~~l~----------------ag~~~~ge~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l~  304 (821)
T CHL00095        241 LDIGLLL----------------AGTKYRGEFEERLKRIFDEIQENNNIILVIDEVHTLIGAGAAEGAIDAANILKPALA  304 (821)
T ss_pred             eeHHHHh----------------ccCCCccHHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCCCCCcccHHHHhHHHHh
Confidence            7765332                12222 3 4343   3444455667899999998442        257899999999


Q ss_pred             cCeEe
Q 003038          758 SGRIV  762 (854)
Q Consensus       758 ~G~l~  762 (854)
                      .|.++
T Consensus       305 rg~l~  309 (821)
T CHL00095        305 RGELQ  309 (821)
T ss_pred             CCCcE
Confidence            98877

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.19  E-value=6.8e-06  Score=87.28  Aligned_cols=80  Identities=11%  Similarity=0.199  Sum_probs=49.8

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      .+++|+||+|+|||.++++++..+.........+.+..+.                     .+...+.+.+.+  +.+++
T Consensus        46 ~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~~~~~---------------------~~~~~~~~~~~~--~dlli  102 (235)
T PRK08084         46 GYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPLDKRA---------------------WFVPEVLEGMEQ--LSLVC  102 (235)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEHHHHh---------------------hhhHHHHHHhhh--CCEEE
Confidence            3799999999999999999999876444444444443221                     011112222322  46999


Q ss_pred             EecCCCCC--HHH----HHHHHHhhhcCe
Q 003038          738 IEDVEQAD--YCS----QKGFKRAIESGR  760 (854)
Q Consensus       738 iDEieka~--~~v----~~~Ll~~le~G~  760 (854)
                      ||||+...  +..    ++.|...++.|+
T Consensus       103 iDdi~~~~~~~~~~~~lf~l~n~~~e~g~  131 (235)
T PRK08084        103 IDNIECIAGDELWEMAIFDLYNRILESGR  131 (235)
T ss_pred             EeChhhhcCCHHHHHHHHHHHHHHHHcCC
Confidence            99999874  333    444455555443

>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.19  E-value=2.5e-06  Score=92.09  Aligned_cols=80  Identities=16%  Similarity=0.231  Sum_probs=61.9

Q ss_pred             HHHHHhhcCcccccHHHHHHHHHHHHHh--hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc
Q 003038          610 TSLCNALEKKVPWQKDTVYDIANTVLKC--RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN  687 (854)
Q Consensus       610 ~~L~~~L~~~V~GQ~~av~~Ia~~v~~~--rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~  687 (854)
                      +.+...|.+.|+||++|.+.|+-+++..  |..+...-+.      .=-+-.+|+.||||||||++||.||++.   ..+
T Consensus         7 reIV~eLd~yIIGQ~~AKkaVAIALRNR~RR~qL~~~lr~------EV~PKNILMIGpTGVGKTEIARRLAkl~---~aP   77 (444)
T COG1220           7 REIVSELDRYIIGQDEAKKAVAIALRNRWRRMQLEEELRD------EVTPKNILMIGPTGVGKTEIARRLAKLA---GAP   77 (444)
T ss_pred             HHHHHHHHhHhcCcHHHHHHHHHHHHHHHHHHhcCHHHhh------ccCccceEEECCCCCcHHHHHHHHHHHh---CCC
Confidence            4667788899999999999999999753  3333221110      0112378999999999999999999998   579


Q ss_pred             eEEEccccccC
Q 003038          688 FVSIALSSFSS  698 (854)
Q Consensus       688 ~i~id~s~~~~  698 (854)
                      |+.+..+.|++
T Consensus        78 FiKVEATKfTE   88 (444)
T COG1220          78 FIKVEATKFTE   88 (444)
T ss_pred             eEEEEeeeeee
Confidence            99999998886

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=98.19  E-value=9.9e-06  Score=87.77  Aligned_cols=146  Identities=14%  Similarity=0.182  Sum_probs=90.1

Q ss_pred             HHHHHHHhhcc---CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccc--------------ccccc-
Q 003038          215 VMYVIENLMSK---RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSIS--------------SFRHM-  276 (854)
Q Consensus       215 i~~v~~~L~r~---~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~--------------~l~~~-  276 (854)
                      +.++-++|...   +-.|.+|||+++.|||++++.+++.--...-++. ....|+.+.+.              .|.+. 
T Consensus        46 L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~-~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP~  124 (302)
T PF05621_consen   46 LDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDA-ERIPVVYVQMPPEPDERRFYSAILEALGAPY  124 (302)
T ss_pred             HHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCC-ccccEEEEecCCCCChHHHHHHHHHHhCccc
Confidence            44444444433   3468999999999999999988875433222221 23467776652              11111 


Q ss_pred             -chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc--cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEec
Q 003038          277 -NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA--EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIA  353 (854)
Q Consensus       277 -~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l--~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgat  353 (854)
                       .+.-..++-..++..++..  +.=+|.|||+|.+  |....               .-++-|+||.-+..-++-+||++
T Consensus       125 ~~~~~~~~~~~~~~~llr~~--~vrmLIIDE~H~lLaGs~~~---------------qr~~Ln~LK~L~NeL~ipiV~vG  187 (302)
T PF05621_consen  125 RPRDRVAKLEQQVLRLLRRL--GVRMLIIDEFHNLLAGSYRK---------------QREFLNALKFLGNELQIPIVGVG  187 (302)
T ss_pred             CCCCCHHHHHHHHHHHHHHc--CCcEEEeechHHHhcccHHH---------------HHHHHHHHHHHhhccCCCeEEec
Confidence             1222222222333444443  3458999999998  54321               22444555430111258999999


Q ss_pred             CHHHHHHhhccCCchhhhhccCCCCCCC
Q 003038          354 TFQSYMRCKSGHPSLETLWSLHPLTIPA  381 (854)
Q Consensus       354 T~~ey~k~~~~~pale~~~~~~~v~i~~  381 (854)
                      |.+.|. .+..||-|++  ||+++.+|.
T Consensus       188 t~~A~~-al~~D~QLa~--RF~~~~Lp~  212 (302)
T PF05621_consen  188 TREAYR-ALRTDPQLAS--RFEPFELPR  212 (302)
T ss_pred             cHHHHH-HhccCHHHHh--ccCCccCCC
Confidence            999998 5799999999  999999984

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK12377 putative replication protein; Provisional

Probab=98.19  E-value=7.4e-06  Score=87.54  Aligned_cols=88  Identities=13%  Similarity=0.272  Sum_probs=60.1

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      .+|+|+||+|+|||.||.+||..+......++.+.+.++.       ...  +.... .+ ...+.+.+.+.  ...|++
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~~~~l~-------~~l--~~~~~-~~-~~~~~~l~~l~--~~dLLi  168 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVPDVM-------SRL--HESYD-NG-QSGEKFLQELC--KVDLLV  168 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEHHHHH-------HHH--HHHHh-cc-chHHHHHHHhc--CCCEEE
Confidence            4899999999999999999999987655666666665444       111  00000 00 01123334333  356999


Q ss_pred             EecC--CCCCHHHHHHHHHhhhc
Q 003038          738 IEDV--EQADYCSQKGFKRAIES  758 (854)
Q Consensus       738 iDEi--eka~~~v~~~Ll~~le~  758 (854)
                      |||+  ++.++..+..|.++|+.
T Consensus       169 IDDlg~~~~s~~~~~~l~~ii~~  191 (248)
T PRK12377        169 LDEIGIQRETKNEQVVLNQIIDR  191 (248)
T ss_pred             EcCCCCCCCCHHHHHHHHHHHHH
Confidence            9999  77788899999999986

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.19  E-value=9.7e-06  Score=91.41  Aligned_cols=145  Identities=8%  Similarity=0.063  Sum_probs=83.8

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC------CceEEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH------NNFVSI  691 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~------~~~i~i  691 (854)
                      +.++|.++-++.|...+..+-.|              ...+.++++||+|+|||.+++.+++.+-...      -.++.+
T Consensus        15 ~~l~gRe~e~~~l~~~l~~~~~~--------------~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~i   80 (365)
T TIGR02928        15 DRIVHRDEQIEELAKALRPILRG--------------SRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYV   80 (365)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHcC--------------CCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEE
Confidence            57899999999999998875432              1124789999999999999999998774221      357888


Q ss_pred             ccccccCcCCCcccccccccc------CCCCCCchHH---HHHHHHH-cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeE
Q 003038          692 ALSSFSSTRADSTEDSRNKRS------RDEQSCSYIE---RFAEAVS-NNPHRVFLIEDVEQADYCSQKGFKRAIESGRI  761 (854)
Q Consensus       692 d~s~~~~~~~~s~e~~~~~rl------~~~~g~g~~e---~L~eav~-~~p~~ViliDEieka~~~v~~~Ll~~le~G~l  761 (854)
                      ++..+.+....  -..-...+      .+..+....+   .+.+.+. .++..||+|||+|.+....+..|...+.-...
T Consensus        81 n~~~~~~~~~~--~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~  158 (365)
T TIGR02928        81 NCQILDTLYQV--LVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSN  158 (365)
T ss_pred             ECCCCCCHHHH--HHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccCCcHHHHhHhccccc
Confidence            88765420000  00000001      0111222222   4555554 35567999999999953333334433321101


Q ss_pred             ecCCCceeecCCeEEEEecCCC
Q 003038          762 VTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       762 ~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                      .     ...-.+.++|+.+|..
T Consensus       159 ~-----~~~~~~v~lI~i~n~~  175 (365)
T TIGR02928       159 G-----DLDNAKVGVIGISNDL  175 (365)
T ss_pred             c-----CCCCCeEEEEEEECCc
Confidence            1     1222456778878754

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.

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=98.18  E-value=1e-05  Score=91.75  Aligned_cols=101  Identities=15%  Similarity=0.146  Sum_probs=70.8

Q ss_pred             CcccccHHHHHHHHHHHHHhhcC--CCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSG--TMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsg--l~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      +.|.|-++|..++-+.|.-.|.-  ..+-.++       =|. -+|+.||||+|||.|||++|-.-   .-+|.....|+
T Consensus       304 ~dVkG~DEAK~ELeEiVefLkdP~kftrLGGK-------LPK-GVLLvGPPGTGKTlLARAvAGEA---~VPFF~~sGSE  372 (752)
T KOG0734|consen  304 EDVKGVDEAKQELEEIVEFLKDPTKFTRLGGK-------LPK-GVLLVGPPGTGKTLLARAVAGEA---GVPFFYASGSE  372 (752)
T ss_pred             ccccChHHHHHHHHHHHHHhcCcHHhhhccCc-------CCC-ceEEeCCCCCchhHHHHHhhccc---CCCeEeccccc
Confidence            67899999999888888654321  0111111       122 36888999999999999999654   46788888888


Q ss_pred             ccCcCCCccccccccccCCCCCCchHH--HHHHHHHcCCCEEEEEecCCCC
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIE--RFAEAVSNNPHRVFLIEDVEQA  744 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e--~L~eav~~~p~~ViliDEieka  744 (854)
                      |.       |-+-        |-|...  .|+.+.+.+..|||||||||-.
T Consensus       373 Fd-------Em~V--------GvGArRVRdLF~aAk~~APcIIFIDEiDav  408 (752)
T KOG0734|consen  373 FD-------EMFV--------GVGARRVRDLFAAAKARAPCIIFIDEIDAV  408 (752)
T ss_pred             hh-------hhhh--------cccHHHHHHHHHHHHhcCCeEEEEechhhh
Confidence            86       3221        123332  6888888888899999999964

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.18  E-value=5.6e-06  Score=87.94  Aligned_cols=122  Identities=11%  Similarity=0.025  Sum_probs=74.8

Q ss_pred             ccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEE
Q 003038          224 SKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLN  303 (854)
Q Consensus       224 r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILf  303 (854)
                      -...++.+|+||||+|||.++.+++..+.+.       +.+++-+++.....        ...++++.+++.    .+|+
T Consensus        42 ~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~-------~~~v~y~~~~~~~~--------~~~~~~~~~~~~----dlli  102 (235)
T PRK08084         42 QEHSGYIYLWSREGAGRSHLLHAACAELSQR-------GRAVGYVPLDKRAW--------FVPEVLEGMEQL----SLVC  102 (235)
T ss_pred             CCCCCeEEEECCCCCCHHHHHHHHHHHHHhC-------CCeEEEEEHHHHhh--------hhHHHHHHhhhC----CEEE
Confidence            3456789999999999999999999876542       34444444433221        122344444432    4799


Q ss_pred             eCccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecCHHHHHHhhccCCchhhhhcc---CCC
Q 003038          304 LGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIATFQSYMRCKSGHPSLETLWSL---HPL  377 (854)
Q Consensus       304 idel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~---~~v  377 (854)
                      |||+|.+ +...               ....+-.++..  ..|  ..++|++++ ..+...-...|.|.+  |+   ..+
T Consensus       103 iDdi~~~~~~~~---------------~~~~lf~l~n~~~e~g--~~~li~ts~-~~p~~l~~~~~~L~S--Rl~~g~~~  162 (235)
T PRK08084        103 IDNIECIAGDEL---------------WEMAIFDLYNRILESG--RTRLLITGD-RPPRQLNLGLPDLAS--RLDWGQIY  162 (235)
T ss_pred             EeChhhhcCCHH---------------HHHHHHHHHHHHHHcC--CCeEEEeCC-CChHHcCcccHHHHH--HHhCCcee
Confidence            9999999 5422               11233334422  233  477888877 333443346799988  77   666


Q ss_pred             CCCCchH
Q 003038          378 TIPAGSL  384 (854)
Q Consensus       378 ~i~~~sl  384 (854)
                      .|.+++.
T Consensus       163 ~l~~~~~  169 (235)
T PRK08084        163 KLQPLSD  169 (235)
T ss_pred             eecCCCH
Confidence            7766653

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

Probab=98.16  E-value=2.6e-06  Score=85.86  Aligned_cols=44  Identities=23%  Similarity=0.419  Sum_probs=32.9

Q ss_pred             cHHHHHHHHHHhh---ccCcCCceeecCCCCCHHHHHHHHHHHHHcC
Q 003038          211 RNEDVMYVIENLM---SKRKRNFVVVGECLASIEGVVRGVIDKIEKG  254 (854)
Q Consensus       211 r~~ei~~v~~~L~---r~~k~n~vLvGe~GvGKta~v~~la~~i~~~  254 (854)
                      |++|++++...|.   ....++++|+|++|+|||++++.++.++...
T Consensus         5 R~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~   51 (185)
T PF13191_consen    5 REEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAER   51 (185)
T ss_dssp             -HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            9999999999993   2267789999999999999999999998875

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=98.15  E-value=6.8e-06  Score=86.49  Aligned_cols=77  Identities=14%  Similarity=0.227  Sum_probs=62.4

Q ss_pred             HHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHh
Q 003038          215 VMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRS  294 (854)
Q Consensus       215 i~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~  294 (854)
                      ++-....+.-...||++|.|+.|+|||++|+++..+...       +|.++|.++-..|..         |.+|++.++.
T Consensus        40 ~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~-------~GLRlIev~k~~L~~---------l~~l~~~l~~  103 (249)
T PF05673_consen   40 IENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYAD-------QGLRLIEVSKEDLGD---------LPELLDLLRD  103 (249)
T ss_pred             HHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhh-------cCceEEEECHHHhcc---------HHHHHHHHhc
Confidence            444444566668899999999999999999999988765       468999998777764         7778888886


Q ss_pred             hhCCCeEEEeCccc
Q 003038          295 CLGRGIVLNLGDLE  308 (854)
Q Consensus       295 ~~~~~~ILfidel~  308 (854)
                      . +...|||+||+-
T Consensus       104 ~-~~kFIlf~DDLs  116 (249)
T PF05673_consen  104 R-PYKFILFCDDLS  116 (249)
T ss_pred             C-CCCEEEEecCCC
Confidence            5 678999999973

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=98.15  E-value=3.5e-06  Score=89.41  Aligned_cols=93  Identities=17%  Similarity=0.215  Sum_probs=64.7

Q ss_pred             ccccHHHHHHHHHHHHHh------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcc
Q 003038          620 VPWQKDTVYDIANTVLKC------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIAL  693 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~~------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~  693 (854)
                      |-|-+.|.+++-++|..-      -.|-            .+|..-+|++||+|+||++||+++|-.-   ..-|.++.-
T Consensus       135 VAGLE~AKeALKEAVILPIKFPqlFtGk------------R~PwrgiLLyGPPGTGKSYLAKAVATEA---nSTFFSvSS  199 (439)
T KOG0739|consen  135 VAGLEGAKEALKEAVILPIKFPQLFTGK------------RKPWRGILLYGPPGTGKSYLAKAVATEA---NSTFFSVSS  199 (439)
T ss_pred             hccchhHHHHHHhheeecccchhhhcCC------------CCcceeEEEeCCCCCcHHHHHHHHHhhc---CCceEEeeh
Confidence            556667777777777532      2221            1566678999999999999999999865   245555544


Q ss_pred             ccccCcCCCccccccccccCCCCCCchHH----HHHHHHHcCCCEEEEEecCCCC
Q 003038          694 SSFSSTRADSTEDSRNKRSRDEQSCSYIE----RFAEAVSNNPHRVFLIEDVEQA  744 (854)
Q Consensus       694 s~~~~~~~~s~e~~~~~rl~~~~g~g~~e----~L~eav~~~p~~ViliDEieka  744 (854)
                      |...            ++..     |-.|    .|++..|++..+||||||||-+
T Consensus       200 SDLv------------SKWm-----GESEkLVknLFemARe~kPSIIFiDEiDsl  237 (439)
T KOG0739|consen  200 SDLV------------SKWM-----GESEKLVKNLFEMARENKPSIIFIDEIDSL  237 (439)
T ss_pred             HHHH------------HHHh-----ccHHHHHHHHHHHHHhcCCcEEEeehhhhh
Confidence            4332            1111     3333    7899999999999999999965

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=98.15  E-value=5.1e-06  Score=101.50  Aligned_cols=117  Identities=12%  Similarity=0.138  Sum_probs=74.7

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .++|.+..+..+...+.+.+                  ....||+||+|||||.+|+.||..+.....++...++.-|..
T Consensus       187 ~liGR~~ei~~~i~iL~r~~------------------~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l  248 (758)
T PRK11034        187 PLIGREKELERAIQVLCRRR------------------KNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSL  248 (758)
T ss_pred             cCcCCCHHHHHHHHHHhccC------------------CCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEec
Confidence            57999988888887666521                  124588999999999999999987644332332223322220


Q ss_pred             cCCCccccccccccCCCCCC-c-hHH---HHHHHHHcCCCEEEEEecCCCC---------CHHHHHHHHHhhhcCeEe
Q 003038          699 TRADSTEDSRNKRSRDEQSC-S-YIE---RFAEAVSNNPHRVFLIEDVEQA---------DYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~g~-g-~~e---~L~eav~~~p~~ViliDEieka---------~~~v~~~Ll~~le~G~l~  762 (854)
                               ....++.+..| | +.+   .+.+.+++....|+||||||.+         ..++.|.|+.++..|.+.
T Consensus       249 ---------~~~~llaG~~~~Ge~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~~g~i~  317 (758)
T PRK11034        249 ---------DIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIR  317 (758)
T ss_pred             ---------cHHHHhcccchhhhHHHHHHHHHHHHHhcCCCEEEeccHHHHhccCCCCCcHHHHHHHHHHHHhCCCeE
Confidence                     01122222222 2 222   3445556677789999999965         356778899999888776

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.14  E-value=7.2e-06  Score=102.37  Aligned_cols=111  Identities=12%  Similarity=0.219  Sum_probs=74.1

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC-------CCceEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS-------HNNFVS  690 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-------~~~~i~  690 (854)
                      ..|+||++.+..+...+.+.                  .....+|+||+|||||.+++.||+.+...       ...++.
T Consensus       173 ~~~igr~~ei~~~~~~l~r~------------------~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~  234 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSRR------------------TKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLA  234 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhcC------------------CCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEE
Confidence            35899998877777765431                  12356899999999999999999987431       345566


Q ss_pred             EccccccCcCCCccccccccccCCCCCC-c-hHHHHH---HHHHc-CCCEEEEEecCCCCC--------HHHHHHHHHhh
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSC-S-YIERFA---EAVSN-NPHRVFLIEDVEQAD--------YCSQKGFKRAI  756 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~-g-~~e~L~---eav~~-~p~~ViliDEieka~--------~~v~~~Ll~~l  756 (854)
                      ++++...                .+..| | +.+++.   ..+.+ ....|+||||||.+.        .++.+.|+.++
T Consensus       235 l~~~~l~----------------a~~~~~g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l  298 (852)
T TIGR03346       235 LDMGALI----------------AGAKYRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPAL  298 (852)
T ss_pred             eeHHHHh----------------hcchhhhhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCCCCcchhHHHHHhchhh
Confidence            6655332                11112 2 222333   33333 456899999999764        35889999999


Q ss_pred             hcCeEe
Q 003038          757 ESGRIV  762 (854)
Q Consensus       757 e~G~l~  762 (854)
                      ..|.+.
T Consensus       299 ~~g~i~  304 (852)
T TIGR03346       299 ARGELH  304 (852)
T ss_pred             hcCceE
Confidence            888776

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.

>KOG0651 consensus 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones]

Probab=98.14  E-value=7.1e-06  Score=87.81  Aligned_cols=114  Identities=15%  Similarity=0.172  Sum_probs=76.2

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCE
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHR  734 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~  734 (854)
                      +|+--++++||+|+|||.+|+++|..+   .-+|+.+-.+++.       +++     ++.++.=..+.+..| ++.-.|
T Consensus       164 k~Pkg~ll~GppGtGKTlla~~Vaa~m---g~nfl~v~ss~lv-------~ky-----iGEsaRlIRemf~yA-~~~~pc  227 (388)
T KOG0651|consen  164 KPPKGLLLYGPPGTGKTLLARAVAATM---GVNFLKVVSSALV-------DKY-----IGESARLIRDMFRYA-REVIPC  227 (388)
T ss_pred             CCCceeEEeCCCCCchhHHHHHHHHhc---CCceEEeeHhhhh-------hhh-----cccHHHHHHHHHHHH-hhhCce
Confidence            444578999999999999999999998   4577777666554       111     111110111233333 334449


Q ss_pred             EEEEecCCC-----------CCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCCCCC
Q 003038          735 VFLIEDVEQ-----------ADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRAC  790 (854)
Q Consensus       735 ViliDEiek-----------a~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~~  790 (854)
                      |||+||||-           ++..+|.-|+..++.-.=.|      .+..+=+|||+|.||..-.+.
T Consensus       228 iifmdeiDAigGRr~se~Ts~dreiqrTLMeLlnqmdgfd------~l~rVk~ImatNrpdtLdpaL  288 (388)
T KOG0651|consen  228 IIFMDEIDAIGGRRFSEGTSSDREIQRTLMELLNQMDGFD------TLHRVKTIMATNRPDTLDPAL  288 (388)
T ss_pred             EEeehhhhhhccEEeccccchhHHHHHHHHHHHHhhccch------hcccccEEEecCCccccchhh
Confidence            999999995           57889999999988321111      245666999999988776553

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=98.13  E-value=2.4e-05  Score=82.49  Aligned_cols=121  Identities=9%  Similarity=0.193  Sum_probs=87.8

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .++|-+.-...|.....++..|.              |...+|++|+.|+|||.+.|+|...+....-++|.+.-...  
T Consensus        28 ~L~Gie~Qk~~l~~Nt~~Fl~G~--------------pannvLL~G~rGtGKSSlVkall~~y~~~GLRlIev~k~~L--   91 (249)
T PF05673_consen   28 DLIGIERQKEALIENTEQFLQGL--------------PANNVLLWGARGTGKSSLVKALLNEYADQGLRLIEVSKEDL--   91 (249)
T ss_pred             HhcCHHHHHHHHHHHHHHHHcCC--------------CCcceEEecCCCCCHHHHHHHHHHHHhhcCceEEEECHHHh--
Confidence            35787777788888888887763              45578999999999999999999988776666666642211  


Q ss_pred             cCCCccccccccccCCCCCCchHHHHHHHHHcCCCE-EEEEecCCCCC-HHHHHHHHHhhhcCeEecCCCceeecCCeEE
Q 003038          699 TRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHR-VFLIEDVEQAD-YCSQKGFKRAIESGRIVTSSGDEVSLGDAIV  776 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~-ViliDEieka~-~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIi  776 (854)
                                          .+...|.+.++..|++ |||+|+.-=-. ..-...|+.+||-| +.      .--.|++|
T Consensus        92 --------------------~~l~~l~~~l~~~~~kFIlf~DDLsFe~~d~~yk~LKs~LeGg-le------~~P~Nvli  144 (249)
T PF05673_consen   92 --------------------GDLPELLDLLRDRPYKFILFCDDLSFEEGDTEYKALKSVLEGG-LE------ARPDNVLI  144 (249)
T ss_pred             --------------------ccHHHHHHHHhcCCCCEEEEecCCCCCCCcHHHHHHHHHhcCc-cc------cCCCcEEE
Confidence                                2344688888888865 89999976433 34456666666633 32      33579999


Q ss_pred             EEecCC
Q 003038          777 ILSCES  782 (854)
Q Consensus       777 IlTsn~  782 (854)
                      ..|||-
T Consensus       145 yATSNR  150 (249)
T PF05673_consen  145 YATSNR  150 (249)
T ss_pred             EEecch
Confidence            999984

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=98.12  E-value=5.4e-06  Score=94.79  Aligned_cols=73  Identities=12%  Similarity=0.144  Sum_probs=56.3

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc-ccchHH-HHHHHHHHHHH----HHhhhCCC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR-HMNRVE-VEQRVEEIKNL----VRSCLGRG  299 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~-~~~rge-~E~rl~~l~~~----~~~~~~~~  299 (854)
                      .+.|++|+||||||||++|+.+|..+          +..|+.++.+.+. ++|.|+ .+..+..++..    +...  .+
T Consensus       107 ~~~~iLl~Gp~GtGKT~lAr~lA~~l----------~~pf~~id~~~l~~~gyvG~d~e~~l~~l~~~~~~~~~~a--~~  174 (412)
T PRK05342        107 QKSNILLIGPTGSGKTLLAQTLARIL----------DVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKA--QR  174 (412)
T ss_pred             CCceEEEEcCCCCCHHHHHHHHHHHh----------CCCceecchhhcccCCcccchHHHHHHHHHHhccccHHHc--CC
Confidence            36789999999999999999999764          4578888888775 468886 55556665543    2222  46


Q ss_pred             eEEEeCccccc
Q 003038          300 IVLNLGDLEWA  310 (854)
Q Consensus       300 ~ILfidel~~l  310 (854)
                      .|||||||+.+
T Consensus       175 gIi~iDEIdkl  185 (412)
T PRK05342        175 GIVYIDEIDKI  185 (412)
T ss_pred             cEEEEechhhh
Confidence            79999999999

>CHL00206 ycf2 Ycf2; Provisional

Probab=98.12  E-value=6.5e-06  Score=105.22  Aligned_cols=124  Identities=15%  Similarity=0.109  Sum_probs=77.4

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcC-----------CCccccc----ccc--------cc
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTR-----------ADSTEDS----RNK--------RS  712 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~-----------~~s~e~~----~~~--------rl  712 (854)
                      |..-+|++||+|||||.|||+||...   +-+|+++.++++....           ..+ ++.    .+.        .+
T Consensus      1629 pPKGILLiGPPGTGKTlLAKALA~es---~VPFIsISgs~fl~~~~~~~~~d~i~iges-~~~~~~~~~~~~~~~e~~e~ 1704 (2281)
T CHL00206       1629 PSRGILVIGSIGTGRSYLVKYLATNS---YVPFITVFLNKFLDNKPKGFLIDDIDIDDS-DDIDDSDDIDRDLDTELLTM 1704 (2281)
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHhc---CCceEEEEHHHHhhcccccccccccccccc-cccccccccccccchhhhhh
Confidence            33457889999999999999999976   6799999999876310           000 000    000        00


Q ss_pred             C-CCCCC---ch----HHHHHHHHHcCCCEEEEEecCCCCCHH-----HHHHHHHhhhcCeEecCCCceeecCCeEEEEe
Q 003038          713 R-DEQSC---SY----IERFAEAVSNNPHRVFLIEDVEQADYC-----SQKGFKRAIESGRIVTSSGDEVSLGDAIVILS  779 (854)
Q Consensus       713 ~-~~~g~---g~----~e~L~eav~~~p~~ViliDEieka~~~-----v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlT  779 (854)
                      . .-.++   +.    ...+.+..+++..|||+|||||.+.+.     ..+.|+..|+..      +...+-++.|||.+
T Consensus      1705 ~n~~~~~m~~~e~~~rIr~lFelARk~SPCIIFIDEIDaL~~~ds~~ltL~qLLneLDg~------~~~~s~~~VIVIAA 1778 (2281)
T CHL00206       1705 MNALTMDMMPKIDRFYITLQFELAKAMSPCIIWIPNIHDLNVNESNYLSLGLLVNSLSRD------CERCSTRNILVIAS 1778 (2281)
T ss_pred             cchhhhhhhhhhhHHHHHHHHHHHHHCCCeEEEEEchhhcCCCccceehHHHHHHHhccc------cccCCCCCEEEEEe
Confidence            0 00000   11    123577778888899999999998754     256666666531      11123467888999


Q ss_pred             cCCCCCCCCC
Q 003038          780 CESFSSRSRA  789 (854)
Q Consensus       780 sn~f~~~s~~  789 (854)
                      ||--+....|
T Consensus      1779 TNRPD~LDPA 1788 (2281)
T CHL00206       1779 THIPQKVDPA 1788 (2281)
T ss_pred             CCCcccCCHh
Confidence            9865555554

>PRK08116 hypothetical protein; Validated

Probab=98.10  E-value=1.1e-05  Score=87.41  Aligned_cols=103  Identities=12%  Similarity=0.136  Sum_probs=67.5

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLI  738 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vili  738 (854)
                      +++|+|++|+|||.||.++|+.+.....+++.++++++.       ...  +......+......+.+.+...  .|++|
T Consensus       116 gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~~~~ll-------~~i--~~~~~~~~~~~~~~~~~~l~~~--dlLvi  184 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQLL-------NRI--KSTYKSSGKEDENEIIRSLVNA--DLLIL  184 (268)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHH-------HHH--HHHHhccccccHHHHHHHhcCC--CEEEE
Confidence            689999999999999999999987556677777766544       111  1001001100111344444443  59999


Q ss_pred             ecC--CCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCC
Q 003038          739 EDV--EQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       739 DEi--eka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      ||+  ++.+...+..|..+|+.. +.         .+.-+|+|||.
T Consensus       185 DDlg~e~~t~~~~~~l~~iin~r-~~---------~~~~~IiTsN~  220 (268)
T PRK08116        185 DDLGAERDTEWAREKVYNIIDSR-YR---------KGLPTIVTTNL  220 (268)
T ss_pred             ecccCCCCCHHHHHHHHHHHHHH-HH---------CCCCEEEECCC
Confidence            999  778888999999999863 21         11237888873

>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=98.08  E-value=8.1e-07  Score=86.02  Aligned_cols=68  Identities=16%  Similarity=0.150  Sum_probs=41.0

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccc------cccch---HHHHHHHHHHHHHHHhhhCCC
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSF------RHMNR---VEVEQRVEEIKNLVRSCLGRG  299 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l------~~~~r---ge~E~rl~~l~~~~~~~~~~~  299 (854)
                      |++|+||||+|||++|+.+|..+          +..++.+.+...      ...+.   |.++-+-..+...++    .+
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~----------~~~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~a~~----~~   66 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALL----------GRPVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVRAMR----KG   66 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH----------TCEEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCTTHH----EE
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh----------hcceEEEEeccccccccceeeeeeccccccccccccccccc----ce
Confidence            58999999999999999999987          345555554432      22221   111111111111222    47


Q ss_pred             eEEEeCccccc
Q 003038          300 IVLNLGDLEWA  310 (854)
Q Consensus       300 ~ILfidel~~l  310 (854)
                      .|+||||++.+
T Consensus        67 ~il~lDEin~a   77 (139)
T PF07728_consen   67 GILVLDEINRA   77 (139)
T ss_dssp             EEEEESSCGG-
T ss_pred             eEEEECCcccC
Confidence            89999999877

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.

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=98.08  E-value=3.6e-06  Score=90.54  Aligned_cols=129  Identities=16%  Similarity=0.166  Sum_probs=82.3

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC---ceEEEcccc
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN---NFVSIALSS  695 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~---~~i~id~s~  695 (854)
                      .|++|++++..+.+-     +++..             ..++||+||||+|||.+..+.|+.+++...   .+..++.| 
T Consensus        42 dv~~~~ei~st~~~~-----~~~~~-------------lPh~L~YgPPGtGktsti~a~a~~ly~~~~~~~m~lelnaS-  102 (360)
T KOG0990|consen   42 IVIKQEPIWSTENRY-----SGMPG-------------LPHLLFYGPPGTGKTSTILANARDFYSPHPTTSMLLELNAS-  102 (360)
T ss_pred             hHhcCCchhhHHHHh-----ccCCC-------------CCcccccCCCCCCCCCchhhhhhhhcCCCCchhHHHHhhcc-
Confidence            468898777765554     33322             238999999999999999999999987311   11111211 


Q ss_pred             ccCcCCCccccccccccCCCCCCchHH---HHHHHHH-------cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCC
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIE---RFAEAVS-------NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSS  765 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e---~L~eav~-------~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~  765 (854)
                                        ++.|-+...   .+....+       ...+..|++||.|.+..+.||+|.++++.  ++   
T Consensus       103 ------------------d~rgid~vr~qi~~fast~~~~~fst~~~fKlvILDEADaMT~~AQnALRRviek--~t---  159 (360)
T KOG0990|consen  103 ------------------DDRGIDPVRQQIHLFASTQQPTTYSTHAAFKLVILDEADAMTRDAQNALRRVIEK--YT---  159 (360)
T ss_pred             ------------------CccCCcchHHHHHHHHhhccceeccccCceeEEEecchhHhhHHHHHHHHHHHHH--hc---
Confidence                              011112221   2222222       23788999999999999999999998774  22   


Q ss_pred             CceeecCCeEEEEecCCCCCCCCC-CCCCcc
Q 003038          766 GDEVSLGDAIVILSCESFSSRSRA-CSPPTK  795 (854)
Q Consensus       766 G~~v~~~~aIiIlTsn~f~~~s~~-~sp~~~  795 (854)
                            .|+.|++-||.....+++ -|.|++
T Consensus       160 ------~n~rF~ii~n~~~ki~pa~qsRctr  184 (360)
T KOG0990|consen  160 ------ANTRFATISNPPQKIHPAQQSRCTR  184 (360)
T ss_pred             ------cceEEEEeccChhhcCchhhccccc
Confidence                  455677778876555554 244443

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=98.07  E-value=3.4e-05  Score=84.64  Aligned_cols=105  Identities=9%  Similarity=0.111  Sum_probs=67.9

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCC--CCCCchHH--HHHHHHHc--
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRD--EQSCSYIE--RFAEAVSN--  730 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~--~~g~g~~e--~L~eav~~--  730 (854)
                      .+.+||+|+.|.||+.+|+.+|+.++.....-  ++-....       ....   .+.  +...+.++  .+.+.+..  
T Consensus        18 ~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~--~~~~~~p-------~n~~---~~d~~g~~i~vd~Ir~l~~~~~~~~   85 (299)
T PRK07132         18 SHSFLLKSNYNEDIDEKILYFLNKFNNLQITN--LNEQELP-------ANII---LFDIFDKDLSKSEFLSAINKLYFSS   85 (299)
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCC--CCCCCCC-------cceE---EeccCCCcCCHHHHHHHHHHhccCC
Confidence            46899999999999999999999997532110  0000000       0000   011  11113332  33333322  


Q ss_pred             ---CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCCC
Q 003038          731 ---NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFS  784 (854)
Q Consensus       731 ---~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~  784 (854)
                         .+++||+||++|+++...+|.|++.||+           .-.+++|||+|+..+
T Consensus        86 ~~~~~~KvvII~~~e~m~~~a~NaLLK~LEE-----------Pp~~t~~il~~~~~~  131 (299)
T PRK07132         86 FVQSQKKILIIKNIEKTSNSLLNALLKTIEE-----------PPKDTYFLLTTKNIN  131 (299)
T ss_pred             cccCCceEEEEecccccCHHHHHHHHHHhhC-----------CCCCeEEEEEeCChH
Confidence               3679999999999999999999999997           236788999886443

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=98.07  E-value=2.7e-05  Score=80.99  Aligned_cols=114  Identities=11%  Similarity=0.206  Sum_probs=80.1

Q ss_pred             EEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEe
Q 003038          660 LFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIE  739 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliD  739 (854)
                      +|++||+|+|||.+|+++|..-   +-.||++..|+..       .++     ++ .|......|+--.|+...+|||+|
T Consensus       184 vlLygppgtGktLlaraVahht---~c~firvsgselv-------qk~-----ig-egsrmvrelfvmarehapsiifmd  247 (404)
T KOG0728|consen  184 VLLYGPPGTGKTLLARAVAHHT---DCTFIRVSGSELV-------QKY-----IG-EGSRMVRELFVMAREHAPSIIFMD  247 (404)
T ss_pred             eEEecCCCCchhHHHHHHHhhc---ceEEEEechHHHH-------HHH-----hh-hhHHHHHHHHHHHHhcCCceEeee
Confidence            5778999999999999999864   5679999888765       333     21 111222356666688888999999


Q ss_pred             cCCCC-----------CHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCCCCCCCCcc
Q 003038          740 DVEQA-----------DYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRACSPPTK  795 (854)
Q Consensus       740 Eieka-----------~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~~sp~~~  795 (854)
                      |||..           |.+||...+..+..=     .|- -..+|.-+||.+|..|....+.=.|-|
T Consensus       248 eidsigs~r~e~~~ggdsevqrtmlellnql-----dgf-eatknikvimatnridild~allrpgr  308 (404)
T KOG0728|consen  248 EIDSIGSSRVESGSGGDSEVQRTMLELLNQL-----DGF-EATKNIKVIMATNRIDILDPALLRPGR  308 (404)
T ss_pred             cccccccccccCCCCccHHHHHHHHHHHHhc-----ccc-ccccceEEEEeccccccccHhhcCCCc
Confidence            99964           678999888887530     010 123577799999998877776444433

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=98.07  E-value=9.9e-06  Score=93.66  Aligned_cols=139  Identities=12%  Similarity=0.134  Sum_probs=89.2

Q ss_pred             ccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc
Q 003038          620 VPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST  699 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~  699 (854)
                      ++|....+..+...+....                .....++++|.+|+||+.+|++|.........+|+.+||+...  
T Consensus       141 lig~s~~~~~~~~~i~~~~----------------~~~~~vli~ge~g~gk~~~a~~ih~~s~~~~~~~i~~~c~~~~--  202 (441)
T PRK10365        141 MVGKSPAMQHLLSEIALVA----------------PSEATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALN--  202 (441)
T ss_pred             eEecCHHHHHHHHHHhhcc----------------CCCCeEEEEecCCCCHHHHHHHHHHcCCCCCCCeeeeeCCCCC--
Confidence            5676666665555554321                1234678899999999999999998877777899999998765  


Q ss_pred             CCCccccccccccCC-CCC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEE
Q 003038          700 RADSTEDSRNKRSRD-EQS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIV  776 (854)
Q Consensus       700 ~~~s~e~~~~~rl~~-~~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIi  776 (854)
                           +....+.+.+ ..| + |....-.+.+......++|||||+.+++.+|..|++++++|.++.-.+...--.++.|
T Consensus       203 -----~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ldei~~l~~~~q~~l~~~l~~~~~~~~~~~~~~~~~~ri  277 (441)
T PRK10365        203 -----ESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPMMQVRLLRAIQEREVQRVGSNQTISVDVRL  277 (441)
T ss_pred             -----HHHHHHHhcCCCCCCcCCCCcCCCCceeECCCCEEEEeccccCCHHHHHHHHHHHccCcEEeCCCCceeeeceEE
Confidence                 1111111111 000 0 1000001123344567999999999999999999999999988753332222335667


Q ss_pred             EEecC
Q 003038          777 ILSCE  781 (854)
Q Consensus       777 IlTsn  781 (854)
                      |+||+
T Consensus       278 i~~t~  282 (441)
T PRK10365        278 IAATH  282 (441)
T ss_pred             EEeCC
Confidence            77764

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.05  E-value=2.7e-05  Score=81.51  Aligned_cols=119  Identities=13%  Similarity=0.189  Sum_probs=79.7

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLI  738 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vili  738 (854)
                      -+|++||+|+|||.+||++|.--   ..-||++=.|+..       +++-      +.|......|++-.|.+.-++|||
T Consensus       213 gvllygppgtgktl~aravanrt---dacfirvigselv-------qkyv------gegarmvrelf~martkkaciiff  276 (435)
T KOG0729|consen  213 GVLLYGPPGTGKTLCARAVANRT---DACFIRVIGSELV-------QKYV------GEGARMVRELFEMARTKKACIIFF  276 (435)
T ss_pred             ceEEeCCCCCchhHHHHHHhccc---CceEEeehhHHHH-------HHHh------hhhHHHHHHHHHHhcccceEEEEe
Confidence            35788999999999999999843   5678888877665       2321      111112236888888899999999


Q ss_pred             ecCCCC-----------CHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCCCCCCCCcc--CCCC
Q 003038          739 EDVEQA-----------DYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRACSPPTK--QKSD  799 (854)
Q Consensus       739 DEieka-----------~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~~sp~~~--~~~~  799 (854)
                      ||||-.           +.+||...|..+-.=-=.|..      .|.-+.|.+|--+....+.=.|-|  +|+.
T Consensus       277 deidaiggarfddg~ggdnevqrtmleli~qldgfdpr------gnikvlmatnrpdtldpallrpgrldrkve  344 (435)
T KOG0729|consen  277 DEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPR------GNIKVLMATNRPDTLDPALLRPGRLDRKVE  344 (435)
T ss_pred             eccccccCccccCCCCCcHHHHHHHHHHHHhccCCCCC------CCeEEEeecCCCCCcCHhhcCCccccccee
Confidence            999964           568999998888631112222      255577888865555555433333  4444

>PRK09862 putative ATP-dependent protease; Provisional

Probab=98.05  E-value=1.9e-05  Score=92.20  Aligned_cols=144  Identities=15%  Similarity=0.167  Sum_probs=86.4

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++||..++..+.-++                    .+...++|.||+|+|||++++.|+..+..... =+.++.+...
T Consensus       191 ~~v~Gq~~~~~al~laa--------------------~~G~~llliG~~GsGKTtLak~L~gllpp~~g-~e~le~~~i~  249 (506)
T PRK09862        191 SDVIGQEQGKRGLEITA--------------------AGGHNLLLIGPPGTGKTMLASRINGLLPDLSN-EEALESAAIL  249 (506)
T ss_pred             EEEECcHHHHhhhheec--------------------cCCcEEEEECCCCCcHHHHHHHHhccCCCCCC-cEEEecchhh
Confidence            35789998776643221                    12347899999999999999999987743221 1223333221


Q ss_pred             C-cCCCccccccccccC-CCCCC-chHH-------HHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEec-CCC
Q 003038          698 S-TRADSTEDSRNKRSR-DEQSC-SYIE-------RFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVT-SSG  766 (854)
Q Consensus       698 ~-~~~~s~e~~~~~rl~-~~~g~-g~~e-------~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d-~~G  766 (854)
                      + .........-..|.. .|... +...       .-...+......|+|+|||+.+++.+|..|++.||+|.++- ..|
T Consensus       250 s~~g~~~~~~~~~~rPfr~ph~~~s~~~l~GGg~~~~pG~l~~A~gGvLfLDEi~e~~~~~~~~L~~~LE~g~v~I~r~g  329 (506)
T PRK09862        250 SLVNAESVQKQWRQRPFRSPHHSASLTAMVGGGAIPGPGEISLAHNGVLFLDELPEFERRTLDALREPIESGQIHLSRTR  329 (506)
T ss_pred             hhhccccccCCcCCCCccCCCccchHHHHhCCCceehhhHhhhccCCEEecCCchhCCHHHHHHHHHHHHcCcEEEecCC
Confidence            1 000000000001111 11110 1000       01234566677899999999999999999999999999874 334


Q ss_pred             ceee-cCCeEEEEecCC
Q 003038          767 DEVS-LGDAIVILSCES  782 (854)
Q Consensus       767 ~~v~-~~~aIiIlTsn~  782 (854)
                      ..+. -.+..+|.|+|.
T Consensus       330 ~~~~~pa~f~lIAa~NP  346 (506)
T PRK09862        330 AKITYPARFQLVAAMNP  346 (506)
T ss_pred             cceeccCCEEEEEeecC
Confidence            4443 368889999985

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.05  E-value=3.1e-05  Score=88.30  Aligned_cols=139  Identities=14%  Similarity=0.112  Sum_probs=84.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC--CCceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS--HNNFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~--~~~~i~id~s~  695 (854)
                      .+++|.++-+..|...+.....|-             ++ ..++++||+|+|||.+++.+++.+-..  .-.++.+++..
T Consensus        30 ~~l~~Re~e~~~l~~~l~~~~~~~-------------~~-~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~   95 (394)
T PRK00411         30 ENLPHREEQIEELAFALRPALRGS-------------RP-LNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQI   95 (394)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhCCC-------------CC-CeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCc
Confidence            567899988888888887653321             22 368999999999999999999887433  24678888876


Q ss_pred             ccCcCCCccccccccccCC----CCCCchHH---HHHHHHHc-CCCEEEEEecCCCCC----HHHHHHHHHhhhcCeEec
Q 003038          696 FSSTRADSTEDSRNKRSRD----EQSCSYIE---RFAEAVSN-NPHRVFLIEDVEQAD----YCSQKGFKRAIESGRIVT  763 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~----~~g~g~~e---~L~eav~~-~p~~ViliDEieka~----~~v~~~Ll~~le~G~l~d  763 (854)
                      +......-  ..-...+..    ..+..+.+   .+.+.+.. ..+.||+|||+|.+.    .+....|++.+++-    
T Consensus        96 ~~~~~~~~--~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~~----  169 (394)
T PRK00411         96 DRTRYAIF--SEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEEY----  169 (394)
T ss_pred             CCCHHHHH--HHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhhcc----
Confidence            54100000  000001111    11223332   45555544 345799999999875    45555666655531    


Q ss_pred             CCCceeecCCeEEEEecCC
Q 003038          764 SSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       764 ~~G~~v~~~~aIiIlTsn~  782 (854)
                       .+     .+..||+++|.
T Consensus       170 -~~-----~~v~vI~i~~~  182 (394)
T PRK00411        170 -PG-----ARIGVIGISSD  182 (394)
T ss_pred             -CC-----CeEEEEEEECC
Confidence             11     25667787765

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=98.03  E-value=3.5e-05  Score=85.22  Aligned_cols=136  Identities=10%  Similarity=0.038  Sum_probs=82.4

Q ss_pred             cHHHHHHHHHHhhccCcCCcee-ecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVV-VGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIK  289 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vL-vGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~  289 (854)
                      .++.+..+...+.+.+..|++| +||||+|||+++++++..+          +..++.++.+.  .. ...+...+.+..
T Consensus        26 ~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~----------~~~~~~i~~~~--~~-~~~i~~~l~~~~   92 (316)
T PHA02544         26 PAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEV----------GAEVLFVNGSD--CR-IDFVRNRLTRFA   92 (316)
T ss_pred             cHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHh----------CccceEeccCc--cc-HHHHHHHHHHHH
Confidence            5566666666666656667777 7999999999999999874          23455665554  11 222333344333


Q ss_pred             HHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCch
Q 003038          290 NLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSL  368 (854)
Q Consensus       290 ~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pal  368 (854)
                      ...... +.+-||+|||+|.+ ...                ....+.+++....+  ..++|.+|+..  .   ...|++
T Consensus        93 ~~~~~~-~~~~vliiDe~d~l~~~~----------------~~~~L~~~le~~~~--~~~~Ilt~n~~--~---~l~~~l  148 (316)
T PHA02544         93 STVSLT-GGGKVIIIDEFDRLGLAD----------------AQRHLRSFMEAYSK--NCSFIITANNK--N---GIIEPL  148 (316)
T ss_pred             Hhhccc-CCCeEEEEECcccccCHH----------------HHHHHHHHHHhcCC--CceEEEEcCCh--h---hchHHH
Confidence            332211 35678999999988 331                11234445532112  47788877632  2   346788


Q ss_pred             hhhhccCCCCCCCchHH
Q 003038          369 ETLWSLHPLTIPAGSLS  385 (854)
Q Consensus       369 e~~~~~~~v~i~~~sl~  385 (854)
                      .+  |++.+.++.|+..
T Consensus       149 ~s--R~~~i~~~~p~~~  163 (316)
T PHA02544        149 RS--RCRVIDFGVPTKE  163 (316)
T ss_pred             Hh--hceEEEeCCCCHH
Confidence            88  7777777666543

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.03  E-value=1.2e-05  Score=75.68  Aligned_cols=77  Identities=13%  Similarity=0.066  Sum_probs=54.9

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc--------------chHHHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM--------------NRVEVEQRVEEIKNLV  292 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~--------------~rge~E~rl~~l~~~~  292 (854)
                      .++++|+||||+|||++++.++..+....       ..++.++.+.....              ....-...+..++..+
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   74 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPG-------GGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALA   74 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCC-------CCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHH
Confidence            57899999999999999999998765432       24566655543321              1223445666777888


Q ss_pred             HhhhCCCeEEEeCccccc-cc
Q 003038          293 RSCLGRGIVLNLGDLEWA-EF  312 (854)
Q Consensus       293 ~~~~~~~~ILfidel~~l-~~  312 (854)
                      +..  .+.||||||++.+ ..
T Consensus        75 ~~~--~~~viiiDei~~~~~~   93 (148)
T smart00382       75 RKL--KPDVLILDEITSLLDA   93 (148)
T ss_pred             Hhc--CCCEEEEECCcccCCH
Confidence            765  4689999999999 54

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.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.03  E-value=3.6e-05  Score=88.83  Aligned_cols=130  Identities=11%  Similarity=0.099  Sum_probs=72.7

Q ss_pred             cHHHHHHHH-HHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCCCc--------------ccCCceEEEccccccc
Q 003038          211 RNEDVMYVI-ENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDVPE--------------ALRDVKCLPLSISSFR  274 (854)
Q Consensus       211 r~~ei~~v~-~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~vp~--------------~L~~~~~~~l~~~~l~  274 (854)
                      ..+.+.+.+ ..+..++-.+ .+|+||+|+|||++|+.+|..+....-+.              ......|+.++.++  
T Consensus        22 GQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~dviEIdaas--   99 (484)
T PRK14956         22 HQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNECTSCLEITKGISSDVLEIDAAS--   99 (484)
T ss_pred             ChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCCCcHHHHHHccCCccceeechhh--
Confidence            455554444 4444434333 69999999999999999999876532110              00111344444321  


Q ss_pred             ccchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEE
Q 003038          275 HMNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMG  351 (854)
Q Consensus       275 ~~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIg  351 (854)
                        .+|  -..++++++.+....  ++.-|+||||+|.+ ..                 +...+-..|....+  .+.+|.
T Consensus       100 --~~g--Vd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~-----------------A~NALLKtLEEPp~--~viFIL  156 (484)
T PRK14956        100 --NRG--IENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQ-----------------SFNALLKTLEEPPA--HIVFIL  156 (484)
T ss_pred             --ccc--HHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHH-----------------HHHHHHHHhhcCCC--ceEEEe
Confidence              111  123455555554321  45679999999999 43                 12233333421123  599999


Q ss_pred             ecCHHHHHHhhccCCchhh
Q 003038          352 IATFQSYMRCKSGHPSLET  370 (854)
Q Consensus       352 atT~~ey~k~~~~~pale~  370 (854)
                      +||.  +.+   .-|++.+
T Consensus       157 aTte--~~k---I~~TI~S  170 (484)
T PRK14956        157 ATTE--FHK---IPETILS  170 (484)
T ss_pred             ecCC--hhh---ccHHHHh
Confidence            9986  333   3466655

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]

Probab=98.03  E-value=9e-06  Score=86.12  Aligned_cols=146  Identities=14%  Similarity=0.192  Sum_probs=96.1

Q ss_pred             cccccHHHHHHHHHHHHH--------hhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEE
Q 003038          619 KVPWQKDTVYDIANTVLK--------CRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVS  690 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~--------~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~  690 (854)
                      .|-|-+.-|.+|-++|..        --.|+.             |+--++++|+||+|||.||+++|..-   ..-|++
T Consensus       186 diGGle~QiQEiKEsvELPLthPE~YeemGik-------------pPKGVIlyG~PGTGKTLLAKAVANqT---SATFlR  249 (440)
T KOG0726|consen  186 DIGGLESQIQEIKESVELPLTHPEYYEEMGIK-------------PPKGVILYGEPGTGKTLLAKAVANQT---SATFLR  249 (440)
T ss_pred             ccccHHHHHHHHHHhhcCCCCCHHHHHHcCCC-------------CCCeeEEeCCCCCchhHHHHHHhccc---chhhhh
Confidence            355666667777777742        223443             33346788999999999999999854   456777


Q ss_pred             EccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCC-----------CHHHHHHHHHhhhcC
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQA-----------DYCSQKGFKRAIESG  759 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka-----------~~~v~~~Ll~~le~G  759 (854)
                      +-.|+..       .++.      +.|.-...+|+....++..+|+||||||-.           ..++|..+|..+..=
T Consensus       250 vvGseLi-------Qkyl------GdGpklvRqlF~vA~e~apSIvFiDEIdAiGtKRyds~SggerEiQrtmLELLNQl  316 (440)
T KOG0726|consen  250 VVGSELI-------QKYL------GDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQL  316 (440)
T ss_pred             hhhHHHH-------HHHh------ccchHHHHHHHHHHHhcCCceEEeehhhhhccccccCCCccHHHHHHHHHHHHHhc
Confidence            7777655       3322      112123346777777888899999999964           357888888887531


Q ss_pred             eEecCCCceeecCCeEEEEecCCCCCCCCCCCCCcc--CCCC
Q 003038          760 RIVTSSGDEVSLGDAIVILSCESFSSRSRACSPPTK--QKSD  799 (854)
Q Consensus       760 ~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~~sp~~~--~~~~  799 (854)
                      -=.|++      .+.-+||.+|-.++...+.=.|-|  +++.
T Consensus       317 dGFdsr------gDvKvimATnrie~LDPaLiRPGrIDrKIe  352 (440)
T KOG0726|consen  317 DGFDSR------GDVKVIMATNRIETLDPALIRPGRIDRKIE  352 (440)
T ss_pred             cCcccc------CCeEEEEecccccccCHhhcCCCccccccc
Confidence            111222      466799999988888777544433  4444

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=98.01  E-value=1.5e-05  Score=87.86  Aligned_cols=126  Identities=12%  Similarity=0.125  Sum_probs=77.7

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc----chHHHHHHHHHHHHHHHhhhCCCeEEE
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM----NRVEVEQRVEEIKNLVRSCLGRGIVLN  303 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~----~rge~E~rl~~l~~~~~~~~~~~~ILf  303 (854)
                      +|++++||||+|||.+++.||++  .|             ||..-+..|    .-.+-=.++.+||+-++.+ .+|.+||
T Consensus       385 RNilfyGPPGTGKTm~ArelAr~--SG-------------lDYA~mTGGDVAPlG~qaVTkiH~lFDWakkS-~rGLllF  448 (630)
T KOG0742|consen  385 RNILFYGPPGTGKTMFARELARH--SG-------------LDYAIMTGGDVAPLGAQAVTKIHKLFDWAKKS-RRGLLLF  448 (630)
T ss_pred             hheeeeCCCCCCchHHHHHHHhh--cC-------------CceehhcCCCccccchHHHHHHHHHHHHHhhc-ccceEEE
Confidence            48999999999999999999986  12             233323322    1223456899999999987 7899999


Q ss_pred             eCccccc-cccccccccccccchhhhHHHHHHHhhc-cc-CCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCC
Q 003038          304 LGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CG-IGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTI  379 (854)
Q Consensus       304 idel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~-~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i  379 (854)
                      |||.+.+ -.++..       |. .+..-.-+..|| .. .-.+ +|.|+-||+-.+     ..|.++..  |+ +.|..
T Consensus       449 IDEADAFLceRnkt-------ym-SEaqRsaLNAlLfRTGdqSr-divLvlAtNrpg-----dlDsAV~D--Ride~veF  512 (630)
T KOG0742|consen  449 IDEADAFLCERNKT-------YM-SEAQRSALNALLFRTGDQSR-DIVLVLATNRPG-----DLDSAVND--RIDEVVEF  512 (630)
T ss_pred             ehhhHHHHHHhchh-------hh-cHHHHHHHHHHHHHhccccc-ceEEEeccCCcc-----chhHHHHh--hhhheeec
Confidence            9999999 333221       11 112223344555 22 2223 688888887544     23556655  44 33444


Q ss_pred             CCchHH
Q 003038          380 PAGSLS  385 (854)
Q Consensus       380 ~~~sl~  385 (854)
                      |=|.-+
T Consensus       513 pLPGeE  518 (630)
T KOG0742|consen  513 PLPGEE  518 (630)
T ss_pred             CCCChH
Confidence            444433

>PRK06893 DNA replication initiation factor; Validated

Probab=98.01  E-value=2.1e-05  Score=83.25  Aligned_cols=118  Identities=14%  Similarity=0.096  Sum_probs=66.9

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCcccc
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEW  309 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~  309 (854)
                      .+|+||||+|||.++++++..+.+..     ..+.+++++  .        ++....++++.+++    .-+|+|||++.
T Consensus        42 l~l~G~~G~GKThL~~ai~~~~~~~~-----~~~~y~~~~--~--------~~~~~~~~~~~~~~----~dlLilDDi~~  102 (229)
T PRK06893         42 FYIWGGKSSGKSHLLKAVSNHYLLNQ-----RTAIYIPLS--K--------SQYFSPAVLENLEQ----QDLVCLDDLQA  102 (229)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcC-----CCeEEeeHH--H--------hhhhhHHHHhhccc----CCEEEEeChhh
Confidence            47999999999999999998865531     234444442  1        11122234444443    45899999999


Q ss_pred             c-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecCHHHHHHhhccCCchhhhhccC---CCCCCCch
Q 003038          310 A-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIATFQSYMRCKSGHPSLETLWSLH---PLTIPAGS  383 (854)
Q Consensus       310 l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~---~v~i~~~s  383 (854)
                      + +...               ....+-.++..  ..+. .+.+|++++......  ...|.|.+  |+.   .+.++.+.
T Consensus       103 ~~~~~~---------------~~~~l~~l~n~~~~~~~-~illits~~~p~~l~--~~~~~L~s--Rl~~g~~~~l~~pd  162 (229)
T PRK06893        103 VIGNEE---------------WELAIFDLFNRIKEQGK-TLLLISADCSPHALS--IKLPDLAS--RLTWGEIYQLNDLT  162 (229)
T ss_pred             hcCChH---------------HHHHHHHHHHHHHHcCC-cEEEEeCCCChHHcc--ccchhHHH--HHhcCCeeeCCCCC
Confidence            8 5422               11123334421  1221 466777765433332  24688888  443   45566655


Q ss_pred             HHH
Q 003038          384 LSL  386 (854)
Q Consensus       384 l~~  386 (854)
                      .+.
T Consensus       163 ~e~  165 (229)
T PRK06893        163 DEQ  165 (229)
T ss_pred             HHH
Confidence            443

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=98.00  E-value=1.6e-05  Score=96.31  Aligned_cols=106  Identities=16%  Similarity=0.165  Sum_probs=69.1

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLI  738 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vili  738 (854)
                      .++|+||+|+|||.+|+++|..+   ..+|+.++.+.|.       +.+.      +.+......+.+..+..+.+||||
T Consensus       187 gill~G~~G~GKt~~~~~~a~~~---~~~f~~is~~~~~-------~~~~------g~~~~~~~~~f~~a~~~~P~IifI  250 (644)
T PRK10733        187 GVLMVGPPGTGKTLLAKAIAGEA---KVPFFTISGSDFV-------EMFV------GVGASRVRDMFEQAKKAAPCIIFI  250 (644)
T ss_pred             cEEEECCCCCCHHHHHHHHHHHc---CCCEEEEehHHhH-------Hhhh------cccHHHHHHHHHHHHhcCCcEEEe
Confidence            38999999999999999999987   3578888887665       2110      001111224555556667799999


Q ss_pred             ecCCCCCH--------------HHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCCCC
Q 003038          739 EDVEQADY--------------CSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRA  789 (854)
Q Consensus       739 DEieka~~--------------~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~  789 (854)
                      ||||....              .+.+.|+.-||.  +.       +-.+.|||.|||.-+....+
T Consensus       251 DEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg--~~-------~~~~vivIaaTN~p~~lD~A  306 (644)
T PRK10733        251 DEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDG--FE-------GNEGIIVIAATNRPDVLDPA  306 (644)
T ss_pred             hhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhc--cc-------CCCCeeEEEecCChhhcCHH
Confidence            99998732              245556555552  11       12357889999975544433

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.00  E-value=4.7e-05  Score=91.72  Aligned_cols=152  Identities=10%  Similarity=0.121  Sum_probs=93.8

Q ss_pred             hhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC-------CCc
Q 003038          615 ALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS-------HNN  687 (854)
Q Consensus       615 ~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-------~~~  687 (854)
                      ++-.+++|.++=+..|+..|..+-.|-             .|...|+++|+||+|||.+++.+.+.|-..       .-.
T Consensus       752 YVPD~LPhREeEIeeLasfL~paIkgs-------------gpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~  818 (1164)
T PTZ00112        752 VVPKYLPCREKEIKEVHGFLESGIKQS-------------GSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFN  818 (1164)
T ss_pred             cCCCcCCChHHHHHHHHHHHHHHHhcC-------------CCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCce
Confidence            445789999999999999998765431             233467899999999999999988776311       134


Q ss_pred             eEEEccccccCcCCCccc-cccccccCCCCCCc---hHHHHHHHHH--cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeE
Q 003038          688 FVSIALSSFSSTRADSTE-DSRNKRSRDEQSCS---YIERFAEAVS--NNPHRVFLIEDVEQADYCSQKGFKRAIESGRI  761 (854)
Q Consensus       688 ~i~id~s~~~~~~~~s~e-~~~~~rl~~~~g~g---~~e~L~eav~--~~p~~ViliDEieka~~~v~~~Ll~~le~G~l  761 (854)
                      ++.|+|..+......-.. -..+....++.+..   +.+.++..+.  .....||+|||||.+...-|..|+..|+--..
T Consensus       819 vVYINCm~Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~~  898 (1164)
T PTZ00112        819 VFEINGMNVVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPTK  898 (1164)
T ss_pred             EEEEeCCccCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCccHHHHHHHHHHHhhc
Confidence            688998765421000000 00010111222321   2234444442  23356999999999987778888888874221


Q ss_pred             ecCCCceeecCCeEEEEecCCCCCCC
Q 003038          762 VTSSGDEVSLGDAIVILSCESFSSRS  787 (854)
Q Consensus       762 ~d~~G~~v~~~~aIiIlTsn~f~~~s  787 (854)
                      .        -...+||..||.++-+.
T Consensus       899 s--------~SKLiLIGISNdlDLpe  916 (1164)
T PTZ00112        899 I--------NSKLVLIAISNTMDLPE  916 (1164)
T ss_pred             c--------CCeEEEEEecCchhcch
Confidence            1        13467888898765444

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=97.99  E-value=8.3e-06  Score=97.60  Aligned_cols=114  Identities=15%  Similarity=0.158  Sum_probs=75.6

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCC------CchHHHHHHHHHc
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQS------CSYIERFAEAVSN  730 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g------~g~~e~L~eav~~  730 (854)
                      +|.+|+.|++|+|||.+|+.|++.+-+ ..+|+++..+...        .    +++++-.      .|....-...+-+
T Consensus        16 ~g~vLl~G~~GtgKs~lar~l~~~~~~-~~pfv~i~~~~t~--------d----~L~G~idl~~~~~~g~~~~~~G~L~~   82 (589)
T TIGR02031        16 LGGVAIRARAGTGKTALARALAEILPP-IMPFVELPLGVTE--------D----RLIGGIDVEESLAGGQRVTQPGLLDE   82 (589)
T ss_pred             cceEEEEcCCCcHHHHHHHHHHHhCCc-CCCeEecCcccch--------h----hcccchhhhhhhhcCcccCCCCCeee
Confidence            789999999999999999999998733 3468888753111        0    1110000      0000000011223


Q ss_pred             CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecC-CCceeec-CCeEEEEecCCC
Q 003038          731 NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTS-SGDEVSL-GDAIVILSCESF  783 (854)
Q Consensus       731 ~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~-~G~~v~~-~~aIiIlTsn~f  783 (854)
                      ....|+|+|||+++++.+|+.|+++|++|.++-. .|....+ .+..+|.|+|.-
T Consensus        83 A~~GvL~lDEi~rl~~~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~  137 (589)
T TIGR02031        83 APRGVLYVDMANLLDDGLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPA  137 (589)
T ss_pred             CCCCcEeccchhhCCHHHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCc
Confidence            3457999999999999999999999999987643 3555544 367788888753

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.

>PF13173 AAA_14: AAA domain

Probab=97.98  E-value=1.9e-05  Score=75.63  Aligned_cols=84  Identities=17%  Similarity=0.288  Sum_probs=58.1

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLI  738 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vili  738 (854)
                      ++++.||.|||||++++.+++.+. ...+++.+++....       ....    ...   ...+.+.+. -.....+|||
T Consensus         4 ~~~l~G~R~vGKTtll~~~~~~~~-~~~~~~yi~~~~~~-------~~~~----~~~---~~~~~~~~~-~~~~~~~i~i   67 (128)
T PF13173_consen    4 IIILTGPRGVGKTTLLKQLAKDLL-PPENILYINFDDPR-------DRRL----ADP---DLLEYFLEL-IKPGKKYIFI   67 (128)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhc-ccccceeeccCCHH-------HHHH----hhh---hhHHHHHHh-hccCCcEEEE
Confidence            688999999999999999998886 55778888887544       1000    000   011112222 1124689999


Q ss_pred             ecCCCCCHHHHHHHHHhhhcC
Q 003038          739 EDVEQADYCSQKGFKRAIESG  759 (854)
Q Consensus       739 DEieka~~~v~~~Ll~~le~G  759 (854)
                      |||++++ +....+....+++
T Consensus        68 DEiq~~~-~~~~~lk~l~d~~   87 (128)
T PF13173_consen   68 DEIQYLP-DWEDALKFLVDNG   87 (128)
T ss_pred             ehhhhhc-cHHHHHHHHHHhc
Confidence            9999996 7888898888865

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=97.97  E-value=3.2e-05  Score=84.18  Aligned_cols=110  Identities=15%  Similarity=0.192  Sum_probs=80.6

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCC----CCCC-chHHHHHHHHHcCC
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRD----EQSC-SYIERFAEAVSNNP  732 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~----~~g~-g~~e~L~eav~~~p  732 (854)
                      ..+|+.|.||+||..+||+--..--....+|+.++|....       +...-+.+.+    ..|+ |+       +....
T Consensus       228 APLLI~GeTGTGKdLlAkaCH~~S~R~~~pFlalNCA~lP-------e~~aEsElFG~apg~~gk~Gf-------fE~An  293 (511)
T COG3283         228 APLLITGETGTGKDLLAKACHLASPRHSKPFLALNCASLP-------EDAAESELFGHAPGDEGKKGF-------FEQAN  293 (511)
T ss_pred             CCeEEecCCCchHHHHHHHHhhcCcccCCCeeEeecCCCc-------hhHhHHHHhcCCCCCCCccch-------hhhcc
Confidence            4689999999999999997665544567899999999887       3333333331    1233 43       22334


Q ss_pred             CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecC
Q 003038          733 HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       733 ~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn  781 (854)
                      ..-||+|||-.++|..|..|++.+.+|.++--.++.=-.-|+.||++|.
T Consensus       294 gGTVlLDeIgEmSp~lQaKLLRFL~DGtFRRVGee~Ev~vdVRVIcatq  342 (511)
T COG3283         294 GGTVLLDEIGEMSPRLQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQ  342 (511)
T ss_pred             CCeEEeehhhhcCHHHHHHHHHHhcCCceeecCCcceEEEEEEEEeccc
Confidence            5678899999999999999999999999996433333344788999884

>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=97.97  E-value=1.3e-05  Score=83.43  Aligned_cols=160  Identities=11%  Similarity=0.150  Sum_probs=86.6

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCC-C---cccCCceEEEcccccc-------------
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDV-P---EALRDVKCLPLSISSF-------------  273 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~v-p---~~L~~~~~~~l~~~~l-------------  273 (854)
                      |++|++++.+++.+...+.++|+||.|+|||++++.+...+..... .   ..+.....  -....+             
T Consensus         4 R~~el~~l~~~l~~~~~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~~~~y~~~~~~~~~--~~~~~~~~~~~~~~~l~~~   81 (234)
T PF01637_consen    4 REKELEKLKELLESGPSQHILLYGPRGSGKTSLLKEFINELKEKGYKVVYIDFLEESNE--SSLRSFIEETSLADELSEA   81 (234)
T ss_dssp             -HHHHHHHHHCHHH--SSEEEEEESTTSSHHHHHHHHHHHCT--EECCCHHCCTTBSHH--HHHHHHHHHHHHHCHCHHH
T ss_pred             HHHHHHHHHHHHHhhcCcEEEEEcCCcCCHHHHHHHHHHHhhhcCCcEEEEecccchhh--hHHHHHHHHHHHHHHHHHH
Confidence            9999999999998766788999999999999999999998744221 1   11111100  000000             


Q ss_pred             cc-------------cchHHHHHHHHHHHHHHHhhhCCCeEEEeCcccccc-ccccccccccccchhhhHHHHHHHhhcc
Q 003038          274 RH-------------MNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWAE-FRASSSEQVRGYYCSIEHIIMEIGKLVC  339 (854)
Q Consensus       274 ~~-------------~~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l~-~~~~~~~~~~~~~~~~~~~~~~~~~ll~  339 (854)
                      ..             .....+...+..+++.+... +..+||+|||++++. .-...           ......+.+++.
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~-~~~~iiviDe~~~~~~~~~~~-----------~~~~~~l~~~~~  149 (234)
T PF01637_consen   82 LGISIPSITLEKISKDLSEDSFSALERLLEKLKKK-GKKVIIVIDEFQYLAIASEED-----------KDFLKSLRSLLD  149 (234)
T ss_dssp             HHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHC-HCCEEEEEETGGGGGBCTTTT-----------HHHHHHHHHHHH
T ss_pred             HhhhcccccchhhhhcchhhHHHHHHHHHHHHHhc-CCcEEEEEecHHHHhhcccch-----------HHHHHHHHHHHh
Confidence            00             01244577788888888875 456999999999994 21110           113344555553


Q ss_pred             c--CCCCceEEEEEecCHHHHHH-hhccCCchhhhhccCCCCCCCchHHHHh
Q 003038          340 G--IGENARFWLMGIATFQSYMR-CKSGHPSLETLWSLHPLTIPAGSLSLSL  388 (854)
Q Consensus       340 ~--~~g~g~l~lIgatT~~ey~k-~~~~~pale~~~~~~~v~i~~~sl~~al  388 (854)
                      .  ...  .+.+|.+++...+.. +...++.+-.  +++.+.+++-+...+.
T Consensus       150 ~~~~~~--~~~~v~~~S~~~~~~~~~~~~~~~~~--~~~~~~l~~l~~~e~~  197 (234)
T PF01637_consen  150 SLLSQQ--NVSIVITGSSDSLMEEFLDDKSPLFG--RFSHIELKPLSKEEAR  197 (234)
T ss_dssp             H----T--TEEEEEEESSHHHHHHTT-TTSTTTT-----EEEE----HHHHH
T ss_pred             hccccC--CceEEEECCchHHHHHhhcccCcccc--ccceEEEeeCCHHHHH
Confidence            2  223  466666666554443 3444454544  5555777765555544

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

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=97.96  E-value=1.7e-05  Score=87.35  Aligned_cols=80  Identities=8%  Similarity=0.045  Sum_probs=49.8

Q ss_pred             cHHHHHHHHHHhh-----ccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHH
Q 003038          211 RNEDVMYVIENLM-----SKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRV  285 (854)
Q Consensus       211 r~~ei~~v~~~L~-----r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl  285 (854)
                      +++.+.++...+.     .+.-++++|+||||||||++++.+|..+.          ..+..++...+.  ..+      
T Consensus         9 ~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~~----------~~~~~~~~~~~~--~~~------   70 (305)
T TIGR00635         9 QEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMG----------VNLKITSGPALE--KPG------   70 (305)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhC----------CCEEEeccchhc--Cch------
Confidence            6666666666554     12345789999999999999999998752          222222221111  112      


Q ss_pred             HHHHHHHHhhhCCCeEEEeCccccc
Q 003038          286 EEIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       286 ~~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                       ++...+... +.+.||||||+|.+
T Consensus        71 -~l~~~l~~~-~~~~vl~iDEi~~l   93 (305)
T TIGR00635        71 -DLAAILTNL-EEGDVLFIDEIHRL   93 (305)
T ss_pred             -hHHHHHHhc-ccCCEEEEehHhhh
Confidence             222333333 45779999999999

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.

>PRK08727 hypothetical protein; Validated

Probab=97.96  E-value=4.4e-05  Score=80.99  Aligned_cols=78  Identities=13%  Similarity=0.178  Sum_probs=52.6

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      -|++|+||+|+|||.++.+++..+.......+.+.+.++.       .             .+. ...+.+  ..+.+|+
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~~~~~-------~-------------~~~-~~~~~l--~~~dlLi   98 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQAAA-------G-------------RLR-DALEAL--EGRSLVA   98 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeHHHhh-------h-------------hHH-HHHHHH--hcCCEEE
Confidence            4899999999999999999998886655555555544332       0             011 112222  3346999


Q ss_pred             EecCCCCC--HHHHHHHHHhhhc
Q 003038          738 IEDVEQAD--YCSQKGFKRAIES  758 (854)
Q Consensus       738 iDEieka~--~~v~~~Ll~~le~  758 (854)
                      ||||+...  +.-+..|+..+..
T Consensus        99 IDDi~~l~~~~~~~~~lf~l~n~  121 (233)
T PRK08727         99 LDGLESIAGQREDEVALFDFHNR  121 (233)
T ss_pred             EeCcccccCChHHHHHHHHHHHH
Confidence            99999874  4556677777764

>PRK05642 DNA replication initiation factor; Validated

Probab=97.96  E-value=2e-05  Score=83.66  Aligned_cols=121  Identities=12%  Similarity=0.089  Sum_probs=76.7

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGD  306 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfide  306 (854)
                      .++++|+|++|+|||.++.+++..+..       ++.+++-++...|...        ...+++.+++.    -+|+|||
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~~~-------~~~~v~y~~~~~~~~~--------~~~~~~~~~~~----d~LiiDD  105 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRFEQ-------RGEPAVYLPLAELLDR--------GPELLDNLEQY----ELVCLDD  105 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHh-------CCCcEEEeeHHHHHhh--------hHHHHHhhhhC----CEEEEec
Confidence            356789999999999999999987653       2456666666655432        23455555543    3799999


Q ss_pred             cccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc---CCCCCCCc
Q 003038          307 LEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL---HPLTIPAG  382 (854)
Q Consensus       307 l~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~---~~v~i~~~  382 (854)
                      ++.+ +...               ...++-.++-....+|...+|++++...+..  ...|.|.+  ||   ..+.|.++
T Consensus       106 i~~~~~~~~---------------~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~--~~~~~L~S--Rl~~gl~~~l~~~  166 (234)
T PRK05642        106 LDVIAGKAD---------------WEEALFHLFNRLRDSGRRLLLAASKSPRELP--IKLPDLKS--RLTLALVFQMRGL  166 (234)
T ss_pred             hhhhcCChH---------------HHHHHHHHHHHHHhcCCEEEEeCCCCHHHcC--ccCccHHH--HHhcCeeeecCCC
Confidence            9988 5432               1223444442211222588888887554432  35799998  77   66666665


Q ss_pred             hHH
Q 003038          383 SLS  385 (854)
Q Consensus       383 sl~  385 (854)
                      +.+
T Consensus       167 ~~e  169 (234)
T PRK05642        167 SDE  169 (234)
T ss_pred             CHH
Confidence            543

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.94  E-value=1e-05  Score=91.01  Aligned_cols=99  Identities=14%  Similarity=0.288  Sum_probs=62.6

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHc-CCCEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSN-NPHRVFL  737 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~-~p~~Vil  737 (854)
                      -+||+||||+|||.|.-|+|..|   +-.+--+++++..       ..               ..|...+.. .+.+||+
T Consensus       237 GYLLYGPPGTGKSS~IaAmAn~L---~ydIydLeLt~v~-------~n---------------~dLr~LL~~t~~kSIiv  291 (457)
T KOG0743|consen  237 GYLLYGPPGTGKSSFIAAMANYL---NYDIYDLELTEVK-------LD---------------SDLRHLLLATPNKSILL  291 (457)
T ss_pred             cceeeCCCCCCHHHHHHHHHhhc---CCceEEeeecccc-------Cc---------------HHHHHHHHhCCCCcEEE
Confidence            37999999999999999999988   2233334443222       00               124444444 4578999


Q ss_pred             EecCCCC----C--------------HHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCCCC
Q 003038          738 IEDVEQA----D--------------YCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRA  789 (854)
Q Consensus       738 iDEieka----~--------------~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~  789 (854)
                      |++||.+    .              +-.+.+||.++| |--..+ |     .--|||||+|-.+-.-.|
T Consensus       292 IEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiD-GlwSsc-g-----~ERIivFTTNh~EkLDPA  354 (457)
T KOG0743|consen  292 IEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLD-GLWSSC-G-----DERIIVFTTNHKEKLDPA  354 (457)
T ss_pred             EeecccccccccccccccccccCCcceeehHHhhhhhc-cccccC-C-----CceEEEEecCChhhcCHh
Confidence            9999976    1              123456777776 322222 1     245899999976655444

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

Probab=97.93  E-value=8.8e-05  Score=83.74  Aligned_cols=148  Identities=11%  Similarity=0.218  Sum_probs=93.0

Q ss_pred             CCcHHHHHHHHHHhhcc----CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc--------
Q 003038          209 PIRNEDVMYVIENLMSK----RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM--------  276 (854)
Q Consensus       209 pvr~~ei~~v~~~L~r~----~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~--------  276 (854)
                      |.||+|++++..+|.-.    ...|++++|+||+|||++++-+++++..-. +    +..++.+++-.+...        
T Consensus        20 ~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~-~----~~~~~yINc~~~~t~~~i~~~i~   94 (366)
T COG1474          20 PHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESS-A----NVEVVYINCLELRTPYQVLSKIL   94 (366)
T ss_pred             cccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhh-c----cCceEEEeeeeCCCHHHHHHHHH
Confidence            44999999999887644    667899999999999999999999987641 1    112555555332211        


Q ss_pred             -------chH-HHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-CCCCce
Q 003038          277 -------NRV-EVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGENAR  346 (854)
Q Consensus       277 -------~rg-e~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~g~  346 (854)
                             ..| -.-+-++.+.+.+... ++.+|+.+||+..| ....                 .-+=.|+.. .....+
T Consensus        95 ~~~~~~p~~g~~~~~~~~~l~~~~~~~-~~~~IvvLDEid~L~~~~~-----------------~~LY~L~r~~~~~~~~  156 (366)
T COG1474          95 NKLGKVPLTGDSSLEILKRLYDNLSKK-GKTVIVILDEVDALVDKDG-----------------EVLYSLLRAPGENKVK  156 (366)
T ss_pred             HHcCCCCCCCCchHHHHHHHHHHHHhc-CCeEEEEEcchhhhccccc-----------------hHHHHHHhhcccccee
Confidence                   111 1122333344444443 57899999999999 5432                 112234422 112236


Q ss_pred             EEEEEecCHHHHHHhhccCCchhhhhccCCCCCCC
Q 003038          347 FWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPA  381 (854)
Q Consensus       347 l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~  381 (854)
                      +-+||.++.-.|..+  -+|.+....+...|..|+
T Consensus       157 v~vi~i~n~~~~~~~--ld~rv~s~l~~~~I~F~p  189 (366)
T COG1474         157 VSIIAVSNDDKFLDY--LDPRVKSSLGPSEIVFPP  189 (366)
T ss_pred             EEEEEEeccHHHHHH--hhhhhhhccCcceeeeCC
Confidence            899999998888654  678887733333344554

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.93  E-value=5.6e-05  Score=84.07  Aligned_cols=95  Identities=12%  Similarity=0.044  Sum_probs=59.9

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccc-------------
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMN-------------  277 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~-------------  277 (854)
                      +++.++++...+.+++-.+++|+||||+|||++++.+++.+....     .+..++.++...+....             
T Consensus        20 ~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l~~~~-----~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~   94 (337)
T PRK12402         20 QDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGDP-----WENNFTEFNVADFFDQGKKYLVEDPRFAHF   94 (337)
T ss_pred             CHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhcCcc-----cccceEEechhhhhhcchhhhhcCcchhhh
Confidence            667777777777665545899999999999999999999875321     12345666655443211             


Q ss_pred             hHH-------HHHHHHHHHHHHHhhh---CCCeEEEeCccccc
Q 003038          278 RVE-------VEQRVEEIKNLVRSCL---GRGIVLNLGDLEWA  310 (854)
Q Consensus       278 rge-------~E~rl~~l~~~~~~~~---~~~~ILfidel~~l  310 (854)
                      .+.       ....+++++.......   +..-||+|||++.+
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l  137 (337)
T PRK12402         95 LGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEAL  137 (337)
T ss_pred             hhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccC
Confidence            111       1223444444443321   23458999999998

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.92  E-value=1.1e-05  Score=86.78  Aligned_cols=84  Identities=10%  Similarity=0.102  Sum_probs=64.8

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhh---CCCeEEEeCc
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCL---GRGIVLNLGD  306 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~---~~~~ILfide  306 (854)
                      ++|+||||+|||++.++|||++.=. .-+.-...+++.++.-+|.+.+.+|.-+-+..+|+.+....   +.-|.+.|||
T Consensus       180 iLlhGPPGTGKTSLCKaLaQkLSIR-~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvLIDE  258 (423)
T KOG0744|consen  180 ILLHGPPGTGKTSLCKALAQKLSIR-TNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVLIDE  258 (423)
T ss_pred             EEEeCCCCCChhHHHHHHHHhheee-ecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEEeHH
Confidence            5899999999999999999997532 12334456899999999999988888877777777666533   3346677899


Q ss_pred             cccc-cccc
Q 003038          307 LEWA-EFRA  314 (854)
Q Consensus       307 l~~l-~~~~  314 (854)
                      +..| -++.
T Consensus       259 VESLa~aR~  267 (423)
T KOG0744|consen  259 VESLAAART  267 (423)
T ss_pred             HHHHHHHHH
Confidence            9999 5553

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.92  E-value=4.5e-05  Score=88.85  Aligned_cols=141  Identities=13%  Similarity=0.083  Sum_probs=77.8

Q ss_pred             cHHHHHHHH-HHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCCCc--------------ccCCceEEEccccccc
Q 003038          211 RNEDVMYVI-ENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDVPE--------------ALRDVKCLPLSISSFR  274 (854)
Q Consensus       211 r~~ei~~v~-~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~vp~--------------~L~~~~~~~l~~~~l~  274 (854)
                      ..+.+.+.+ ..+.+.+-.+ .+|+||||+|||++|+.+|..+.....+.              ......++.++.++  
T Consensus        18 Gq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~dv~el~aa~--   95 (472)
T PRK14962         18 GQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVIELDAAS--   95 (472)
T ss_pred             CcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCccEEEeCcc--
Confidence            445554444 4444444434 59999999999999999999876432110              00112455554431  


Q ss_pred             ccchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEE
Q 003038          275 HMNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMG  351 (854)
Q Consensus       275 ~~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIg  351 (854)
                        .+|-  ..++++++.+....  +..-||||||+|.+ ...                 ...+-..+....+  .+.+|+
T Consensus        96 --~~gi--d~iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt~~a-----------------~~~LLk~LE~p~~--~vv~Il  152 (472)
T PRK14962         96 --NRGI--DEIRKIRDAVGYRPMEGKYKVYIIDEVHMLTKEA-----------------FNALLKTLEEPPS--HVVFVL  152 (472)
T ss_pred             --cCCH--HHHHHHHHHHhhChhcCCeEEEEEEChHHhHHHH-----------------HHHHHHHHHhCCC--cEEEEE
Confidence              2221  12344555554321  34579999999999 421                 1122333321123  588888


Q ss_pred             ecCHHHHHHhhccCCchhhhhccCCCCCCCch
Q 003038          352 IATFQSYMRCKSGHPSLETLWSLHPLTIPAGS  383 (854)
Q Consensus       352 atT~~ey~k~~~~~pale~~~~~~~v~i~~~s  383 (854)
                      +||...     ...|++.+  |++.+.+...+
T Consensus       153 attn~~-----kl~~~L~S--R~~vv~f~~l~  177 (472)
T PRK14962        153 ATTNLE-----KVPPTIIS--RCQVIEFRNIS  177 (472)
T ss_pred             EeCChH-----hhhHHHhc--CcEEEEECCcc
Confidence            887422     23677777  66666655443

>PRK06526 transposase; Provisional

Probab=97.92  E-value=1.1e-05  Score=86.70  Aligned_cols=87  Identities=9%  Similarity=0.109  Sum_probs=55.1

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      ..++|+||+|+|||.+|.+|+..+......+..+.++++.       +.....  . ..+ .+...+ ..+  ..+.|++
T Consensus        99 ~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t~~~l~-------~~l~~~--~-~~~-~~~~~l-~~l--~~~dlLI  164 (254)
T PRK06526         99 ENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQWV-------ARLAAA--H-HAG-RLQAEL-VKL--GRYPLLI  164 (254)
T ss_pred             ceEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhhHHHHH-------HHHHHH--H-hcC-cHHHHH-HHh--ccCCEEE
Confidence            3789999999999999999998876544444444444332       111100  0 001 111122 112  3468999


Q ss_pred             EecCCCC--CHHHHHHHHHhhhc
Q 003038          738 IEDVEQA--DYCSQKGFKRAIES  758 (854)
Q Consensus       738 iDEieka--~~~v~~~Ll~~le~  758 (854)
                      |||++..  ++..++.|.++++.
T Consensus       165 IDD~g~~~~~~~~~~~L~~li~~  187 (254)
T PRK06526        165 VDEVGYIPFEPEAANLFFQLVSS  187 (254)
T ss_pred             EcccccCCCCHHHHHHHHHHHHH
Confidence            9999976  57888899999974

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=97.91  E-value=5.6e-06  Score=93.75  Aligned_cols=152  Identities=17%  Similarity=0.209  Sum_probs=88.4

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhC-CCC------ceEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFG-SHN------NFVS  690 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg-~~~------~~i~  690 (854)
                      +.|+||+.|...+--+-.    |                .+.+||+||||+|||.+|+-|..+|-- +..      .+.+
T Consensus       179 ~DV~GQ~~AKrAleiAAA----G----------------gHnLl~~GpPGtGKTmla~Rl~~lLPpls~~E~lE~s~I~s  238 (490)
T COG0606         179 KDVKGQEQAKRALEIAAA----G----------------GHNLLLVGPPGTGKTMLASRLPGLLPPLSIPEALEVSAIHS  238 (490)
T ss_pred             hhhcCcHHHHHHHHHHHh----c----------------CCcEEEecCCCCchHHhhhhhcccCCCCChHHHHHHHHHhh
Confidence            468999999887654422    2                247999999999999999988765521 000      1111


Q ss_pred             Ecccccc-----CcCCCccccccc--cccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEec
Q 003038          691 IALSSFS-----STRADSTEDSRN--KRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVT  763 (854)
Q Consensus       691 id~s~~~-----~~~~~s~e~~~~--~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d  763 (854)
                      ++...+.     ..+..-.-.|+.  ..++++.+    .-....|....+.|+||||+-...+.+.+.|.+-||+|.++-
T Consensus       239 ~~g~~~~~~~~~~~rPFr~PHHsaS~~aLvGGG~----~p~PGeIsLAH~GVLFLDElpef~~~iLe~LR~PLE~g~i~I  314 (490)
T COG0606         239 LAGDLHEGCPLKIHRPFRAPHHSASLAALVGGGG----VPRPGEISLAHNGVLFLDELPEFKRSILEALREPLENGKIII  314 (490)
T ss_pred             hcccccccCccceeCCccCCCccchHHHHhCCCC----CCCCCceeeecCCEEEeeccchhhHHHHHHHhCccccCcEEE
Confidence            1111000     000000000111  11221110    011223444557899999999999999999999999999986


Q ss_pred             CC-Cceee-cCCeEEEEecCC-----CCCCCCC--CCCC
Q 003038          764 SS-GDEVS-LGDAIVILSCES-----FSSRSRA--CSPP  793 (854)
Q Consensus       764 ~~-G~~v~-~~~aIiIlTsn~-----f~~~s~~--~sp~  793 (854)
                      +. +..|. .-+-++|++.|.     .....+.  |+|.
T Consensus       315 sRa~~~v~ypa~Fqlv~AmNpcpcG~~~~~~~~C~c~~~  353 (490)
T COG0606         315 SRAGSKVTYPARFQLVAAMNPCPCGNLGAPLRRCPCSPR  353 (490)
T ss_pred             EEcCCeeEEeeeeEEhhhcCCCCccCCCCCCCCcCCCHH
Confidence            53 33444 457778888884     3444444  5554

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=97.91  E-value=1.4e-05  Score=85.90  Aligned_cols=75  Identities=9%  Similarity=0.092  Sum_probs=57.8

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc-ccchHH-HHHHHHHHHHHHHhhh--CCCeE
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR-HMNRVE-VEQRVEEIKNLVRSCL--GRGIV  301 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~-~~~rge-~E~rl~~l~~~~~~~~--~~~~I  301 (854)
                      .|.|++|+||.|+|||-+++-||..+          ++.|---|..+|. |||.|| +|.=+..|+..+.-..  ...=|
T Consensus        96 ~KSNILLiGPTGsGKTlLAqTLAk~L----------nVPFaiADATtLTEAGYVGEDVENillkLlqaadydV~rAerGI  165 (408)
T COG1219          96 SKSNILLIGPTGSGKTLLAQTLAKIL----------NVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVERAERGI  165 (408)
T ss_pred             eeccEEEECCCCCcHHHHHHHHHHHh----------CCCeeeccccchhhccccchhHHHHHHHHHHHcccCHHHHhCCe
Confidence            69999999999999999999999764          4556666666664 789987 8888888877643111  12338


Q ss_pred             EEeCccccc
Q 003038          302 LNLGDLEWA  310 (854)
Q Consensus       302 Lfidel~~l  310 (854)
                      +|||||+-+
T Consensus       166 IyIDEIDKI  174 (408)
T COG1219         166 IYIDEIDKI  174 (408)
T ss_pred             EEEechhhh
Confidence            999999999

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

Probab=97.88  E-value=1.2e-05  Score=76.49  Aligned_cols=103  Identities=14%  Similarity=0.152  Sum_probs=65.4

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCC-----CCceEEEccccccCcCCCccccccccccC--CCCC-C---chHHHHH
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGS-----HNNFVSIALSSFSSTRADSTEDSRNKRSR--DEQS-C---SYIERFA  725 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-----~~~~i~id~s~~~~~~~~s~e~~~~~rl~--~~~g-~---g~~e~L~  725 (854)
                      .+.++++||+|+|||.+++.+++.+...     ...++.+++.........   -..+....  .... .   ...+.+.
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~i~~~l~~~~~~~~~~~~l~~~~~   80 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDF---AQEILEALGLPLKSRQTSDELRSLLI   80 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHH---HHHHHHHHT-SSSSTS-HHHHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHH---HHHHHHHhCccccccCCHHHHHHHHH
Confidence            3588999999999999999999887421     456777777654410000   00111111  1111 1   1113677


Q ss_pred             HHHHcCCCEEEEEecCCCC-CHHHHHHHHHhhhcCeEe
Q 003038          726 EAVSNNPHRVFLIEDVEQA-DYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       726 eav~~~p~~ViliDEieka-~~~v~~~Ll~~le~G~l~  762 (854)
                      +.+.+....||+|||+|.+ +..+.+.|+..+++..+.
T Consensus        81 ~~l~~~~~~~lviDe~~~l~~~~~l~~l~~l~~~~~~~  118 (131)
T PF13401_consen   81 DALDRRRVVLLVIDEADHLFSDEFLEFLRSLLNESNIK  118 (131)
T ss_dssp             HHHHHCTEEEEEEETTHHHHTHHHHHHHHHHTCSCBEE
T ss_pred             HHHHhcCCeEEEEeChHhcCCHHHHHHHHHHHhCCCCe
Confidence            7888887789999999999 999999998888854443

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.87  E-value=3e-05  Score=81.65  Aligned_cols=77  Identities=14%  Similarity=0.159  Sum_probs=52.4

Q ss_pred             cHHHHHHHHHHhhc--cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMS--KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEI  288 (854)
Q Consensus       211 r~~ei~~v~~~L~r--~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l  288 (854)
                      +++++...+.-+.+  ...++++|+||+|||||+++++++......       +..++.++...+..        .    
T Consensus        24 ~~~~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~-------~~~~~~i~~~~~~~--------~----   84 (227)
T PRK08903         24 ENAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADASYG-------GRNARYLDAASPLL--------A----   84 (227)
T ss_pred             CcHHHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHHHHhC-------CCcEEEEehHHhHH--------H----
Confidence            45566666666654  456789999999999999999999876442       34566665554321        1    


Q ss_pred             HHHHHhhhCCCeEEEeCccccc
Q 003038          289 KNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       289 ~~~~~~~~~~~~ILfidel~~l  310 (854)
                      +...    ..+-+|+|||+|++
T Consensus        85 ~~~~----~~~~~liiDdi~~l  102 (227)
T PRK08903         85 FDFD----PEAELYAVDDVERL  102 (227)
T ss_pred             Hhhc----ccCCEEEEeChhhc
Confidence            1111    23458999999999

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=97.86  E-value=7.1e-05  Score=90.15  Aligned_cols=63  Identities=8%  Similarity=0.101  Sum_probs=43.6

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccc
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSF  273 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l  273 (854)
                      ++..+++++..+......+++|+||||||||++++.+............-.+..++.++...+
T Consensus       159 qs~~~~~l~~~ia~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l  221 (615)
T TIGR02903       159 QERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTL  221 (615)
T ss_pred             CcHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhc
Confidence            667777777777766677899999999999999999886643211111112456777776544

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.

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=97.86  E-value=3.3e-05  Score=85.14  Aligned_cols=157  Identities=11%  Similarity=0.117  Sum_probs=90.5

Q ss_pred             CCCCC---cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc--chHH
Q 003038          206 SLDPI---RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM--NRVE  280 (854)
Q Consensus       206 ~ldpv---r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~--~rge  280 (854)
                      +.||-   +.+.++.|+.-|..  +++++|.|+||+|||++++.||.++          +..++.+++..-...  ..|.
T Consensus        42 ~~d~~y~f~~~~~~~vl~~l~~--~~~ilL~G~pGtGKTtla~~lA~~l----------~~~~~rV~~~~~l~~~DliG~  109 (327)
T TIGR01650        42 DIDPAYLFDKATTKAICAGFAY--DRRVMVQGYHGTGKSTHIEQIAARL----------NWPCVRVNLDSHVSRIDLVGK  109 (327)
T ss_pred             CCCCCccCCHHHHHHHHHHHhc--CCcEEEEeCCCChHHHHHHHHHHHH----------CCCeEEEEecCCCChhhcCCC
Confidence            45553   66777778877763  6789999999999999999999986          345555544322211  1111


Q ss_pred             H---------HHH-HHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhc-ccCC-----C
Q 003038          281 V---------EQR-VEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CGIG-----E  343 (854)
Q Consensus       281 ~---------E~r-l~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~~~-----g  343 (854)
                      .         ... ....+-.+..   .|++|++||+..+ ..-...           =+.+.|...-+ -+..     .
T Consensus       110 ~~~~l~~g~~~~~f~~GpL~~A~~---~g~illlDEin~a~p~~~~~-----------L~~lLE~~~~l~i~~~~~~i~~  175 (327)
T TIGR01650       110 DAIVLKDGKQITEFRDGILPWALQ---HNVALCFDEYDAGRPDVMFV-----------IQRVLEAGGKLTLLDQNRVIRA  175 (327)
T ss_pred             ceeeccCCcceeEEecCcchhHHh---CCeEEEechhhccCHHHHHH-----------HHHHhccCCeEEECCCceEecC
Confidence            0         000 1112333333   4789999999888 221100           01122211111 0000     1


Q ss_pred             CceEEEEEecCHHH-------HHHhhccCCchhhhhccC-CCCCCCchHHHHh
Q 003038          344 NARFWLMGIATFQS-------YMRCKSGHPSLETLWSLH-PLTIPAGSLSLSL  388 (854)
Q Consensus       344 ~g~l~lIgatT~~e-------y~k~~~~~pale~~~~~~-~v~i~~~sl~~al  388 (854)
                      ...|++|+++++.+       |.=...-+.|+-.+|.+- .+.-+++..+..+
T Consensus       176 hp~FrviAT~Np~g~Gd~~G~y~Gt~~l~~A~lDRF~i~~~~~Yp~~e~E~~I  228 (327)
T TIGR01650       176 HPAFRLFATANTIGLGDTTGLYHGTQQINQAQMDRWSIVTTLNYLEHDNEAAI  228 (327)
T ss_pred             CCCeEEEEeeCCCCcCCCCcceeeeecCCHHHHhheeeEeeCCCCCHHHHHHH
Confidence            12599999999866       777777888998844432 4666666555544

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.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=97.85  E-value=3.4e-05  Score=86.07  Aligned_cols=80  Identities=9%  Similarity=0.004  Sum_probs=50.9

Q ss_pred             cHHHHHHHHHHhhc-----cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHH
Q 003038          211 RNEDVMYVIENLMS-----KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRV  285 (854)
Q Consensus       211 r~~ei~~v~~~L~r-----~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl  285 (854)
                      +++++.++...+..     ...++++|+||||+|||++++.+|..+.          ..++..+...+.  ..+    .+
T Consensus        30 ~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l~----------~~~~~~~~~~~~--~~~----~l   93 (328)
T PRK00080         30 QEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMG----------VNIRITSGPALE--KPG----DL   93 (328)
T ss_pred             cHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHhC----------CCeEEEeccccc--ChH----HH
Confidence            77777776665542     2345799999999999999999998752          233332222111  112    22


Q ss_pred             HHHHHHHHhhhCCCeEEEeCccccc
Q 003038          286 EEIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       286 ~~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                      ..++..   . +.+.||||||+|.+
T Consensus        94 ~~~l~~---l-~~~~vl~IDEi~~l  114 (328)
T PRK00080         94 AAILTN---L-EEGDVLFIDEIHRL  114 (328)
T ss_pred             HHHHHh---c-ccCCEEEEecHhhc
Confidence            233332   2 35779999999999

>PRK05642 DNA replication initiation factor; Validated

Probab=97.85  E-value=8.7e-05  Score=78.82  Aligned_cols=78  Identities=6%  Similarity=0.112  Sum_probs=54.8

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      ..++|+||+|+|||.|+++++..+.......+.+++.++.       .              +...+.+.++.  ..+++
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~~~~~-------~--------------~~~~~~~~~~~--~d~Li  102 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPLAELL-------D--------------RGPELLDNLEQ--YELVC  102 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeHHHHH-------h--------------hhHHHHHhhhh--CCEEE
Confidence            4689999999999999999998776555667777766554       1              01123344443  36999


Q ss_pred             EecCCCCC--HHHHHHHHHhhhc
Q 003038          738 IEDVEQAD--YCSQKGFKRAIES  758 (854)
Q Consensus       738 iDEieka~--~~v~~~Ll~~le~  758 (854)
                      ||||+...  +..+..|+..+..
T Consensus       103 iDDi~~~~~~~~~~~~Lf~l~n~  125 (234)
T PRK05642        103 LDDLDVIAGKADWEEALFHLFNR  125 (234)
T ss_pred             EechhhhcCChHHHHHHHHHHHH
Confidence            99998663  5666778887753

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=97.85  E-value=2.4e-05  Score=89.25  Aligned_cols=73  Identities=11%  Similarity=0.129  Sum_probs=53.8

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc-ccchHH-HHHHHHHHHHH----HHhhhCCC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR-HMNRVE-VEQRVEEIKNL----VRSCLGRG  299 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~-~~~rge-~E~rl~~l~~~----~~~~~~~~  299 (854)
                      .+.|++|+||||||||.+|+.||..+          +..++.++...+. ++|.|+ .+.-+..++..    +...  .+
T Consensus       115 ~~~~iLL~GP~GsGKT~lAraLA~~l----------~~pf~~~da~~L~~~gyvG~d~e~~L~~~~~~~~~~l~~a--~~  182 (413)
T TIGR00382       115 SKSNILLIGPTGSGKTLLAQTLARIL----------NVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKA--QK  182 (413)
T ss_pred             CCceEEEECCCCcCHHHHHHHHHHhc----------CCCeEEechhhccccccccccHHHHHHHHHHhCcccHHhc--cc
Confidence            46799999999999999999999764          3466777776664 368776 56666665543    2222  45


Q ss_pred             eEEEeCccccc
Q 003038          300 IVLNLGDLEWA  310 (854)
Q Consensus       300 ~ILfidel~~l  310 (854)
                      .|||||||+.+
T Consensus       183 gIV~lDEIdkl  193 (413)
T TIGR00382       183 GIIYIDEIDKI  193 (413)
T ss_pred             ceEEecccchh
Confidence            68999999988

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.84  E-value=1.9e-05  Score=87.83  Aligned_cols=75  Identities=12%  Similarity=0.120  Sum_probs=59.7

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccc-cccchHH-HHHHHHHHHHHHHhhh--CCCeE
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSF-RHMNRVE-VEQRVEEIKNLVRSCL--GRGIV  301 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l-~~~~rge-~E~rl~~l~~~~~~~~--~~~~I  301 (854)
                      .|.|++|+||+|+|||-+++-||+-+          ++.|.--|...| +|||.|| +|-=+..|+..+.-..  ...=|
T Consensus       225 eKSNvLllGPtGsGKTllaqTLAr~l----------dVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVekAQqGI  294 (564)
T KOG0745|consen  225 EKSNVLLLGPTGSGKTLLAQTLARVL----------DVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGI  294 (564)
T ss_pred             ecccEEEECCCCCchhHHHHHHHHHh----------CCCeEEecccchhhcccccccHHHHHHHHHHHccCCHHHHhcCe
Confidence            79999999999999999999999653          566777777777 6799987 8888888887754221  12348


Q ss_pred             EEeCccccc
Q 003038          302 LNLGDLEWA  310 (854)
Q Consensus       302 Lfidel~~l  310 (854)
                      +||||++-+
T Consensus       295 VflDEvDKi  303 (564)
T KOG0745|consen  295 VFLDEVDKI  303 (564)
T ss_pred             EEEehhhhh
Confidence            999999988

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=97.82  E-value=4.8e-05  Score=91.35  Aligned_cols=53  Identities=21%  Similarity=0.162  Sum_probs=43.3

Q ss_pred             HHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC
Q 003038          612 LCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS  684 (854)
Q Consensus       612 L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~  684 (854)
                      +.+.|...|+||++++..+..++...                    ..++|+||+|+|||++|++||+.+...
T Consensus        12 ~~~~~~~~viG~~~a~~~l~~a~~~~--------------------~~~ll~G~pG~GKT~la~~la~~l~~~   64 (608)
T TIGR00764        12 VPERLIDQVIGQEEAVEIIKKAAKQK--------------------RNVLLIGEPGVGKSMLAKAMAELLPDE   64 (608)
T ss_pred             cchhhHhhccCHHHHHHHHHHHHHcC--------------------CCEEEECCCCCCHHHHHHHHHHHcCch
Confidence            34467789999999999888877641                    167899999999999999999988644

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.82  E-value=0.00011  Score=87.43  Aligned_cols=120  Identities=13%  Similarity=0.006  Sum_probs=70.5

Q ss_pred             cHHHHHHHHHHhhccCcCCc-eeecCCCCCHHHHHHHHHHHHHcCCCCc--------------ccCCceEEEcccccccc
Q 003038          211 RNEDVMYVIENLMSKRKRNF-VVVGECLASIEGVVRGVIDKIEKGDVPE--------------ALRDVKCLPLSISSFRH  275 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~-vLvGe~GvGKta~v~~la~~i~~~~vp~--------------~L~~~~~~~l~~~~l~~  275 (854)
                      .+.-++.+...+.+.+-.+. +|+||+|||||++++.+|..+....-+.              .-....|+.++.++-. 
T Consensus        20 Qe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hpDviEIDAAs~~-   98 (702)
T PRK14960         20 QNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFIDLIEIDAASRT-   98 (702)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCCceEEecccccC-
Confidence            44455556666665554444 9999999999999999999886422110              0122345666554221 


Q ss_pred             cchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEe
Q 003038          276 MNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGI  352 (854)
Q Consensus       276 ~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIga  352 (854)
                       ..    ..++++++.+....  ++.-|++|||+|++ ..                 +...+-++|..-.+  .+.+|.+
T Consensus        99 -~V----ddIReli~~~~y~P~~gk~KV~IIDEVh~LS~~-----------------A~NALLKtLEEPP~--~v~FILa  154 (702)
T PRK14960         99 -KV----EDTRELLDNVPYAPTQGRFKVYLIDEVHMLSTH-----------------SFNALLKTLEEPPE--HVKFLFA  154 (702)
T ss_pred             -CH----HHHHHHHHHHhhhhhcCCcEEEEEechHhcCHH-----------------HHHHHHHHHhcCCC--CcEEEEE
Confidence             11    23455555554221  45679999999999 43                 22234455521122  4788888


Q ss_pred             cCH
Q 003038          353 ATF  355 (854)
Q Consensus       353 tT~  355 (854)
                      ||.
T Consensus       155 Ttd  157 (702)
T PRK14960        155 TTD  157 (702)
T ss_pred             ECC
Confidence            875

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=97.80  E-value=8.7e-05  Score=76.71  Aligned_cols=130  Identities=13%  Similarity=0.090  Sum_probs=88.9

Q ss_pred             HHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc-----chHHHH---------H
Q 003038          218 VIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM-----NRVEVE---------Q  283 (854)
Q Consensus       218 v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~-----~rge~E---------~  283 (854)
                      ++..|.-+..-|.+++|||+||||++.+.+|+-+..|--  .+..+++.-+|-.+=+++     ..=++-         -
T Consensus       128 li~~ly~~g~lntLiigpP~~GKTTlLRdiaR~~s~g~~--~~l~kkv~IiDersEIag~~~gvpq~~~g~R~dVld~cp  205 (308)
T COG3854         128 LIKDLYQNGWLNTLIIGPPQVGKTTLLRDIARLLSDGIN--QFLPKKVGIIDERSEIAGCLNGVPQHGRGRRMDVLDPCP  205 (308)
T ss_pred             HHHHHHhcCceeeEEecCCCCChHHHHHHHHHHhhcccc--ccCCceEEEEeccchhhccccCCchhhhhhhhhhcccch
Confidence            677888889999999999999999999999998887732  455667777776554443     111222         3


Q ss_pred             HHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-CCCCceEEEEEecCHHHHHHh
Q 003038          284 RVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGENARFWLMGIATFQSYMRC  361 (854)
Q Consensus       284 rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~g~l~lIgatT~~ey~k~  361 (854)
                      +-..++..+++.  .|-|+.+|||-+- ++                      -.++.. ..|   +.+|+++.=..... 
T Consensus       206 k~~gmmmaIrsm--~PEViIvDEIGt~~d~----------------------~A~~ta~~~G---Vkli~TaHG~~ied-  257 (308)
T COG3854         206 KAEGMMMAIRSM--SPEVIIVDEIGTEEDA----------------------LAILTALHAG---VKLITTAHGNGIED-  257 (308)
T ss_pred             HHHHHHHHHHhc--CCcEEEEeccccHHHH----------------------HHHHHHHhcC---cEEEEeeccccHHH-
Confidence            344567778876  5778999999554 32                      222211 345   99999875333222 


Q ss_pred             hccCCchhhhhccCCC
Q 003038          362 KSGHPSLETLWSLHPL  377 (854)
Q Consensus       362 ~~~~pale~~~~~~~v  377 (854)
                      +.+.|+|.++|..|.+
T Consensus       258 l~krp~lkdlv~i~af  273 (308)
T COG3854         258 LIKRPTLKDLVEIQAF  273 (308)
T ss_pred             hhcChhHHHHHhhhHH
Confidence            3578999997765544

>PRK08181 transposase; Validated

Probab=97.80  E-value=3.9e-05  Score=83.04  Aligned_cols=86  Identities=8%  Similarity=0.120  Sum_probs=56.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLI  738 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vili  738 (854)
                      .++|+||+|+|||.||.+|+..+......++.+.+.++.       +.....    .....+ +.+.+.+.  ...+++|
T Consensus       108 nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~~~L~-------~~l~~a----~~~~~~-~~~l~~l~--~~dLLII  173 (269)
T PRK08181        108 NLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLV-------QKLQVA----RRELQL-ESAIAKLD--KFDLLIL  173 (269)
T ss_pred             eEEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeHHHHH-------HHHHHH----HhCCcH-HHHHHHHh--cCCEEEE
Confidence            699999999999999999999887655566666665444       111100    000122 12333333  3469999


Q ss_pred             ecCCCCC--HHHHHHHHHhhhc
Q 003038          739 EDVEQAD--YCSQKGFKRAIES  758 (854)
Q Consensus       739 DEieka~--~~v~~~Ll~~le~  758 (854)
                      ||+....  +..+..|.++|+.
T Consensus       174 DDlg~~~~~~~~~~~Lf~lin~  195 (269)
T PRK08181        174 DDLAYVTKDQAETSVLFELISA  195 (269)
T ss_pred             eccccccCCHHHHHHHHHHHHH
Confidence            9998764  4566789999974

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=97.79  E-value=7.6e-05  Score=79.15  Aligned_cols=136  Identities=15%  Similarity=0.247  Sum_probs=96.0

Q ss_pred             hhhhhhhHHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHH
Q 003038          599 HKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELA  678 (854)
Q Consensus       599 ~~~~~~~~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA  678 (854)
                      .+|.+.-.+.|.-|..-+..+=+.-...|++|-..-.+.|                   ..+|+.||+|.||+.+|+.+-
T Consensus       169 srfa~ere~tl~~lksgiatrnp~fnrmieqierva~rsr-------------------~p~ll~gptgagksflarriy  229 (531)
T COG4650         169 SRFAEEREQTLDFLKSGIATRNPHFNRMIEQIERVAIRSR-------------------APILLNGPTGAGKSFLARRIY  229 (531)
T ss_pred             HHHHHHHHHHHHHHHhcccccChHHHHHHHHHHHHHhhcc-------------------CCeEeecCCCcchhHHHHHHH
Confidence            7787776777888888887776666666666655544433                   257999999999999999653


Q ss_pred             -----HHHhCCCCceEEEccccccCcCCCccccccccccCCC-CC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHH
Q 003038          679 -----RLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDE-QS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQK  750 (854)
Q Consensus       679 -----~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~-~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~  750 (854)
                           +.-|  ..+||.+||....       .+..++-+.+. .| + |..+.-...+|.....++|+|||..+..+-|.
T Consensus       230 elk~arhq~--sg~fvevncatlr-------gd~amsalfghvkgaftga~~~r~gllrsadggmlfldeigelgadeqa  300 (531)
T COG4650         230 ELKQARHQF--SGAFVEVNCATLR-------GDTAMSALFGHVKGAFTGARESREGLLRSADGGMLFLDEIGELGADEQA  300 (531)
T ss_pred             HHHHHHHhc--CCceEEEeeeeec-------CchHHHHHHhhhccccccchhhhhhhhccCCCceEehHhhhhcCccHHH
Confidence                 4444  3579999998665       33333333311 01 1 33333445567777899999999999999999


Q ss_pred             HHHHhhhcCeEe
Q 003038          751 GFKRAIESGRIV  762 (854)
Q Consensus       751 ~Ll~~le~G~l~  762 (854)
                      .|+++||+-++-
T Consensus       301 mllkaieekrf~  312 (531)
T COG4650         301 MLLKAIEEKRFY  312 (531)
T ss_pred             HHHHHHHhhccC
Confidence            999999987765

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=97.78  E-value=0.00018  Score=80.82  Aligned_cols=149  Identities=14%  Similarity=0.048  Sum_probs=89.5

Q ss_pred             HHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          613 CNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       613 ~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      .+.+.+-++||+.....|    ..+..   +|           ..+-.|+.|+.|+|||+++|+||.+|- .  .-+.++
T Consensus        12 ~~~pf~aivGqd~lk~aL----~l~av---~P-----------~iggvLI~G~kGtaKSt~~Rala~LLp-~--~~~V~g   70 (423)
T COG1239          12 ENLPFTAIVGQDPLKLAL----GLNAV---DP-----------QIGGALIAGEKGTAKSTLARALADLLP-E--IEVVIG   70 (423)
T ss_pred             hccchhhhcCchHHHHHH----hhhhc---cc-----------ccceeEEecCCCccHHHHHHHHHHhCC-c--cceecC
Confidence            346678899999665543    33321   22           256788999999999999999999992 1  112223


Q ss_pred             cccccCcCCC--cc-----------ccccccc---cCC-CCCCchHH------HHHHHHH------------cCCCEEEE
Q 003038          693 LSSFSSTRAD--ST-----------EDSRNKR---SRD-EQSCSYIE------RFAEAVS------------NNPHRVFL  737 (854)
Q Consensus       693 ~s~~~~~~~~--s~-----------e~~~~~r---l~~-~~g~g~~e------~L~eav~------------~~p~~Vil  737 (854)
                      |.-...+...  ..           .-+.-++   ++. |.+- -.+      .+..+++            +....|++
T Consensus        71 c~f~cdP~~P~~~c~~c~~k~~e~~~~~~~~r~v~~v~lPl~a-teDrvvGslDi~ka~~~g~~af~PGlLa~AnRGIlY  149 (423)
T COG1239          71 CPFNCDPDDPEEMCDECRAKGDELEWLPREKRKVPFVALPLGA-TEDRLVGSLDIEKALEEGPKAFQPGLLARANRGILY  149 (423)
T ss_pred             CCCCCCCCChhhhhHHHHhhccccccccccceecceecCCCcc-chhhhccccCHHHHHhcCccccCCcchhhccCCEEE
Confidence            3211110000  00           0000011   111 2111 111      1233333            33457999


Q ss_pred             EecCCCCCHHHHHHHHHhhhcC-eEecCCCceeec-CCeEEEEecCCC
Q 003038          738 IEDVEQADYCSQKGFKRAIESG-RIVTSSGDEVSL-GDAIVILSCESF  783 (854)
Q Consensus       738 iDEieka~~~v~~~Ll~~le~G-~l~d~~G~~v~~-~~aIiIlTsn~f  783 (854)
                      ||||.-++..+++.||.++++| ...--.|..+.. -+.++|.|.|.-
T Consensus       150 vDEvnlL~d~lvd~LLd~aaeG~n~vereGisi~hpa~fvligTmNPE  197 (423)
T COG1239         150 VDEVNLLDDHLVDALLDVAAEGVNDVEREGISIRHPARFLLIGTMNPE  197 (423)
T ss_pred             EeccccccHHHHHHHHHHHHhCCceeeeCceeeccCccEEEEeecCcc
Confidence            9999999999999999999999 334456766665 488999999953

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.78  E-value=4.3e-05  Score=88.49  Aligned_cols=127  Identities=9%  Similarity=0.041  Sum_probs=74.4

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHH-HHHHHHHHHHhhhCCCeEEEeC
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQ-RVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~-rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      .|..+|+||||+|||.++++++..+...       +.+++.++...|...+...+.. .+..+....+    ...+|+||
T Consensus       141 ~npl~L~G~~G~GKTHLl~Ai~~~l~~~-------~~~v~yi~~~~f~~~~~~~l~~~~~~~f~~~~~----~~dvLiID  209 (445)
T PRK12422        141 FNPIYLFGPEGSGKTHLMQAAVHALRES-------GGKILYVRSELFTEHLVSAIRSGEMQRFRQFYR----NVDALFIE  209 (445)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHHHHHc-------CCCEEEeeHHHHHHHHHHHHhcchHHHHHHHcc----cCCEEEEc
Confidence            3567899999999999999999988652       4677777766554432222221 1111111222    34589999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEec-CHHHHHHhhccCCchhhhhcc---CCCC
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIA-TFQSYMRCKSGHPSLETLWSL---HPLT  378 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgat-T~~ey~k~~~~~pale~~~~~---~~v~  378 (854)
                      |+|.+ +....               ..++-.++..  ..|  ...+|+++ .+.++..   .++.|.+  ||   ..+.
T Consensus       210 Diq~l~~k~~~---------------qeelf~l~N~l~~~~--k~IIlts~~~p~~l~~---l~~rL~S--R~~~Gl~~~  267 (445)
T PRK12422        210 DIEVFSGKGAT---------------QEEFFHTFNSLHTEG--KLIVISSTCAPQDLKA---MEERLIS--RFEWGIAIP  267 (445)
T ss_pred             chhhhcCChhh---------------HHHHHHHHHHHHHCC--CcEEEecCCCHHHHhh---hHHHHHh--hhcCCeEEe
Confidence            99999 64321               1122233211  123  34455444 4666653   4778877  77   4666


Q ss_pred             CCCchHHH
Q 003038          379 IPAGSLSL  386 (854)
Q Consensus       379 i~~~sl~~  386 (854)
                      |..++.+.
T Consensus       268 l~~pd~e~  275 (445)
T PRK12422        268 LHPLTKEG  275 (445)
T ss_pred             cCCCCHHH
Confidence            76666544

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.77  E-value=0.00024  Score=81.10  Aligned_cols=125  Identities=15%  Similarity=0.140  Sum_probs=76.3

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHcCCC---Cc------------ccCCceEEEcccccccccchHHHHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEKGDV---PE------------ALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLV  292 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~~~v---p~------------~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~  292 (854)
                      ...+|+||||+|||++++.+|+.+...+.   |-            .--+.+++.-+...   ...++    ++++++.+
T Consensus        37 ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~~hpD~~~i~~~~~~---i~i~~----iR~l~~~~  109 (394)
T PRK07940         37 HAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAGTHPDVRVVAPEGLS---IGVDE----VRELVTIA  109 (394)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEecccccc---CCHHH----HHHHHHHH
Confidence            45889999999999999999998876431   10            00112222222110   12222    55676666


Q ss_pred             Hhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhc-ccCCCCceEEEEEecCHHHHHHhhccCCch
Q 003038          293 RSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CGIGENARFWLMGIATFQSYMRCKSGHPSL  368 (854)
Q Consensus       293 ~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~~~g~g~l~lIgatT~~ey~k~~~~~pal  368 (854)
                      ....  ++.-|+||||+|.+ ...                 ...+-+.| .|..+  .+++++|+++..      ..|++
T Consensus       110 ~~~p~~~~~kViiIDead~m~~~a-----------------anaLLk~LEep~~~--~~fIL~a~~~~~------llpTI  164 (394)
T PRK07940        110 ARRPSTGRWRIVVIEDADRLTERA-----------------ANALLKAVEEPPPR--TVWLLCAPSPED------VLPTI  164 (394)
T ss_pred             HhCcccCCcEEEEEechhhcCHHH-----------------HHHHHHHhhcCCCC--CeEEEEECChHH------ChHHH
Confidence            5421  44569999999999 431                 12344445 23222  588888888543      45888


Q ss_pred             hhhhccCCCCCCCchHHH
Q 003038          369 ETLWSLHPLTIPAGSLSL  386 (854)
Q Consensus       369 e~~~~~~~v~i~~~sl~~  386 (854)
                      .+  |.+.+.++.++.+.
T Consensus       165 rS--Rc~~i~f~~~~~~~  180 (394)
T PRK07940        165 RS--RCRHVALRTPSVEA  180 (394)
T ss_pred             Hh--hCeEEECCCCCHHH
Confidence            87  77888888776554

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.77  E-value=4.4e-05  Score=84.92  Aligned_cols=90  Identities=17%  Similarity=0.221  Sum_probs=60.6

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      .+++|+||+|+|||.||.++|..+......++.+.+.++.       ......+.  ... ...+...+.+.+  ..+++
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~l~-------~~l~~~~~--~~~-~~~~~~~~~l~~--~DLLI  251 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADELI-------EILREIRF--NND-KELEEVYDLLIN--CDLLI  251 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHHHH-------HHHHHHHh--ccc-hhHHHHHHHhcc--CCEEE
Confidence            5799999999999999999999998777777887776554       11110000  000 000112344443  36999


Q ss_pred             EecC--CCCCHHHHHHHHHhhhcC
Q 003038          738 IEDV--EQADYCSQKGFKRAIESG  759 (854)
Q Consensus       738 iDEi--eka~~~v~~~Ll~~le~G  759 (854)
                      |||+  +..++..+..|..+|+.-
T Consensus       252 IDDlG~e~~t~~~~~~Lf~iin~R  275 (329)
T PRK06835        252 IDDLGTEKITEFSKSELFNLINKR  275 (329)
T ss_pred             EeccCCCCCCHHHHHHHHHHHHHH
Confidence            9999  666788888899988753

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=97.77  E-value=5.7e-05  Score=89.52  Aligned_cols=62  Identities=10%  Similarity=0.156  Sum_probs=43.3

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccc
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISS  272 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~  272 (854)
                      .++.++.+...+......+++|+||||||||++|+.+.....+...-..-.+..|+.+|...
T Consensus        70 qs~~i~~l~~al~~~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~~~~~~~fi~id~~~  131 (531)
T TIGR02902        70 QEEGIKALKAALCGPNPQHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAAFVEIDATT  131 (531)
T ss_pred             cHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhhhccCCCcCCCCCEEEEcccc
Confidence            55667777776776677899999999999999999997653322110111246788888753

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.76  E-value=0.00018  Score=87.91  Aligned_cols=118  Identities=14%  Similarity=0.027  Sum_probs=67.8

Q ss_pred             HHHHHHHhhccCcCCc-eeecCCCCCHHHHHHHHHHHHHcCCC----Ccc----------cCCceEEEcccccccccchH
Q 003038          215 VMYVIENLMSKRKRNF-VVVGECLASIEGVVRGVIDKIEKGDV----PEA----------LRDVKCLPLSISSFRHMNRV  279 (854)
Q Consensus       215 i~~v~~~L~r~~k~n~-vLvGe~GvGKta~v~~la~~i~~~~v----p~~----------L~~~~~~~l~~~~l~~~~rg  279 (854)
                      ++.+...+..++-.+. ||+||||||||++++.+|..+.....    |-.          ....-++.++..+-.  ...
T Consensus        25 v~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~DviEidAas~~--kVD  102 (944)
T PRK14949         25 LHALTNALTQQRLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFVDLIEVDAASRT--KVD  102 (944)
T ss_pred             HHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCceEEEecccccc--CHH
Confidence            3444455555555665 89999999999999999999865321    110          111223334332110  111


Q ss_pred             HHHHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhc-ccCCCCceEEEEEecCH
Q 003038          280 EVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CGIGENARFWLMGIATF  355 (854)
Q Consensus       280 e~E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~~~g~g~l~lIgatT~  355 (854)
                          .++++++.+....  ++.-|++|||+|.+ ..                 +...+-+.| .| .+  .+++|++||.
T Consensus       103 ----dIReLie~v~~~P~~gk~KViIIDEAh~LT~e-----------------AqNALLKtLEEP-P~--~vrFILaTTe  158 (944)
T PRK14949        103 ----DTRELLDNVQYRPSRGRFKVYLIDEVHMLSRS-----------------SFNALLKTLEEP-PE--HVKFLLATTD  158 (944)
T ss_pred             ----HHHHHHHHHHhhhhcCCcEEEEEechHhcCHH-----------------HHHHHHHHHhcc-CC--CeEEEEECCC
Confidence                2344555544221  45679999999999 33                 122344444 22 23  4889999886


Q ss_pred             HHH
Q 003038          356 QSY  358 (854)
Q Consensus       356 ~ey  358 (854)
                      ...
T Consensus       159 ~~k  161 (944)
T PRK14949        159 PQK  161 (944)
T ss_pred             chh
Confidence            553

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.76  E-value=9.1e-05  Score=79.03  Aligned_cols=89  Identities=10%  Similarity=0.206  Sum_probs=57.7

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      .+++|+|++|+|||.||.+||..+......++.+++.++.       ....  ......... .+.+.+.+.  ...|++
T Consensus       100 ~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~it~~~l~-------~~l~--~~~~~~~~~-~~~~l~~l~--~~dlLv  167 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIITVADIM-------SAMK--DTFSNSETS-EEQLLNDLS--NVDLLV  167 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEHHHHH-------HHHH--HHHhhcccc-HHHHHHHhc--cCCEEE
Confidence            3799999999999999999999987666777777766554       1110  000000001 123444444  367999


Q ss_pred             EecCCCCC--HHHHHHHHHhhhc
Q 003038          738 IEDVEQAD--YCSQKGFKRAIES  758 (854)
Q Consensus       738 iDEieka~--~~v~~~Ll~~le~  758 (854)
                      |||+....  ......|.++|+.
T Consensus       168 IDDig~~~~s~~~~~~l~~Ii~~  190 (244)
T PRK07952        168 IDEIGVQTESRYEKVIINQIVDR  190 (244)
T ss_pred             EeCCCCCCCCHHHHHHHHHHHHH
Confidence            99997754  3345577888875

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.75  E-value=3.6e-05  Score=89.61  Aligned_cols=128  Identities=13%  Similarity=0.088  Sum_probs=77.6

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHH-HHHHHHHHHHhhhCCCeEEEeCc
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQ-RVEEIKNLVRSCLGRGIVLNLGD  306 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~-rl~~l~~~~~~~~~~~~ILfide  306 (854)
                      |+++|+||||+|||.++++++..+.+..     .+..++.++...|...+...+.. .+.++.+..++    ..+|+|||
T Consensus       149 ~~l~l~G~~G~GKThL~~ai~~~~~~~~-----~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~----~dlLiiDD  219 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHAIGNYILEKN-----PNAKVVYVTSEKFTNDFVNALRNNTMEEFKEKYRS----VDVLLIDD  219 (450)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhC-----CCCeEEEEEHHHHHHHHHHHHHcCcHHHHHHHHhc----CCEEEEeh
Confidence            5578899999999999999999886532     15678888777665543333321 22334444442    45899999


Q ss_pred             cccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecC-HHHHHHhhccCCchhhhhccC---CCCC
Q 003038          307 LEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIAT-FQSYMRCKSGHPSLETLWSLH---PLTI  379 (854)
Q Consensus       307 l~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT-~~ey~k~~~~~pale~~~~~~---~v~i  379 (854)
                      ||.+ +...               ...++-.++-.  ..+  ...+|+++. +.+...   .+|.|.+  ||.   .|.|
T Consensus       220 i~~l~~~~~---------------~~~~l~~~~n~l~~~~--~~iiits~~~p~~l~~---l~~~l~S--Rl~~gl~v~i  277 (450)
T PRK00149        220 IQFLAGKER---------------TQEEFFHTFNALHEAG--KQIVLTSDRPPKELPG---LEERLRS--RFEWGLTVDI  277 (450)
T ss_pred             hhhhcCCHH---------------HHHHHHHHHHHHHHCC--CcEEEECCCCHHHHHH---HHHHHHh--HhcCCeeEEe
Confidence            9999 6432               11233344321  223  345665554 344332   3577877  773   5667


Q ss_pred             CCchHHH
Q 003038          380 PAGSLSL  386 (854)
Q Consensus       380 ~~~sl~~  386 (854)
                      ..|+.+.
T Consensus       278 ~~pd~~~  284 (450)
T PRK00149        278 EPPDLET  284 (450)
T ss_pred             cCCCHHH
Confidence            7776554

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=97.74  E-value=0.00016  Score=72.93  Aligned_cols=79  Identities=11%  Similarity=0.139  Sum_probs=49.6

Q ss_pred             HHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHH----------
Q 003038          216 MYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRV----------  285 (854)
Q Consensus       216 ~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl----------  285 (854)
                      .+.+.-++ ....+++|+||+|+||+.+|+.+-..-.+       ++..|+.++++.+-.   ..+|..|          
T Consensus        12 ~~~~~~~a-~~~~pVlI~GE~GtGK~~lA~~IH~~s~r-------~~~pfi~vnc~~~~~---~~~e~~LFG~~~~~~~~   80 (168)
T PF00158_consen   12 REQAKRAA-SSDLPVLITGETGTGKELLARAIHNNSPR-------KNGPFISVNCAALPE---ELLESELFGHEKGAFTG   80 (168)
T ss_dssp             HHHHHHHT-TSTS-EEEECSTTSSHHHHHHHHHHCSTT-------TTS-EEEEETTTS-H---HHHHHHHHEBCSSSSTT
T ss_pred             HHHHHHHh-CCCCCEEEEcCCCCcHHHHHHHHHHhhhc-------ccCCeEEEehhhhhc---chhhhhhhccccccccc
Confidence            33333344 36689999999999999999988764222       456899999987632   1122111          


Q ss_pred             -----HHHHHHHHhhhCCCeEEEeCccccc
Q 003038          286 -----EEIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       286 -----~~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                           ..+++.+.     +=+||||||..|
T Consensus        81 ~~~~~~G~l~~A~-----~GtL~Ld~I~~L  105 (168)
T PF00158_consen   81 ARSDKKGLLEQAN-----GGTLFLDEIEDL  105 (168)
T ss_dssp             TSSEBEHHHHHTT-----TSEEEEETGGGS
T ss_pred             cccccCCceeecc-----ceEEeecchhhh
Confidence                 12333332     337999999999

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

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

Probab=97.74  E-value=9.7e-05  Score=83.41  Aligned_cols=137  Identities=11%  Similarity=0.101  Sum_probs=90.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc--eEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN--FVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~--~i~id~s~  695 (854)
                      .++++-++-+..++..+.-.-.|.             +| ..++++||||+|||.+++.+.+.+......  .++|||-.
T Consensus        17 ~~l~~Re~ei~~l~~~l~~~~~~~-------------~p-~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~   82 (366)
T COG1474          17 EELPHREEEINQLASFLAPALRGE-------------RP-SNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLE   82 (366)
T ss_pred             ccccccHHHHHHHHHHHHHHhcCC-------------CC-ccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeee
Confidence            457888888888888876654432             23 358999999999999999999999865322  69999998


Q ss_pred             ccCcCCCccccccccc-c------CCCCCCchH---HHHHHHHHc-CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecC
Q 003038          696 FSSTRADSTEDSRNKR-S------RDEQSCSYI---ERFAEAVSN-NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTS  764 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~r-l------~~~~g~g~~---e~L~eav~~-~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~  764 (854)
                      +.+       ...+.. +      ++..|....   +.|.+.+.+ ...-||++||+|.+-..-++.|+..+.-..--  
T Consensus        83 ~~t-------~~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~~~~LY~L~r~~~~~--  153 (366)
T COG1474          83 LRT-------PYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRAPGEN--  153 (366)
T ss_pred             CCC-------HHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhccccchHHHHHHhhcccc--
Confidence            873       222111 1      112233222   366777765 56679999999998766545555555421110  


Q ss_pred             CCceeecCCeEEEEecCCC
Q 003038          765 SGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       765 ~G~~v~~~~aIiIlTsn~f  783 (854)
                            -.+.++|+.+|..
T Consensus       154 ------~~~v~vi~i~n~~  166 (366)
T COG1474         154 ------KVKVSIIAVSNDD  166 (366)
T ss_pred             ------ceeEEEEEEeccH
Confidence                  3456788888864

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=97.73  E-value=7.4e-05  Score=89.67  Aligned_cols=53  Identities=21%  Similarity=0.186  Sum_probs=43.0

Q ss_pred             HHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC
Q 003038          612 LCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS  684 (854)
Q Consensus       612 L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~  684 (854)
                      +...+...|+||++++..|..++...                    ..++|+||+|+|||++|++|++.++..
T Consensus        25 ~~~~~~~~vigq~~a~~~L~~~~~~~--------------------~~~l~~G~~G~GKttla~~l~~~l~~~   77 (637)
T PRK13765         25 VPERLIDQVIGQEHAVEVIKKAAKQR--------------------RHVMMIGSPGTGKSMLAKAMAELLPKE   77 (637)
T ss_pred             cCcccHHHcCChHHHHHHHHHHHHhC--------------------CeEEEECCCCCcHHHHHHHHHHHcChH
Confidence            33456678999999999888877641                    158999999999999999999988643

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.73  E-value=5.9e-05  Score=82.92  Aligned_cols=69  Identities=19%  Similarity=0.346  Sum_probs=50.6

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHH----HcC
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAV----SNN  731 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav----~~~  731 (854)
                      |.--+|++||+|+|||.+|+++|+..   ..+||.+.|+..+       ++.          ||-.+.|..++    .+-
T Consensus       126 p~kGiLL~GPpG~GKTmlAKA~Akea---ga~fInv~~s~lt-------~KW----------fgE~eKlv~AvFslAsKl  185 (386)
T KOG0737|consen  126 PPKGILLYGPPGTGKTMLAKAIAKEA---GANFINVSVSNLT-------SKW----------FGEAQKLVKAVFSLASKL  185 (386)
T ss_pred             CCccceecCCCCchHHHHHHHHHHHc---CCCcceeeccccc-------hhh----------HHHHHHHHHHHHhhhhhc
Confidence            33456778999999999999999976   5789999999777       221          14444455554    333


Q ss_pred             CCEEEEEecCCCC
Q 003038          732 PHRVFLIEDVEQA  744 (854)
Q Consensus       732 p~~ViliDEieka  744 (854)
                      ..+||||||||.+
T Consensus       186 ~P~iIFIDEvds~  198 (386)
T KOG0737|consen  186 QPSIIFIDEVDSF  198 (386)
T ss_pred             CcceeehhhHHHH
Confidence            4589999999965

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=97.72  E-value=9.2e-05  Score=77.56  Aligned_cols=79  Identities=14%  Similarity=0.121  Sum_probs=53.4

Q ss_pred             HHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHH
Q 003038          213 EDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLV  292 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~  292 (854)
                      .-+.++-..+.-+..++++|+||||||||++++.++......       +..++.+++..+..        +..+++..+
T Consensus        24 ~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~~~~~-------~~~~~~i~~~~~~~--------~~~~~~~~~   88 (226)
T TIGR03420        24 ELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEER-------GKSAIYLPLAELAQ--------ADPEVLEGL   88 (226)
T ss_pred             HHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHHHHhc-------CCcEEEEeHHHHHH--------hHHHHHhhc
Confidence            334444444444577889999999999999999999876432       34566676665542        223444444


Q ss_pred             HhhhCCCeEEEeCccccc
Q 003038          293 RSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       293 ~~~~~~~~ILfidel~~l  310 (854)
                      ..    .-+|||||++++
T Consensus        89 ~~----~~lLvIDdi~~l  102 (226)
T TIGR03420        89 EQ----ADLVCLDDVEAI  102 (226)
T ss_pred             cc----CCEEEEeChhhh
Confidence            32    348999999999

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.

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.72  E-value=4.4e-05  Score=82.21  Aligned_cols=106  Identities=14%  Similarity=0.225  Sum_probs=64.1

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHh----CC--CCceEEEccccccCcCCCccccccccccCCCCCC---chHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLVF----GS--HNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSC---SYIERFAEAVS  729 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lf----g~--~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~---g~~e~L~eav~  729 (854)
                      .+|++||||+|||.|+|+||+.|-    +.  +..+|.|+....            .++..+..|.   -.-+++.|.+.
T Consensus       179 liLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEinshsL------------FSKWFsESgKlV~kmF~kI~ELv~  246 (423)
T KOG0744|consen  179 LILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINSHSL------------FSKWFSESGKLVAKMFQKIQELVE  246 (423)
T ss_pred             EEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEehhHH------------HHHHHhhhhhHHHHHHHHHHHHHh
Confidence            589999999999999999999872    11  122333332211            1111122222   01124556555


Q ss_pred             cCCCE-EEEEecCCCCC---------------HHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCCCC
Q 003038          730 NNPHR-VFLIEDVEQAD---------------YCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFSS  785 (854)
Q Consensus       730 ~~p~~-ViliDEieka~---------------~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~  785 (854)
                      ....= .|+|||||.+.               -.|-|+||.-||.         --...|.+|..|||--++
T Consensus       247 d~~~lVfvLIDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlDr---------lK~~~NvliL~TSNl~~s  309 (423)
T KOG0744|consen  247 DRGNLVFVLIDEVESLAAARTSASSRNEPSDAIRVVNALLTQLDR---------LKRYPNVLILATSNLTDS  309 (423)
T ss_pred             CCCcEEEEEeHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHH---------hccCCCEEEEeccchHHH
Confidence            53333 47899999642               1478899988884         224578888889996444

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=97.71  E-value=0.0001  Score=68.47  Aligned_cols=96  Identities=19%  Similarity=0.289  Sum_probs=60.2

Q ss_pred             EEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccc-cccCCCCCC-chHHHHHHHHHcCCCEEEE
Q 003038          660 LFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRN-KRSRDEQSC-SYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~-~rl~~~~g~-g~~e~L~eav~~~p~~Vil  737 (854)
                      +.|+||+|+|||.+|+.||+.+.....         ..       ....+ .+.....-+ ||          ..+.|++
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~~~---------~~-------~~~~vy~~~~~~~~w~gY----------~~q~vvi   54 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKHIG---------EP-------TKDSVYTRNPGDKFWDGY----------QGQPVVI   54 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHHhc---------cC-------CCCcEEeCCCccchhhcc----------CCCcEEE
Confidence            368999999999999999998853210         00       00000 000000001 44          1357999


Q ss_pred             EecCCCCCHH----HHHHHHHhhhcCeEecC----CCceeecCCeEEEEecC
Q 003038          738 IEDVEQADYC----SQKGFKRAIESGRIVTS----SGDEVSLGDAIVILSCE  781 (854)
Q Consensus       738 iDEieka~~~----v~~~Ll~~le~G~l~d~----~G~~v~~~~aIiIlTsn  781 (854)
                      +||+......    ....|+++++...+.-.    ......|.--+||+|||
T Consensus        55 ~DD~~~~~~~~~~~~~~~l~~l~s~~~~~~~~a~~~~K~~~~~s~~vi~tsN  106 (107)
T PF00910_consen   55 IDDFGQDNDGYNYSDESELIRLISSNPFQPNMADLEDKGTPFNSKLVIITSN  106 (107)
T ss_pred             EeecCccccccchHHHHHHHHHHhcCCcccccccHhhCCCccCCCEEEEcCC
Confidence            9999998854    67888999988766531    11225566678888888

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

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.71  E-value=0.00026  Score=84.10  Aligned_cols=92  Identities=15%  Similarity=0.110  Sum_probs=55.6

Q ss_pred             HHHHHHHHHhhccCcCCc-eeecCCCCCHHHHHHHHHHHHHcCC------C---Cc----------ccCCceEEEccccc
Q 003038          213 EDVMYVIENLMSKRKRNF-VVVGECLASIEGVVRGVIDKIEKGD------V---PE----------ALRDVKCLPLSISS  272 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~-vLvGe~GvGKta~v~~la~~i~~~~------v---p~----------~L~~~~~~~l~~~~  272 (854)
                      .-++.+...+...+-.+. ||+|++|+|||++++.||+.+....      +   |-          .-....++.++.++
T Consensus        23 ~vv~~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC~~I~aG~hpDviEIdAas  102 (700)
T PRK12323         23 HVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEIDAGRFVDYIEMDAAS  102 (700)
T ss_pred             HHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccHHHHHHHcCCCCcceEecccc
Confidence            334455556665555565 8999999999999999999986521      0   10          00112455555442


Q ss_pred             ccccchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          273 FRHMNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       273 l~~~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                      -.  ...    .++++++.+....  ++.-|++|||+|.+
T Consensus       103 ~~--gVD----dIReLie~~~~~P~~gr~KViIIDEah~L  136 (700)
T PRK12323        103 NR--GVD----EMAQLLDKAVYAPTAGRFKVYMIDEVHML  136 (700)
T ss_pred             cC--CHH----HHHHHHHHHHhchhcCCceEEEEEChHhc
Confidence            11  222    2444555543211  45679999999999

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=97.70  E-value=0.00011  Score=90.55  Aligned_cols=138  Identities=7%  Similarity=0.002  Sum_probs=82.7

Q ss_pred             HHHHHHHHHHhhc------cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc---------c
Q 003038          212 NEDVMYVIENLMS------KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH---------M  276 (854)
Q Consensus       212 ~~ei~~v~~~L~r------~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~---------~  276 (854)
                      ++--++|++.|.-      .+...++|+||||+|||++++.+|..+          +..++.++++.+..         .
T Consensus       328 ~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~l----------~~~~~~i~~~~~~d~~~i~g~~~~  397 (784)
T PRK10787        328 ERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKAT----------GRKYVRMALGGVRDEAEIRGHRRT  397 (784)
T ss_pred             HHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHHh----------CCCEEEEEcCCCCCHHHhccchhc
Confidence            3334445555542      134568999999999999999999764          33566666554321         1


Q ss_pred             chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc---------------
Q 003038          277 NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG---------------  340 (854)
Q Consensus       277 ~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~---------------  340 (854)
                      |.|....++...+..+..   .+.|+||||++.+ ....+.             ....+-.++.+               
T Consensus       398 ~~g~~~G~~~~~l~~~~~---~~~villDEidk~~~~~~g~-------------~~~aLlevld~~~~~~~~d~~~~~~~  461 (784)
T PRK10787        398 YIGSMPGKLIQKMAKVGV---KNPLFLLDEIDKMSSDMRGD-------------PASALLEVLDPEQNVAFSDHYLEVDY  461 (784)
T ss_pred             cCCCCCcHHHHHHHhcCC---CCCEEEEEChhhcccccCCC-------------HHHHHHHHhccccEEEEecccccccc
Confidence            455555555444444332   2347899999999 432211             11122233322               


Q ss_pred             CCCCceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHH
Q 003038          341 IGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLS  385 (854)
Q Consensus       341 ~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~  385 (854)
                      ..+  .+.+|++|++      +...|+|-.  |+..|++...+..
T Consensus       462 dls--~v~~i~TaN~------~~i~~aLl~--R~~ii~~~~~t~e  496 (784)
T PRK10787        462 DLS--DVMFVATSNS------MNIPAPLLD--RMEVIRLSGYTED  496 (784)
T ss_pred             cCC--ceEEEEcCCC------CCCCHHHhc--ceeeeecCCCCHH
Confidence            123  5888886643      247999999  8888888766543

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=97.69  E-value=0.00014  Score=85.76  Aligned_cols=147  Identities=16%  Similarity=0.136  Sum_probs=91.7

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|-|.+++..++.+.|--.+..-++..    -+. .=|.| .|+.||||+|||.|||++|-.-   +-+|.++..|+|.
T Consensus       150 ~DVAG~dEakeel~EiVdfLk~p~ky~~----lGa-kiPkG-vlLvGpPGTGKTLLAkAvAgEA---~VPFf~iSGS~FV  220 (596)
T COG0465         150 ADVAGVDEAKEELSELVDFLKNPKKYQA----LGA-KIPKG-VLLVGPPGTGKTLLAKAVAGEA---GVPFFSISGSDFV  220 (596)
T ss_pred             hhhcCcHHHHHHHHHHHHHHhCchhhHh----ccc-ccccc-eeEecCCCCCcHHHHHHHhccc---CCCceeccchhhh
Confidence            4579999999999999876543211100    000 02334 4678999999999999999765   5678888888776


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCH--------------HHHHHHHHhhhcCeEec
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADY--------------CSQKGFKRAIESGRIVT  763 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~--------------~v~~~Ll~~le~G~l~d  763 (854)
                             +-+-      +-|......|++.-+++-.|||||||||....              +..|-||.-||-     
T Consensus       221 -------emfV------GvGAsRVRdLF~qAkk~aP~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlLvEmDG-----  282 (596)
T COG0465         221 -------EMFV------GVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDG-----  282 (596)
T ss_pred             -------hhhc------CCCcHHHHHHHHHhhccCCCeEEEehhhhcccccCCCCCCCchHHHHHHHHHHhhhcc-----
Confidence                   3221      22223333566666666669999999997532              356666666651     


Q ss_pred             CCCceeecCCeEEEEecCCCCCCCCCCCCCcc
Q 003038          764 SSGDEVSLGDAIVILSCESFSSRSRACSPPTK  795 (854)
Q Consensus       764 ~~G~~v~~~~aIiIlTsn~f~~~s~~~sp~~~  795 (854)
                       .|   .=...|+|-.||--|..-++.-.|-|
T Consensus       283 -F~---~~~gviviaaTNRpdVlD~ALlRpgR  310 (596)
T COG0465         283 -FG---GNEGVIVIAATNRPDVLDPALLRPGR  310 (596)
T ss_pred             -CC---CCCceEEEecCCCcccchHhhcCCCC
Confidence             11   00234555566655666666665644

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.69  E-value=0.00012  Score=87.77  Aligned_cols=50  Identities=12%  Similarity=0.130  Sum_probs=39.6

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHH
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .|+||++.+..|...+.....+.             ++...++|.||+|+|||++++.||+.+
T Consensus        85 el~~~~~ki~~l~~~l~~~~~~~-------------~~~~illL~GP~GsGKTTl~~~la~~l  134 (637)
T TIGR00602        85 ELAVHKKKIEEVETWLKAQVLEN-------------APKRILLITGPSGCGKSTTIKILSKEL  134 (637)
T ss_pred             HhcCcHHHHHHHHHHHHhccccc-------------CCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            47999999999888876543221             233368999999999999999999876

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.68  E-value=8.4e-05  Score=85.34  Aligned_cols=86  Identities=19%  Similarity=0.283  Sum_probs=56.3

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCC--CCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGS--HNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRV  735 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~--~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~V  735 (854)
                      .+++|+||+|+|||.|+++++..+...  ...++++++.+|.       .... ..+..    +-.+.+.+.++.  ..|
T Consensus       137 n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~~~~-------~~~~-~~~~~----~~~~~~~~~~~~--~dl  202 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSSEKFT-------NDFV-NALRN----NKMEEFKEKYRS--VDL  202 (405)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEHHHHH-------HHHH-HHHHc----CCHHHHHHHHHh--CCE
Confidence            478999999999999999999988654  4567788776554       1110 00000    111234444443  579


Q ss_pred             EEEecCCCCCH--HHHHHHHHhhh
Q 003038          736 FLIEDVEQADY--CSQKGFKRAIE  757 (854)
Q Consensus       736 iliDEieka~~--~v~~~Ll~~le  757 (854)
                      ++||||+....  ..|..|+..|+
T Consensus       203 LiiDDi~~l~~~~~~~~~l~~~~n  226 (405)
T TIGR00362       203 LLIDDIQFLAGKERTQEEFFHTFN  226 (405)
T ss_pred             EEEehhhhhcCCHHHHHHHHHHHH
Confidence            99999997643  46677777775

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).

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=97.68  E-value=3e-05  Score=78.93  Aligned_cols=87  Identities=14%  Similarity=0.187  Sum_probs=57.9

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      .+++|+||+|+|||.||.+++..+.........++++++.       +.....  .   ..+-.+.+...+.+.  .+++
T Consensus        48 ~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~~L~-------~~l~~~--~---~~~~~~~~~~~l~~~--dlLi  113 (178)
T PF01695_consen   48 ENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFITASDLL-------DELKQS--R---SDGSYEELLKRLKRV--DLLI  113 (178)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHH-------HHHHCC--H---CCTTHCHHHHHHHTS--SCEE
T ss_pred             eEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecCcee-------cccccc--c---cccchhhhcCccccc--cEec
Confidence            3799999999999999999999887777777777777554       221111  0   111112344555543  5999


Q ss_pred             EecCCCC--CHHHHHHHHHhhhc
Q 003038          738 IEDVEQA--DYCSQKGFKRAIES  758 (854)
Q Consensus       738 iDEieka--~~~v~~~Ll~~le~  758 (854)
                      |||+-..  +....+.|.++|+.
T Consensus       114 lDDlG~~~~~~~~~~~l~~ii~~  136 (178)
T PF01695_consen  114 LDDLGYEPLSEWEAELLFEIIDE  136 (178)
T ss_dssp             EETCTSS---HHHHHCTHHHHHH
T ss_pred             ccccceeeecccccccchhhhhH
Confidence            9999865  46677888888875

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.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.68  E-value=0.00013  Score=80.47  Aligned_cols=102  Identities=15%  Similarity=0.147  Sum_probs=61.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      ..++|+||+|+|||.||.+||..+.........+.++++.       ...  +..+.. + .+ +.+.+.+.+  ..|++
T Consensus       157 ~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~~~~l~-------~~l--k~~~~~-~-~~-~~~l~~l~~--~dlLi  222 (306)
T PRK08939        157 KGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFPEFI-------REL--KNSISD-G-SV-KEKIDAVKE--APVLM  222 (306)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEHHHHH-------HHH--HHHHhc-C-cH-HHHHHHhcC--CCEEE
Confidence            3689999999999999999999987555556666666544       111  111100 0 12 223344444  45999


Q ss_pred             EecCC--CCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCC
Q 003038          738 IEDVE--QADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       738 iDEie--ka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      |||+.  .+++-+.+.++..|-+.|+.         .+--.|+|||.
T Consensus       223 IDDiG~e~~s~~~~~~ll~~Il~~R~~---------~~~~ti~TSNl  260 (306)
T PRK08939        223 LDDIGAEQMSSWVRDEVLGVILQYRMQ---------EELPTFFTSNF  260 (306)
T ss_pred             EecCCCccccHHHHHHHHHHHHHHHHH---------CCCeEEEECCC
Confidence            99996  45566665566555332321         11226888984

>PRK04195 replication factor C large subunit; Provisional

Probab=97.67  E-value=0.0002  Score=84.20  Aligned_cols=85  Identities=13%  Similarity=0.122  Sum_probs=57.2

Q ss_pred             cHHHHHHHHHHhhccC----cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKR----KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVE  286 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~----k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~  286 (854)
                      .++.+.++.+.+.+..    .++++|+||||+|||++|+.||+.+          +..++.++.+....  ..    .+.
T Consensus        19 ~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el----------~~~~ielnasd~r~--~~----~i~   82 (482)
T PRK04195         19 NEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDY----------GWEVIELNASDQRT--AD----VIE   82 (482)
T ss_pred             CHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHc----------CCCEEEEccccccc--HH----HHH
Confidence            5666667666665432    6789999999999999999999875          45677777664432  11    223


Q ss_pred             HHHHHHHhhh---C-CCeEEEeCccccc-c
Q 003038          287 EIKNLVRSCL---G-RGIVLNLGDLEWA-E  311 (854)
Q Consensus       287 ~l~~~~~~~~---~-~~~ILfidel~~l-~  311 (854)
                      .++..+....   + .+.||+|||++.+ +
T Consensus        83 ~~i~~~~~~~sl~~~~~kvIiIDEaD~L~~  112 (482)
T PRK04195         83 RVAGEAATSGSLFGARRKLILLDEVDGIHG  112 (482)
T ss_pred             HHHHHhhccCcccCCCCeEEEEecCccccc
Confidence            3333332211   2 4679999999999 5

>PLN03025 replication factor C subunit; Provisional

Probab=97.64  E-value=0.00028  Score=78.42  Aligned_cols=93  Identities=15%  Similarity=0.100  Sum_probs=54.7

Q ss_pred             cHHH-HHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHH
Q 003038          211 RNED-VMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIK  289 (854)
Q Consensus       211 r~~e-i~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~  289 (854)
                      ..++ +.++-.++..++..|.+|+||||+|||++++++|..+.....     ...++.++.+...  ....+.+.++...
T Consensus        17 g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l~~~~~-----~~~~~eln~sd~~--~~~~vr~~i~~~~   89 (319)
T PLN03025         17 GNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGPNY-----KEAVLELNASDDR--GIDVVRNKIKMFA   89 (319)
T ss_pred             CcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhcccC-----ccceeeecccccc--cHHHHHHHHHHHH
Confidence            3344 444444555556678999999999999999999988753211     1235555554322  2223333333321


Q ss_pred             HHHHhh-hCCCeEEEeCccccc
Q 003038          290 NLVRSC-LGRGIVLNLGDLEWA  310 (854)
Q Consensus       290 ~~~~~~-~~~~~ILfidel~~l  310 (854)
                      ...... .++.-|++|||+|.+
T Consensus        90 ~~~~~~~~~~~kviiiDE~d~l  111 (319)
T PLN03025         90 QKKVTLPPGRHKIVILDEADSM  111 (319)
T ss_pred             hccccCCCCCeEEEEEechhhc
Confidence            111000 023579999999999

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.64  E-value=0.00016  Score=81.86  Aligned_cols=143  Identities=10%  Similarity=0.042  Sum_probs=77.7

Q ss_pred             cHHH-HHHHHHHhhccCcCCc-eeecCCCCCHHHHHHHHHHHHHcCCCC--c-c---------cC--CceEEEccccccc
Q 003038          211 RNED-VMYVIENLMSKRKRNF-VVVGECLASIEGVVRGVIDKIEKGDVP--E-A---------LR--DVKCLPLSISSFR  274 (854)
Q Consensus       211 r~~e-i~~v~~~L~r~~k~n~-vLvGe~GvGKta~v~~la~~i~~~~vp--~-~---------L~--~~~~~~l~~~~l~  274 (854)
                      ..+. ++.+...+..++-.+. +|+||||+|||++++.+|..+.....+  . .         ..  ...++.++.++  
T Consensus        20 Gq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c~~c~~~~~~~~~d~~~~~~~~--   97 (363)
T PRK14961         20 GQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKCIICKEIEKGLCLDLIEIDAAS--   97 (363)
T ss_pred             ChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceEEecccc--
Confidence            3344 4445555555454554 899999999999999999987532111  0 0         00  12344443321  


Q ss_pred             ccchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEE
Q 003038          275 HMNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMG  351 (854)
Q Consensus       275 ~~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIg  351 (854)
                         +.-+ ..++++++.+....  ++.-|++|||+|.+ ...                 ...+-..+....+  .+++|.
T Consensus        98 ---~~~v-~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~~a-----------------~naLLk~lEe~~~--~~~fIl  154 (363)
T PRK14961         98 ---RTKV-EEMREILDNIYYSPSKSRFKVYLIDEVHMLSRHS-----------------FNALLKTLEEPPQ--HIKFIL  154 (363)
T ss_pred             ---cCCH-HHHHHHHHHHhcCcccCCceEEEEEChhhcCHHH-----------------HHHHHHHHhcCCC--CeEEEE
Confidence               1111 12455655554321  33569999999999 421                 1123333321122  477888


Q ss_pred             ecCHHHHHHhhccCCchhhhhccCCCCCCCchHH
Q 003038          352 IATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLS  385 (854)
Q Consensus       352 atT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~  385 (854)
                      +||...  +   -.+++..  |.+.+.++..+..
T Consensus       155 ~t~~~~--~---l~~tI~S--Rc~~~~~~~l~~~  181 (363)
T PRK14961        155 ATTDVE--K---IPKTILS--RCLQFKLKIISEE  181 (363)
T ss_pred             EcCChH--h---hhHHHHh--hceEEeCCCCCHH
Confidence            776422  2   3456665  6667777665533

>PRK06921 hypothetical protein; Provisional

Probab=97.64  E-value=8.7e-05  Score=80.36  Aligned_cols=86  Identities=12%  Similarity=0.114  Sum_probs=53.4

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCC-CCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEE
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGS-HNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRV  735 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~V  735 (854)
                      ..+++|+||+|+|||.||.++|..+... ...++.+...+..       ..     +..  .++..+...+.+.  ...|
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~~~l~-------~~-----l~~--~~~~~~~~~~~~~--~~dl  180 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPFVEGF-------GD-----LKD--DFDLLEAKLNRMK--KVEV  180 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEHHHHH-------HH-----HHH--HHHHHHHHHHHhc--CCCE
Confidence            3589999999999999999999988654 4455555543322       10     000  0011112223333  3569


Q ss_pred             EEEecCCC-------CCHHHHHHHHHhhhc
Q 003038          736 FLIEDVEQ-------ADYCSQKGFKRAIES  758 (854)
Q Consensus       736 iliDEiek-------a~~~v~~~Ll~~le~  758 (854)
                      ++|||++.       ++...+..|..+|+.
T Consensus       181 LiIDDl~~~~~g~e~~t~~~~~~lf~iin~  210 (266)
T PRK06921        181 LFIDDLFKPVNGKPRATEWQIEQMYSVLNY  210 (266)
T ss_pred             EEEeccccccCCCccCCHHHHHHHHHHHHH
Confidence            99999943       555566778888864

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=97.64  E-value=7e-05  Score=80.49  Aligned_cols=100  Identities=10%  Similarity=0.107  Sum_probs=65.8

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCC-chHHHHHHHHHcCCCEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSC-SYIERFAEAVSNNPHRVF  736 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~~e~L~eav~~~p~~Vi  736 (854)
                      ..++|+||+|||||.||-+|+..+.....+++.+...++.            .++.....+ ...++|...+.  ...|+
T Consensus       106 ~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~~el~------------~~Lk~~~~~~~~~~~l~~~l~--~~dlL  171 (254)
T COG1484         106 ENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLL------------SKLKAAFDEGRLEEKLLRELK--KVDLL  171 (254)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEHHHHH------------HHHHHHHhcCchHHHHHHHhh--cCCEE
Confidence            3789999999999999999999887545666666665544            111111111 12224444443  45699


Q ss_pred             EEecCCC--CCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCC
Q 003038          737 LIEDVEQ--ADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       737 liDEiek--a~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      +|||+-.  .++...+.|.++|..-+..          ... |+|||.
T Consensus       172 IiDDlG~~~~~~~~~~~~~q~I~~r~~~----------~~~-~~tsN~  208 (254)
T COG1484         172 IIDDIGYEPFSQEEADLLFQLISRRYES----------RSL-IITSNL  208 (254)
T ss_pred             EEecccCccCCHHHHHHHHHHHHHHHhh----------ccc-eeecCC
Confidence            9999987  5666788888988753322          223 888884

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=97.64  E-value=0.00031  Score=73.82  Aligned_cols=102  Identities=13%  Similarity=0.148  Sum_probs=69.5

Q ss_pred             ceeEEEecCCC-chHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccC--C--CCCCchHH--HHHHHHH
Q 003038          657 ETWLFFQGVDA-DAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSR--D--EQSCSYIE--RFAEAVS  729 (854)
Q Consensus       657 ~~~lLf~Gp~G-vGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~--~--~~g~g~~e--~L~eav~  729 (854)
                      ...+||.|..+ .||..++.-+++.+|...     ++...+.       +-+.+..-.  .  +...+.++  .+.+.+.
T Consensus        15 shAYLfeG~n~~~~~~~~~~f~~~~l~~~~-----i~~~~HP-------D~~~I~pe~~~~~~~~~I~IdqIReL~~~l~   82 (263)
T PRK06581         15 YNSWLIEAENIEQALKDLEKFIYIKLFKNS-----IPLENNP-------DYHFIARETSATSNAKNISIEQIRKLQDFLS   82 (263)
T ss_pred             hheeeEeCCChhhHHHHHHHHHHHHHhccC-----cccCCCC-------CEEEEeccccccccCCcccHHHHHHHHHHHh
Confidence            46899999998 999999999999998642     2333222       111111000  0  00114444  4566665


Q ss_pred             cC----CCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecC
Q 003038          730 NN----PHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       730 ~~----p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn  781 (854)
                      ..    +++|++|+++|+++....|+||+.+|+.           -.+++|||+|+
T Consensus        83 ~~p~~g~~KViII~~ae~mt~~AANALLKtLEEP-----------P~~t~fILit~  127 (263)
T PRK06581         83 KTSAISGYKVAIIYSAELMNLNAANSCLKILEDA-----------PKNSYIFLITS  127 (263)
T ss_pred             hCcccCCcEEEEEechHHhCHHHHHHHHHhhcCC-----------CCCeEEEEEeC
Confidence            44    5789999999999999999999999973           35788888774

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=97.61  E-value=0.00025  Score=83.54  Aligned_cols=102  Identities=18%  Similarity=0.251  Sum_probs=69.0

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHc--------
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSN--------  730 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~--------  730 (854)
                      .+|++||+|-|||+||+.+|+.-   .-.++.||.|.--          +.        ..+.+++..++..        
T Consensus       328 ilLL~GppGlGKTTLAHViAkqa---GYsVvEINASDeR----------t~--------~~v~~kI~~avq~~s~l~ads  386 (877)
T KOG1969|consen  328 ILLLCGPPGLGKTTLAHVIAKQA---GYSVVEINASDER----------TA--------PMVKEKIENAVQNHSVLDADS  386 (877)
T ss_pred             eEEeecCCCCChhHHHHHHHHhc---CceEEEecccccc----------cH--------HHHHHHHHHHHhhccccccCC
Confidence            79999999999999999999975   4577888877321          11        1233455555543        


Q ss_pred             CCCEEEEEecCCCCCHHHHHHHHHhhhc-C-eEecCCC---------ceeecCCeEEEEecCCC
Q 003038          731 NPHRVFLIEDVEQADYCSQKGFKRAIES-G-RIVTSSG---------DEVSLGDAIVILSCESF  783 (854)
Q Consensus       731 ~p~~ViliDEieka~~~v~~~Ll~~le~-G-~l~d~~G---------~~v~~~~aIiIlTsn~f  783 (854)
                      +|.| +++||||=+++...+.|+..+.. + ..+...+         +.--+.+.||-. ||..
T Consensus       387 rP~C-LViDEIDGa~~~~Vdvilslv~a~~k~~~Gkq~~~~~~rkkkr~~~L~RPIICI-CNdL  448 (877)
T KOG1969|consen  387 RPVC-LVIDEIDGAPRAAVDVILSLVKATNKQATGKQAKKDKKRKKKRSKLLTRPIICI-CNDL  448 (877)
T ss_pred             Ccce-EEEecccCCcHHHHHHHHHHHHhhcchhhcCcccchhhhhhhccccccCCEEEE-ecCc
Confidence            4544 56999999999999999998872 2 2222222         122366777666 6653

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.61  E-value=0.00017  Score=83.78  Aligned_cols=76  Identities=18%  Similarity=0.209  Sum_probs=52.6

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHH---HHHHHHHHHHhhhCCCeEEEe
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQ---RVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~---rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      |+++|+|++|+|||.++++++..+....     .+.+++.++...|...+...+..   .+.++.+..+    ...+|+|
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~-----~~~~v~yv~~~~f~~~~~~~l~~~~~~~~~~~~~~~----~~dvLiI  212 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESNF-----SDLKVSYMSGDEFARKAVDILQKTHKEIEQFKNEIC----QNDVLII  212 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHhC-----CCCeEEEEEHHHHHHHHHHHHHHhhhHHHHHHHHhc----cCCEEEE
Confidence            4566899999999999999999876532     35788888877776554433322   2333333333    3458999


Q ss_pred             Cccccc-cc
Q 003038          305 GDLEWA-EF  312 (854)
Q Consensus       305 del~~l-~~  312 (854)
                      ||+|.+ +.
T Consensus       213 DDiq~l~~k  221 (450)
T PRK14087        213 DDVQFLSYK  221 (450)
T ss_pred             eccccccCC
Confidence            999999 54

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.61  E-value=0.00039  Score=83.66  Aligned_cols=121  Identities=12%  Similarity=0.003  Sum_probs=69.3

Q ss_pred             cHHHHHHHHHHhhccCcCCc-eeecCCCCCHHHHHHHHHHHHHcCC----CCcc----------cCCceEEEcccccccc
Q 003038          211 RNEDVMYVIENLMSKRKRNF-VVVGECLASIEGVVRGVIDKIEKGD----VPEA----------LRDVKCLPLSISSFRH  275 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~-vLvGe~GvGKta~v~~la~~i~~~~----vp~~----------L~~~~~~~l~~~~l~~  275 (854)
                      .+.-++.+...+..++..+. ||+|++|||||++++.||+.+....    .|..          -....++.+|-.+-. 
T Consensus        21 Qe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C~sCr~I~~G~h~DviEIDAas~r-   99 (830)
T PRK07003         21 QEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCRACREIDEGRFVDYVEMDAASNR-   99 (830)
T ss_pred             cHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcccHHHHHHhcCCCceEEEecccccc-
Confidence            34445556666665555555 8999999999999999999886421    1100          011235555543211 


Q ss_pred             cchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEe
Q 003038          276 MNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGI  352 (854)
Q Consensus       276 ~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIga  352 (854)
                       ...+    ++++++.+....  ++.-|++|||+|+| ..                 +...+-+.|..-..  .+.+|.+
T Consensus       100 -gVDd----IReLIe~a~~~P~~gr~KVIIIDEah~LT~~-----------------A~NALLKtLEEPP~--~v~FILa  155 (830)
T PRK07003        100 -GVDE----MAALLERAVYAPVDARFKVYMIDEVHMLTNH-----------------AFNAMLKTLEEPPP--HVKFILA  155 (830)
T ss_pred             -cHHH----HHHHHHHHHhccccCCceEEEEeChhhCCHH-----------------HHHHHHHHHHhcCC--CeEEEEE
Confidence             1222    344555443211  34568999999999 42                 12234444421122  4888888


Q ss_pred             cCHH
Q 003038          353 ATFQ  356 (854)
Q Consensus       353 tT~~  356 (854)
                      ||..
T Consensus       156 Ttd~  159 (830)
T PRK07003        156 TTDP  159 (830)
T ss_pred             ECCh
Confidence            8853

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=97.60  E-value=0.0002  Score=79.35  Aligned_cols=65  Identities=20%  Similarity=0.197  Sum_probs=49.1

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      -++||.+|-++..-.+...+.|-..             --.+||.||||+|||.+|-++|+.| |..-+|+.+..|+..
T Consensus        25 GlVGQ~~AReAagiiv~mIk~~K~a-------------Gr~iLiaGppGtGKTAlA~~ia~eL-G~~~PF~~isgSEiy   89 (398)
T PF06068_consen   25 GLVGQEKAREAAGIIVDMIKEGKIA-------------GRAILIAGPPGTGKTALAMAIAKEL-GEDVPFVSISGSEIY   89 (398)
T ss_dssp             TEES-HHHHHHHHHHHHHHHTT--T-------------T-EEEEEE-TTSSHHHHHHHHHHHC-TTTS-EEEEEGGGG-
T ss_pred             cccChHHHHHHHHHHHHHHhccccc-------------CcEEEEeCCCCCCchHHHHHHHHHh-CCCCCeeEcccceee
Confidence            4799999888777777666654211             1278999999999999999999999 889999999999765

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>PRK08727 hypothetical protein; Validated

Probab=97.60  E-value=0.00041  Score=73.64  Aligned_cols=120  Identities=10%  Similarity=0.053  Sum_probs=71.2

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEe
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      +..+.++|+|++|+|||.++.+++....+.       +.+++-+++        .++..++.++++.+.+    ..+|+|
T Consensus        39 ~~~~~l~l~G~~G~GKThL~~a~~~~~~~~-------~~~~~y~~~--------~~~~~~~~~~~~~l~~----~dlLiI   99 (233)
T PRK08727         39 QSSDWLYLSGPAGTGKTHLALALCAAAEQA-------GRSSAYLPL--------QAAAGRLRDALEALEG----RSLVAL   99 (233)
T ss_pred             cCCCeEEEECCCCCCHHHHHHHHHHHHHHc-------CCcEEEEeH--------HHhhhhHHHHHHHHhc----CCEEEE
Confidence            344568999999999999999998876542       334444433        2344556666666654    358999


Q ss_pred             Cccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecCHHHHHHhhccCCchhhhhcc---CCCC
Q 003038          305 GDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIATFQSYMRCKSGHPSLETLWSL---HPLT  378 (854)
Q Consensus       305 del~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~---~~v~  378 (854)
                      ||++++ +....               ...+-+++..  ..+. .+.+.+-.-+.++..   .+|.|.+  ||   ..+.
T Consensus       100 DDi~~l~~~~~~---------------~~~lf~l~n~~~~~~~-~vI~ts~~~p~~l~~---~~~dL~S--Rl~~~~~~~  158 (233)
T PRK08727        100 DGLESIAGQRED---------------EVALFDFHNRARAAGI-TLLYTARQMPDGLAL---VLPDLRS--RLAQCIRIG  158 (233)
T ss_pred             eCcccccCChHH---------------HHHHHHHHHHHHHcCC-eEEEECCCChhhhhh---hhHHHHH--HHhcCceEE
Confidence            999999 54321               1122233311  1221 244444444666653   5788887  53   4456


Q ss_pred             CCCchH
Q 003038          379 IPAGSL  384 (854)
Q Consensus       379 i~~~sl  384 (854)
                      ++++..
T Consensus       159 l~~~~~  164 (233)
T PRK08727        159 LPVLDD  164 (233)
T ss_pred             ecCCCH
Confidence            665543

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

Probab=97.60  E-value=0.00012  Score=85.93  Aligned_cols=90  Identities=8%  Similarity=0.093  Sum_probs=67.9

Q ss_pred             cHHHHHHHHHHhhccCcC------CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc-----c---
Q 003038          211 RNEDVMYVIENLMSKRKR------NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH-----M---  276 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~------n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~-----~---  276 (854)
                      -++-=.||++-++=++=+      =..++||||||||+|++.+|+.+          |..|+.++++-+..     |   
T Consensus       416 m~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~AL----------nRkFfRfSvGG~tDvAeIkGHRR  485 (906)
T KOG2004|consen  416 MEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARAL----------NRKFFRFSVGGMTDVAEIKGHRR  485 (906)
T ss_pred             hHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHh----------CCceEEEeccccccHHhhcccce
Confidence            444456788877544222      25789999999999999999885          56899999886642     2   


Q ss_pred             -chHHHHHHHHHHHHHHHhhhCCCeEEEeCcccccccc
Q 003038          277 -NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWAEFR  313 (854)
Q Consensus       277 -~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l~~~  313 (854)
                       |.|-.--|+-.-++.+.-.   +-++.||||+-+|.|
T Consensus       486 TYVGAMPGkiIq~LK~v~t~---NPliLiDEvDKlG~g  520 (906)
T KOG2004|consen  486 TYVGAMPGKIIQCLKKVKTE---NPLILIDEVDKLGSG  520 (906)
T ss_pred             eeeccCChHHHHHHHhhCCC---CceEEeehhhhhCCC
Confidence             8888888988888877754   445779999999543

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=97.59  E-value=0.00019  Score=78.43  Aligned_cols=66  Identities=21%  Similarity=0.221  Sum_probs=51.7

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      .-++||.+|-++-.-.+...++|-..             -..+||.||+|+|||.||-.+|+.| |..-+|+.+..|+..
T Consensus        39 dG~VGQ~~AReAaGvIv~mik~gk~a-------------GrgiLi~GppgTGKTAlA~gIa~eL-G~dvPF~~isgsEiY  104 (450)
T COG1224          39 DGLVGQEEAREAAGVIVKMIKQGKMA-------------GRGILIVGPPGTGKTALAMGIAREL-GEDVPFVAISGSEIY  104 (450)
T ss_pred             CcccchHHHHHhhhHHHHHHHhCccc-------------ccEEEEECCCCCcHHHHHHHHHHHh-CCCCCceeeccceee
Confidence            34699998876655555555554211             1268999999999999999999999 999999999999765

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.59  E-value=0.00053  Score=80.83  Aligned_cols=92  Identities=12%  Similarity=0.006  Sum_probs=56.0

Q ss_pred             HHHHHHHHHhhccCcCCc-eeecCCCCCHHHHHHHHHHHHHcCCCCcc--------------cCCceEEEcccccccccc
Q 003038          213 EDVMYVIENLMSKRKRNF-VVVGECLASIEGVVRGVIDKIEKGDVPEA--------------LRDVKCLPLSISSFRHMN  277 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~-vLvGe~GvGKta~v~~la~~i~~~~vp~~--------------L~~~~~~~l~~~~l~~~~  277 (854)
                      .-++.+...+...+-.+. +|+||+|||||++++.+|..+.....+..              -....++.++.++-.  .
T Consensus        23 ~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~eidaas~~--~  100 (509)
T PRK14958         23 PVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLFEVDAASRT--K  100 (509)
T ss_pred             HHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceEEEEcccccC--C
Confidence            335556666666566664 89999999999999999998865321110              011235666543211  1


Q ss_pred             hHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          278 RVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       278 rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                      ..+    ++++++.+.-..  ++.-|++|||+|.+
T Consensus       101 v~~----iR~l~~~~~~~p~~~~~kV~iIDE~~~l  131 (509)
T PRK14958        101 VED----TRELLDNIPYAPTKGRFKVYLIDEVHML  131 (509)
T ss_pred             HHH----HHHHHHHHhhccccCCcEEEEEEChHhc
Confidence            222    445555544221  34568999999999

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=97.59  E-value=0.00011  Score=78.94  Aligned_cols=81  Identities=14%  Similarity=0.210  Sum_probs=57.7

Q ss_pred             HHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccc-----hHHHHHHHHHH
Q 003038          214 DVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMN-----RVEVEQRVEEI  288 (854)
Q Consensus       214 ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~-----rge~E~rl~~l  288 (854)
                      .+....+-+.  +++|++|+|+||||||-++-+++.++.+       +|.+++-+....|+.-.     .|..+.+|.  
T Consensus        94 ~~~~~~~~~~--~~~nl~l~G~~G~GKThLa~Ai~~~l~~-------~g~sv~f~~~~el~~~Lk~~~~~~~~~~~l~--  162 (254)
T COG1484          94 DLASLVEFFE--RGENLVLLGPPGVGKTHLAIAIGNELLK-------AGISVLFITAPDLLSKLKAAFDEGRLEEKLL--  162 (254)
T ss_pred             HHHHHHHHhc--cCCcEEEECCCCCcHHHHHHHHHHHHHH-------cCCeEEEEEHHHHHHHHHHHHhcCchHHHHH--
Confidence            3444443444  7999999999999999999999999874       36788888877776532     234455543  


Q ss_pred             HHHHHhhhCCCeEEEeCccccc
Q 003038          289 KNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       289 ~~~~~~~~~~~~ILfidel~~l  310 (854)
                       +.+++.    -+|+||||-..
T Consensus       163 -~~l~~~----dlLIiDDlG~~  179 (254)
T COG1484         163 -RELKKV----DLLIIDDIGYE  179 (254)
T ss_pred             -HHhhcC----CEEEEecccCc
Confidence             334433    38999999776

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

Probab=97.57  E-value=0.00028  Score=74.21  Aligned_cols=86  Identities=17%  Similarity=0.248  Sum_probs=57.7

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhC--CCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFG--SHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVF  736 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg--~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vi  736 (854)
                      +++++||+|+|||.|..+++..+..  ....++++++.+|.       .... .-+..    +..+.+.+.++  ...++
T Consensus        36 ~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~~f~-------~~~~-~~~~~----~~~~~~~~~~~--~~DlL  101 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAEEFI-------REFA-DALRD----GEIEEFKDRLR--SADLL  101 (219)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHHHHH-------HHHH-HHHHT----TSHHHHHHHHC--TSSEE
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHHHHH-------HHHH-HHHHc----ccchhhhhhhh--cCCEE
Confidence            5789999999999999999988753  45678888887775       2111 00000    11123334333  57799


Q ss_pred             EEecCCCCCH--HHHHHHHHhhhc
Q 003038          737 LIEDVEQADY--CSQKGFKRAIES  758 (854)
Q Consensus       737 liDEieka~~--~v~~~Ll~~le~  758 (854)
                      +||+|+....  ..|..|...++.
T Consensus       102 ~iDDi~~l~~~~~~q~~lf~l~n~  125 (219)
T PF00308_consen  102 IIDDIQFLAGKQRTQEELFHLFNR  125 (219)
T ss_dssp             EEETGGGGTTHHHHHHHHHHHHHH
T ss_pred             EEecchhhcCchHHHHHHHHHHHH
Confidence            9999998864  357888888764

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.

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

Probab=97.55  E-value=0.00032  Score=84.81  Aligned_cols=110  Identities=15%  Similarity=0.229  Sum_probs=80.9

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC-------CCceEEE
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS-------HNNFVSI  691 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-------~~~~i~i  691 (854)
                      -|||-++-|..+...+.|.+.              +.|    +|.|++|||||.++.-||..+-..       ...++.+
T Consensus       171 PvIGRd~EI~r~iqIL~RR~K--------------NNP----vLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sL  232 (786)
T COG0542         171 PVIGRDEEIRRTIQILSRRTK--------------NNP----VLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSL  232 (786)
T ss_pred             CCcChHHHHHHHHHHHhccCC--------------CCC----eEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEEe
Confidence            469999877777777665321              245    588999999999999999876432       3556677


Q ss_pred             ccccccCcCCCccccccccccCCCCCC--chHHH---HHHHHHcCCCEEEEEecCCCC---------CHHHHHHHHHhhh
Q 003038          692 ALSSFSSTRADSTEDSRNKRSRDEQSC--SYIER---FAEAVSNNPHRVFLIEDVEQA---------DYCSQKGFKRAIE  757 (854)
Q Consensus       692 d~s~~~~~~~~s~e~~~~~rl~~~~g~--g~~e~---L~eav~~~p~~ViliDEieka---------~~~v~~~Ll~~le  757 (854)
                      ||+...                ++..|  -|+++   +.+.+.+.+.-|+||||||..         .-+.-|.|+.++.
T Consensus       233 D~g~Lv----------------AGakyRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~~G~a~DAaNiLKPaLA  296 (786)
T COG0542         233 DLGSLV----------------AGAKYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGGAMDAANLLKPALA  296 (786)
T ss_pred             cHHHHh----------------ccccccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCcccccccchhhhhHHHHh
Confidence            766433                34455  45554   556667788889999999963         2669999999999


Q ss_pred             cCeEe
Q 003038          758 SGRIV  762 (854)
Q Consensus       758 ~G~l~  762 (854)
                      .|.+.
T Consensus       297 RGeL~  301 (786)
T COG0542         297 RGELR  301 (786)
T ss_pred             cCCeE
Confidence            99988

>PRK09183 transposase/IS protein; Provisional

Probab=97.55  E-value=0.0002  Score=77.19  Aligned_cols=120  Identities=10%  Similarity=0.039  Sum_probs=67.6

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccch-HHHHHHHHHHHHHHHhhhCCCeEEE
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNR-VEVEQRVEEIKNLVRSCLGRGIVLN  303 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~r-ge~E~rl~~l~~~~~~~~~~~~ILf  303 (854)
                      ....|++|+||||+|||.++.+++.....       +|..+.-++...+...+. ...+.++..++....   ..+.+|+
T Consensus       100 ~~~~~v~l~Gp~GtGKThLa~al~~~a~~-------~G~~v~~~~~~~l~~~l~~a~~~~~~~~~~~~~~---~~~dlLi  169 (259)
T PRK09183        100 ERNENIVLLGPSGVGKTHLAIALGYEAVR-------AGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRGV---MAPRLLI  169 (259)
T ss_pred             hcCCeEEEEeCCCCCHHHHHHHHHHHHHH-------cCCeEEEEeHHHHHHHHHHHHHCCcHHHHHHHHh---cCCCEEE
Confidence            35789999999999999999999876432       345565555555543321 112223444443322   2456999


Q ss_pred             eCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchh
Q 003038          304 LGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLE  369 (854)
Q Consensus       304 idel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale  369 (854)
                      |||++.. ....               ....+-+++..--+++.+.+-+-.++.+|.+++..||.+.
T Consensus       170 iDdlg~~~~~~~---------------~~~~lf~li~~r~~~~s~iiTsn~~~~~w~~~~~~d~~~~  221 (259)
T PRK09183        170 IDEIGYLPFSQE---------------EANLFFQVIAKRYEKGSMILTSNLPFGQWDQTFAGDAALT  221 (259)
T ss_pred             EcccccCCCChH---------------HHHHHHHHHHHHHhcCcEEEecCCCHHHHHHHhcCchhHH
Confidence            9999776 2211               1223444442101122332222235788888776666553

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=97.55  E-value=0.00019  Score=77.18  Aligned_cols=122  Identities=12%  Similarity=0.128  Sum_probs=79.5

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc--chHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM--NRVEVEQRVEEI  288 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~--~rge~E~rl~~l  288 (854)
                      -+..+.-+...+.||.-.|.+++||||+|||+.+.++|+.+-.    +.+.-.++.+++.+...+.  .|+- -+.+..+
T Consensus        41 Qe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~~----~~~~~~rvl~lnaSderGisvvr~K-ik~fakl  115 (346)
T KOG0989|consen   41 QEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARALNC----EQLFPCRVLELNASDERGISVVREK-IKNFAKL  115 (346)
T ss_pred             hHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhcC----ccccccchhhhcccccccccchhhh-hcCHHHH
Confidence            4566777777788888889999999999999999999988754    5677788888888766553  2221 1112222


Q ss_pred             HHHHHhhh----CCCeEEEeCccccc--cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHH
Q 003038          289 KNLVRSCL----GRGIVLNLGDLEWA--EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQS  357 (854)
Q Consensus       289 ~~~~~~~~----~~~~ILfidel~~l--~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~e  357 (854)
                      ........    +..=|+.|||.+.+  ++|+                  .+.+.+.....  ..++|-.|+|-+
T Consensus       116 ~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~------------------aLrr~mE~~s~--~trFiLIcnyls  170 (346)
T KOG0989|consen  116 TVLLKRSDGYPCPPFKIIILDECDSMTSDAQA------------------ALRRTMEDFSR--TTRFILICNYLS  170 (346)
T ss_pred             hhccccccCCCCCcceEEEEechhhhhHHHHH------------------HHHHHHhcccc--ceEEEEEcCChh
Confidence            22221110    22268999999999  6664                  24455532222  477777787655

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.53  E-value=0.00054  Score=82.28  Aligned_cols=119  Identities=15%  Similarity=0.057  Sum_probs=68.1

Q ss_pred             HHHHHHHHHHhhccCcCCc-eeecCCCCCHHHHHHHHHHHHHcCCCC---ccc-----------CCceEEEccccccccc
Q 003038          212 NEDVMYVIENLMSKRKRNF-VVVGECLASIEGVVRGVIDKIEKGDVP---EAL-----------RDVKCLPLSISSFRHM  276 (854)
Q Consensus       212 ~~ei~~v~~~L~r~~k~n~-vLvGe~GvGKta~v~~la~~i~~~~vp---~~L-----------~~~~~~~l~~~~l~~~  276 (854)
                      +.-++.+...+..++-.+. ||+||+|||||++++.+|..+......   ...           ....++.++.++    
T Consensus        22 e~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~~C~~i~~g~~~D~ieidaas----   97 (647)
T PRK07994         22 EHVLTALANALDLGRLHHAYLFSGTRGVGKTTIARLLAKGLNCETGITATPCGECDNCREIEQGRFVDLIEIDAAS----   97 (647)
T ss_pred             HHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCCCCCCCHHHHHHHcCCCCCceeecccc----
Confidence            3344555555655555554 899999999999999999988763211   000           111334444321    


Q ss_pred             chHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEec
Q 003038          277 NRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIA  353 (854)
Q Consensus       277 ~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgat  353 (854)
                       +.-++ .++++++.+....  ++.-|++|||+|.+ ..                 +...+-+.|..-.+  .+.+|.+|
T Consensus        98 -~~~Vd-diR~li~~~~~~p~~g~~KV~IIDEah~Ls~~-----------------a~NALLKtLEEPp~--~v~FIL~T  156 (647)
T PRK07994         98 -RTKVE-DTRELLDNVQYAPARGRFKVYLIDEVHMLSRH-----------------SFNALLKTLEEPPE--HVKFLLAT  156 (647)
T ss_pred             -cCCHH-HHHHHHHHHHhhhhcCCCEEEEEechHhCCHH-----------------HHHHHHHHHHcCCC--CeEEEEec
Confidence             11112 2455555554321  45679999999999 43                 22234444421123  48888888


Q ss_pred             CH
Q 003038          354 TF  355 (854)
Q Consensus       354 T~  355 (854)
                      |.
T Consensus       157 t~  158 (647)
T PRK07994        157 TD  158 (647)
T ss_pred             CC
Confidence            75

>PRK08181 transposase; Validated

Probab=97.53  E-value=9.4e-05  Score=80.07  Aligned_cols=74  Identities=12%  Similarity=0.082  Sum_probs=51.7

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccch-HHHHHHHHHHHHHHHhhhCCCeEEEe
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNR-VEVEQRVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~r-ge~E~rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      .+.|++|+||||+|||.++.+++..+.+       +|..++-++...|....+ ...+..+.++++.+.+    .-+|+|
T Consensus       105 ~~~nlll~Gp~GtGKTHLa~Aia~~a~~-------~g~~v~f~~~~~L~~~l~~a~~~~~~~~~l~~l~~----~dLLII  173 (269)
T PRK08181        105 KGANLLLFGPPGGGKSHLAAAIGLALIE-------NGWRVLFTRTTDLVQKLQVARRELQLESAIAKLDK----FDLLIL  173 (269)
T ss_pred             cCceEEEEecCCCcHHHHHHHHHHHHHH-------cCCceeeeeHHHHHHHHHHHHhCCcHHHHHHHHhc----CCEEEE
Confidence            6789999999999999999999987654       355666666666655321 1222334445555543    458999


Q ss_pred             Cccccc
Q 003038          305 GDLEWA  310 (854)
Q Consensus       305 del~~l  310 (854)
                      ||++.+
T Consensus       174 DDlg~~  179 (269)
T PRK08181        174 DDLAYV  179 (269)
T ss_pred             eccccc
Confidence            999877

>PRK06526 transposase; Provisional

Probab=97.53  E-value=0.00013  Score=78.38  Aligned_cols=74  Identities=12%  Similarity=0.056  Sum_probs=46.5

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccch-HHHHHHHHHHHHHHHhhhCCCeEEEe
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNR-VEVEQRVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~r-ge~E~rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      .+.|++|+||||||||.++.+++..+.+       +|.+++-.....+..... ......+...+..+.    +..+|+|
T Consensus        97 ~~~nlll~Gp~GtGKThLa~al~~~a~~-------~g~~v~f~t~~~l~~~l~~~~~~~~~~~~l~~l~----~~dlLII  165 (254)
T PRK06526         97 GKENVVFLGPPGTGKTHLAIGLGIRACQ-------AGHRVLFATAAQWVARLAAAHHAGRLQAELVKLG----RYPLLIV  165 (254)
T ss_pred             cCceEEEEeCCCCchHHHHHHHHHHHHH-------CCCchhhhhHHHHHHHHHHHHhcCcHHHHHHHhc----cCCEEEE
Confidence            6789999999999999999999988764       234444444444443211 111112222223222    3568999


Q ss_pred             Cccccc
Q 003038          305 GDLEWA  310 (854)
Q Consensus       305 del~~l  310 (854)
                      ||++.+
T Consensus       166 DD~g~~  171 (254)
T PRK06526        166 DEVGYI  171 (254)
T ss_pred             cccccC
Confidence            999887

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

Probab=97.53  E-value=9.6e-05  Score=87.14  Aligned_cols=82  Identities=11%  Similarity=0.097  Sum_probs=60.8

Q ss_pred             HHHHHHhhcc------CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc-----c----chHH
Q 003038          216 MYVIENLMSK------RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH-----M----NRVE  280 (854)
Q Consensus       216 ~~v~~~L~r~------~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~-----~----~rge  280 (854)
                      .||++-|+=+      +..=.+||||||||||++++.+|..+          |..|+.++++-+..     |    |.|-
T Consensus       333 eRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al----------~RkfvR~sLGGvrDEAEIRGHRRTYIGa  402 (782)
T COG0466         333 ERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKAL----------GRKFVRISLGGVRDEAEIRGHRRTYIGA  402 (782)
T ss_pred             HHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHh----------CCCEEEEecCccccHHHhcccccccccc
Confidence            4566655432      11235789999999999999999886          56899998887653     2    7788


Q ss_pred             HHHHHHHHHHHHHhhhCCCeEEEeCccccc
Q 003038          281 VEQRVEEIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       281 ~E~rl~~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                      .--|+-.-+..+...   +-+..+|||+-+
T Consensus       403 mPGrIiQ~mkka~~~---NPv~LLDEIDKm  429 (782)
T COG0466         403 MPGKIIQGMKKAGVK---NPVFLLDEIDKM  429 (782)
T ss_pred             CChHHHHHHHHhCCc---CCeEEeechhhc
Confidence            888877766666653   456789999999

>PHA02244 ATPase-like protein

Probab=97.52  E-value=0.00025  Score=79.26  Aligned_cols=80  Identities=4%  Similarity=0.086  Sum_probs=47.8

Q ss_pred             HHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccc----cccc--cchHHHHHHHH
Q 003038          213 EDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSIS----SFRH--MNRVEVEQRVE  286 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~----~l~~--~~rge~E~rl~  286 (854)
                      ...+++...+.  ...+++|+||||||||++|+++|..+          +..++.++.-    .+..  ...|.|+  -.
T Consensus       107 ~~~~ri~r~l~--~~~PVLL~GppGtGKTtLA~aLA~~l----------g~pfv~In~l~d~~~L~G~i~~~g~~~--dg  172 (383)
T PHA02244        107 YETADIAKIVN--ANIPVFLKGGAGSGKNHIAEQIAEAL----------DLDFYFMNAIMDEFELKGFIDANGKFH--ET  172 (383)
T ss_pred             HHHHHHHHHHh--cCCCEEEECCCCCCHHHHHHHHHHHh----------CCCEEEEecChHHHhhccccccccccc--ch
Confidence            34445555544  46789999999999999999999873          3345554411    1110  0112221  01


Q ss_pred             HHHHHHHhhhCCCeEEEeCccccc
Q 003038          287 EIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       287 ~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                      .++..++    .+-+|||||+..+
T Consensus       173 pLl~A~~----~GgvLiLDEId~a  192 (383)
T PHA02244        173 PFYEAFK----KGGLFFIDEIDAS  192 (383)
T ss_pred             HHHHHhh----cCCEEEEeCcCcC
Confidence            2333333    3569999999877

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.51  E-value=0.00081  Score=78.47  Aligned_cols=94  Identities=7%  Similarity=0.053  Sum_probs=59.4

Q ss_pred             cHHHHHHHHH-HhhccCcC-CceeecCCCCCHHHHHHHHHHHHHcCCCCc--------------ccCCceEEEccccccc
Q 003038          211 RNEDVMYVIE-NLMSKRKR-NFVVVGECLASIEGVVRGVIDKIEKGDVPE--------------ALRDVKCLPLSISSFR  274 (854)
Q Consensus       211 r~~ei~~v~~-~L~r~~k~-n~vLvGe~GvGKta~v~~la~~i~~~~vp~--------------~L~~~~~~~l~~~~l~  274 (854)
                      ..+.+.+.+. .+..++-. ..+|+||+|+|||++++.+|+.+....-|.              ......|+.+|.++-.
T Consensus        17 GQe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~eidaas~~   96 (491)
T PRK14964         17 GQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEIDAASNT   96 (491)
T ss_pred             CcHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEEEEecccCC
Confidence            4455555554 44444333 589999999999999999999876433221              1234566777665322


Q ss_pred             ccchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          275 HMNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       275 ~~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                        ..    ..++++++.+....  +..-|++|||+|.+
T Consensus        97 --~v----ddIR~Iie~~~~~P~~~~~KVvIIDEah~L  128 (491)
T PRK14964         97 --SV----DDIKVILENSCYLPISSKFKVYIIDEVHML  128 (491)
T ss_pred             --CH----HHHHHHHHHHHhccccCCceEEEEeChHhC
Confidence              12    23556666665321  34568999999999

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

Probab=97.49  E-value=0.00038  Score=74.93  Aligned_cols=94  Identities=13%  Similarity=0.212  Sum_probs=52.9

Q ss_pred             HHHHHHHHHHhh---ccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEE--cccccccc------c----
Q 003038          212 NEDVMYVIENLM---SKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLP--LSISSFRH------M----  276 (854)
Q Consensus       212 ~~ei~~v~~~L~---r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~--l~~~~l~~------~----  276 (854)
                      ....++++..|.   +.....++|+||+|+|||++++.++..+..+.+.    .+.++.  ++...+..      |    
T Consensus        25 ~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~~l~~~l~~~~~~----~~~~~~~~~~~~~~l~~i~~~lG~~~~  100 (269)
T TIGR03015        25 SKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIRNLLKRLDQERVV----AAKLVNTRVDAEDLLRMVAADFGLETE  100 (269)
T ss_pred             CHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHHHHHhcCCCCeE----EeeeeCCCCCHHHHHHHHHHHcCCCCC
Confidence            344444554443   4445578999999999999999999876543321    011111  11111110      1    


Q ss_pred             --chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc
Q 003038          277 --NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       277 --~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                        .+.+.-.++.+.+...... ++++||+|||+|++
T Consensus       101 ~~~~~~~~~~l~~~l~~~~~~-~~~~vliiDe~~~l  135 (269)
T TIGR03015       101 GRDKAALLRELEDFLIEQFAA-GKRALLVVDEAQNL  135 (269)
T ss_pred             CCCHHHHHHHHHHHHHHHHhC-CCCeEEEEECcccC
Confidence              1222333444444333322 56899999999999

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.

>PRK09183 transposase/IS protein; Provisional

Probab=97.49  E-value=0.00018  Score=77.52  Aligned_cols=87  Identities=11%  Similarity=0.119  Sum_probs=52.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLI  738 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vili  738 (854)
                      .++|+||+|+|||.+|.+|+..+......+..+++.++.       ......  ... + ++...+...+  ....+++|
T Consensus       104 ~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~~~~l~-------~~l~~a--~~~-~-~~~~~~~~~~--~~~dlLii  170 (259)
T PRK09183        104 NIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLL-------LQLSTA--QRQ-G-RYKTTLQRGV--MAPRLLII  170 (259)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeHHHHH-------HHHHHH--HHC-C-cHHHHHHHHh--cCCCEEEE
Confidence            688999999999999999988764444444455544332       110000  000 0 1111122211  33479999


Q ss_pred             ecCCC--CCHHHHHHHHHhhhc
Q 003038          739 EDVEQ--ADYCSQKGFKRAIES  758 (854)
Q Consensus       739 DEiek--a~~~v~~~Ll~~le~  758 (854)
                      ||+..  .+....+.|+++++.
T Consensus       171 Ddlg~~~~~~~~~~~lf~li~~  192 (259)
T PRK09183        171 DEIGYLPFSQEEANLFFQVIAK  192 (259)
T ss_pred             cccccCCCChHHHHHHHHHHHH
Confidence            99986  556677789999875

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.49  E-value=0.00027  Score=81.15  Aligned_cols=128  Identities=13%  Similarity=0.101  Sum_probs=74.6

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHH-HHHHHHHHHHHhhhCCCeEEEeCc
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVE-QRVEEIKNLVRSCLGRGIVLNLGD  306 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E-~rl~~l~~~~~~~~~~~~ILfide  306 (854)
                      |+.+|+|+||+|||.++++++..+.+..     .+..++.++...+...+...+. ..+.++.+.++.    .-+|+|||
T Consensus       137 n~l~l~G~~G~GKThL~~ai~~~l~~~~-----~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~----~dlLiiDD  207 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLHAIGNEILENN-----PNAKVVYVSSEKFTNDFVNALRNNKMEEFKEKYRS----VDLLLIDD  207 (405)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHhC-----CCCcEEEEEHHHHHHHHHHHHHcCCHHHHHHHHHh----CCEEEEeh
Confidence            4457999999999999999999886531     2467777776665443222221 122233333432    34899999


Q ss_pred             cccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEec-CHHHHHHhhccCCchhhhhccC---CCCC
Q 003038          307 LEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIA-TFQSYMRCKSGHPSLETLWSLH---PLTI  379 (854)
Q Consensus       307 l~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgat-T~~ey~k~~~~~pale~~~~~~---~v~i  379 (854)
                      ||.+ +...               ...++-.++..  ..+  ...+|.++ .+.+...   .++.|.+  ||.   .|.|
T Consensus       208 i~~l~~~~~---------------~~~~l~~~~n~~~~~~--~~iiits~~~p~~l~~---l~~~l~S--Rl~~g~~v~i  265 (405)
T TIGR00362       208 IQFLAGKER---------------TQEEFFHTFNALHENG--KQIVLTSDRPPKELPG---LEERLRS--RFEWGLVVDI  265 (405)
T ss_pred             hhhhcCCHH---------------HHHHHHHHHHHHHHCC--CCEEEecCCCHHHHhh---hhhhhhh--hccCCeEEEe
Confidence            9999 5422               11233344421  223  23444443 4555443   3677777  664   4677


Q ss_pred             CCchHHH
Q 003038          380 PAGSLSL  386 (854)
Q Consensus       380 ~~~sl~~  386 (854)
                      +.|+.+.
T Consensus       266 ~~pd~~~  272 (405)
T TIGR00362       266 EPPDLET  272 (405)
T ss_pred             CCCCHHH
Confidence            7666544

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).

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.48  E-value=0.00081  Score=79.53  Aligned_cols=119  Identities=11%  Similarity=0.037  Sum_probs=68.1

Q ss_pred             HHHHHHHHHHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCC----Cc----------ccCCceEEEccccccccc
Q 003038          212 NEDVMYVIENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDV----PE----------ALRDVKCLPLSISSFRHM  276 (854)
Q Consensus       212 ~~ei~~v~~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~v----p~----------~L~~~~~~~l~~~~l~~~  276 (854)
                      +.-+..+...+..++-.+ .+|+||+|||||++++.+|..+....-    |-          ......++.++..+-.  
T Consensus        22 ~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dlieidaas~~--   99 (546)
T PRK14957         22 QHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIEIDAASRT--   99 (546)
T ss_pred             HHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEEeeccccc--
Confidence            344555666665544444 679999999999999999998764211    10          0011244444432111  


Q ss_pred             chHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEec
Q 003038          277 NRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIA  353 (854)
Q Consensus       277 ~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgat  353 (854)
                      ...    .++++++.+....  ++.-|++|||+|.+ ..                 +...+-+.|..-.+  .+.+|.+|
T Consensus       100 gvd----~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~-----------------a~naLLK~LEepp~--~v~fIL~T  156 (546)
T PRK14957        100 GVE----ETKEILDNIQYMPSQGRYKVYLIDEVHMLSKQ-----------------SFNALLKTLEEPPE--YVKFILAT  156 (546)
T ss_pred             CHH----HHHHHHHHHHhhhhcCCcEEEEEechhhccHH-----------------HHHHHHHHHhcCCC--CceEEEEE
Confidence            111    2445555554321  45679999999999 42                 12234444521112  48888888


Q ss_pred             CH
Q 003038          354 TF  355 (854)
Q Consensus       354 T~  355 (854)
                      |.
T Consensus       157 td  158 (546)
T PRK14957        157 TD  158 (546)
T ss_pred             CC
Confidence            74

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.48  E-value=0.0008  Score=83.23  Aligned_cols=119  Identities=11%  Similarity=0.013  Sum_probs=69.2

Q ss_pred             HHHHHHHHHHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCCCcc----------------cCCceEEEccccccc
Q 003038          212 NEDVMYVIENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDVPEA----------------LRDVKCLPLSISSFR  274 (854)
Q Consensus       212 ~~ei~~v~~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~vp~~----------------L~~~~~~~l~~~~l~  274 (854)
                      +.-++.+...+..++.++ .||+|++|||||++++.||+.+...+-+..                -....|+.++..+..
T Consensus        21 e~v~~~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~~g~~~~~dv~eidaas~~  100 (824)
T PRK07764         21 EHVTEPLSTALDSGRINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAPGGPGSLDVTEIDAASHG  100 (824)
T ss_pred             HHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHHcCCCCCCcEEEecccccC
Confidence            444555666666667777 589999999999999999999875321110                012345555443221


Q ss_pred             ccchHHHHHHHHHHHHHHHhh--hCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEE
Q 003038          275 HMNRVEVEQRVEEIKNLVRSC--LGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMG  351 (854)
Q Consensus       275 ~~~rge~E~rl~~l~~~~~~~--~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIg  351 (854)
                        ...    .+++|++.+...  .++.-|+||||+|.| ..                 +...+-++|+.-..  .+.+|.
T Consensus       101 --~Vd----~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~~-----------------a~NaLLK~LEEpP~--~~~fIl  155 (824)
T PRK07764        101 --GVD----DARELRERAFFAPAESRYKIFIIDEAHMVTPQ-----------------GFNALLKIVEEPPE--HLKFIF  155 (824)
T ss_pred             --CHH----HHHHHHHHHHhchhcCCceEEEEechhhcCHH-----------------HHHHHHHHHhCCCC--CeEEEE
Confidence              111    223343333211  034568999999999 43                 22345566632112  488888


Q ss_pred             ecCH
Q 003038          352 IATF  355 (854)
Q Consensus       352 atT~  355 (854)
                      +||.
T Consensus       156 ~tt~  159 (824)
T PRK07764        156 ATTE  159 (824)
T ss_pred             EeCC
Confidence            7764

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.48  E-value=0.00023  Score=82.51  Aligned_cols=86  Identities=15%  Similarity=0.226  Sum_probs=55.1

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      -+++|+||+|+|||.|+++++..+......++++.+..|.       ... ... +.   .+..+.+.+..  ....|++
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~f~-------~~~-~~~-l~---~~~~~~f~~~~--~~~dvLi  207 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELFT-------EHL-VSA-IR---SGEMQRFRQFY--RNVDALF  207 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHHHH-------HHH-HHH-Hh---cchHHHHHHHc--ccCCEEE
Confidence            4689999999999999999999886545667777765554       110 000 00   01112233322  2356999


Q ss_pred             EecCCCCC--HHHHHHHHHhhh
Q 003038          738 IEDVEQAD--YCSQKGFKRAIE  757 (854)
Q Consensus       738 iDEieka~--~~v~~~Ll~~le  757 (854)
                      ||||+...  ...|..|+..|.
T Consensus       208 IDDiq~l~~k~~~qeelf~l~N  229 (445)
T PRK12422        208 IEDIEVFSGKGATQEEFFHTFN  229 (445)
T ss_pred             EcchhhhcCChhhHHHHHHHHH
Confidence            99999874  346777777665

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.47  E-value=0.00028  Score=81.85  Aligned_cols=78  Identities=13%  Similarity=0.223  Sum_probs=50.7

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHH-HHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEV-EQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~-E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      -|+.+|+||||+|||.++++++..+.+.. |    +.+++.++...|...+...+ ...+.++....+.   .+-||+||
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~l~~~~-~----~~~v~yi~~~~f~~~~~~~~~~~~~~~f~~~~~~---~~dvLlID  201 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNE-P----DLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRK---KVDVLLID  201 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHHHHhC-C----CCeEEEEEHHHHHHHHHHHHhcccHHHHHHHHHh---cCCEEEEe
Confidence            36788999999999999999999876532 2    45777777666544321111 1122233333332   35689999


Q ss_pred             ccccc-cc
Q 003038          306 DLEWA-EF  312 (854)
Q Consensus       306 el~~l-~~  312 (854)
                      |++.+ +.
T Consensus       202 Di~~l~~~  209 (440)
T PRK14088        202 DVQFLIGK  209 (440)
T ss_pred             chhhhcCc
Confidence            99988 54

>PRK12377 putative replication protein; Provisional

Probab=97.45  E-value=0.0003  Score=75.28  Aligned_cols=74  Identities=9%  Similarity=0.083  Sum_probs=49.9

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHH--HHHHHHHHHHhhhCCCeEEE
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQ--RVEEIKNLVRSCLGRGIVLN  303 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~--rl~~l~~~~~~~~~~~~ILf  303 (854)
                      ..+|++|+|+||||||.++.+++..+.+       ++..++-+++..|....+..+..  ...++++.+.+    .-+|+
T Consensus       100 ~~~~l~l~G~~GtGKThLa~AIa~~l~~-------~g~~v~~i~~~~l~~~l~~~~~~~~~~~~~l~~l~~----~dLLi  168 (248)
T PRK12377        100 GCTNFVFSGKPGTGKNHLAAAIGNRLLA-------KGRSVIVVTVPDVMSRLHESYDNGQSGEKFLQELCK----VDLLV  168 (248)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHHHH-------cCCCeEEEEHHHHHHHHHHHHhccchHHHHHHHhcC----CCEEE
Confidence            4578999999999999999999998865       34556666666665543222211  12234555543    45899


Q ss_pred             eCccccc
Q 003038          304 LGDLEWA  310 (854)
Q Consensus       304 idel~~l  310 (854)
                      ||||...
T Consensus       169 IDDlg~~  175 (248)
T PRK12377        169 LDEIGIQ  175 (248)
T ss_pred             EcCCCCC
Confidence            9999665

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.45  E-value=0.00025  Score=82.61  Aligned_cols=86  Identities=19%  Similarity=0.274  Sum_probs=55.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCC--CCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGS--HNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRV  735 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~--~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~V  735 (854)
                      .+++|+||+|+|||.|+++++..+...  ...++.+++.+|.       .... .. +..   +-.+.+.+.++  ...|
T Consensus       149 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~~~~-------~~~~-~~-~~~---~~~~~~~~~~~--~~dl  214 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSEKFT-------NDFV-NA-LRN---NTMEEFKEKYR--SVDV  214 (450)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHHHHH-------HHHH-HH-HHc---CcHHHHHHHHh--cCCE
Confidence            479999999999999999999988643  4557777776554       1110 00 000   11123444444  3569


Q ss_pred             EEEecCCCCC--HHHHHHHHHhhh
Q 003038          736 FLIEDVEQAD--YCSQKGFKRAIE  757 (854)
Q Consensus       736 iliDEieka~--~~v~~~Ll~~le  757 (854)
                      ++||||+...  ...+..|+..|+
T Consensus       215 LiiDDi~~l~~~~~~~~~l~~~~n  238 (450)
T PRK00149        215 LLIDDIQFLAGKERTQEEFFHTFN  238 (450)
T ss_pred             EEEehhhhhcCCHHHHHHHHHHHH
Confidence            9999999763  335666666664

>PRK06620 hypothetical protein; Validated

Probab=97.45  E-value=0.00032  Score=73.57  Aligned_cols=118  Identities=11%  Similarity=0.096  Sum_probs=69.3

Q ss_pred             HHHHHHHHHHhhcc-C----cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHH
Q 003038          212 NEDVMYVIENLMSK-R----KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVE  286 (854)
Q Consensus       212 ~~ei~~v~~~L~r~-~----k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~  286 (854)
                      .++....++-+.+. .    ++..+|+||||+|||.++++++...          +..+++.  .     ...  +    
T Consensus        24 N~~a~~~~~~~~~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~----------~~~~~~~--~-----~~~--~----   80 (214)
T PRK06620         24 NDQAYNIIKNWQCGFGVNPYKFTLLIKGPSSSGKTYLTKIWQNLS----------NAYIIKD--I-----FFN--E----   80 (214)
T ss_pred             HHHHHHHHHHHHHccccCCCcceEEEECCCCCCHHHHHHHHHhcc----------CCEEcch--h-----hhc--h----
Confidence            44555555555542 1    2457999999999999999876542          1222210  0     000  0    


Q ss_pred             HHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccC
Q 003038          287 EIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGH  365 (854)
Q Consensus       287 ~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~  365 (854)
                          ....   ...+|+|||||.+ +.                 ..-.+=|.+.. .|  ...+|+++|+..+..   - 
T Consensus        81 ----~~~~---~~d~lliDdi~~~~~~-----------------~lf~l~N~~~e-~g--~~ilits~~~p~~l~---l-  129 (214)
T PRK06620         81 ----EILE---KYNAFIIEDIENWQEP-----------------ALLHIFNIINE-KQ--KYLLLTSSDKSRNFT---L-  129 (214)
T ss_pred             ----hHHh---cCCEEEEeccccchHH-----------------HHHHHHHHHHh-cC--CEEEEEcCCCccccc---h-
Confidence                1111   2458999999966 32                 11222233321 33  588999999888653   3 


Q ss_pred             CchhhhhccC---CCCCCCchHH
Q 003038          366 PSLETLWSLH---PLTIPAGSLS  385 (854)
Q Consensus       366 pale~~~~~~---~v~i~~~sl~  385 (854)
                      |.|.+  ||+   .+.|.+++.+
T Consensus       130 ~~L~S--Rl~~gl~~~l~~pd~~  150 (214)
T PRK06620        130 PDLSS--RIKSVLSILLNSPDDE  150 (214)
T ss_pred             HHHHH--HHhCCceEeeCCCCHH
Confidence            88988  777   5666666543

>PRK13531 regulatory ATPase RavA; Provisional

Probab=97.45  E-value=9.7e-05  Score=85.16  Aligned_cols=42  Identities=7%  Similarity=0.086  Sum_probs=37.9

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcC
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKG  254 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~  254 (854)
                      |++.|+.++.++.  ...|++|.||||+|||.+|++|+..+...
T Consensus        25 re~vI~lll~aal--ag~hVLL~GpPGTGKT~LAraLa~~~~~~   66 (498)
T PRK13531         25 RSHAIRLCLLAAL--SGESVFLLGPPGIAKSLIARRLKFAFQNA   66 (498)
T ss_pred             cHHHHHHHHHHHc--cCCCEEEECCCChhHHHHHHHHHHHhccc
Confidence            8999999999987  68899999999999999999999886543

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=97.45  E-value=0.00025  Score=80.41  Aligned_cols=58  Identities=12%  Similarity=0.202  Sum_probs=50.9

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc-ccchH-HHHHHHHHHHHHHHh
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR-HMNRV-EVEQRVEEIKNLVRS  294 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~-~~~rg-e~E~rl~~l~~~~~~  294 (854)
                      ++|++|+||||||||++++.||..+          +..++.++...+. .+|.| +.|..++.+++.+..
T Consensus        47 p~~ILLiGppG~GKT~lAraLA~~l----------~~~fi~vdat~~~e~g~vG~dvE~i~r~l~e~A~~  106 (441)
T TIGR00390        47 PKNILMIGPTGVGKTEIARRLAKLA----------NAPFIKVEATKFTEVGYVGRDVESMVRDLTDAAVK  106 (441)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHh----------CCeEEEeecceeecCCcccCCHHHHHHHHHHHHHH
Confidence            4799999999999999999999764          6789999998787 47888 899999999998864

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.

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.44  E-value=0.00089  Score=78.64  Aligned_cols=94  Identities=9%  Similarity=0.123  Sum_probs=57.0

Q ss_pred             cHHHHHHHHHH-hhccC-cCCceeecCCCCCHHHHHHHHHHHHHcCCC--------C----------cccCCceEEEccc
Q 003038          211 RNEDVMYVIEN-LMSKR-KRNFVVVGECLASIEGVVRGVIDKIEKGDV--------P----------EALRDVKCLPLSI  270 (854)
Q Consensus       211 r~~ei~~v~~~-L~r~~-k~n~vLvGe~GvGKta~v~~la~~i~~~~v--------p----------~~L~~~~~~~l~~  270 (854)
                      ..+.+.+.+.. +...+ ....+|+||||||||++++.+|..+.....        |          .......++.+|.
T Consensus        25 Gq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~~C~~i~~~~h~Dv~eida  104 (507)
T PRK06645         25 GQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCTNCISFNNHNHPDIIEIDA  104 (507)
T ss_pred             CcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCChHHHHHhcCCCCcEEEeec
Confidence            55665555554 33322 257899999999999999999998865321        1          0111234555544


Q ss_pred             ccccccchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          271 SSFRHMNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       271 ~~l~~~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                      ++-  ....    .++++++.+....  +..-|++|||+|.+
T Consensus       105 as~--~~vd----~Ir~iie~a~~~P~~~~~KVvIIDEa~~L  140 (507)
T PRK06645        105 ASK--TSVD----DIRRIIESAEYKPLQGKHKIFIIDEVHML  140 (507)
T ss_pred             cCC--CCHH----HHHHHHHHHHhccccCCcEEEEEEChhhc
Confidence            321  1222    3555666665321  44678999999999

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=97.40  E-value=0.0012  Score=71.54  Aligned_cols=97  Identities=9%  Similarity=0.198  Sum_probs=66.8

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc-cccccCcCCCccccccccccCC-CCCCchHHHHHHHHHcCCC
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA-LSSFSSTRADSTEDSRNKRSRD-EQSCSYIERFAEAVSNNPH  733 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id-~s~~~~~~~~s~e~~~~~rl~~-~~g~g~~e~L~eav~~~p~  733 (854)
                      +.+.++|.||+|+|||++.+++...+......++.+. -.|+.-       +....-.+. ..++.|.+-+..++|.+| 
T Consensus        79 ~~GlilisG~tGSGKTT~l~all~~i~~~~~~iitiEdp~E~~~-------~~~~q~~v~~~~~~~~~~~l~~~lR~~P-  150 (264)
T cd01129          79 PHGIILVTGPTGSGKTTTLYSALSELNTPEKNIITVEDPVEYQI-------PGINQVQVNEKAGLTFARGLRAILRQDP-  150 (264)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEECCCceecC-------CCceEEEeCCcCCcCHHHHHHHHhccCC-
Confidence            3468999999999999999999888755445666663 223321       110000011 223467677888888887 


Q ss_pred             EEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          734 RVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       734 ~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                      .+|++.||.  +++....++++..+|...
T Consensus       151 D~i~vgEiR--~~e~a~~~~~aa~tGh~v  177 (264)
T cd01129         151 DIIMVGEIR--DAETAEIAVQAALTGHLV  177 (264)
T ss_pred             CEEEeccCC--CHHHHHHHHHHHHcCCcE
Confidence            788899998  777778888999888654

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=97.40  E-value=0.00058  Score=84.27  Aligned_cols=98  Identities=13%  Similarity=0.207  Sum_probs=62.2

Q ss_pred             EEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCC-chHH----HHHHHHHcCCCE
Q 003038          660 LFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSC-SYIE----RFAEAVSNNPHR  734 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~~e----~L~eav~~~p~~  734 (854)
                      +||+||+|+|||.+|++||...-..+.+ +.+.|....       +.  .+      .| |..|    .|++-.+++.++
T Consensus       302 vL~~GppGTGkTl~araLa~~~s~~~~k-isffmrkga-------D~--ls------kwvgEaERqlrllFeeA~k~qPS  365 (1080)
T KOG0732|consen  302 VLFHGPPGTGKTLMARALAAACSRGNRK-ISFFMRKGA-------DC--LS------KWVGEAERQLRLLFEEAQKTQPS  365 (1080)
T ss_pred             eeecCCCCCchhHHHHhhhhhhcccccc-cchhhhcCc-------hh--hc------cccCcHHHHHHHHHHHHhccCce
Confidence            6899999999999999999988433332 333333222       00  11      12 4444    467777888889


Q ss_pred             EEEEecCCC-----------CCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCC
Q 003038          735 VFLIEDVEQ-----------ADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       735 ViliDEiek-----------a~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      |||||||+=           .|..+...||-.|+-   .++      .+..++|=++|-
T Consensus       366 IIffdeIdGlapvrSskqEqih~SIvSTLLaLmdG---lds------RgqVvvigATnR  415 (1080)
T KOG0732|consen  366 IIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDG---LDS------RGQVVVIGATNR  415 (1080)
T ss_pred             EEeccccccccccccchHHHhhhhHHHHHHHhccC---CCC------CCceEEEcccCC
Confidence            999999993           344566666666652   111      234556667764

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

Probab=97.40  E-value=0.00013  Score=69.28  Aligned_cols=82  Identities=10%  Similarity=0.133  Sum_probs=48.9

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc------------c----chHHHHHHHHHH
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH------------M----NRVEVEQRVEEI  288 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~------------~----~rge~E~rl~~l  288 (854)
                      ++++.++++||||+|||++++.+++....-..+..  ...++.+++.....            +    .....++-...+
T Consensus         2 ~~~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~   79 (131)
T PF13401_consen    2 QSQRILVISGPPGSGKTTLIKRLARQLNAEAEIKN--HPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLL   79 (131)
T ss_dssp             -----EEEEE-TTSSHHHHHHHHHHHHHHHHHHCC--CEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHH
T ss_pred             CCCcccEEEcCCCCCHHHHHHHHHHHhHHhhhccC--CCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHH
Confidence            46788999999999999999999988653100000  45666666543221            0    112344555666


Q ss_pred             HHHHHhhhCCCeEEEeCccccc
Q 003038          289 KNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       289 ~~~~~~~~~~~~ILfidel~~l  310 (854)
                      .+.+...  +..+|+|||+|.+
T Consensus        80 ~~~l~~~--~~~~lviDe~~~l   99 (131)
T PF13401_consen   80 IDALDRR--RVVLLVIDEADHL   99 (131)
T ss_dssp             HHHHHHC--TEEEEEEETTHHH
T ss_pred             HHHHHhc--CCeEEEEeChHhc
Confidence            6666664  3469999999998

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=97.40  E-value=7.9e-05  Score=75.32  Aligned_cols=75  Identities=16%  Similarity=0.271  Sum_probs=50.8

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHH-cCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHH----HhhhCCC
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIE-KGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLV----RSCLGRG  299 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~-~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~----~~~~~~~  299 (854)
                      |.+-|.+|+||+|||||.+++.||+.+. .+       ...++.+|++.+..  .++.+.-+..++...    ... ..+
T Consensus         1 ~p~~~~ll~GpsGvGKT~la~~la~~l~~~~-------~~~~~~~d~s~~~~--~~~~~~~~~~l~~~~~~~v~~~-~~g   70 (171)
T PF07724_consen    1 RPKSNFLLAGPSGVGKTELAKALAELLFVGS-------ERPLIRIDMSEYSE--GDDVESSVSKLLGSPPGYVGAE-EGG   70 (171)
T ss_dssp             S-SEEEEEESSTTSSHHHHHHHHHHHHT-SS-------CCEEEEEEGGGHCS--HHHCSCHCHHHHHHTTCHHHHH-HHT
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHhccCC-------ccchHHHhhhcccc--cchHHhhhhhhhhcccceeecc-chh
Confidence            3567899999999999999999999875 32       35899999988876  222222222222211    111 112


Q ss_pred             eEEEeCccccc
Q 003038          300 IVLNLGDLEWA  310 (854)
Q Consensus       300 ~ILfidel~~l  310 (854)
                       |||+|||+-+
T Consensus        71 -VVllDEidKa   80 (171)
T PF07724_consen   71 -VVLLDEIDKA   80 (171)
T ss_dssp             -EEEEETGGGC
T ss_pred             -hhhhHHHhhc
Confidence             8999999999

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.39  E-value=0.00035  Score=78.95  Aligned_cols=65  Identities=9%  Similarity=0.207  Sum_probs=51.1

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      =||.-+|+||||+|||+++.++|.-          -+..|+-|+++....    ..|  |+.|+-...    ..-||.|.
T Consensus       234 wKRGYLLYGPPGTGKSS~IaAmAn~----------L~ydIydLeLt~v~~----n~d--Lr~LL~~t~----~kSIivIE  293 (457)
T KOG0743|consen  234 WKRGYLLYGPPGTGKSSFIAAMANY----------LNYDIYDLELTEVKL----DSD--LRHLLLATP----NKSILLIE  293 (457)
T ss_pred             hhccceeeCCCCCCHHHHHHHHHhh----------cCCceEEeeeccccC----cHH--HHHHHHhCC----CCcEEEEe
Confidence            4788999999999999999999965          366888888876543    334  666665544    46799999


Q ss_pred             ccccc
Q 003038          306 DLEWA  310 (854)
Q Consensus       306 el~~l  310 (854)
                      ||+.-
T Consensus       294 DIDcs  298 (457)
T KOG0743|consen  294 DIDCS  298 (457)
T ss_pred             ecccc
Confidence            99988

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.39  E-value=0.00054  Score=71.46  Aligned_cols=77  Identities=12%  Similarity=0.189  Sum_probs=61.8

Q ss_pred             HHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHh
Q 003038          215 VMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRS  294 (854)
Q Consensus       215 i~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~  294 (854)
                      ++...+-+.-..-||++|.|-=|+||+++|+++-..+..       ++.++|.++...+..         |-.|+++++.
T Consensus        73 ~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e~~~-------~glrLVEV~k~dl~~---------Lp~l~~~Lr~  136 (287)
T COG2607          73 VRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNEYAD-------EGLRLVEVDKEDLAT---------LPDLVELLRA  136 (287)
T ss_pred             HHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHHHHh-------cCCeEEEEcHHHHhh---------HHHHHHHHhc
Confidence            444444445457899999999999999999999888765       466799998877764         6778888887


Q ss_pred             hhCCCeEEEeCccc
Q 003038          295 CLGRGIVLNLGDLE  308 (854)
Q Consensus       295 ~~~~~~ILfidel~  308 (854)
                      . +..+|||+||+-
T Consensus       137 ~-~~kFIlFcDDLS  149 (287)
T COG2607         137 R-PEKFILFCDDLS  149 (287)
T ss_pred             C-CceEEEEecCCC
Confidence            6 778999999983

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=97.38  E-value=0.00022  Score=79.67  Aligned_cols=140  Identities=11%  Similarity=0.038  Sum_probs=80.9

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc--cchHH--HHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH--MNRVE--VEQRVE  286 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~--~~rge--~E~rl~  286 (854)
                      +++.+..++..+.  .+.+++|.||||||||.+|+.+|+.+.          ..++.+.+.....  -..|.  +..+..
T Consensus        29 ~~~~~~~~l~a~~--~~~~vll~G~PG~gKT~la~~lA~~l~----------~~~~~i~~t~~l~p~d~~G~~~~~~~~~   96 (329)
T COG0714          29 DEEVIELALLALL--AGGHVLLEGPPGVGKTLLARALARALG----------LPFVRIQCTPDLLPSDLLGTYAYAALLL   96 (329)
T ss_pred             cHHHHHHHHHHHH--cCCCEEEECCCCccHHHHHHHHHHHhC----------CCeEEEecCCCCCHHHhcCchhHhhhhc
Confidence            6777777777766  588999999999999999999998863          4566665543332  12332  222221


Q ss_pred             H--HHHHHHhhhCCCe--EEEeCccccc-c-ccccccccccccchhhhHHHHHHHhhc-c------cCC---CCceEEEE
Q 003038          287 E--IKNLVRSCLGRGI--VLNLGDLEWA-E-FRASSSEQVRGYYCSIEHIIMEIGKLV-C------GIG---ENARFWLM  350 (854)
Q Consensus       287 ~--l~~~~~~~~~~~~--ILfidel~~l-~-~~~~~~~~~~~~~~~~~~~~~~~~~ll-~------~~~---g~g~l~lI  350 (854)
                      +  .+..+....-..+  |||+|||... . ..+                  .+-.+| .      ..+   -...+.+|
T Consensus        97 ~~~~~~~~~gpl~~~~~~ill~DEInra~p~~q~------------------aLl~~l~e~~vtv~~~~~~~~~~~f~vi  158 (329)
T COG0714          97 EPGEFRFVPGPLFAAVRVILLLDEINRAPPEVQN------------------ALLEALEERQVTVPGLTTIRLPPPFIVI  158 (329)
T ss_pred             cCCeEEEecCCcccccceEEEEeccccCCHHHHH------------------HHHHHHhCcEEEECCcCCcCCCCCCEEE
Confidence            1  1111110001123  9999999887 2 211                  111111 1      001   01258888


Q ss_pred             EecCHHHHHHhhccCCchhhhh-ccCCCCCC
Q 003038          351 GIATFQSYMRCKSGHPSLETLW-SLHPLTIP  380 (854)
Q Consensus       351 gatT~~ey~k~~~~~pale~~~-~~~~v~i~  380 (854)
                      ++.++.+|.--..-..|+-++| -.+-|..|
T Consensus       159 aT~Np~e~~g~~~l~eA~ldRf~~~~~v~yp  189 (329)
T COG0714         159 ATQNPGEYEGTYPLPEALLDRFLLRIYVDYP  189 (329)
T ss_pred             EccCccccCCCcCCCHHHHhhEEEEEecCCC
Confidence            8888888776555567777744 22555555

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.38  E-value=0.0015  Score=78.06  Aligned_cols=120  Identities=12%  Similarity=0.045  Sum_probs=69.4

Q ss_pred             HHH-HHHHHHHhhccCcCCc-eeecCCCCCHHHHHHHHHHHHHcCCCCc----c------------cCCceEEEcccccc
Q 003038          212 NED-VMYVIENLMSKRKRNF-VVVGECLASIEGVVRGVIDKIEKGDVPE----A------------LRDVKCLPLSISSF  273 (854)
Q Consensus       212 ~~e-i~~v~~~L~r~~k~n~-vLvGe~GvGKta~v~~la~~i~~~~vp~----~------------L~~~~~~~l~~~~l  273 (854)
                      .+. ++.+...+.+.+..+. +|+||+|+|||++++.+|..+....-|.    .            -....|+.++.++.
T Consensus        18 q~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~~~~~~~dvieidaas~   97 (584)
T PRK14952         18 QEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCESCVALAPNGPGSIDVVELDAASH   97 (584)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccccHHHHHhhcccCCCceEEEeccccc
Confidence            344 4445555565566774 8999999999999999999887422111    0            01235666655432


Q ss_pred             cccchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEE
Q 003038          274 RHMNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLM  350 (854)
Q Consensus       274 ~~~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lI  350 (854)
                      .  ...+    +++|++.+....  +..-|++|||+|.+ ..                 +...+-+.|..-.+  .+.+|
T Consensus        98 ~--gvd~----iRel~~~~~~~P~~~~~KVvIIDEah~Lt~~-----------------A~NALLK~LEEpp~--~~~fI  152 (584)
T PRK14952         98 G--GVDD----TRELRDRAFYAPAQSRYRIFIVDEAHMVTTA-----------------GFNALLKIVEEPPE--HLIFI  152 (584)
T ss_pred             c--CHHH----HHHHHHHHHhhhhcCCceEEEEECCCcCCHH-----------------HHHHHHHHHhcCCC--CeEEE
Confidence            1  1222    334555544321  34568999999999 43                 12233344421122  48888


Q ss_pred             EecCHH
Q 003038          351 GIATFQ  356 (854)
Q Consensus       351 gatT~~  356 (854)
                      .+||..
T Consensus       153 L~tte~  158 (584)
T PRK14952        153 FATTEP  158 (584)
T ss_pred             EEeCCh
Confidence            888754

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.38  E-value=0.00034  Score=81.10  Aligned_cols=86  Identities=19%  Similarity=0.209  Sum_probs=53.1

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCC--CCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGS--HNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVF  736 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~--~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vi  736 (854)
                      +++|+||+|+|||.|+++++..+-..  ...++.+++..|.       .... ..+..    +-.+.+.+..+ ....|+
T Consensus       132 ~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~~~f~-------~~~~-~~~~~----~~~~~f~~~~~-~~~dvL  198 (440)
T PRK14088        132 PLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFL-------NDLV-DSMKE----GKLNEFREKYR-KKVDVL  198 (440)
T ss_pred             eEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHH-------HHHH-HHHhc----ccHHHHHHHHH-hcCCEE
Confidence            59999999999999999999987532  3466777766554       1110 00000    11123334333 245799


Q ss_pred             EEecCCCCC--HHHHHHHHHhhh
Q 003038          737 LIEDVEQAD--YCSQKGFKRAIE  757 (854)
Q Consensus       737 liDEieka~--~~v~~~Ll~~le  757 (854)
                      +|||++..-  ...|..|+..|.
T Consensus       199 lIDDi~~l~~~~~~q~elf~~~n  221 (440)
T PRK14088        199 LIDDVQFLIGKTGVQTELFHTFN  221 (440)
T ss_pred             EEechhhhcCcHHHHHHHHHHHH
Confidence            999999763  345566666654

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.36  E-value=0.0013  Score=78.98  Aligned_cols=94  Identities=13%  Similarity=0.138  Sum_probs=55.1

Q ss_pred             cHHHHHHHHHHhhccC-cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcc--------------cCCceEEEcccccccc
Q 003038          211 RNEDVMYVIENLMSKR-KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEA--------------LRDVKCLPLSISSFRH  275 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~-k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~--------------L~~~~~~~l~~~~l~~  275 (854)
                      .+.-++.+...+..++ ....||+|++|||||++++.||..+.....+..              -+...++.++.++-. 
T Consensus        21 Qe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~~DvlEidaAs~~-   99 (709)
T PRK08691         21 QEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLLEIDAASNT-   99 (709)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCccceEEEeccccC-
Confidence            3444555555555444 345799999999999999999998764321100              001233444432211 


Q ss_pred             cchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          276 MNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       276 ~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                       ..    ..++++++.+....  ++.-|++|||+|.+
T Consensus       100 -gV----d~IRelle~a~~~P~~gk~KVIIIDEad~L  131 (709)
T PRK08691        100 -GI----DNIREVLENAQYAPTAGKYKVYIIDEVHML  131 (709)
T ss_pred             -CH----HHHHHHHHHHHhhhhhCCcEEEEEECcccc
Confidence             11    24556666554221  44579999999998

>PRK06921 hypothetical protein; Provisional

Probab=97.36  E-value=0.00033  Score=75.87  Aligned_cols=73  Identities=15%  Similarity=0.120  Sum_probs=48.5

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..+|++|+|+||+|||.++.++|..+.+.      .+..++-+....+....+..+ ..+.+.++.+.+    -.+|+||
T Consensus       116 ~~~~l~l~G~~G~GKThLa~aia~~l~~~------~g~~v~y~~~~~l~~~l~~~~-~~~~~~~~~~~~----~dlLiID  184 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTAAANELMRK------KGVPVLYFPFVEGFGDLKDDF-DLLEAKLNRMKK----VEVLFID  184 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHhhh------cCceEEEEEHHHHHHHHHHHH-HHHHHHHHHhcC----CCEEEEe
Confidence            46889999999999999999999987642      145666666555444322222 223333444433    4589999


Q ss_pred             cccc
Q 003038          306 DLEW  309 (854)
Q Consensus       306 el~~  309 (854)
                      ||+.
T Consensus       185 Dl~~  188 (266)
T PRK06921        185 DLFK  188 (266)
T ss_pred             cccc
Confidence            9966

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=97.35  E-value=0.0015  Score=66.82  Aligned_cols=135  Identities=15%  Similarity=0.066  Sum_probs=75.9

Q ss_pred             HHHhhccCc-CCceeecCCCCCHHHHHHHHHHHHHcCC----CCc------------ccCCceEEEcccccccccchHHH
Q 003038          219 IENLMSKRK-RNFVVVGECLASIEGVVRGVIDKIEKGD----VPE------------ALRDVKCLPLSISSFRHMNRVEV  281 (854)
Q Consensus       219 ~~~L~r~~k-~n~vLvGe~GvGKta~v~~la~~i~~~~----vp~------------~L~~~~~~~l~~~~l~~~~rge~  281 (854)
                      .+.+.+++- +..+|+||+|+|||++++.++..+....    .|-            .-.+..++..+...+   ..   
T Consensus         5 ~~~i~~~~~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~---~~---   78 (188)
T TIGR00678         5 KRALEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSI---KV---   78 (188)
T ss_pred             HHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccCcC---CH---
Confidence            344444444 5689999999999999999999987531    110            001122222221110   11   


Q ss_pred             HHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHH
Q 003038          282 EQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSY  358 (854)
Q Consensus       282 E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey  358 (854)
                       +.++++++.+....  ++.-|++|||+|.+ ..                 +...+-..+.....  ...+|.+|+..  
T Consensus        79 -~~i~~i~~~~~~~~~~~~~kviiide~~~l~~~-----------------~~~~Ll~~le~~~~--~~~~il~~~~~--  136 (188)
T TIGR00678        79 -DQVRELVEFLSRTPQESGRRVVIIEDAERMNEA-----------------AANALLKTLEEPPP--NTLFILITPSP--  136 (188)
T ss_pred             -HHHHHHHHHHccCcccCCeEEEEEechhhhCHH-----------------HHHHHHHHhcCCCC--CeEEEEEECCh--
Confidence             34555666665421  45678999999999 43                 12234444522111  35555555422  


Q ss_pred             HHhhccCCchhhhhccCCCCCCCchHHH
Q 003038          359 MRCKSGHPSLETLWSLHPLTIPAGSLSL  386 (854)
Q Consensus       359 ~k~~~~~pale~~~~~~~v~i~~~sl~~  386 (854)
                      .   ...|++.+  |.+.|.++..+-..
T Consensus       137 ~---~l~~~i~s--r~~~~~~~~~~~~~  159 (188)
T TIGR00678       137 E---KLLPTIRS--RCQVLPFPPLSEEA  159 (188)
T ss_pred             H---hChHHHHh--hcEEeeCCCCCHHH
Confidence            2   24678887  77778887765443

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.34  E-value=0.0008  Score=75.01  Aligned_cols=128  Identities=11%  Similarity=0.088  Sum_probs=74.3

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHH-HH--HHHHHHHHHHHhhhCCCeEE
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVE-VE--QRVEEIKNLVRSCLGRGIVL  302 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge-~E--~rl~~l~~~~~~~~~~~~IL  302 (854)
                      .++|++|+|+||+|||.++.++|..+.+       +|..|+-++...|....+.. ++  ......++.+.+    --+|
T Consensus       182 ~~~~Lll~G~~GtGKThLa~aIa~~l~~-------~g~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~~~l~~----~DLL  250 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLSNCIAKELLD-------RGKSVIYRTADELIEILREIRFNNDKELEEVYDLLIN----CDLL  250 (329)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHH-------CCCeEEEEEHHHHHHHHHHHHhccchhHHHHHHHhcc----CCEE
Confidence            4589999999999999999999998865       35677777776665432211 11  111222444443    3489


Q ss_pred             EeCccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEec--CHHHHHHhhccCCchhhh-hccCC
Q 003038          303 NLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIA--TFQSYMRCKSGHPSLETL-WSLHP  376 (854)
Q Consensus       303 fidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgat--T~~ey~k~~~~~pale~~-~~~~~  376 (854)
                      +|||+... ...               +....+-+++-.  ..+   ..+|-+|  +++++...+ .++-+.|+ |.+..
T Consensus       251 IIDDlG~e~~t~---------------~~~~~Lf~iin~R~~~~---k~tIiTSNl~~~el~~~~-~eri~SRL~~~~~~  311 (329)
T PRK06835        251 IIDDLGTEKITE---------------FSKSELFNLINKRLLRQ---KKMIISTNLSLEELLKTY-SERISSRLLGNFTL  311 (329)
T ss_pred             EEeccCCCCCCH---------------HHHHHHHHHHHHHHHCC---CCEEEECCCCHHHHHHHH-hHHHHHHHHcCCEE
Confidence            99999776 321               123345556522  222   2344444  467776542 23333443 55555


Q ss_pred             CCCCCch
Q 003038          377 LTIPAGS  383 (854)
Q Consensus       377 v~i~~~s  383 (854)
                      |.+...+
T Consensus       312 i~~~G~d  318 (329)
T PRK06835        312 LKFYGED  318 (329)
T ss_pred             EEecCcC
Confidence            6555444

>PRK08116 hypothetical protein; Validated

Probab=97.33  E-value=0.00049  Score=74.65  Aligned_cols=71  Identities=11%  Similarity=0.111  Sum_probs=49.1

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHH----HHHHHHHHHHHHhhhCCCeEEEe
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEV----EQRVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~----E~rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      .++|+|+||+|||.++.+++..+.+.       +..++-++...|...++..+    .....++++.+.+.    -+|+|
T Consensus       116 gl~l~G~~GtGKThLa~aia~~l~~~-------~~~v~~~~~~~ll~~i~~~~~~~~~~~~~~~~~~l~~~----dlLvi  184 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAACIANELIEK-------GVPVIFVNFPQLLNRIKSTYKSSGKEDENEIIRSLVNA----DLLIL  184 (268)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHc-------CCeEEEEEHHHHHHHHHHHHhccccccHHHHHHHhcCC----CEEEE
Confidence            49999999999999999999998652       45667777666655433222    22334455555543    38999


Q ss_pred             Cccccc
Q 003038          305 GDLEWA  310 (854)
Q Consensus       305 del~~l  310 (854)
                      ||++..
T Consensus       185 DDlg~e  190 (268)
T PRK08116        185 DDLGAE  190 (268)
T ss_pred             ecccCC
Confidence            999654

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.33  E-value=0.0012  Score=74.87  Aligned_cols=141  Identities=9%  Similarity=0.050  Sum_probs=78.4

Q ss_pred             cHHHHHHHHHHhhccCc-CCceeecCCCCCHHHHHHHHHHHHHcCCCCcccC--CceEEEcccccccccchHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRK-RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALR--DVKCLPLSISSFRHMNRVEVEQRVEE  287 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k-~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~--~~~~~~l~~~~l~~~~rge~E~rl~~  287 (854)
                      .++-++.+...+..++. ++.+|+||||+|||++++.++..+.....+..-.  +..++.++...    ..+  ...+++
T Consensus        22 ~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~----~~~--~~~i~~   95 (367)
T PRK14970         22 QSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAAS----NNS--VDDIRN   95 (367)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEecccc----CCC--HHHHHH
Confidence            44555666666655433 4688999999999999999999886633221111  23344443221    111  134555


Q ss_pred             HHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhcc
Q 003038          288 IKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSG  364 (854)
Q Consensus       288 l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~  364 (854)
                      +++++....  ++.-|++|||++.+ ..                 ....+-+.+.....  ...+|.+|+..  .   ..
T Consensus        96 l~~~~~~~p~~~~~kiviIDE~~~l~~~-----------------~~~~ll~~le~~~~--~~~~Il~~~~~--~---kl  151 (367)
T PRK14970         96 LIDQVRIPPQTGKYKIYIIDEVHMLSSA-----------------AFNAFLKTLEEPPA--HAIFILATTEK--H---KI  151 (367)
T ss_pred             HHHHHhhccccCCcEEEEEeChhhcCHH-----------------HHHHHHHHHhCCCC--ceEEEEEeCCc--c---cC
Confidence            666554321  34568999999888 42                 11222233421112  35666666531  1   23


Q ss_pred             CCchhhhhccCCCCCCCch
Q 003038          365 HPSLETLWSLHPLTIPAGS  383 (854)
Q Consensus       365 ~pale~~~~~~~v~i~~~s  383 (854)
                      .|++.+  |.+.|.++.++
T Consensus       152 ~~~l~s--r~~~v~~~~~~  168 (367)
T PRK14970        152 IPTILS--RCQIFDFKRIT  168 (367)
T ss_pred             CHHHHh--cceeEecCCcc
Confidence            467766  66666666544

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.32  E-value=0.0021  Score=76.71  Aligned_cols=43  Identities=9%  Similarity=0.115  Sum_probs=30.9

Q ss_pred             cHHHHHHHHHHhhccC--cCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          211 RNEDVMYVIENLMSKR--KRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~--k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ..+.+..++.-.....  ..+.+|+||+|||||++++.+|+.+..
T Consensus        20 GQe~v~~~L~~ai~~~ri~ha~Lf~GPpG~GKTtiArilAk~L~C   64 (624)
T PRK14959         20 GQETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNC   64 (624)
T ss_pred             CCHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhccc
Confidence            3455544444433332  456788999999999999999999865

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

Probab=97.32  E-value=0.00082  Score=72.32  Aligned_cols=94  Identities=7%  Similarity=0.142  Sum_probs=53.1

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcc--ccccCcCCCcccc-ccccccCC--CCCCch---HHHHH---
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIAL--SSFSSTRADSTED-SRNKRSRD--EQSCSY---IERFA---  725 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~--s~~~~~~~~s~e~-~~~~rl~~--~~g~g~---~e~L~---  725 (854)
                      .+.++++||+|+|||++++.+++.+-..  .++...+  ..+.     ..+- ..+....+  ..+...   ...|.   
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~l~~~l~~~--~~~~~~~~~~~~~-----~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l  115 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRNLLKRLDQE--RVVAAKLVNTRVD-----AEDLLRMVAADFGLETEGRDKAALLRELEDFL  115 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHhcCCC--CeEEeeeeCCCCC-----HHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHH
Confidence            4588999999999999999999887421  2222111  1111     0000 00111111  111111   11232   


Q ss_pred             -HHHHcCCCEEEEEecCCCCCHHHHHHHHHhhh
Q 003038          726 -EAVSNNPHRVFLIEDVEQADYCSQKGFKRAIE  757 (854)
Q Consensus       726 -eav~~~p~~ViliDEieka~~~v~~~Ll~~le  757 (854)
                       .....+...||+|||++.+++...+.|....+
T Consensus       116 ~~~~~~~~~~vliiDe~~~l~~~~~~~l~~l~~  148 (269)
T TIGR03015       116 IEQFAAGKRALLVVDEAQNLTPELLEELRMLSN  148 (269)
T ss_pred             HHHHhCCCCeEEEEECcccCCHHHHHHHHHHhC
Confidence             33345666899999999999998887765443

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.32  E-value=0.00054  Score=73.19  Aligned_cols=73  Identities=10%  Similarity=0.132  Sum_probs=52.3

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHH---HHHHHHHHHHHhhhCCCeEEE
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVE---QRVEEIKNLVRSCLGRGIVLN  303 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E---~rl~~l~~~~~~~~~~~~ILf  303 (854)
                      .++.+|.|+||||||.++.++|..+.+       ++..++-+++..+....++.+.   ....++++.+..    .-+|+
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~l~~-------~g~~v~~it~~~l~~~l~~~~~~~~~~~~~~l~~l~~----~dlLv  167 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNELLL-------RGKSVLIITVADIMSAMKDTFSNSETSEEQLLNDLSN----VDLLV  167 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHh-------cCCeEEEEEHHHHHHHHHHHHhhccccHHHHHHHhcc----CCEEE
Confidence            358999999999999999999998765       2457777777777665444432   223345555553    45899


Q ss_pred             eCccccc
Q 003038          304 LGDLEWA  310 (854)
Q Consensus       304 idel~~l  310 (854)
                      |||+...
T Consensus       168 IDDig~~  174 (244)
T PRK07952        168 IDEIGVQ  174 (244)
T ss_pred             EeCCCCC
Confidence            9999776

>PF13173 AAA_14: AAA domain

Probab=97.31  E-value=0.00038  Score=66.69  Aligned_cols=72  Identities=6%  Similarity=0.071  Sum_probs=45.6

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGD  306 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfide  306 (854)
                      ++.++|.|+.|||||++++.+++...        ...+++.+++.........+.+  +.+.+.....  .++.+|||||
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~--------~~~~~~yi~~~~~~~~~~~~~~--~~~~~~~~~~--~~~~~i~iDE   69 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL--------PPENILYINFDDPRDRRLADPD--LLEYFLELIK--PGKKYIFIDE   69 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc--------ccccceeeccCCHHHHHHhhhh--hHHHHHHhhc--cCCcEEEEeh
Confidence            45689999999999999999998764        1235666666544331111111  2222222211  2578999999


Q ss_pred             cccc
Q 003038          307 LEWA  310 (854)
Q Consensus       307 l~~l  310 (854)
                      +|.+
T Consensus        70 iq~~   73 (128)
T PF13173_consen   70 IQYL   73 (128)
T ss_pred             hhhh
Confidence            9998

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.31  E-value=0.0017  Score=72.90  Aligned_cols=94  Identities=12%  Similarity=0.152  Sum_probs=57.7

Q ss_pred             cHHHHHHHHHHhhccCcC-CceeecCCCCCHHHHHHHHHHHHHcCCCCcc--------------cCCceEEEcccccccc
Q 003038          211 RNEDVMYVIENLMSKRKR-NFVVVGECLASIEGVVRGVIDKIEKGDVPEA--------------LRDVKCLPLSISSFRH  275 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~-n~vLvGe~GvGKta~v~~la~~i~~~~vp~~--------------L~~~~~~~l~~~~l~~  275 (854)
                      .++.++.+...+.+++.. ..+|+||||+|||++++.+++.+...+.+..              .....++.++..... 
T Consensus        19 ~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~~~~~~~~~~~-   97 (355)
T TIGR02397        19 QEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDVIEIDAASNN-   97 (355)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEeeccccC-
Confidence            566677777777655444 4688999999999999999999865432210              112234444332110 


Q ss_pred             cchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          276 MNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       276 ~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                       ..    ..++++++.+....  ++.-|++|||++.+
T Consensus        98 -~~----~~~~~l~~~~~~~p~~~~~~vviidea~~l  129 (355)
T TIGR02397        98 -GV----DDIREILDNVKYAPSSGKYKVYIIDEVHML  129 (355)
T ss_pred             -CH----HHHHHHHHHHhcCcccCCceEEEEeChhhc
Confidence             11    12455666665431  34568999999888

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.

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=97.31  E-value=0.00036  Score=79.20  Aligned_cols=59  Identities=10%  Similarity=0.207  Sum_probs=52.2

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc-cchH-HHHHHHHHHHHHHHhh
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH-MNRV-EVEQRVEEIKNLVRSC  295 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~-~~rg-e~E~rl~~l~~~~~~~  295 (854)
                      +.|++|+||||||||++++.||..+          +..|+.+|...|.. ||.| +.|..++++++.+...
T Consensus        50 ~~~ILliGp~G~GKT~LAr~LAk~l----------~~~fi~vD~t~f~e~GyvG~d~e~~ir~L~~~A~~~  110 (443)
T PRK05201         50 PKNILMIGPTGVGKTEIARRLAKLA----------NAPFIKVEATKFTEVGYVGRDVESIIRDLVEIAVKM  110 (443)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHh----------CChheeecchhhccCCcccCCHHHHHHHHHHHHHHH
Confidence            5799999999999999999999874          67899999998885 7999 8999999999998654

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=97.30  E-value=0.0014  Score=73.18  Aligned_cols=51  Identities=12%  Similarity=0.120  Sum_probs=36.7

Q ss_pred             HHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc
Q 003038          216 MYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR  274 (854)
Q Consensus       216 ~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~  274 (854)
                      .+.+.-++ +...+++|+||+|+||+.+|+.+-..-.+       ++..|+.++++.+-
T Consensus        12 ~~~~~~~a-~~~~pVLI~GE~GtGK~~lAr~iH~~s~r-------~~~pfv~vnc~~~~   62 (329)
T TIGR02974        12 LEQVSRLA-PLDRPVLIIGERGTGKELIAARLHYLSKR-------WQGPLVKLNCAALS   62 (329)
T ss_pred             HHHHHHHh-CCCCCEEEECCCCChHHHHHHHHHHhcCc-------cCCCeEEEeCCCCC
Confidence            33334444 36778999999999999999988654221       35689999988653

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

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=97.29  E-value=0.0019  Score=78.33  Aligned_cols=90  Identities=8%  Similarity=0.109  Sum_probs=53.5

Q ss_pred             HHHHHHHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCCCcc-----------cCCceEEEcccccccccchHHHH
Q 003038          215 VMYVIENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDVPEA-----------LRDVKCLPLSISSFRHMNRVEVE  282 (854)
Q Consensus       215 i~~v~~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~vp~~-----------L~~~~~~~l~~~~l~~~~rge~E  282 (854)
                      ++.+...+...+-.+ .|++||+|+|||++++.+|..+.....+..           -....++.++.+    +..|  -
T Consensus        27 v~~L~~aI~~~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~~~~~~~~Dvieidaa----sn~~--v  100 (725)
T PRK07133         27 VQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIENVNNSLDIIEMDAA----SNNG--V  100 (725)
T ss_pred             HHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHHHhhcCCCcEEEEecc----ccCC--H
Confidence            444555555444444 489999999999999999999875331110           011223333321    1111  1


Q ss_pred             HHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          283 QRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       283 ~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                      .-+++|++.+....  ++.-|++|||+|.+
T Consensus       101 d~IReLie~~~~~P~~g~~KV~IIDEa~~L  130 (725)
T PRK07133        101 DEIRELIENVKNLPTQSKYKIYIIDEVHML  130 (725)
T ss_pred             HHHHHHHHHHHhchhcCCCEEEEEEChhhC
Confidence            22566666666431  44568999999999

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=97.28  E-value=0.00011  Score=74.66  Aligned_cols=75  Identities=13%  Similarity=0.189  Sum_probs=46.6

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchH-HHHHHHHHHHHHHHhhhCCCeEEE
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRV-EVEQRVEEIKNLVRSCLGRGIVLN  303 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rg-e~E~rl~~l~~~~~~~~~~~~ILf  303 (854)
                      +.+.|++|+|+||+|||.++.+++..+.+       +|..++-++...|....+. ....+..++++.+...    -+|+
T Consensus        45 ~~~~~l~l~G~~G~GKThLa~ai~~~~~~-------~g~~v~f~~~~~L~~~l~~~~~~~~~~~~~~~l~~~----dlLi  113 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHLAVAIANEAIR-------KGYSVLFITASDLLDELKQSRSDGSYEELLKRLKRV----DLLI  113 (178)
T ss_dssp             SC--EEEEEESTTSSHHHHHHHHHHHHHH-------TT--EEEEEHHHHHHHHHCCHCCTTHCHHHHHHHTS----SCEE
T ss_pred             ccCeEEEEEhhHhHHHHHHHHHHHHHhcc-------CCcceeEeecCceeccccccccccchhhhcCccccc----cEec
Confidence            36789999999999999999999987765       3455666666666543110 0111233344555543    4799


Q ss_pred             eCccccc
Q 003038          304 LGDLEWA  310 (854)
Q Consensus       304 idel~~l  310 (854)
                      |||+-..
T Consensus       114 lDDlG~~  120 (178)
T PF01695_consen  114 LDDLGYE  120 (178)
T ss_dssp             EETCTSS
T ss_pred             cccccee
Confidence            9999443

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.

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.28  E-value=0.0022  Score=76.07  Aligned_cols=94  Identities=16%  Similarity=0.137  Sum_probs=54.1

Q ss_pred             cHHHHH-HHHHHhhccCcCCc-eeecCCCCCHHHHHHHHHHHHHcCCC----Ccc----------cCCceEEEccccccc
Q 003038          211 RNEDVM-YVIENLMSKRKRNF-VVVGECLASIEGVVRGVIDKIEKGDV----PEA----------LRDVKCLPLSISSFR  274 (854)
Q Consensus       211 r~~ei~-~v~~~L~r~~k~n~-vLvGe~GvGKta~v~~la~~i~~~~v----p~~----------L~~~~~~~l~~~~l~  274 (854)
                      ..+.+. .+...+..++-.+. +|+||||+|||++++.+|..+....-    |-.          -....++.++.++  
T Consensus        20 Gq~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d~~ei~~~~--   97 (527)
T PRK14969         20 GQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDLIEVDAAS--   97 (527)
T ss_pred             CcHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceeEeeccc--
Confidence            344444 44444444444554 89999999999999999988754211    100          0111344444321  


Q ss_pred             ccchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          275 HMNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       275 ~~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                        ..+  -..++++++.+....  ++.-|++|||+|.+
T Consensus        98 --~~~--vd~ir~l~~~~~~~p~~~~~kVvIIDEad~l  131 (527)
T PRK14969         98 --NTQ--VDAMRELLDNAQYAPTRGRFKVYIIDEVHML  131 (527)
T ss_pred             --cCC--HHHHHHHHHHHhhCcccCCceEEEEcCcccC
Confidence              111  123556666654321  34569999999999

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.27  E-value=0.00088  Score=79.62  Aligned_cols=86  Identities=14%  Similarity=0.238  Sum_probs=54.8

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhC--CCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFG--SHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVF  736 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg--~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vi  736 (854)
                      +++|+|++|+|||.|+.+++..+..  ....++++.+.+|.       .... ..+..    +-.+.+.+.++.  ..||
T Consensus       316 pL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitaeef~-------~el~-~al~~----~~~~~f~~~y~~--~DLL  381 (617)
T PRK14086        316 PLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSEEFT-------NEFI-NSIRD----GKGDSFRRRYRE--MDIL  381 (617)
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHH-------HHHH-HHHHh----ccHHHHHHHhhc--CCEE
Confidence            5899999999999999999998753  23566777776654       1111 00000    111223333333  5899


Q ss_pred             EEecCCCCC--HHHHHHHHHhhhc
Q 003038          737 LIEDVEQAD--YCSQKGFKRAIES  758 (854)
Q Consensus       737 liDEieka~--~~v~~~Ll~~le~  758 (854)
                      +||||+...  ...+..|+.+|+.
T Consensus       382 lIDDIq~l~gke~tqeeLF~l~N~  405 (617)
T PRK14086        382 LVDDIQFLEDKESTQEEFFHTFNT  405 (617)
T ss_pred             EEehhccccCCHHHHHHHHHHHHH
Confidence            999999874  3446667776664

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.24  E-value=0.00075  Score=78.49  Aligned_cols=89  Identities=17%  Similarity=0.218  Sum_probs=55.9

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhC--CCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFG--SHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRV  735 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg--~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~V  735 (854)
                      .+++|+|++|+|||.|+++++..+..  ....++++.+.+|.       .... .. +.. ..+..+.+.+.++  ...|
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~~f~-------~~~~-~~-l~~-~~~~~~~~~~~~~--~~dv  209 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDEFA-------RKAV-DI-LQK-THKEIEQFKNEIC--QNDV  209 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHH-------HHHH-HH-HHH-hhhHHHHHHHHhc--cCCE
Confidence            36899999999999999999997752  34566777766554       1110 00 000 0011122333333  3569


Q ss_pred             EEEecCCCCC--HHHHHHHHHhhhc
Q 003038          736 FLIEDVEQAD--YCSQKGFKRAIES  758 (854)
Q Consensus       736 iliDEieka~--~~v~~~Ll~~le~  758 (854)
                      ++||||+...  ...+..|...|..
T Consensus       210 LiIDDiq~l~~k~~~~e~lf~l~N~  234 (450)
T PRK14087        210 LIIDDVQFLSYKEKTNEIFFTIFNN  234 (450)
T ss_pred             EEEeccccccCCHHHHHHHHHHHHH
Confidence            9999999876  6677778777764

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=97.24  E-value=0.00098  Score=69.98  Aligned_cols=134  Identities=10%  Similarity=0.148  Sum_probs=76.8

Q ss_pred             cccccHHHHHHHHHHHHHh--------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEE
Q 003038          619 KVPWQKDTVYDIANTVLKC--------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVS  690 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~--------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~  690 (854)
                      .|-|-+.-|.++.++|..-        ..|+             +|+--+|++||||+|||.|||+-|..-   ..-|+.
T Consensus       172 DiGGldkQIqELvEAiVLpmth~ekF~~lgi-------------~pPKGvLmYGPPGTGKTlmARAcAaqT---~aTFLK  235 (424)
T KOG0652|consen  172 DIGGLDKQIQELVEAIVLPMTHKEKFENLGI-------------RPPKGVLMYGPPGTGKTLMARACAAQT---NATFLK  235 (424)
T ss_pred             ccccHHHHHHHHHHHhccccccHHHHHhcCC-------------CCCCceEeeCCCCCcHHHHHHHHHHhc---cchHHH
Confidence            3566666667777776421        2333             333346889999999999999988643   222332


Q ss_pred             EccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCC-----------CHHHHHHHHHhhhc-
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQA-----------DYCSQKGFKRAIES-  758 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka-----------~~~v~~~Ll~~le~-  758 (854)
                      +.....            +.-.| +.|.-....-+...+++..+||||||+|-.           +++||...+..+.. 
T Consensus       236 LAgPQL------------VQMfI-GdGAkLVRDAFaLAKEkaP~IIFIDElDAIGtKRfDSek~GDREVQRTMLELLNQL  302 (424)
T KOG0652|consen  236 LAGPQL------------VQMFI-GDGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQL  302 (424)
T ss_pred             hcchHH------------Hhhhh-cchHHHHHHHHHHhhccCCeEEEEechhhhccccccccccccHHHHHHHHHHHHhh
Confidence            222111            11111 111111111222334566699999999843           67899988888853 


Q ss_pred             -CeEecCCCceeecCCeEEEEecCCCCCCCCC
Q 003038          759 -GRIVTSSGDEVSLGDAIVILSCESFSSRSRA  789 (854)
Q Consensus       759 -G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~  789 (854)
                       |.-.+        .+.-+|..+|..|....+
T Consensus       303 DGFss~--------~~vKviAATNRvDiLDPA  326 (424)
T KOG0652|consen  303 DGFSSD--------DRVKVIAATNRVDILDPA  326 (424)
T ss_pred             cCCCCc--------cceEEEeecccccccCHH
Confidence             32221        234477788877766555

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.23  E-value=0.0025  Score=76.51  Aligned_cols=92  Identities=18%  Similarity=0.138  Sum_probs=54.7

Q ss_pred             HHHHHHHHHhhccCcCCc-eeecCCCCCHHHHHHHHHHHHHcCCC---------C----------cccCCceEEEccccc
Q 003038          213 EDVMYVIENLMSKRKRNF-VVVGECLASIEGVVRGVIDKIEKGDV---------P----------EALRDVKCLPLSISS  272 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~-vLvGe~GvGKta~v~~la~~i~~~~v---------p----------~~L~~~~~~~l~~~~  272 (854)
                      .-++.+...+..++-.+. +|+|++|+|||++++.+|+.+....-         |          ..-....++.++.++
T Consensus        23 ~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C~~C~~i~~g~h~D~~eldaas  102 (618)
T PRK14951         23 HVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVCQACRDIDSGRFVDYTELDAAS  102 (618)
T ss_pred             HHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCccHHHHHHHcCCCCceeecCccc
Confidence            344555555665555565 89999999999999999998875210         1          000112345554332


Q ss_pred             ccccchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          273 FRHMNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       273 l~~~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                      -    +| + ..++++++.+....  ++.-|++|||+|.+
T Consensus       103 ~----~~-V-d~iReli~~~~~~p~~g~~KV~IIDEvh~L  136 (618)
T PRK14951        103 N----RG-V-DEVQQLLEQAVYKPVQGRFKVFMIDEVHML  136 (618)
T ss_pred             c----cC-H-HHHHHHHHHHHhCcccCCceEEEEEChhhC
Confidence            1    11 1 12455555544321  34568999999999

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=97.22  E-value=0.00053  Score=77.56  Aligned_cols=131  Identities=14%  Similarity=0.120  Sum_probs=82.9

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc---------chHHHHHHH---HHHHHHH
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM---------NRVEVEQRV---EEIKNLV  292 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~---------~rge~E~rl---~~l~~~~  292 (854)
                      ....++++.||+|+||+-+++.+- .+....     .+..|++++++.+-..         -+|-|--+.   ..+++.+
T Consensus        99 p~~~~vLi~GetGtGKel~A~~iH-~~s~r~-----~~~PFI~~NCa~~~en~~~~eLFG~~kGaftGa~~~k~Glfe~A  172 (403)
T COG1221          99 PSGLPVLIIGETGTGKELFARLIH-ALSARR-----AEAPFIAFNCAAYSENLQEAELFGHEKGAFTGAQGGKAGLFEQA  172 (403)
T ss_pred             CCCCcEEEecCCCccHHHHHHHHH-Hhhhcc-----cCCCEEEEEHHHhCcCHHHHHHhccccceeecccCCcCchheec
Confidence            578899999999999999999887 444331     4678999999766431         111111111   1233333


Q ss_pred             HhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhc-cc--C--CC----CceEEEEEecCHHHHHHhh
Q 003038          293 RSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CG--I--GE----NARFWLMGIATFQSYMRCK  362 (854)
Q Consensus       293 ~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~--~--~g----~g~l~lIgatT~~ey~k~~  362 (854)
                      .     |=+||+||||.+ -.+.                 .-+-++| ..  .  ++    ...+++|+|||..-=...+
T Consensus       173 ~-----GGtLfLDEI~~LP~~~Q-----------------~kLl~~le~g~~~rvG~~~~~~~dVRli~AT~~~l~~~~~  230 (403)
T COG1221         173 N-----GGTLFLDEIHRLPPEGQ-----------------EKLLRVLEEGEYRRVGGSQPRPVDVRLICATTEDLEEAVL  230 (403)
T ss_pred             C-----CCEEehhhhhhCCHhHH-----------------HHHHHHHHcCceEecCCCCCcCCCceeeeccccCHHHHHH
Confidence            2     337999999999 4332                 1233344 11  0  11    1369999999987777766


Q ss_pred             ccCCchhhhhccCCCCCCCchHHH
Q 003038          363 SGHPSLETLWSLHPLTIPAGSLSL  386 (854)
Q Consensus       363 ~~~pale~~~~~~~v~i~~~sl~~  386 (854)
                      .+ .-|.+  |+.+++|.=|+|..
T Consensus       231 ~g-~dl~~--rl~~~~I~LPpLrE  251 (403)
T COG1221         231 AG-ADLTR--RLNILTITLPPLRE  251 (403)
T ss_pred             hh-cchhh--hhcCceecCCChhh
Confidence            66 55666  67777777666654

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=97.20  E-value=0.002  Score=71.85  Aligned_cols=56  Identities=11%  Similarity=0.124  Sum_probs=37.9

Q ss_pred             cHHHHHHHHHHhhc--cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccc
Q 003038          211 RNEDVMYVIENLMS--KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSF  273 (854)
Q Consensus       211 r~~ei~~v~~~L~r--~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l  273 (854)
                      +...++++++-+.+  +...+++|+||+|+||+.+|+.+-..-.       -.+..|+.+|++.+
T Consensus        11 ~S~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~~s~-------r~~~pfv~v~c~~~   68 (326)
T PRK11608         11 EANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYLSS-------RWQGPFISLNCAAL   68 (326)
T ss_pred             CCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhCC-------ccCCCeEEEeCCCC
Confidence            33444444444332  3566799999999999999998864311       13568999998876

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=97.20  E-value=0.0062  Score=69.25  Aligned_cols=142  Identities=15%  Similarity=0.043  Sum_probs=85.2

Q ss_pred             hhhhhhhhhhHHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHH
Q 003038          596 EYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAK  675 (854)
Q Consensus       596 ~~~~~~~~~~~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr  675 (854)
                      +.+..|+.+|--.+..-.--++-.-......+..++..+-....                 .-.+++.||+|+|||.+|.
T Consensus       165 ~~R~~FT~dEWid~LlrSiG~~P~~~~~r~k~~~L~rl~~fve~-----------------~~Nli~lGp~GTGKThla~  227 (449)
T TIGR02688       165 EGRKEFTLEEWIDVLIRSIGYEPEGFEARQKLLLLARLLPLVEP-----------------NYNLIELGPKGTGKSYIYN  227 (449)
T ss_pred             HHHhhcCHHHHHHHHHHhcCCCcccCChHHHHHHHHhhHHHHhc-----------------CCcEEEECCCCCCHHHHHH
Confidence            44577876655444332223333344556666666666444321                 2478999999999999999


Q ss_pred             HHHHH-HhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCC----CHHHHH
Q 003038          676 ELARL-VFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQA----DYCSQK  750 (854)
Q Consensus       676 ~LA~~-lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka----~~~v~~  750 (854)
                      +|+.. ..-+.         .|.          +...|+.    .-..+....  -..+.+|+|||+-..    +.+...
T Consensus       228 ~l~~~~a~~sG---------~f~----------T~a~Lf~----~L~~~~lg~--v~~~DlLI~DEvgylp~~~~~~~v~  282 (449)
T TIGR02688       228 NLSPYVILISG---------GTI----------TVAKLFY----NISTRQIGL--VGRWDVVAFDEVATLKFAKPKELIG  282 (449)
T ss_pred             HHhHHHHHHcC---------CcC----------cHHHHHH----HHHHHHHhh--hccCCEEEEEcCCCCcCCchHHHHH
Confidence            99876 22111         111          1111110    000011111  134689999999984    345778


Q ss_pred             HHHHhhhcCeEecCCCceeecCCeEEEEecC
Q 003038          751 GFKRAIESGRIVTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       751 ~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn  781 (854)
                      .++..|++|.++-  |...--.+|=+||.-|
T Consensus       283 imK~yMesg~fsR--G~~~~~a~as~vfvGN  311 (449)
T TIGR02688       283 ILKNYMESGSFTR--GDETKSSDASFVFLGN  311 (449)
T ss_pred             HHHHHHHhCceec--cceeeeeeeEEEEEcc
Confidence            9999999999994  5455557888888666

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=97.19  E-value=0.0026  Score=65.80  Aligned_cols=97  Identities=15%  Similarity=0.247  Sum_probs=60.9

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCC-CCceEEEccc-cccCcCCCcccccccc-ccCCCCCCchHHHHHHHHHcCCCE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGS-HNNFVSIALS-SFSSTRADSTEDSRNK-RSRDEQSCSYIERFAEAVSNNPHR  734 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~-~~~~i~id~s-~~~~~~~~s~e~~~~~-rl~~~~g~g~~e~L~eav~~~p~~  734 (854)
                      |.++|.||+|+|||++.++|+..+... ...++.+.-. +|....    ....+. +-++.....|.+.+..+++.+| .
T Consensus         2 GlilI~GptGSGKTTll~~ll~~~~~~~~~~i~t~e~~~E~~~~~----~~~~i~q~~vg~~~~~~~~~i~~aLr~~p-d   76 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDYINKNKTHHILTIEDPIEFVHES----KRSLINQREVGLDTLSFENALKAALRQDP-D   76 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhhhcCCcEEEEEcCCccccccC----ccceeeecccCCCccCHHHHHHHHhcCCc-C
Confidence            689999999999999999999887432 2344444322 222000    000000 0011112256667888888877 6


Q ss_pred             EEEEecCCCCCHHHHHHHHHhhhcCeE
Q 003038          735 VFLIEDVEQADYCSQKGFKRAIESGRI  761 (854)
Q Consensus       735 ViliDEieka~~~v~~~Ll~~le~G~l  761 (854)
                      +|++||+-  +++....++++...|..
T Consensus        77 ~ii~gEir--d~e~~~~~l~~a~~G~~  101 (198)
T cd01131          77 VILVGEMR--DLETIRLALTAAETGHL  101 (198)
T ss_pred             EEEEcCCC--CHHHHHHHHHHHHcCCE
Confidence            99999995  77777887888877643

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.

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.19  E-value=0.0019  Score=73.78  Aligned_cols=119  Identities=7%  Similarity=0.097  Sum_probs=72.1

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEc-ccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCcc
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPL-SISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDL  307 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l-~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfidel  307 (854)
                      .++|.||||+||||+|-.+|..          .+..|+.+ +...++...--.==.-++.+|+.+.++  .-.|+.||||
T Consensus       540 SvLl~Gp~~sGKTaLAA~iA~~----------S~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DAYkS--~lsiivvDdi  607 (744)
T KOG0741|consen  540 SVLLEGPPGSGKTALAAKIALS----------SDFPFVKIISPEDMIGLSESAKCAHIKKIFEDAYKS--PLSIIVVDDI  607 (744)
T ss_pred             EEEEecCCCCChHHHHHHHHhh----------cCCCeEEEeChHHccCccHHHHHHHHHHHHHHhhcC--cceEEEEcch
Confidence            5799999999999999888754          23344443 333444322111124567778887775  5678999999


Q ss_pred             ccc-cccccccccccccchhhhHHHHHHHh-hcc--cCCCCceEEEEEecCHHHHHHhhccCCch
Q 003038          308 EWA-EFRASSSEQVRGYYCSIEHIIMEIGK-LVC--GIGENARFWLMGIATFQSYMRCKSGHPSL  368 (854)
Q Consensus       308 ~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~-ll~--~~~g~g~l~lIgatT~~ey~k~~~~~pal  368 (854)
                      ..| +...-+ ..    |+   ..+..+-. |||  |-.|+ ++.++|+|+.-++++-...-..|
T Consensus       608 ErLiD~vpIG-PR----fS---N~vlQaL~VllK~~ppkg~-kLli~~TTS~~~vL~~m~i~~~F  663 (744)
T KOG0741|consen  608 ERLLDYVPIG-PR----FS---NLVLQALLVLLKKQPPKGR-KLLIFGTTSRREVLQEMGILDCF  663 (744)
T ss_pred             hhhhcccccC-ch----hh---HHHHHHHHHHhccCCCCCc-eEEEEecccHHHHHHHcCHHHhh
Confidence            998 654321 01    11   13333332 333  22344 79999999999988754433333

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=97.18  E-value=0.0026  Score=75.93  Aligned_cols=94  Identities=6%  Similarity=0.081  Sum_probs=58.1

Q ss_pred             cHHHHHHHHHHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCCCcc--------------cCCceEEEcccccccc
Q 003038          211 RNEDVMYVIENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDVPEA--------------LRDVKCLPLSISSFRH  275 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~vp~~--------------L~~~~~~~l~~~~l~~  275 (854)
                      .+.-++.+...+...+-.+ .+|+||+|+|||++++.+|..+...+-+..              .....|+.++.++.. 
T Consensus        21 q~~v~~~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~pC~~C~~C~~i~~g~~~dv~eidaas~~-   99 (559)
T PRK05563         21 QEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGEPCNECEICKAITNGSLMDVIEIDAASNN-   99 (559)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccHHHHHHhcCCCCCeEEeeccccC-
Confidence            3444455555555444445 577999999999999999998875432211              123345555543211 


Q ss_pred             cchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          276 MNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       276 ~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                         |  -..++++++.+....  ++.-|++|||+|.+
T Consensus       100 ---~--vd~ir~i~~~v~~~p~~~~~kViIIDE~~~L  131 (559)
T PRK05563        100 ---G--VDEIRDIRDKVKYAPSEAKYKVYIIDEVHML  131 (559)
T ss_pred             ---C--HHHHHHHHHHHhhCcccCCeEEEEEECcccC
Confidence               1  124556666665321  45678999999999

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

Probab=97.16  E-value=0.00077  Score=70.92  Aligned_cols=146  Identities=14%  Similarity=0.147  Sum_probs=80.1

Q ss_pred             HHHHHHHHHHhhccCc---CCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHH-HHHHH
Q 003038          212 NEDVMYVIENLMSKRK---RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVE-QRVEE  287 (854)
Q Consensus       212 ~~ei~~v~~~L~r~~k---~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E-~rl~~  287 (854)
                      .+.....+..++....   +.++|+|++|+|||.+..+++..+.+..     .+.+++.++...|...+...+. ..+.+
T Consensus        16 N~~a~~~~~~ia~~~~~~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~-----~~~~v~y~~~~~f~~~~~~~~~~~~~~~   90 (219)
T PF00308_consen   16 NELAYAAAKAIAENPGERYNPLFLYGPSGLGKTHLLQAIANEAQKQH-----PGKRVVYLSAEEFIREFADALRDGEIEE   90 (219)
T ss_dssp             THHHHHHHHHHHHSTTTSSSEEEEEESTTSSHHHHHHHHHHHHHHHC-----TTS-EEEEEHHHHHHHHHHHHHTTSHHH
T ss_pred             HHHHHHHHHHHHhcCCCCCCceEEECCCCCCHHHHHHHHHHHHHhcc-----ccccceeecHHHHHHHHHHHHHcccchh
Confidence            3445555555554422   3468999999999999999999886521     3568888887766553222211 23444


Q ss_pred             HHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecCHHHHHHhhcc
Q 003038          288 IKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIATFQSYMRCKSG  364 (854)
Q Consensus       288 l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT~~ey~k~~~~  364 (854)
                      +++.+++    --+|+|||||.+ +...               ....+-.++..  ..|. .+.+-+-..+.+...   .
T Consensus        91 ~~~~~~~----~DlL~iDDi~~l~~~~~---------------~q~~lf~l~n~~~~~~k-~li~ts~~~P~~l~~---~  147 (219)
T PF00308_consen   91 FKDRLRS----ADLLIIDDIQFLAGKQR---------------TQEELFHLFNRLIESGK-QLILTSDRPPSELSG---L  147 (219)
T ss_dssp             HHHHHCT----SSEEEEETGGGGTTHHH---------------HHHHHHHHHHHHHHTTS-EEEEEESS-TTTTTT---S
T ss_pred             hhhhhhc----CCEEEEecchhhcCchH---------------HHHHHHHHHHHHHhhCC-eEEEEeCCCCccccc---c
Confidence            5555554    358999999999 6432               11233344422  2332 344444456666542   4


Q ss_pred             CCchhhh--hccCCCCCCCchHHH
Q 003038          365 HPSLETL--WSLHPLTIPAGSLSL  386 (854)
Q Consensus       365 ~pale~~--~~~~~v~i~~~sl~~  386 (854)
                      .|-|.++  |++. +.|.+|+.+.
T Consensus       148 ~~~L~SRl~~Gl~-~~l~~pd~~~  170 (219)
T PF00308_consen  148 LPDLRSRLSWGLV-VELQPPDDED  170 (219)
T ss_dssp             -HHHHHHHHCSEE-EEE----HHH
T ss_pred             ChhhhhhHhhcch-hhcCCCCHHH
Confidence            5667661  3322 5555555433

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.

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]

Probab=97.15  E-value=0.00053  Score=80.31  Aligned_cols=109  Identities=16%  Similarity=0.283  Sum_probs=80.0

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHH-HHH--------HH
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIE-RFA--------EA  727 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e-~L~--------ea  727 (854)
                      ...+++.|.||+||..+||++-+.-- -..+||-++|..+.       +.+.-+.+.     ||.. .++        ..
T Consensus       336 ~~pvll~GEtGtGKe~laraiH~~s~-~~gpfvAvNCaAip-------~~liesELF-----Gy~~GafTga~~kG~~g~  402 (606)
T COG3284         336 DLPVLLQGETGTGKEVLARAIHQNSE-AAGPFVAVNCAAIP-------EALIESELF-----GYVAGAFTGARRKGYKGK  402 (606)
T ss_pred             CCCeEecCCcchhHHHHHHHHHhccc-ccCCeEEEEeccch-------HHhhhHHHh-----ccCccccccchhcccccc
Confidence            34789999999999999999988664 67899999999887       333333333     2221 122        23


Q ss_pred             HHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCC--ceeecCCeEEEEecC
Q 003038          728 VSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSG--DEVSLGDAIVILSCE  781 (854)
Q Consensus       728 v~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G--~~v~~~~aIiIlTsn  781 (854)
                      +...+..-+|+|||.-++-..|..||+++++|.++==.|  .+||+   -||-+|+
T Consensus       403 ~~~A~gGtlFldeIgd~p~~~Qs~LLrVl~e~~v~p~g~~~~~vdi---rvi~ath  455 (606)
T COG3284         403 LEQADGGTLFLDEIGDMPLALQSRLLRVLQEGVVTPLGGTRIKVDI---RVIAATH  455 (606)
T ss_pred             ceecCCCccHHHHhhhchHHHHHHHHHHHhhCceeccCCcceeEEE---EEEeccC
Confidence            344556789999999999999999999999999995444  45554   4777664

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=97.14  E-value=0.00038  Score=67.60  Aligned_cols=99  Identities=13%  Similarity=0.110  Sum_probs=59.7

Q ss_pred             HHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHH
Q 003038          214 DVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVR  293 (854)
Q Consensus       214 ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~  293 (854)
                      ++++-++-++ +...+++|+||+|+||+.+|+.+...-..       ....++.++...+-           .++++.+ 
T Consensus         9 ~l~~~l~~~a-~~~~pvli~GE~GtGK~~~A~~lh~~~~~-------~~~~~~~~~~~~~~-----------~~~l~~a-   68 (138)
T PF14532_consen    9 RLRRQLERLA-KSSSPVLITGEPGTGKSLLARALHRYSGR-------ANGPFIVIDCASLP-----------AELLEQA-   68 (138)
T ss_dssp             HHHHHHHHHH-CSSS-EEEECCTTSSHHHHHHCCHHTTTT-------CCS-CCCCCHHCTC-----------HHHHHHC-
T ss_pred             HHHHHHHHHh-CCCCcEEEEcCCCCCHHHHHHHHHhhcCc-------cCCCeEEechhhCc-----------HHHHHHc-
Confidence            3444455555 58889999999999999999988765222       12233444444322           2333333 


Q ss_pred             hhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-CCCCceEEEEEecCH
Q 003038          294 SCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGENARFWLMGIATF  355 (854)
Q Consensus       294 ~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~g~l~lIgatT~  355 (854)
                          .+-.|||+||+.+ ...                 ...+..+|+. ...  ++++|.+++.
T Consensus        69 ----~~gtL~l~~i~~L~~~~-----------------Q~~L~~~l~~~~~~--~~RlI~ss~~  109 (138)
T PF14532_consen   69 ----KGGTLYLKNIDRLSPEA-----------------QRRLLDLLKRQERS--NVRLIASSSQ  109 (138)
T ss_dssp             ----TTSEEEEECGCCS-HHH-----------------HHHHHHHHHHCTTT--TSEEEEEECC
T ss_pred             ----CCCEEEECChHHCCHHH-----------------HHHHHHHHHhcCCC--CeEEEEEeCC
Confidence                2447999999999 432                 2345566643 223  5788888764

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=97.14  E-value=0.00053  Score=80.23  Aligned_cols=51  Identities=18%  Similarity=0.265  Sum_probs=44.7

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHH
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|+++++..|.+.+.....|+..+          +  ..++|+||+|+|||+||+.||+.+
T Consensus        77 d~yGlee~ieriv~~l~~Aa~gl~~~----------~--~IL~LvGPpG~GKSsLa~~la~~l  127 (644)
T PRK15455         77 EFYGMEEAIEQIVSYFRHAAQGLEEK----------K--QILYLLGPVGGGKSSLAERLKSLM  127 (644)
T ss_pred             cccCcHHHHHHHHHHHHHHHHhcCCC----------C--ceEEEecCCCCCchHHHHHHHHHH
Confidence            47999999999999998888888553          2  389999999999999999999876

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.13  E-value=0.00057  Score=75.46  Aligned_cols=74  Identities=16%  Similarity=0.249  Sum_probs=49.4

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHH-HHHHHHHHHHHHhhhCCCeEEEe
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEV-EQRVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~-E~rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      ..++++|+|++|||||.++.++|..+.+       +|..+.-+.+..|....+.-+ ...+.+.++.+++    --||+|
T Consensus       155 ~~~gl~L~G~~G~GKThLa~Aia~~l~~-------~g~~v~~~~~~~l~~~lk~~~~~~~~~~~l~~l~~----~dlLiI  223 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSYLLAAIANELAK-------KGVSSTLLHFPEFIRELKNSISDGSVKEKIDAVKE----APVLML  223 (306)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHH-------cCCCEEEEEHHHHHHHHHHHHhcCcHHHHHHHhcC----CCEEEE
Confidence            4578999999999999999999999865       345555555555544322111 1123445555554    358999


Q ss_pred             Cccccc
Q 003038          305 GDLEWA  310 (854)
Q Consensus       305 del~~l  310 (854)
                      |||..-
T Consensus       224 DDiG~e  229 (306)
T PRK08939        224 DDIGAE  229 (306)
T ss_pred             ecCCCc
Confidence            999544

>PRK09087 hypothetical protein; Validated

Probab=97.13  E-value=0.0018  Score=68.51  Aligned_cols=125  Identities=13%  Similarity=0.057  Sum_probs=70.7

Q ss_pred             HHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHH
Q 003038          212 NEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNL  291 (854)
Q Consensus       212 ~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~  291 (854)
                      +..+..+++-+.....+.++|+|++|+|||.++++++...          ++.+++..  .+..           +++..
T Consensus        29 N~~a~~~l~~~~~~~~~~l~l~G~~GsGKThLl~~~~~~~----------~~~~i~~~--~~~~-----------~~~~~   85 (226)
T PRK09087         29 NRAAVSLVDHWPNWPSPVVVLAGPVGSGKTHLASIWREKS----------DALLIHPN--EIGS-----------DAANA   85 (226)
T ss_pred             hHHHHHHHHhcccCCCCeEEEECCCCCCHHHHHHHHHHhc----------CCEEecHH--Hcch-----------HHHHh
Confidence            3444444443332222237999999999999999887542          23343332  1111           12222


Q ss_pred             HHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhh
Q 003038          292 VRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLET  370 (854)
Q Consensus       292 ~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~  370 (854)
                      +..     -+|.|||++.+ ....               ..-.+-|.+. ..|  ...+|++++...|...  ..|.|..
T Consensus        86 ~~~-----~~l~iDDi~~~~~~~~---------------~lf~l~n~~~-~~g--~~ilits~~~p~~~~~--~~~dL~S  140 (226)
T PRK09087         86 AAE-----GPVLIEDIDAGGFDET---------------GLFHLINSVR-QAG--TSLLMTSRLWPSSWNV--KLPDLKS  140 (226)
T ss_pred             hhc-----CeEEEECCCCCCCCHH---------------HHHHHHHHHH-hCC--CeEEEECCCChHHhcc--ccccHHH
Confidence            221     26888999987 3211               2223333332 223  5888888887666543  4688988


Q ss_pred             hhcc---CCCCCCCchHHH
Q 003038          371 LWSL---HPLTIPAGSLSL  386 (854)
Q Consensus       371 ~~~~---~~v~i~~~sl~~  386 (854)
                        ||   ..+.|..++.+.
T Consensus       141 --Rl~~gl~~~l~~pd~e~  157 (226)
T PRK09087        141 --RLKAATVVEIGEPDDAL  157 (226)
T ss_pred             --HHhCCceeecCCCCHHH
Confidence              77   777777776544

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.12  E-value=0.00091  Score=75.28  Aligned_cols=93  Identities=14%  Similarity=0.209  Sum_probs=57.1

Q ss_pred             HHHHHHhhc-cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccc---------------cccc-ch
Q 003038          216 MYVIENLMS-KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISS---------------FRHM-NR  278 (854)
Q Consensus       216 ~~v~~~L~r-~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~---------------l~~~-~r  278 (854)
                      .|+|+.|.- .+....+|+||||||||++++.++..+.... +    ++.+|-+-...               +++. +-
T Consensus       157 ~rvID~l~PIGkGQR~lIvgppGvGKTTLaK~Ian~I~~nh-F----Dv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d  231 (416)
T PRK09376        157 TRIIDLIAPIGKGQRGLIVAPPKAGKTVLLQNIANSITTNH-P----EVHLIVLLIDERPEEVTDMQRSVKGEVVASTFD  231 (416)
T ss_pred             eeeeeeecccccCceEEEeCCCCCChhHHHHHHHHHHHhhc-C----CeEEEEEEeCCchhHHHHHHHHhcCcEEEECCC
Confidence            356666542 2667789999999999999999999887651 1    23333221211               1221 22


Q ss_pred             HHHHHHHH---HHHHHHHhhh--CCCeEEEeCccccc-ccc
Q 003038          279 VEVEQRVE---EIKNLVRSCL--GRGIVLNLGDLEWA-EFR  313 (854)
Q Consensus       279 ge~E~rl~---~l~~~~~~~~--~~~~ILfidel~~l-~~~  313 (854)
                      +..+.+++   .++..++...  |..|||||||||.+ .+.
T Consensus       232 ~~~~~~~~~a~~~ie~Ae~~~e~G~dVlL~iDsItR~arAq  272 (416)
T PRK09376        232 EPAERHVQVAEMVIEKAKRLVEHGKDVVILLDSITRLARAY  272 (416)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEChHHHHHHH
Confidence            33334444   3344433321  78999999999999 654

>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=97.11  E-value=0.0011  Score=72.11  Aligned_cols=109  Identities=10%  Similarity=0.156  Sum_probs=67.0

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCC-------CCCCchHHHHHHHHHcC
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRD-------EQSCSYIERFAEAVSNN  731 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~-------~~g~g~~e~L~eav~~~  731 (854)
                      .+||+||+|+|||.+++.+-+.+-........+.++.++.+       ..+.+.+.       +..||-        ..+
T Consensus        35 pvLl~G~~GtGKT~li~~~l~~l~~~~~~~~~~~~s~~Tts-------~~~q~~ie~~l~k~~~~~~gP--------~~~   99 (272)
T PF12775_consen   35 PVLLVGPSGTGKTSLIQNFLSSLDSDKYLVITINFSAQTTS-------NQLQKIIESKLEKRRGRVYGP--------PGG   99 (272)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHCSTTCCEEEEEEES-TTHHH-------HHHHHCCCTTECECTTEEEEE--------ESS
T ss_pred             cEEEECCCCCchhHHHHhhhccCCccccceeEeeccCCCCH-------HHHHHHHhhcEEcCCCCCCCC--------CCC
Confidence            57999999999999998755544222223456777765521       11111110       000110        123


Q ss_pred             CCEEEEEecCCCCCHH------HHHHHHHhhhcCeEecCCC-ceeecCCeEEEEecCC
Q 003038          732 PHRVFLIEDVEQADYC------SQKGFKRAIESGRIVTSSG-DEVSLGDAIVILSCES  782 (854)
Q Consensus       732 p~~ViliDEieka~~~------v~~~Ll~~le~G~l~d~~G-~~v~~~~aIiIlTsn~  782 (854)
                      ...|+||||+.-..++      ....|.|.|+.|-+-|... .-..+.|+-||.+++.
T Consensus       100 k~lv~fiDDlN~p~~d~ygtq~~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~~p  157 (272)
T PF12775_consen  100 KKLVLFIDDLNMPQPDKYGTQPPIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAMNP  157 (272)
T ss_dssp             SEEEEEEETTT-S---TTS--HHHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEESS
T ss_pred             cEEEEEecccCCCCCCCCCCcCHHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEecCC
Confidence            3569999999976543      5689999999988888543 4568899999988864

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=97.11  E-value=0.00035  Score=78.13  Aligned_cols=157  Identities=15%  Similarity=0.189  Sum_probs=83.8

Q ss_pred             HHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCce
Q 003038          609 LTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNF  688 (854)
Q Consensus       609 l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~  688 (854)
                      +..|-+.|--.|+|++.+...|.-.+.   +|..+....   +...|...++||.|.||+||+.|.+.+++..    .+-
T Consensus        15 ~~~l~~s~aP~i~g~~~iK~aill~L~---~~~~~~~~~---~~~~r~~ihiLlvGdpg~gKS~ll~~~~~~~----pr~   84 (331)
T PF00493_consen   15 FDRLANSIAPSIYGHEDIKKAILLQLF---GGVEKNDPD---GTRIRGNIHILLVGDPGTGKSQLLKYVAKLA----PRS   84 (331)
T ss_dssp             HHCCHHHCSSTTTT-HHHHHHHCCCCT---T--SCCCCT----TEE--S--EEEECSCHHCHHHHHHCCCCT-----SSE
T ss_pred             HHHHHHHhCCcCcCcHHHHHHHHHHHH---hcccccccc---ccccccccceeeccchhhhHHHHHHHHHhhC----Cce
Confidence            456677777889999876665543332   333321100   0112445699999999999999999776544    233


Q ss_pred             EEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCC-Cc
Q 003038          689 VSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSS-GD  767 (854)
Q Consensus       689 i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~-G~  767 (854)
                      ++..+...+..+- .   -.+.+-....+|.. +  .+++-.....|++|||+||++.+.+..|+++||.|.++-.+ |-
T Consensus        85 v~~~g~~~s~~gL-t---a~~~~d~~~~~~~l-e--aGalvlad~GiccIDe~dk~~~~~~~~l~eaMEqq~isi~kagi  157 (331)
T PF00493_consen   85 VYTSGKGSSAAGL-T---ASVSRDPVTGEWVL-E--AGALVLADGGICCIDEFDKMKEDDRDALHEAMEQQTISIAKAGI  157 (331)
T ss_dssp             EEEECCGSTCCCC-C---EEECCCGGTSSECE-E--E-HHHHCTTSEEEECTTTT--CHHHHHHHHHHHCSCEEECTSSS
T ss_pred             EEECCCCcccCCc-c---ceeccccccceeEE-e--CCchhcccCceeeecccccccchHHHHHHHHHHcCeeccchhhh
Confidence            4444332221000 0   01111000111100 0  12333345689999999999999999999999999999865 44


Q ss_pred             eeec-CCeEEEEecCC
Q 003038          768 EVSL-GDAIVILSCES  782 (854)
Q Consensus       768 ~v~~-~~aIiIlTsn~  782 (854)
                      ...+ .++-|+.++|.
T Consensus       158 ~~~l~ar~svlaa~NP  173 (331)
T PF00493_consen  158 VTTLNARCSVLAAANP  173 (331)
T ss_dssp             EEEEE---EEEEEE--
T ss_pred             cccccchhhhHHHHhh
Confidence            4454 36777778874

; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.10  E-value=0.004  Score=73.42  Aligned_cols=94  Identities=17%  Similarity=0.144  Sum_probs=54.1

Q ss_pred             cHHHHHHH-HHHhhccCcCCc-eeecCCCCCHHHHHHHHHHHHHc-CCCCc------------ccCCceEEEcccccccc
Q 003038          211 RNEDVMYV-IENLMSKRKRNF-VVVGECLASIEGVVRGVIDKIEK-GDVPE------------ALRDVKCLPLSISSFRH  275 (854)
Q Consensus       211 r~~ei~~v-~~~L~r~~k~n~-vLvGe~GvGKta~v~~la~~i~~-~~vp~------------~L~~~~~~~l~~~~l~~  275 (854)
                      ..+.+... ...+.+++-.+. +|+||||+|||++++.+|..+.. +..+.            ......++.++...-. 
T Consensus        18 Gq~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~dv~el~~~~~~-   96 (504)
T PRK14963         18 GQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPDVLEIDAASNN-   96 (504)
T ss_pred             ChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCCCCceEEecccccC-
Confidence            34454444 444444444444 99999999999999999999864 21110            0122345555543111 


Q ss_pred             cchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          276 MNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       276 ~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                       ..    ..++++.+.+....  +..-|++|||+|.+
T Consensus        97 -~v----d~iR~l~~~~~~~p~~~~~kVVIIDEad~l  128 (504)
T PRK14963         97 -SV----EDVRDLREKVLLAPLRGGRKVYILDEAHMM  128 (504)
T ss_pred             -CH----HHHHHHHHHHhhccccCCCeEEEEECcccc
Confidence             11    12444545444321  45678999999888

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.10  E-value=0.0046  Score=73.61  Aligned_cols=94  Identities=9%  Similarity=0.047  Sum_probs=55.7

Q ss_pred             cHHHHHHHHHHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCC----C----------cccCCceEEEcccccccc
Q 003038          211 RNEDVMYVIENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDV----P----------EALRDVKCLPLSISSFRH  275 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~v----p----------~~L~~~~~~~l~~~~l~~  275 (854)
                      .+.-++.+...+.+.+-.+ .+++||+|+|||++|+.+|+.+....-    |          .......++.++.++-. 
T Consensus        21 Qe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~~Cg~C~sCr~i~~~~h~DiieIdaas~i-   99 (605)
T PRK05896         21 QELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSVCESINTNQSVDIVELDAASNN-   99 (605)
T ss_pred             cHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHHcCCCCceEEecccccc-
Confidence            4444556666665544343 678999999999999999999864321    1          00112345555543211 


Q ss_pred             cchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          276 MNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       276 ~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                       ..++    ++++++.+....  ++.=|++|||+|.+
T Consensus       100 -gVd~----IReIi~~~~~~P~~~~~KVIIIDEad~L  131 (605)
T PRK05896        100 -GVDE----IRNIIDNINYLPTTFKYKVYIIDEAHML  131 (605)
T ss_pred             -CHHH----HHHHHHHHHhchhhCCcEEEEEechHhC
Confidence             2222    445555554321  23447999999999

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.08  E-value=0.00074  Score=76.68  Aligned_cols=95  Identities=17%  Similarity=0.194  Sum_probs=61.5

Q ss_pred             CcccccHHHHHHHHHHHHHh------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEE
Q 003038          618 KKVPWQKDTVYDIANTVLKC------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSI  691 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~i  691 (854)
                      .-+.|.+.+...+-+.+..-      -.|++            .|...+|+.||+|+|||.|++++|-..   ...|..|
T Consensus       153 ~di~gl~~~k~~l~e~vi~p~lr~d~F~glr------------~p~rglLLfGPpgtGKtmL~~aiAsE~---~atff~i  217 (428)
T KOG0740|consen  153 DDIAGLEDAKQSLKEAVILPLLRPDLFLGLR------------EPVRGLLLFGPPGTGKTMLAKAIATES---GATFFNI  217 (428)
T ss_pred             cCCcchhhHHHHhhhhhhhcccchHhhhccc------------cccchhheecCCCCchHHHHHHHHhhh---cceEeec
Confidence            44677777777777776542      12332            244578888999999999999999876   3445544


Q ss_pred             ccccccCcCCCccccccccccCCCCCCchHH----HHHHHHHcCCCEEEEEecCCCC
Q 003038          692 ALSSFSSTRADSTEDSRNKRSRDEQSCSYIE----RFAEAVSNNPHRVFLIEDVEQA  744 (854)
Q Consensus       692 d~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e----~L~eav~~~p~~ViliDEieka  744 (854)
                      ..+...       .++        +  |-.+    .|+...+...++||||||||+.
T Consensus       218 SassLt-------sK~--------~--Ge~eK~vralf~vAr~~qPsvifidEidsl  257 (428)
T KOG0740|consen  218 SASSLT-------SKY--------V--GESEKLVRALFKVARSLQPSVIFIDEIDSL  257 (428)
T ss_pred             cHHHhh-------hhc--------c--ChHHHHHHHHHHHHHhcCCeEEEechhHHH
Confidence            444333       111        1  3333    3455556777899999999963

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.08  E-value=0.0037  Score=75.46  Aligned_cols=94  Identities=11%  Similarity=0.104  Sum_probs=54.8

Q ss_pred             cHHH-HHHHHHHhhccC-cCCceeecCCCCCHHHHHHHHHHHHHcCCC--C---ccc-----------CCceEEEccccc
Q 003038          211 RNED-VMYVIENLMSKR-KRNFVVVGECLASIEGVVRGVIDKIEKGDV--P---EAL-----------RDVKCLPLSISS  272 (854)
Q Consensus       211 r~~e-i~~v~~~L~r~~-k~n~vLvGe~GvGKta~v~~la~~i~~~~v--p---~~L-----------~~~~~~~l~~~~  272 (854)
                      ..++ +..+...+..++ ....||+||+|+|||++++.+|+.+.....  +   ...           ....++.++.. 
T Consensus        20 Gq~~i~~~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg~C~~C~~i~~g~h~D~~ei~~~-   98 (620)
T PRK14948         20 GQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCGKCELCRAIAAGNALDVIEIDAA-   98 (620)
T ss_pred             ChHHHHHHHHHHHHcCCCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCcccHHHHHHhcCCCccEEEEecc-
Confidence            3444 444444444332 246789999999999999999999865211  1   010           01123333221 


Q ss_pred             ccccchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          273 FRHMNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       273 l~~~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                           .+..-..++++++.+....  +..-|++|||+|.+
T Consensus        99 -----~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~L  133 (620)
T PRK14948         99 -----SNTGVDNIRELIERAQFAPVQARWKVYVIDECHML  133 (620)
T ss_pred             -----ccCCHHHHHHHHHHHhhChhcCCceEEEEECcccc
Confidence                 1111245667776665321  34568999999999

>PF05729 NACHT: NACHT domain

Probab=97.08  E-value=0.0023  Score=62.93  Aligned_cols=109  Identities=13%  Similarity=0.163  Sum_probs=63.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCC------CceEEEccccccCcCCCccccccccccCC---CCCCchHH-HHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSH------NNFVSIALSSFSSTRADSTEDSRNKRSRD---EQSCSYIE-RFAEAV  728 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~------~~~i~id~s~~~~~~~~s~e~~~~~rl~~---~~g~g~~e-~L~eav  728 (854)
                      .+++.|++|+|||.+++.++..+-...      .-.+.+.+..+.....    ...+..++.   ....+... .+....
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~l~~~l~~~~~~~~~~~~~~~~~~~   77 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNN----SRSLADLLFDQLPESIAPIEELLQELL   77 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccc----cchHHHHHHHhhccchhhhHHHHHHHH
Confidence            578999999999999999997764332      1233455554441100    011222221   11112222 345566


Q ss_pred             HcCCCEEEEEecCCCCCHHHHH--------HHHHhhhcCeEecCCCceeecCCeEEEEecC
Q 003038          729 SNNPHRVFLIEDVEQADYCSQK--------GFKRAIESGRIVTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       729 ~~~p~~ViliDEieka~~~v~~--------~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn  781 (854)
                      .+++.-+|+||.+|.+......        .|.+.+..          ..+.++-+|+||.
T Consensus        78 ~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~----------~~~~~~~liit~r  128 (166)
T PF05729_consen   78 EKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQ----------ALPPGVKLIITSR  128 (166)
T ss_pred             HcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhh----------ccCCCCeEEEEEc
Confidence            7788889999999999875433        45555543          1234566777774

>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=97.05  E-value=0.00088  Score=72.67  Aligned_cols=94  Identities=17%  Similarity=0.236  Sum_probs=58.3

Q ss_pred             cHHHHHHHHHHhhc--cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccc-c---cc----cc---c
Q 003038          211 RNEDVMYVIENLMS--KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSIS-S---FR----HM---N  277 (854)
Q Consensus       211 r~~ei~~v~~~L~r--~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~-~---l~----~~---~  277 (854)
                      ||.++++|.+.|..  +..+-+.|+|.+|+|||++|..++++....   ....++-.+.+.-. .   +.    ..   .
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~---~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~   77 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIK---NRFDGVIWVSLSKNPSLEQLLEQILRQLGEP   77 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHC---CCCTEEEEEEEES-SCCHHHHHHHHHHHTCC
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccccccc---ccccccccccccccccccccccccccccccc
Confidence            79999999999998  566678999999999999999999873321   12212222222211 0   10    00   1


Q ss_pred             ------hHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc
Q 003038          278 ------RVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       278 ------rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                            ..+.+.....|.+.++   +++++|++|++...
T Consensus        78 ~~~~~~~~~~~~~~~~l~~~L~---~~~~LlVlDdv~~~  113 (287)
T PF00931_consen   78 DSSISDPKDIEELQDQLRELLK---DKRCLLVLDDVWDE  113 (287)
T ss_dssp             -STSSCCSSHHHHHHHHHHHHC---CTSEEEEEEEE-SH
T ss_pred             ccccccccccccccccchhhhc---cccceeeeeeeccc
Confidence                  1234455555555554   35999999998544

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.

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.04  E-value=0.0028  Score=75.48  Aligned_cols=76  Identities=9%  Similarity=0.096  Sum_probs=52.0

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHH-HHHHHHHHHHhhhCCCeEEEeCc
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQ-RVEEIKNLVRSCLGRGIVLNLGD  306 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~-rl~~l~~~~~~~~~~~~ILfide  306 (854)
                      |.++|+|++|+|||.++.+++..+.+..     .+.+++.++...|...+...+.. .+..+.+..++    .-||+|||
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~~~~-----~g~~V~Yitaeef~~el~~al~~~~~~~f~~~y~~----~DLLlIDD  385 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYARRLY-----PGTRVRYVSSEEFTNEFINSIRDGKGDSFRRRYRE----MDILLVDD  385 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHhC-----CCCeEEEeeHHHHHHHHHHHHHhccHHHHHHHhhc----CCEEEEeh
Confidence            4577889999999999999999876421     35678888877776543333222 23333333333    45899999


Q ss_pred             cccc-cc
Q 003038          307 LEWA-EF  312 (854)
Q Consensus       307 l~~l-~~  312 (854)
                      |+.+ +.
T Consensus       386 Iq~l~gk  392 (617)
T PRK14086        386 IQFLEDK  392 (617)
T ss_pred             hccccCC
Confidence            9999 54

>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes

Probab=97.02  E-value=0.00094  Score=53.47  Aligned_cols=38  Identities=32%  Similarity=0.678  Sum_probs=33.6

Q ss_pred             ccCHHHHHHHhccCC--hHHHHHHHhCCCHHHHHHHHHHH
Q 003038          129 KIELEQLIISILDDP--SVSRVMREAGFSSTQVKSNVEQA  166 (854)
Q Consensus       129 ~I~~eHLLLALL~d~--~~~~iL~~~Gi~~~~l~~~v~~~  166 (854)
                      +|+++|||+||++++  .+.++|+++|+++..++..+.+.
T Consensus        12 ~i~~eHlL~all~~~~~~~~~il~~~~id~~~l~~~i~~~   51 (53)
T PF02861_consen   12 YISPEHLLLALLEDPDSIAARILKKLGIDPEQLKAAIEKA   51 (53)
T ss_dssp             SE-HHHHHHHHHHHTTSHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHhhhhHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            599999999999975  78999999999999999998863

The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=97.02  E-value=0.0034  Score=70.61  Aligned_cols=99  Identities=15%  Similarity=0.245  Sum_probs=62.9

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCC-CCceEEEc-cccccCcCCCcccccccc-ccCCCCCCchHHHHHHHHHcCC
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGS-HNNFVSIA-LSSFSSTRADSTEDSRNK-RSRDEQSCSYIERFAEAVSNNP  732 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-~~~~i~id-~s~~~~~~~~s~e~~~~~-rl~~~~g~g~~e~L~eav~~~p  732 (854)
                      +.+.++|.||+|+|||++.++|.+.+-.. ...++.+. --++....    ....+. +-++.....|.+.+..++|.+|
T Consensus       121 ~~g~ili~G~tGSGKTT~l~al~~~i~~~~~~~i~tiEdp~E~~~~~----~~~~i~q~evg~~~~~~~~~l~~~lr~~p  196 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTLASMIDYINKNAAGHIITIEDPIEYVHRN----KRSLINQREVGLDTLSFANALRAALREDP  196 (343)
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHhhCcCCCCEEEEEcCChhhhccC----ccceEEccccCCCCcCHHHHHHHhhccCC
Confidence            34789999999999999999999877422 34455543 22222000    000000 0011111256667788888877


Q ss_pred             CEEEEEecCCCCCHHHHHHHHHhhhcCeE
Q 003038          733 HRVFLIEDVEQADYCSQKGFKRAIESGRI  761 (854)
Q Consensus       733 ~~ViliDEieka~~~v~~~Ll~~le~G~l  761 (854)
                       .||++||+-  +++.....+++...|..
T Consensus       197 -d~i~vgEir--d~~~~~~~l~aa~tGh~  222 (343)
T TIGR01420       197 -DVILIGEMR--DLETVELALTAAETGHL  222 (343)
T ss_pred             -CEEEEeCCC--CHHHHHHHHHHHHcCCc
Confidence             789999997  88888888888877754

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.02  E-value=0.0051  Score=72.59  Aligned_cols=94  Identities=14%  Similarity=0.098  Sum_probs=53.1

Q ss_pred             cHHHHHH-HHHHhhccCcCCc-eeecCCCCCHHHHHHHHHHHHHcCCCCc--------------ccCCceEEEccccccc
Q 003038          211 RNEDVMY-VIENLMSKRKRNF-VVVGECLASIEGVVRGVIDKIEKGDVPE--------------ALRDVKCLPLSISSFR  274 (854)
Q Consensus       211 r~~ei~~-v~~~L~r~~k~n~-vLvGe~GvGKta~v~~la~~i~~~~vp~--------------~L~~~~~~~l~~~~l~  274 (854)
                      ..+.+.+ +...+..++-.+. +|+||+|+|||++++.+|..+...+-+.              ...+..++.++.++  
T Consensus        18 Gqe~v~~~L~~~I~~grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~dv~eldaas--   95 (535)
T PRK08451         18 GQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHIDIIEMDAAS--   95 (535)
T ss_pred             CcHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCCeEEEecccc--
Confidence            4455444 4444444333444 8999999999999999999987543221              11233455554321  


Q ss_pred             ccchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          275 HMNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       275 ~~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                        .+|  -.-++++++.+....  ++.-|++|||+|.+
T Consensus        96 --~~g--Id~IRelie~~~~~P~~~~~KVvIIDEad~L  129 (535)
T PRK08451         96 --NRG--IDDIRELIEQTKYKPSMARFKIFIIDEVHML  129 (535)
T ss_pred             --ccC--HHHHHHHHHHHhhCcccCCeEEEEEECcccC
Confidence              111  012333433332110  34568999999999

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.02  E-value=0.0019  Score=71.27  Aligned_cols=93  Identities=12%  Similarity=0.046  Sum_probs=56.4

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKN  290 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~  290 (854)
                      +++.+..+...+.+.+..+++|+||||+|||++++.++..+....     ....++.++.+.-.  ...-+...+.++..
T Consensus        22 ~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~-----~~~~~i~~~~~~~~--~~~~~~~~i~~~~~   94 (319)
T PRK00440         22 QEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGED-----WRENFLELNASDER--GIDVIRNKIKEFAR   94 (319)
T ss_pred             cHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCc-----cccceEEecccccc--chHHHHHHHHHHHh
Confidence            677777777777766667899999999999999999998875432     12234444433211  11112223332222


Q ss_pred             HHHhhhCCCeEEEeCccccc
Q 003038          291 LVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       291 ~~~~~~~~~~ILfidel~~l  310 (854)
                      ..-......-+|+|||++.+
T Consensus        95 ~~~~~~~~~~vviiDe~~~l  114 (319)
T PRK00440         95 TAPVGGAPFKIIFLDEADNL  114 (319)
T ss_pred             cCCCCCCCceEEEEeCcccC
Confidence            11000013568999999998

>PHA00729 NTP-binding motif containing protein

Probab=97.01  E-value=0.0023  Score=67.22  Aligned_cols=37  Identities=8%  Similarity=-0.016  Sum_probs=31.3

Q ss_pred             HHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          216 MYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       216 ~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      +++++-|.-....|++|+|+||||||+++.+|+.++.
T Consensus         6 k~~~~~l~~~~f~nIlItG~pGvGKT~LA~aLa~~l~   42 (226)
T PHA00729          6 KKIVSAYNNNGFVSAVIFGKQGSGKTTYALKVARDVF   42 (226)
T ss_pred             HHHHHHHhcCCeEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4566666666777999999999999999999999864

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

Probab=97.00  E-value=0.0013  Score=70.62  Aligned_cols=37  Identities=14%  Similarity=0.205  Sum_probs=28.6

Q ss_pred             HHHHHhhc-cCcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          217 YVIENLMS-KRKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       217 ~v~~~L~r-~~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      |+|+.|.- .+....+|+||+|||||++++.++..+..
T Consensus         5 ~~id~~~~i~~Gqr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128           5 RVVDLFAPIGKGQRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             hheeeecccCCCCEEEEECCCCCCHHHHHHHHHhcccc
Confidence            45555532 36678999999999999999999887654

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.

>KOG0480 consensus DNA replication licensing factor, MCM6 component [Replication, recombination and repair]

Probab=96.99  E-value=0.0035  Score=73.14  Aligned_cols=151  Identities=16%  Similarity=0.175  Sum_probs=92.0

Q ss_pred             HHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC
Q 003038          607 ENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN  686 (854)
Q Consensus       607 e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~  686 (854)
                      .-++.|.+-|.-.|.|++.+...|.-.+.-   |..+..+   ...+-|....++++|.||+||+.+-++.+..+    .
T Consensus       334 nly~~lv~Sl~PsIyGhe~VK~GilL~LfG---Gv~K~a~---eg~~lRGDinv~iVGDPgt~KSQfLk~v~~fs----P  403 (764)
T KOG0480|consen  334 NLYKNLVNSLFPSIYGHELVKAGILLSLFG---GVHKSAG---EGTSLRGDINVCIVGDPGTGKSQFLKAVCAFS----P  403 (764)
T ss_pred             hHHHHHHHhhCccccchHHHHhhHHHHHhC---CccccCC---CCccccCCceEEEeCCCCccHHHHHHHHhccC----C
Confidence            346889999999999999998887666543   4443221   01234667899999999999999999887654    1


Q ss_pred             ceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCC
Q 003038          687 NFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSG  766 (854)
Q Consensus       687 ~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G  766 (854)
                      +=|+.....-+ +     ..-...-..++-...|. -=.+|+--.-..|-.|||+|||+-.-|.+|..+||.-.      
T Consensus       404 R~vYtsGkaSS-a-----AGLTaaVvkD~esgdf~-iEAGALmLADnGICCIDEFDKMd~~dqvAihEAMEQQt------  470 (764)
T KOG0480|consen  404 RSVYTSGKASS-A-----AGLTAAVVKDEESGDFT-IEAGALMLADNGICCIDEFDKMDVKDQVAIHEAMEQQT------  470 (764)
T ss_pred             cceEecCcccc-c-----ccceEEEEecCCCCcee-eecCcEEEccCceEEechhcccChHhHHHHHHHHHhhe------
Confidence            21222211111 0     00000000011110110 00223333446799999999999999999999999744      


Q ss_pred             ceeecCCeEEEEecCC
Q 003038          767 DEVSLGDAIVILSCES  782 (854)
Q Consensus       767 ~~v~~~~aIiIlTsn~  782 (854)
                        |+...|=|+.|-|.
T Consensus       471 --ISIaKAGv~aTLnA  484 (764)
T KOG0480|consen  471 --ISIAKAGVVATLNA  484 (764)
T ss_pred             --ehheecceEEeecc
Confidence              55555557776654

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=96.99  E-value=0.0041  Score=73.03  Aligned_cols=98  Identities=8%  Similarity=0.195  Sum_probs=68.1

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc-cccccCcCCCccccccccccCC-CCCCchHHHHHHHHHcCC
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA-LSSFSSTRADSTEDSRNKRSRD-EQSCSYIERFAEAVSNNP  732 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id-~s~~~~~~~~s~e~~~~~rl~~-~~g~g~~e~L~eav~~~p  732 (854)
                      ++.|.++|.||+|+|||++..++-..+-....+++.+. --||.-       +......+. ..|..|.+-+..++|..|
T Consensus       240 ~~~GlilitGptGSGKTTtL~a~L~~l~~~~~~iiTiEDpvE~~~-------~~~~q~~v~~~~g~~f~~~lr~~LR~dP  312 (486)
T TIGR02533       240 RPHGIILVTGPTGSGKTTTLYAALSRLNTPERNILTVEDPVEYQI-------EGIGQIQVNPKIGLTFAAGLRAILRQDP  312 (486)
T ss_pred             cCCCEEEEEcCCCCCHHHHHHHHHhccCCCCCcEEEEcCCeeeec-------CCCceEEEccccCccHHHHHHHHHhcCC
Confidence            34678999999999999999977666644445666663 223331       100000111 223467778888999888


Q ss_pred             CEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          733 HRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       733 ~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                       .||++.||-  +++.....+++..+|.+.
T Consensus       313 -DvI~vGEiR--d~eta~~a~~aa~tGHlv  339 (486)
T TIGR02533       313 -DIIMVGEIR--DLETAQIAIQASLTGHLV  339 (486)
T ss_pred             -CEEEEeCCC--CHHHHHHHHHHHHhCCcE
Confidence             799999999  788888888999998765

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=96.97  E-value=0.0059  Score=73.28  Aligned_cols=94  Identities=17%  Similarity=0.146  Sum_probs=58.5

Q ss_pred             cHHHHHHHHHHhhccCcC-CceeecCCCCCHHHHHHHHHHHHHcCCC-----C----c----------ccCCceEEEccc
Q 003038          211 RNEDVMYVIENLMSKRKR-NFVVVGECLASIEGVVRGVIDKIEKGDV-----P----E----------ALRDVKCLPLSI  270 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~-n~vLvGe~GvGKta~v~~la~~i~~~~v-----p----~----------~L~~~~~~~l~~  270 (854)
                      .+.-++.+...+.+.+.. ..+|+||+|+|||++++.+|+.+.....     |    .          .-....|+.++.
T Consensus        29 q~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~cg~c~~C~~i~~g~h~Dv~e~~a  108 (598)
T PRK09111         29 QEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLCGVGEHCQAIMEGRHVDVLEMDA  108 (598)
T ss_pred             cHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccCcccHHHHHHhcCCCCceEEecc
Confidence            555666666667665544 4899999999999999999998864210     1    0          011223444444


Q ss_pred             ccccccchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          271 SSFRHMNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       271 ~~l~~~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                      .+-.  ..    ..++++++.++...  ++.-|++|||+|.+
T Consensus       109 ~s~~--gv----d~IReIie~~~~~P~~a~~KVvIIDEad~L  144 (598)
T PRK09111        109 ASHT--GV----DDIREIIESVRYRPVSARYKVYIIDEVHML  144 (598)
T ss_pred             cccC--CH----HHHHHHHHHHHhchhcCCcEEEEEEChHhC
Confidence            3211  12    23566776665431  34568999999999

>TIGR01817 nifA Nif-specific regulatory protein

Probab=96.96  E-value=0.0023  Score=76.30  Aligned_cols=57  Identities=7%  Similarity=0.133  Sum_probs=41.4

Q ss_pred             cHHHHHHHHHHhhc--cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc
Q 003038          211 RNEDVMYVIENLMS--KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR  274 (854)
Q Consensus       211 r~~ei~~v~~~L~r--~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~  274 (854)
                      +..-++++++-+.+  +...+++|+||+|+|||.+|+.+...-..       ++..|+.+|++.+-
T Consensus       201 ~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~s~r-------~~~pfv~i~c~~~~  259 (534)
T TIGR01817       201 KSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLSPR-------AKRPFVKVNCAALS  259 (534)
T ss_pred             CCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHhCCC-------CCCCeEEeecCCCC
Confidence            55555555555432  36678999999999999999999865321       45689999988763

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.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.96  E-value=0.0065  Score=69.68  Aligned_cols=43  Identities=16%  Similarity=0.166  Sum_probs=31.1

Q ss_pred             cHHHHHHHHHH-hhccCcCC-ceeecCCCCCHHHHHHHHHHHHHc
Q 003038          211 RNEDVMYVIEN-LMSKRKRN-FVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       211 r~~ei~~v~~~-L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ..+.+...+.- +.+.+-.+ .+|+||||+|||++|+.+|+.+..
T Consensus        20 Gq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c   64 (397)
T PRK14955         20 AQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNC   64 (397)
T ss_pred             ChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHHhcC
Confidence            44555444444 34334444 789999999999999999999865

>PRK06620 hypothetical protein; Validated

Probab=96.91  E-value=0.0027  Score=66.61  Aligned_cols=24  Identities=21%  Similarity=0.245  Sum_probs=21.3

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+++|+||+|+|||.++++++...
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~   68 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLS   68 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhcc
Confidence            479999999999999999987754

>PRK09087 hypothetical protein; Validated

Probab=96.90  E-value=0.0019  Score=68.35  Aligned_cols=24  Identities=13%  Similarity=0.098  Sum_probs=21.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+++|+||+|+|||.|++++++..
T Consensus        45 ~~l~l~G~~GsGKThLl~~~~~~~   68 (226)
T PRK09087         45 PVVVLAGPVGSGKTHLASIWREKS   68 (226)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhc
Confidence            368999999999999999988753

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.89  E-value=0.0015  Score=72.58  Aligned_cols=69  Identities=16%  Similarity=0.233  Sum_probs=43.8

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCC-chH--HHHHHHHHcC
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSC-SYI--ERFAEAVSNN  731 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~~--e~L~eav~~~  731 (854)
                      .|.-.+||+||||+|||..||.||+.- |-...    =|+.-         +      +.|-|. +.-  ..|+++-.+.
T Consensus       382 apfRNilfyGPPGTGKTm~ArelAr~S-GlDYA----~mTGG---------D------VAPlG~qaVTkiH~lFDWakkS  441 (630)
T KOG0742|consen  382 APFRNILFYGPPGTGKTMFARELARHS-GLDYA----IMTGG---------D------VAPLGAQAVTKIHKLFDWAKKS  441 (630)
T ss_pred             chhhheeeeCCCCCCchHHHHHHHhhc-CCcee----hhcCC---------C------ccccchHHHHHHHHHHHHHhhc
Confidence            566789999999999999999999965 21111    11100         0      123333 222  2677777665


Q ss_pred             CC-EEEEEecCCC
Q 003038          732 PH-RVFLIEDVEQ  743 (854)
Q Consensus       732 p~-~ViliDEiek  743 (854)
                      .. =++||||.|-
T Consensus       442 ~rGLllFIDEADA  454 (630)
T KOG0742|consen  442 RRGLLLFIDEADA  454 (630)
T ss_pred             ccceEEEehhhHH
Confidence            54 4788999883

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.89  E-value=0.007  Score=72.68  Aligned_cols=94  Identities=13%  Similarity=0.111  Sum_probs=54.1

Q ss_pred             cHHHHHH-HHHHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCCC---cc-----------cCCceEEEccccccc
Q 003038          211 RNEDVMY-VIENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDVP---EA-----------LRDVKCLPLSISSFR  274 (854)
Q Consensus       211 r~~ei~~-v~~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~vp---~~-----------L~~~~~~~l~~~~l~  274 (854)
                      ..+.+.+ +...+..++-.+ .||+||+|+|||++++.+|..+...+-+   +.           -....++.++..+- 
T Consensus        20 Gq~~v~~~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c~~c~~i~~g~~~d~~eid~~s~-   98 (576)
T PRK14965         20 GQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVCPPCVEITEGRSVDVFEIDGASN-   98 (576)
T ss_pred             CcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCccHHHHHHhcCCCCCeeeeeccCc-
Confidence            3344444 444444444444 4899999999999999999998653211   00           01122444433221 


Q ss_pred             ccchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          275 HMNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       275 ~~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                         .|  -..+++|++.++...  +..=|++|||+|.+
T Consensus        99 ---~~--v~~ir~l~~~~~~~p~~~~~KVvIIdev~~L  131 (576)
T PRK14965         99 ---TG--VDDIRELRENVKYLPSRSRYKIFIIDEVHML  131 (576)
T ss_pred             ---cC--HHHHHHHHHHHHhccccCCceEEEEEChhhC
Confidence               11  123556666665321  33458999999999

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.88  E-value=0.011  Score=62.01  Aligned_cols=120  Identities=13%  Similarity=0.204  Sum_probs=85.8

Q ss_pred             ccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc
Q 003038          620 VPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST  699 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~  699 (854)
                      ++|-+...+.+...-.+.-.|.              |.-.+|++|..|+||+.+.|++-..+.+..-.+|.++-.+..  
T Consensus        62 l~Gvd~qk~~L~~NT~~F~~G~--------------pANnVLLwGaRGtGKSSLVKA~~~e~~~~glrLVEV~k~dl~--  125 (287)
T COG2607          62 LVGVDRQKEALVRNTEQFAEGL--------------PANNVLLWGARGTGKSSLVKALLNEYADEGLRLVEVDKEDLA--  125 (287)
T ss_pred             HhCchHHHHHHHHHHHHHHcCC--------------cccceEEecCCCCChHHHHHHHHHHHHhcCCeEEEEcHHHHh--
Confidence            4666666666666666666653              455889999999999999999999888877888877643222  


Q ss_pred             CCCccccccccccCCCCCCchHHHHHHHHHcCCCE-EEEEecCCCC-CHHHHHHHHHhhhcCeEecCCCceeecCCeEEE
Q 003038          700 RADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHR-VFLIEDVEQA-DYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVI  777 (854)
Q Consensus       700 ~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~-ViliDEieka-~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiI  777 (854)
                                 .         .-.|.+.++..|.+ |||+|+.--= +.+....|+.++|-| +      +---.|++|.
T Consensus       126 -----------~---------Lp~l~~~Lr~~~~kFIlFcDDLSFe~gd~~yK~LKs~LeG~-v------e~rP~NVl~Y  178 (287)
T COG2607         126 -----------T---------LPDLVELLRARPEKFILFCDDLSFEEGDDAYKALKSALEGG-V------EGRPANVLFY  178 (287)
T ss_pred             -----------h---------HHHHHHHHhcCCceEEEEecCCCCCCCchHHHHHHHHhcCC-c------ccCCCeEEEE
Confidence                       1         11478888888876 5677876533 455778888888743 2      2345799999


Q ss_pred             EecCC
Q 003038          778 LSCES  782 (854)
Q Consensus       778 lTsn~  782 (854)
                      .|||-
T Consensus       179 ATSNR  183 (287)
T COG2607         179 ATSNR  183 (287)
T ss_pred             EecCC
Confidence            99984

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=96.87  E-value=0.01  Score=66.88  Aligned_cols=43  Identities=7%  Similarity=0.045  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHhhccCcC-CceeecCCCCCHHHHHHHHHHHHHcC
Q 003038          212 NEDVMYVIENLMSKRKR-NFVVVGECLASIEGVVRGVIDKIEKG  254 (854)
Q Consensus       212 ~~ei~~v~~~L~r~~k~-n~vLvGe~GvGKta~v~~la~~i~~~  254 (854)
                      ++-+..+...+.+.+-. ..+|+||+|+|||+++..+|+.+...
T Consensus        29 ~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~lA~~Llc~   72 (351)
T PRK09112         29 EEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHILSH   72 (351)
T ss_pred             HHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHHHHHHcCC
Confidence            34456666666655444 48899999999999999999999874

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=96.87  E-value=0.0051  Score=75.56  Aligned_cols=144  Identities=12%  Similarity=0.114  Sum_probs=81.3

Q ss_pred             cHHHHHHHHHHhhc--cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc------------
Q 003038          211 RNEDVMYVIENLMS--KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM------------  276 (854)
Q Consensus       211 r~~ei~~v~~~L~r--~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~------------  276 (854)
                      +..-++++++-+.+  +...+++|+||+|||||.+|+++...-.       .++..++.+++..+...            
T Consensus       381 ~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s~-------r~~~~~v~i~c~~~~~~~~~~~lfg~~~~  453 (686)
T PRK15429        381 RSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSG-------RNNRRMVKMNCAAMPAGLLESDLFGHERG  453 (686)
T ss_pred             cCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhcC-------CCCCCeEEEecccCChhHhhhhhcCcccc
Confidence            45555555443332  3566899999999999999999876421       24668999888766321            


Q ss_pred             -chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-----CCC----Cc
Q 003038          277 -NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-----IGE----NA  345 (854)
Q Consensus       277 -~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-----~~g----~g  345 (854)
                       +.|....++.    .+...  .+-.||||||+.+ ...                 ...+.++|..     .++    ..
T Consensus       454 ~~~g~~~~~~g----~le~a--~~GtL~Ldei~~L~~~~-----------------Q~~L~~~l~~~~~~~~g~~~~~~~  510 (686)
T PRK15429        454 AFTGASAQRIG----RFELA--DKSSLFLDEVGDMPLEL-----------------QPKLLRVLQEQEFERLGSNKIIQT  510 (686)
T ss_pred             cccccccchhh----HHHhc--CCCeEEEechhhCCHHH-----------------HHHHHHHHHhCCEEeCCCCCcccc
Confidence             1111112221    22222  2346999999999 332                 1234445521     011    12


Q ss_pred             eEEEEEecCHHHHHHhhccCCchhh-h-hccCCCCCCCchHHH
Q 003038          346 RFWLMGIATFQSYMRCKSGHPSLET-L-WSLHPLTIPAGSLSL  386 (854)
Q Consensus       346 ~l~lIgatT~~ey~k~~~~~pale~-~-~~~~~v~i~~~sl~~  386 (854)
                      ++++|++|+.+--..  ..+..|.+ + ++|..++|.=|+|..
T Consensus       511 ~~RiI~~t~~~l~~~--~~~~~f~~~L~~~l~~~~i~lPpLre  551 (686)
T PRK15429        511 DVRLIAATNRDLKKM--VADREFRSDLYYRLNVFPIHLPPLRE  551 (686)
T ss_pred             eEEEEEeCCCCHHHH--HHcCcccHHHHhccCeeEEeCCChhh
Confidence            689999998754322  23344433 2 266666665555443

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.86  E-value=0.0034  Score=70.54  Aligned_cols=95  Identities=13%  Similarity=0.169  Sum_probs=58.5

Q ss_pred             HHHHHHHHHhhc-cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEE--cc-----ccc--------cccc
Q 003038          213 EDVMYVIENLMS-KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLP--LS-----ISS--------FRHM  276 (854)
Q Consensus       213 ~ei~~v~~~L~r-~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~--l~-----~~~--------l~~~  276 (854)
                      .-..|+|+.|.- .+..+.+|+||||||||++++.+++.|.++.     .++.++.  ++     +..        +.+.
T Consensus       118 ~~~~RvID~l~PiGkGQR~LIvG~pGtGKTTLl~~la~~i~~~~-----~dv~~vv~lIgER~~EV~df~~~i~~~Vvas  192 (380)
T PRK12608        118 DLSMRVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQIAAAVAANH-----PEVHLMVLLIDERPEEVTDMRRSVKGEVYAS  192 (380)
T ss_pred             chhHhhhhheeecCCCceEEEECCCCCCHHHHHHHHHHHHHhcC-----CCceEEEEEecCCCCCHHHHHHHHhhhEEee
Confidence            345668888874 3556889999999999999999999987752     1233222  11     111        1111


Q ss_pred             -------chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-ccc
Q 003038          277 -------NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFR  313 (854)
Q Consensus       277 -------~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~  313 (854)
                             .+-..-.-+.++.+..... |+.|||++||++++ .+.
T Consensus       193 t~de~~~~~~~v~~~~~~~Ae~f~~~-GkdVVLvlDsltr~A~A~  236 (380)
T PRK12608        193 TFDRPPDEHIRVAELVLERAKRLVEQ-GKDVVILLDSLTRLARAY  236 (380)
T ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHHc-CCCEEEEEeCcHHHHHHH
Confidence                   1111112233344444444 78999999999998 654

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=96.85  E-value=0.0096  Score=71.13  Aligned_cols=90  Identities=13%  Similarity=0.090  Sum_probs=50.6

Q ss_pred             HHHHHHHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCCCc--------------ccCCceEEEcccccccccchH
Q 003038          215 VMYVIENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDVPE--------------ALRDVKCLPLSISSFRHMNRV  279 (854)
Q Consensus       215 i~~v~~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~vp~--------------~L~~~~~~~l~~~~l~~~~rg  279 (854)
                      +..+...+.+++-.+ .+|+||+|+|||++++.+|..+....-+.              ......++.++..+-  ....
T Consensus        25 v~~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~C~~C~~i~~~~~~dv~~idgas~--~~vd  102 (563)
T PRK06647         25 VETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGECSSCKSIDNDNSLDVIEIDGASN--TSVQ  102 (563)
T ss_pred             HHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCccchHHHHHHcCCCCCeEEecCccc--CCHH
Confidence            344444444444444 68999999999999999999986532111              111223343332210  0111


Q ss_pred             HHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          280 EVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       280 e~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                          .++++++.+....  ++.-|++|||+|.+
T Consensus       103 ----dIr~l~e~~~~~p~~~~~KVvIIDEa~~L  131 (563)
T PRK06647        103 ----DVRQIKEEIMFPPASSRYRVYIIDEVHML  131 (563)
T ss_pred             ----HHHHHHHHHHhchhcCCCEEEEEEChhhc
Confidence                2334444444221  45678999999999

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=96.84  E-value=0.0059  Score=68.94  Aligned_cols=101  Identities=17%  Similarity=0.212  Sum_probs=65.0

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHh---CCCCceEEEc-cccccCcCCCccccc-cccc-cCCCCCCchHHHHHHHHHc
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVF---GSHNNFVSIA-LSSFSSTRADSTEDS-RNKR-SRDEQSCSYIERFAEAVSN  730 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lf---g~~~~~i~id-~s~~~~~~~~s~e~~-~~~r-l~~~~g~g~~e~L~eav~~  730 (854)
                      .+.+++.||+|+|||++.++|.+.+.   +....++.+. --+|... ... ... .+.. .++....+|.+-+..++|.
T Consensus       134 ~glilI~GpTGSGKTTtL~aLl~~i~~~~~~~~~Ivt~EdpiE~~~~-~~~-~~~~~v~Q~~v~~~~~~~~~~l~~aLR~  211 (358)
T TIGR02524       134 EGIVFITGATGSGKSTLLAAIIRELAEAPDSHRKILTYEAPIEFVYD-EIE-TISASVCQSEIPRHLNNFAAGVRNALRR  211 (358)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHhhcCCCCcEEEEeCCCceEecc-ccc-cccceeeeeeccccccCHHHHHHHHhcc
Confidence            47899999999999999999999883   2223444432 2222200 000 000 0000 0111122677778889999


Q ss_pred             CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          731 NPHRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       731 ~p~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                      .|. +|++.|+.  +.+.....+++...|.+.
T Consensus       212 ~Pd-~i~vGEiR--d~et~~~al~aa~tGh~v  240 (358)
T TIGR02524       212 KPH-AILVGEAR--DAETISAALEAALTGHPV  240 (358)
T ss_pred             CCC-EEeeeeeC--CHHHHHHHHHHHHcCCcE
Confidence            996 88899877  888888899999988654

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=96.83  E-value=0.0019  Score=67.83  Aligned_cols=87  Identities=13%  Similarity=0.102  Sum_probs=49.3

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCC-chHHHHHHHHH--cCCC
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSC-SYIERFAEAVS--NNPH  733 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~~e~L~eav~--~~p~  733 (854)
                      ..++||+|++|+|||++|+.|+     ....++..|.+...-.   ......+.+.-.+..+ .+.+.+ +.+.  .++|
T Consensus        12 ~~~~liyG~~G~GKtt~a~~~~-----~~~~~~~~d~~~~~l~---g~~~~~v~~~d~~~~~~~~~d~l-~~~~~~~~~y   82 (220)
T TIGR01618        12 PNMYLIYGKPGTGKTSTIKYLP-----GKTLVLSFDMSSKVLI---GDENVDIADHDDMPPIQAMVEFY-VMQNIQAVKY   82 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHhcC-----CCCEEEeccccchhcc---CCCCCceeecCCCCCHHHHHHHH-HHHHhccccC
Confidence            3589999999999999999886     2334566666532200   0011111111111111 222333 3333  3669


Q ss_pred             EEEEEecCCCCCHHHHHHH
Q 003038          734 RVFLIEDVEQADYCSQKGF  752 (854)
Q Consensus       734 ~ViliDEieka~~~v~~~L  752 (854)
                      .+|+||+|+.+-..+...+
T Consensus        83 dtVVIDsI~~l~~~~~~~~  101 (220)
T TIGR01618        83 DNIVIDNISALQNLWLENI  101 (220)
T ss_pred             CEEEEecHHHHHHHHHHHH
Confidence            9999999999866554433

This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=96.83  E-value=0.0065  Score=72.80  Aligned_cols=98  Identities=10%  Similarity=0.187  Sum_probs=68.9

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc-cccccCcCCCccccccccccCC-CCCCchHHHHHHHHHcCC
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA-LSSFSSTRADSTEDSRNKRSRD-EQSCSYIERFAEAVSNNP  732 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id-~s~~~~~~~~s~e~~~~~rl~~-~~g~g~~e~L~eav~~~p  732 (854)
                      ++.|.+||.||+|+|||++..++.+.+.....+++.+. --||.-       +......+. ..|.+|.+-|..++|..|
T Consensus       314 ~~~Glilv~G~tGSGKTTtl~a~l~~~~~~~~~i~tiEdpvE~~~-------~~~~q~~v~~~~g~~~~~~l~~~LR~dP  386 (564)
T TIGR02538       314 KPQGMVLVTGPTGSGKTVSLYTALNILNTEEVNISTAEDPVEINL-------PGINQVNVNPKIGLTFAAALRSFLRQDP  386 (564)
T ss_pred             hcCCeEEEECCCCCCHHHHHHHHHHhhCCCCceEEEecCCceecC-------CCceEEEeccccCCCHHHHHHHHhccCC
Confidence            35689999999999999998877777754445666553 223331       110000111 224477778888889888


Q ss_pred             CEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          733 HRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       733 ~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                       .||++.||-  +++.....+++..+|.+.
T Consensus       387 -DvI~vGEiR--d~eta~~a~~aa~tGHlv  413 (564)
T TIGR02538       387 -DIIMVGEIR--DLETAEIAIKAAQTGHLV  413 (564)
T ss_pred             -CEEEeCCCC--CHHHHHHHHHHHHcCCcE
Confidence             799999999  899888889999998765

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.83  E-value=0.0059  Score=70.40  Aligned_cols=97  Identities=10%  Similarity=0.209  Sum_probs=70.7

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc-cccccCcCCCcccccccccc-CC-CCCCchHHHHHHHHHcC
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA-LSSFSSTRADSTEDSRNKRS-RD-EQSCSYIERFAEAVSNN  731 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id-~s~~~~~~~~s~e~~~~~rl-~~-~~g~g~~e~L~eav~~~  731 (854)
                      +|.|-+||.||+|+|||++-.++-..++....+++.+. -=||..        ..+... +. .-|..|..-|.-.+|+.
T Consensus       256 ~p~GliLvTGPTGSGKTTTLY~~L~~ln~~~~nI~TiEDPVE~~~--------~gI~Q~qVN~k~gltfa~~LRa~LRqD  327 (500)
T COG2804         256 RPQGLILVTGPTGSGKTTTLYAALSELNTPERNIITIEDPVEYQL--------PGINQVQVNPKIGLTFARALRAILRQD  327 (500)
T ss_pred             CCCeEEEEeCCCCCCHHHHHHHHHHHhcCCCceEEEeeCCeeeec--------CCcceeecccccCCCHHHHHHHHhccC
Confidence            67899999999999999999988888888777777763 222320        001111 11 22346766677777777


Q ss_pred             CCEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          732 PHRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       732 p~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                      | .||++.||.  |.+.-....++--+|.+.
T Consensus       328 P-DvImVGEIR--D~ETAeiavqAalTGHLV  355 (500)
T COG2804         328 P-DVIMVGEIR--DLETAEIAVQAALTGHLV  355 (500)
T ss_pred             C-CeEEEeccC--CHHHHHHHHHHHhcCCeE
Confidence            7 899999999  888888899999888775

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.82  E-value=0.0096  Score=69.96  Aligned_cols=94  Identities=13%  Similarity=0.133  Sum_probs=52.6

Q ss_pred             cHHHHHHHH-HHhhccCcCCc-eeecCCCCCHHHHHHHHHHHHHc--CCC--Cc----------ccCCceEEEccccccc
Q 003038          211 RNEDVMYVI-ENLMSKRKRNF-VVVGECLASIEGVVRGVIDKIEK--GDV--PE----------ALRDVKCLPLSISSFR  274 (854)
Q Consensus       211 r~~ei~~v~-~~L~r~~k~n~-vLvGe~GvGKta~v~~la~~i~~--~~v--p~----------~L~~~~~~~l~~~~l~  274 (854)
                      ..+.+.+.+ ..+..++-.+. +|+||+|+|||++++.+|..+..  +..  |-          ......++.++.++  
T Consensus        20 Gq~~i~~~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~i~~g~~~d~~eidaas--   97 (486)
T PRK14953         20 GQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGSFPDLIEIDAAS--   97 (486)
T ss_pred             ChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHHHhcCCCCcEEEEeCcc--
Confidence            445544444 44444344454 68999999999999999988763  111  10          00112344444322  


Q ss_pred             ccchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          275 HMNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       275 ~~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                        .+| . ..++.+.+.+....  +..-|++|||+|.+
T Consensus        98 --~~g-v-d~ir~I~~~~~~~P~~~~~KVvIIDEad~L  131 (486)
T PRK14953         98 --NRG-I-DDIRALRDAVSYTPIKGKYKVYIIDEAHML  131 (486)
T ss_pred             --CCC-H-HHHHHHHHHHHhCcccCCeeEEEEEChhhc
Confidence              122 1 12334555554321  34579999999999

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.82  E-value=0.0094  Score=71.77  Aligned_cols=94  Identities=14%  Similarity=0.117  Sum_probs=53.3

Q ss_pred             cHHHH-HHHHHHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCC-Cc--------------ccCCceEEEcccccc
Q 003038          211 RNEDV-MYVIENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDV-PE--------------ALRDVKCLPLSISSF  273 (854)
Q Consensus       211 r~~ei-~~v~~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~v-p~--------------~L~~~~~~~l~~~~l  273 (854)
                      ..+.+ ..+...+.+++..+ .||+||+|+|||++++.+|+.+....- +.              .-.+..++.++.+..
T Consensus        20 Gq~~~~~~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~~c~~c~~i~~~~~~d~~~i~~~~~   99 (585)
T PRK14950         20 GQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGTCEMCRAIAEGSAVDVIEMDAASH   99 (585)
T ss_pred             CCHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccCHHHHHHhcCCCCeEEEEecccc
Confidence            34444 44555555544444 489999999999999999988753210 10              001123444443211


Q ss_pred             cccchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          274 RHMNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       274 ~~~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                      .  ...    .++++++.+....  +..-|++|||+|.+
T Consensus       100 ~--~vd----~ir~ii~~~~~~p~~~~~kVvIIDEa~~L  132 (585)
T PRK14950        100 T--SVD----DAREIIERVQFRPALARYKVYIIDEVHML  132 (585)
T ss_pred             C--CHH----HHHHHHHHHhhCcccCCeEEEEEeChHhC
Confidence            1  112    2445555444321  34568999999999

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=96.81  E-value=0.0049  Score=71.12  Aligned_cols=144  Identities=9%  Similarity=0.118  Sum_probs=84.4

Q ss_pred             HHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc--------c-chHHHHH
Q 003038          213 EDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH--------M-NRVEVEQ  283 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~--------~-~rge~E~  283 (854)
                      .++++.+.-++ .+.-++++.||+||||+.+++++=+.=.+       ++..|+.++++++-.        | -+|-|.-
T Consensus       151 ~~l~~~i~kvA-~s~a~VLI~GESGtGKElvAr~IH~~S~R-------~~~PFVavNcaAip~~l~ESELFGhekGAFTG  222 (464)
T COG2204         151 QQLRRLIAKVA-PSDASVLITGESGTGKELVARAIHQASPR-------AKGPFIAVNCAAIPENLLESELFGHEKGAFTG  222 (464)
T ss_pred             HHHHHHHHHHh-CCCCCEEEECCCCCcHHHHHHHHHhhCcc-------cCCCceeeecccCCHHHHHHHhhcccccCcCC
Confidence            45666666666 48889999999999999999988654222       356899999876632        1 2333332


Q ss_pred             HHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-----CCCC----ceEEEEEec
Q 003038          284 RVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-----IGEN----ARFWLMGIA  353 (854)
Q Consensus       284 rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-----~~g~----g~l~lIgat  353 (854)
                      -...-...++.. . |=.||+|||..+ -.                 +...+-+.|..     -+|+    =++++|+||
T Consensus       223 A~~~r~G~fE~A-~-GGTLfLDEI~~mpl~-----------------~Q~kLLRvLqe~~~~rvG~~~~i~vdvRiIaaT  283 (464)
T COG2204         223 AITRRIGRFEQA-N-GGTLFLDEIGEMPLE-----------------LQVKLLRVLQEREFERVGGNKPIKVDVRIIAAT  283 (464)
T ss_pred             cccccCcceeEc-C-CceEEeeccccCCHH-----------------HHHHHHHHHHcCeeEecCCCcccceeeEEEeec
Confidence            222211222322 2 336999999777 21                 12234444421     1221    269999999


Q ss_pred             CHHHHHHhhccCCchhh--hhccCCCCCCCchHH
Q 003038          354 TFQSYMRCKSGHPSLET--LWSLHPLTIPAGSLS  385 (854)
Q Consensus       354 T~~ey~k~~~~~pale~--~~~~~~v~i~~~sl~  385 (854)
                      +-+=...  ..+.-|..  .+||..|+|.-|.|.
T Consensus       284 ~~dL~~~--v~~G~FReDLyyRLnV~~i~iPpLR  315 (464)
T COG2204         284 NRDLEEE--VAAGRFREDLYYRLNVVPLRLPPLR  315 (464)
T ss_pred             CcCHHHH--HHcCCcHHHHHhhhccceecCCccc
Confidence            8543222  23344433  258888887766654

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=96.80  E-value=0.013  Score=66.44  Aligned_cols=44  Identities=7%  Similarity=0.030  Sum_probs=34.0

Q ss_pred             cHHHH-HHHHHHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcC
Q 003038          211 RNEDV-MYVIENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKG  254 (854)
Q Consensus       211 r~~ei-~~v~~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~  254 (854)
                      ..+++ +.+...+.+.+-.+ .+|+||+|+||++++..+|+.+...
T Consensus        23 Gq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~   68 (365)
T PRK07471         23 GHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFLLAT   68 (365)
T ss_pred             ChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHhCC
Confidence            33444 55666667666566 7899999999999999999999754

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.79  E-value=0.008  Score=58.56  Aligned_cols=36  Identities=17%  Similarity=0.233  Sum_probs=28.1

Q ss_pred             EEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          660 LFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      ++++||+|+|||.+++.++..+-.....++.+++..
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~e~   37 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEE   37 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCc
Confidence            689999999999999999987754445666666543

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.

>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=96.78  E-value=0.00043  Score=75.17  Aligned_cols=139  Identities=16%  Similarity=0.270  Sum_probs=69.6

Q ss_pred             HHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHH-HH
Q 003038          215 VMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNL-VR  293 (854)
Q Consensus       215 i~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~-~~  293 (854)
                      ...+++.|.. .+++++|+||+|+|||++++...+.+...       ...+..+.++....      -..++.+++. +.
T Consensus        22 ~~~ll~~l~~-~~~pvLl~G~~GtGKT~li~~~l~~l~~~-------~~~~~~~~~s~~Tt------s~~~q~~ie~~l~   87 (272)
T PF12775_consen   22 YSYLLDLLLS-NGRPVLLVGPSGTGKTSLIQNFLSSLDSD-------KYLVITINFSAQTT------SNQLQKIIESKLE   87 (272)
T ss_dssp             HHHHHHHHHH-CTEEEEEESSTTSSHHHHHHHHHHCSTTC-------CEEEEEEES-TTHH------HHHHHHCCCTTEC
T ss_pred             HHHHHHHHHH-cCCcEEEECCCCCchhHHHHhhhccCCcc-------ccceeEeeccCCCC------HHHHHHHHhhcEE
Confidence            4567777775 68899999999999999999876543221       11233344433211      0112222111 00


Q ss_pred             hh---h-----CCCeEEEeCccccc--cccccccccccccchhhhHHHHHHHhhcc--c--CCCC------ceEEEEEec
Q 003038          294 SC---L-----GRGIVLNLGDLEWA--EFRASSSEQVRGYYCSIEHIIMEIGKLVC--G--IGEN------ARFWLMGIA  353 (854)
Q Consensus       294 ~~---~-----~~~~ILfidel~~l--~~~~~~~~~~~~~~~~~~~~~~~~~~ll~--~--~~g~------g~l~lIgat  353 (854)
                      +.   .     ++.+|+||||++.-  +.+++.         +   ...=+..++.  .  .+.+      -++.+|||.
T Consensus        88 k~~~~~~gP~~~k~lv~fiDDlN~p~~d~ygtq---------~---~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~  155 (272)
T PF12775_consen   88 KRRGRVYGPPGGKKLVLFIDDLNMPQPDKYGTQ---------P---PIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAM  155 (272)
T ss_dssp             ECTTEEEEEESSSEEEEEEETTT-S---TTS-----------H---HHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEE
T ss_pred             cCCCCCCCCCCCcEEEEEecccCCCCCCCCCCc---------C---HHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEec
Confidence            10   0     45789999999988  554421         1   1222333331  1  1111      158899998


Q ss_pred             CHHHHHHhhccCCchhhhhccCCCCCCCch
Q 003038          354 TFQSYMRCKSGHPSLETLWSLHPLTIPAGS  383 (854)
Q Consensus       354 T~~ey~k~~~~~pale~~~~~~~v~i~~~s  383 (854)
                      ++.. =+ ....|.|-|  -|+.+.++.|+
T Consensus       156 ~p~~-Gr-~~is~R~~r--~f~i~~~~~p~  181 (272)
T PF12775_consen  156 NPTG-GR-NPISPRFLR--HFNILNIPYPS  181 (272)
T ss_dssp             SSTT-T---SHHHHHHT--TEEEEE----T
T ss_pred             CCCC-CC-CCCChHHhh--heEEEEecCCC
Confidence            7632 11 112344445  66777777665

>PRK10436 hypothetical protein; Provisional

Probab=96.77  E-value=0.006  Score=71.04  Aligned_cols=98  Identities=11%  Similarity=0.183  Sum_probs=67.3

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc-cccccCcCCCccccccccccCCC-CCCchHHHHHHHHHcCC
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA-LSSFSSTRADSTEDSRNKRSRDE-QSCSYIERFAEAVSNNP  732 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id-~s~~~~~~~~s~e~~~~~rl~~~-~g~g~~e~L~eav~~~p  732 (854)
                      +|.|.+||.||+|+|||++..++-+.+.....+++.+. --||.-       +......+.+ .|..|..-|..++|..|
T Consensus       216 ~~~GliLvtGpTGSGKTTtL~a~l~~~~~~~~~i~TiEDPvE~~l-------~gi~Q~~v~~~~g~~f~~~lr~~LR~dP  288 (462)
T PRK10436        216 QPQGLILVTGPTGSGKTVTLYSALQTLNTAQINICSVEDPVEIPL-------AGINQTQIHPKAGLTFQRVLRALLRQDP  288 (462)
T ss_pred             hcCCeEEEECCCCCChHHHHHHHHHhhCCCCCEEEEecCCccccC-------CCcceEeeCCccCcCHHHHHHHHhcCCC
Confidence            35689999999999999988877676655455666653 223321       0000001221 23467677888888888


Q ss_pred             CEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          733 HRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       733 ~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                       .||++.||-  +++.....+++..+|.+.
T Consensus       289 -DvI~vGEIR--D~eta~~al~AA~TGHlV  315 (462)
T PRK10436        289 -DVIMVGEIR--DGETAEIAIKAAQTGHLV  315 (462)
T ss_pred             -CEEEECCCC--CHHHHHHHHHHHHcCCcE
Confidence             799999998  788888888888888776

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=96.76  E-value=0.0027  Score=68.71  Aligned_cols=96  Identities=15%  Similarity=0.256  Sum_probs=63.1

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc-cccccCcCCCccccccccccC-CCCCCchHHHHHHHHHcCCCE
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA-LSSFSSTRADSTEDSRNKRSR-DEQSCSYIERFAEAVSNNPHR  734 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id-~s~~~~~~~~s~e~~~~~rl~-~~~g~g~~e~L~eav~~~p~~  734 (854)
                      .+.++|.||+|+|||++.++|...+-.....++.+. -.|+.-.     ..+. ..+. ....+.|.+.+..++|.+| .
T Consensus       127 ~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~E~~l~-----~~~~-~~~~~~~~~~~~~~~l~~~LR~~p-D  199 (270)
T PF00437_consen  127 RGNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPPELRLP-----GPNQ-IQIQTRRDEISYEDLLKSALRQDP-D  199 (270)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS-S--S-----CSSE-EEEEEETTTBSHHHHHHHHTTS---S
T ss_pred             ceEEEEECCCccccchHHHHHhhhccccccceEEeccccceeec-----ccce-EEEEeecCcccHHHHHHHHhcCCC-C
Confidence            468999999999999999999998865536666664 2333310     0110 1111 1234477778888899888 6


Q ss_pred             EEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          735 VFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       735 ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                      +|++.||-  ++++... ++++..|...
T Consensus       200 ~iiigEiR--~~e~~~~-~~a~~tGh~~  224 (270)
T PF00437_consen  200 VIIIGEIR--DPEAAEA-IQAANTGHLG  224 (270)
T ss_dssp             EEEESCE---SCHHHHH-HHHHHTT-EE
T ss_pred             cccccccC--CHhHHHH-HHhhccCCce
Confidence            88899999  5578777 9999988653

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=96.72  E-value=0.0053  Score=74.81  Aligned_cols=142  Identities=11%  Similarity=0.116  Sum_probs=82.6

Q ss_pred             cHHHHHHHHHHhhc--cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMS--KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEI  288 (854)
Q Consensus       211 r~~ei~~v~~~L~r--~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l  288 (854)
                      ....++++++-..+  +...+++|+||+||||+.+|+++-..-..       ++..|+.+|++.+-.   ..++.   ++
T Consensus       330 ~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~s~r-------~~~pfv~vnc~~~~~---~~~~~---el  396 (638)
T PRK11388        330 DSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNESER-------AAGPYIAVNCQLYPD---EALAE---EF  396 (638)
T ss_pred             CCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHhCCc-------cCCCeEEEECCCCCh---HHHHH---Hh
Confidence            56566666655443  36667999999999999999998765221       346899999887632   11111   12


Q ss_pred             HH------------HHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-----CCCC----ce
Q 003038          289 KN------------LVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-----IGEN----AR  346 (854)
Q Consensus       289 ~~------------~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-----~~g~----g~  346 (854)
                      +.            .++..  .+-.||||||+.+ ...                 ...+.++|..     .++.    -+
T Consensus       397 fg~~~~~~~~~~~g~~~~a--~~GtL~ldei~~l~~~~-----------------Q~~Ll~~l~~~~~~~~~~~~~~~~~  457 (638)
T PRK11388        397 LGSDRTDSENGRLSKFELA--HGGTLFLEKVEYLSPEL-----------------QSALLQVLKTGVITRLDSRRLIPVD  457 (638)
T ss_pred             cCCCCcCccCCCCCceeEC--CCCEEEEcChhhCCHHH-----------------HHHHHHHHhcCcEEeCCCCceEEee
Confidence            21            12121  2346999999999 432                 1234455521     1110    15


Q ss_pred             EEEEEecCHHHHHHhhccCCchhh--hhccCCCCCCCchHHH
Q 003038          347 FWLMGIATFQSYMRCKSGHPSLET--LWSLHPLTIPAGSLSL  386 (854)
Q Consensus       347 l~lIgatT~~ey~k~~~~~pale~--~~~~~~v~i~~~sl~~  386 (854)
                      +++|++|+.+-... . ....|.+  .++|..++|.=|+|..
T Consensus       458 ~riI~~t~~~l~~~-~-~~~~f~~dL~~~l~~~~i~lPpLre  497 (638)
T PRK11388        458 VRVIATTTADLAML-V-EQNRFSRQLYYALHAFEITIPPLRM  497 (638)
T ss_pred             EEEEEeccCCHHHH-H-hcCCChHHHhhhhceeEEeCCChhh
Confidence            89999998754322 1 2233333  1367777766555543

>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A

Probab=96.71  E-value=0.0048  Score=65.47  Aligned_cols=97  Identities=13%  Similarity=0.166  Sum_probs=60.8

Q ss_pred             EEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEec
Q 003038          661 FFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIED  740 (854)
Q Consensus       661 Lf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDE  740 (854)
                      .+.||.|+|||++.|.||+.+   ...++.+++++-.       +-..+.+           -+..++.-  ..-+.|||
T Consensus        36 ~~~GpagtGKtetik~La~~l---G~~~~vfnc~~~~-------~~~~l~r-----------il~G~~~~--GaW~cfde   92 (231)
T PF12774_consen   36 ALSGPAGTGKTETIKDLARAL---GRFVVVFNCSEQM-------DYQSLSR-----------ILKGLAQS--GAWLCFDE   92 (231)
T ss_dssp             EEESSTTSSHHHHHHHHHHCT---T--EEEEETTSSS--------HHHHHH-----------HHHHHHHH--T-EEEEET
T ss_pred             CCcCCCCCCchhHHHHHHHHh---CCeEEEecccccc-------cHHHHHH-----------HHHHHhhc--Cchhhhhh
Confidence            368999999999999999988   4678899998655       2222222           12333332  56899999


Q ss_pred             CCCCCHHHHHHHHHhhh-------cC--eEecCCCceeecC-CeEEEEecC
Q 003038          741 VEQADYCSQKGFKRAIE-------SG--RIVTSSGDEVSLG-DAIVILSCE  781 (854)
Q Consensus       741 ieka~~~v~~~Ll~~le-------~G--~l~d~~G~~v~~~-~aIiIlTsn  781 (854)
                      +++++.++...+.+-+.       .+  ++.- .|+++.+. ++-|.+|.|
T Consensus        93 fnrl~~~vLS~i~~~i~~i~~al~~~~~~~~~-~g~~i~l~~~~~iFiT~n  142 (231)
T PF12774_consen   93 FNRLSEEVLSVISQQIQSIQDALRAKQKSFTL-EGQEIKLNPNCGIFITMN  142 (231)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHCTSSEEEE-TTCEEE--TT-EEEEEE-
T ss_pred             hhhhhHHHHHHHHHHHHHHHHhhccccccccc-CCCEEEEccceeEEEeec
Confidence            99999998887765543       22  2322 47778775 433444565

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=96.69  E-value=0.0097  Score=70.57  Aligned_cols=147  Identities=9%  Similarity=0.063  Sum_probs=79.5

Q ss_pred             HHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHH-cCCCCcccCCceEEEccccccccc---------chHHHHHH
Q 003038          215 VMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIE-KGDVPEALRDVKCLPLSISSFRHM---------NRVEVEQR  284 (854)
Q Consensus       215 i~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~-~~~vp~~L~~~~~~~l~~~~l~~~---------~rge~E~r  284 (854)
                      +++.++-++ +...+++|+||+|+||+.+|+.+-.... ....+..-++..|+.+|++.+-..         -.|.|..-
T Consensus       231 ~~~~i~~~A-~s~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~inCaal~e~lleseLFG~~~gaftga  309 (538)
T PRK15424        231 VRQTILLYA-RSSAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAVNCGAIAESLLEAELFGYEEGAFTGS  309 (538)
T ss_pred             HHHHHHHHh-CCCCcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEeecccCChhhHHHHhcCCccccccCc
Confidence            344444444 3677999999999999999999876411 111112235678999998876321         01111100


Q ss_pred             ----HHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-----CCCC----ceEEEE
Q 003038          285 ----VEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-----IGEN----ARFWLM  350 (854)
Q Consensus       285 ----l~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-----~~g~----g~l~lI  350 (854)
                          -..+++.+    . +=.||||||+.+ ....                 ..+.++|..     -++.    -++++|
T Consensus       310 ~~~~~~Gl~e~A----~-gGTLfLdeI~~Lp~~~Q-----------------~kLl~~L~e~~~~r~G~~~~~~~dvRiI  367 (538)
T PRK15424        310 RRGGRAGLFEIA----H-GGTLFLDEIGEMPLPLQ-----------------TRLLRVLEEKEVTRVGGHQPVPVDVRVI  367 (538)
T ss_pred             cccccCCchhcc----C-CCEEEEcChHhCCHHHH-----------------HHHHhhhhcCeEEecCCCceeccceEEE
Confidence                01122222    2 235999999999 4322                 234445521     0111    147999


Q ss_pred             EecCHHHHHHhhccCCchhh--hhccCCCCCCCchHHH
Q 003038          351 GIATFQSYMRCKSGHPSLET--LWSLHPLTIPAGSLSL  386 (854)
Q Consensus       351 gatT~~ey~k~~~~~pale~--~~~~~~v~i~~~sl~~  386 (854)
                      ++|+.+--..  .....|..  .++|..++|.=|+|..
T Consensus       368 aat~~~L~~~--v~~g~Fr~dL~yrL~~~~I~lPPLRe  403 (538)
T PRK15424        368 SATHCDLEED--VRQGRFRRDLFYRLSILRLQLPPLRE  403 (538)
T ss_pred             EecCCCHHHH--HhcccchHHHHHHhcCCeecCCChhh
Confidence            9997653211  23334433  1367666666555543

>PRK04296 thymidine kinase; Provisional

Probab=96.65  E-value=0.0098  Score=61.13  Aligned_cols=97  Identities=14%  Similarity=0.025  Sum_probs=52.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCcccccccccc-CC-CC-CCchHHHHHHHH--HcCCC
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRS-RD-EQ-SCSYIERFAEAV--SNNPH  733 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl-~~-~~-g~g~~e~L~eav--~~~p~  733 (854)
                      ..++.||+|+|||+++..++..+-+.....+.+.. .+.. +. . +....+++ +. +. .....+.+...+  ....+
T Consensus         4 i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~k~-~~d~-~~-~-~~~i~~~lg~~~~~~~~~~~~~~~~~~~~~~~~~   79 (190)
T PRK04296          4 LEFIYGAMNSGKSTELLQRAYNYEERGMKVLVFKP-AIDD-RY-G-EGKVVSRIGLSREAIPVSSDTDIFELIEEEGEKI   79 (190)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEEec-cccc-cc-c-CCcEecCCCCcccceEeCChHHHHHHHHhhCCCC
Confidence            56889999999999998888766555556555532 1110 00 0 11111111 00 00 011112333333  34567


Q ss_pred             EEEEEecCCCCCHH-HHHHHHHhhhcC
Q 003038          734 RVFLIEDVEQADYC-SQKGFKRAIESG  759 (854)
Q Consensus       734 ~ViliDEieka~~~-v~~~Ll~~le~G  759 (854)
                      .||+|||+..++.+ +...+..+-+.|
T Consensus        80 dvviIDEaq~l~~~~v~~l~~~l~~~g  106 (190)
T PRK04296         80 DCVLIDEAQFLDKEQVVQLAEVLDDLG  106 (190)
T ss_pred             CEEEEEccccCCHHHHHHHHHHHHHcC
Confidence            89999999998776 544443334445

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=96.63  E-value=0.0081  Score=75.94  Aligned_cols=107  Identities=19%  Similarity=0.237  Sum_probs=83.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCC-----CCCC-chHH-HHHHHHHcC
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRD-----EQSC-SYIE-RFAEAVSNN  731 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~-----~~g~-g~~e-~L~eav~~~  731 (854)
                      .+++.|+.|.|||.|..+|+..+ |  ..+|+|+.++.++       ..   -+++     .||- -|.. .|++++.. 
T Consensus       151 pI~l~g~~gsgksfLisel~~~~-G--~~iV~Ihl~e~TD-------ak---~LiGtYts~KpG~fEw~~GvL~~avv~-  216 (4600)
T COG5271         151 PIYLEGGRGSGKSFLISELCDEG-G--QRIVEIHLREITD-------AK---VLIGTYTSPKPGDFEWMKGVLIEAVVS-  216 (4600)
T ss_pred             ceEEecCccccHHHHHHHHHHHh-C--ceEEEEecccccC-------ch---heeeeccCCCCCceeeccchhhhhhhc-
Confidence            57899999999999999999988 4  7899999998773       21   1221     1221 2211 58888765 


Q ss_pred             CCEEEEEecCCCCCHHHHHHHHHhhhcCeEec-CCCceeecCCeEEEEec
Q 003038          732 PHRVFLIEDVEQADYCSQKGFKRAIESGRIVT-SSGDEVSLGDAIVILSC  780 (854)
Q Consensus       732 p~~ViliDEieka~~~v~~~Ll~~le~G~l~d-~~G~~v~~~~aIiIlTs  780 (854)
                       .+-|+|.+|||++.+|...|+..++..+++. ++|++|--.+..=||.+
T Consensus       217 -G~WILf~~Idkap~~vLs~Ll~llekR~L~ipsrGEtV~A~~~Fqif~T  265 (4600)
T COG5271         217 -GDWILFKRIDKAPHGVLSYLLTLLEKRRLLIPSRGETVLAHDNFQIFFT  265 (4600)
T ss_pred             -CcEEEEeecccCchhHHHHHHHHHHhhhhccCCCCceEEecCCEEEEEe
Confidence             4589999999999999999999999999998 78999988776655544

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=96.61  E-value=0.016  Score=67.53  Aligned_cols=43  Identities=12%  Similarity=0.088  Sum_probs=32.0

Q ss_pred             cHHHHHHHHHHhhccCc-CCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          211 RNEDVMYVIENLMSKRK-RNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k-~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      .+.-+..+...+.+++- +..+|+||||+|||++++.+|+.+..
T Consensus        22 q~~~v~~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c   65 (451)
T PRK06305         22 QDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFAKALNC   65 (451)
T ss_pred             cHHHHHHHHHHHHcCCCceEEEEEcCCCCCHHHHHHHHHHHhcC
Confidence            34445555656655443 44789999999999999999999865

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=96.59  E-value=0.012  Score=60.15  Aligned_cols=93  Identities=11%  Similarity=0.176  Sum_probs=58.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcc-ccccCcCCCccccccccccC-CC------CCCchHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIAL-SSFSSTRADSTEDSRNKRSR-DE------QSCSYIERFAEAVS  729 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~-s~~~~~~~~s~e~~~~~rl~-~~------~g~g~~e~L~eav~  729 (854)
                      ..++|.||+|+|||++.++|...+.. ....+.+.- .++..    . ....+ .+. .+      +...+.+.+..++|
T Consensus        26 ~~i~I~G~tGSGKTTll~aL~~~i~~-~~~~i~ied~~E~~~----~-~~~~~-~~~~~~~~~~~~~~~~~~~~l~~~lR   98 (186)
T cd01130          26 KNILISGGTGSGKTTLLNALLAFIPP-DERIITIEDTAELQL----P-HPNWV-RLVTRPGNVEGSGEVTMADLLRSALR   98 (186)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhcCC-CCCEEEECCccccCC----C-CCCEE-EEEEecCCCCCCCccCHHHHHHHHhc
Confidence            48999999999999999999998753 345555532 12220    0 01100 111 01      11245556777788


Q ss_pred             cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeE
Q 003038          730 NNPHRVFLIEDVEQADYCSQKGFKRAIESGRI  761 (854)
Q Consensus       730 ~~p~~ViliDEieka~~~v~~~Ll~~le~G~l  761 (854)
                      .+| .+|++.||-  +++... +++++..|..
T Consensus        99 ~~p-d~i~igEir--~~ea~~-~~~a~~tGh~  126 (186)
T cd01130          99 MRP-DRIIVGEVR--GGEALD-LLQAMNTGHP  126 (186)
T ss_pred             cCC-CEEEEEccC--cHHHHH-HHHHHhcCCC
Confidence            887 778899998  466654 6778887743

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=96.58  E-value=0.0039  Score=60.73  Aligned_cols=90  Identities=19%  Similarity=0.286  Sum_probs=58.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCC-chHHHHHHHHHcCCCEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSC-SYIERFAEAVSNNPHRVF  736 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~~e~L~eav~~~p~~Vi  736 (854)
                      ..+|+.|-||+|||++|..||+..     .|..|++|.+..      +.+         -| ||++         .|.--
T Consensus         8 PNILvtGTPG~GKstl~~~lae~~-----~~~~i~isd~vk------En~---------l~~gyDE---------~y~c~   58 (176)
T KOG3347|consen    8 PNILVTGTPGTGKSTLAERLAEKT-----GLEYIEISDLVK------ENN---------LYEGYDE---------EYKCH   58 (176)
T ss_pred             CCEEEeCCCCCCchhHHHHHHHHh-----CCceEehhhHHh------hhc---------chhcccc---------cccCc
Confidence            479999999999999999999765     577888887761      111         12 5533         23344


Q ss_pred             EEecCCCCCHHHHHHHHHhhhc-CeEecCCCce-ee--cCCeEEEEecC
Q 003038          737 LIEDVEQADYCSQKGFKRAIES-GRIVTSSGDE-VS--LGDAIVILSCE  781 (854)
Q Consensus       737 liDEieka~~~v~~~Ll~~le~-G~l~d~~G~~-v~--~~~aIiIlTsn  781 (854)
                      +|||     ..+.+.|-..|.+ |.+.|-+|=. +.  .=+.+|||+|.
T Consensus        59 i~DE-----dkv~D~Le~~m~~Gg~IVDyHgCd~FperwfdlVvVLr~~  102 (176)
T KOG3347|consen   59 ILDE-----DKVLDELEPLMIEGGNIVDYHGCDFFPERWFDLVVVLRTP  102 (176)
T ss_pred             cccH-----HHHHHHHHHHHhcCCcEEeecccCccchhheeEEEEEecC
Confidence            5665     3456666655554 6777766521 11  22678999883

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=96.54  E-value=0.011  Score=69.95  Aligned_cols=57  Identities=14%  Similarity=0.170  Sum_probs=41.1

Q ss_pred             cHHHHHHHHHHhhc--cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc
Q 003038          211 RNEDVMYVIENLMS--KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR  274 (854)
Q Consensus       211 r~~ei~~v~~~L~r--~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~  274 (854)
                      +...++++.+-+.+  ....+++|+||+|||||.+++.+-..-.+       .+..|+.+++..+-
T Consensus       192 ~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~r-------~~~p~v~v~c~~~~  250 (509)
T PRK05022        192 QSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPR-------ADKPLVYLNCAALP  250 (509)
T ss_pred             cCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCCc-------CCCCeEEEEcccCC
Confidence            55556555555443  36778899999999999999998865221       45588999887663

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=96.54  E-value=0.01  Score=67.18  Aligned_cols=98  Identities=11%  Similarity=0.106  Sum_probs=64.9

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhC--CCCceEEEcc-ccccCcCCCccccccc----cccCCCCCCchHHHHHHHHH
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFG--SHNNFVSIAL-SSFSSTRADSTEDSRN----KRSRDEQSCSYIERFAEAVS  729 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg--~~~~~i~id~-s~~~~~~~~s~e~~~~----~rl~~~~g~g~~e~L~eav~  729 (854)
                      .+.+++.||+|+|||++.++|.+.+-.  ...+++.+.- .||.-.+     .+.+    .+-++.....|.+-+..++|
T Consensus       149 ~GlilI~G~TGSGKTT~l~al~~~i~~~~~~~~IvtiEdp~E~~~~~-----~~~~~~~~q~evg~~~~~~~~~l~~aLR  223 (372)
T TIGR02525       149 AGLGLICGETGSGKSTLAASIYQHCGETYPDRKIVTYEDPIEYILGS-----PDDLLPPAQSQIGRDVDSFANGIRLALR  223 (372)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEecCchhccCC-----CceeecccccccCCCccCHHHHHHHhhc
Confidence            357899999999999999999988742  2345666632 2333100     0111    01111111156567788888


Q ss_pred             cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          730 NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       730 ~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                      .+| .+|++.|+-  +++.....+++...|...
T Consensus       224 ~~P-D~I~vGEiR--d~et~~~al~aa~TGH~v  253 (372)
T TIGR02525       224 RAP-KIIGVGEIR--DLETFQAAVLAGQSGHFC  253 (372)
T ss_pred             cCC-CEEeeCCCC--CHHHHHHHHHHHhcCCcE
Confidence            888 788899999  778888889999998654

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>PF05729 NACHT: NACHT domain

Probab=96.49  E-value=0.0085  Score=58.82  Aligned_cols=119  Identities=13%  Similarity=0.113  Sum_probs=62.7

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc------------cchHHHHHHHHHHHHHHHhhh
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH------------MNRVEVEQRVEEIKNLVRSCL  296 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~------------~~rge~E~rl~~l~~~~~~~~  296 (854)
                      -++|+|+||+|||++++.++..+..+.-+..- -.-++.+.+..+..            ....+....+...+..+... 
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~-   79 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEEEPPPSK-FPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPIEELLQELLEK-   79 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhcCccccc-ceEEEEEeehhhhhccccchHHHHHHHhhccchhhhHHHHHHHHHc-
Confidence            36899999999999999999999887643211 12233333322211            00011111111122222222 


Q ss_pred             CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-CCCCceEEEEEecCHHHHHH
Q 003038          297 GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGENARFWLMGIATFQSYMR  360 (854)
Q Consensus       297 ~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~g~l~lIgatT~~ey~k  360 (854)
                      .+.++|+||.++-+ +.....  +    .   .....-+..++.. ...  .+.+|-++++..+..
T Consensus        80 ~~~~llilDglDE~~~~~~~~--~----~---~~~~~~l~~l~~~~~~~--~~~liit~r~~~~~~  134 (166)
T PF05729_consen   80 NKRVLLILDGLDELEEQDQSQ--E----R---QRLLDLLSQLLPQALPP--GVKLIITSRPRAFPD  134 (166)
T ss_pred             CCceEEEEechHhcccchhhh--H----H---HHHHHHHHHHhhhccCC--CCeEEEEEcCChHHH
Confidence            56899999999988 533210  0    0   0122235556632 112  377777777666544

>TIGR00767 rho transcription termination factor Rho

Probab=96.46  E-value=0.0075  Score=68.37  Aligned_cols=38  Identities=11%  Similarity=0.152  Sum_probs=30.1

Q ss_pred             HHHHHhhc-cCcCCceeecCCCCCHHHHHHHHHHHHHcC
Q 003038          217 YVIENLMS-KRKRNFVVVGECLASIEGVVRGVIDKIEKG  254 (854)
Q Consensus       217 ~v~~~L~r-~~k~n~vLvGe~GvGKta~v~~la~~i~~~  254 (854)
                      |+|+++.. .+....+||||||+|||++++.++..+..+
T Consensus       157 R~id~~~pig~Gq~~~IvG~~g~GKTtL~~~i~~~I~~n  195 (415)
T TIGR00767       157 RVLDLFAPIGKGQRGLIVAPPKAGKTVLLQKIAQAITRN  195 (415)
T ss_pred             eeeeeEEEeCCCCEEEEECCCCCChhHHHHHHHHhhccc
Confidence            45566543 366679999999999999999999987654

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

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

Probab=96.45  E-value=0.0055  Score=63.64  Aligned_cols=102  Identities=16%  Similarity=0.155  Sum_probs=53.6

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcc-ccccCcCCCcc-----cccc----ccccCCCC----------
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIAL-SSFSSTRADST-----EDSR----NKRSRDEQ----------  716 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~-s~~~~~~~~s~-----e~~~----~~rl~~~~----------  716 (854)
                      ...++++||.|+|||.+.+.+.+.+-......+.++. ...........     ....    ....+...          
T Consensus        20 ~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~   99 (234)
T PF01637_consen   20 SQHILLYGPRGSGKTSLLKEFINELKEKGYKVVYIDFLEESNESSLRSFIEETSLADELSEALGISIPSITLEKISKDLS   99 (234)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHCT--EECCCHHCCTTBSHHHHHHHHHHHHHHHCHCHHHHHHHCCTSTTEEEECTS-
T ss_pred             CcEEEEEcCCcCCHHHHHHHHHHHhhhcCCcEEEEecccchhhhHHHHHHHHHHHHHHHHHHHhhhcccccchhhhhcch
Confidence            3478899999999999999999887222111222221 11100000000     0000    00000000          


Q ss_pred             --CCchHHHHHHHHHcCC-CEEEEEecCCCCC------HHHHHHHHHhhhc
Q 003038          717 --SCSYIERFAEAVSNNP-HRVFLIEDVEQAD------YCSQKGFKRAIES  758 (854)
Q Consensus       717 --g~g~~e~L~eav~~~p-~~ViliDEieka~------~~v~~~Ll~~le~  758 (854)
                        .......+.+.+.+.. .-||+|||++.+.      +.....|...++.
T Consensus       100 ~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~  150 (234)
T PF01637_consen  100 EDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDS  150 (234)
T ss_dssp             GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhh
Confidence              0011235666665543 4899999999988      5677777777775

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

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=96.44  E-value=0.014  Score=69.13  Aligned_cols=139  Identities=12%  Similarity=0.125  Sum_probs=77.2

Q ss_pred             HHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc--------c-chHHHHH--
Q 003038          215 VMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH--------M-NRVEVEQ--  283 (854)
Q Consensus       215 i~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~--------~-~rge~E~--  283 (854)
                      +++.++-++ +...+++|.||+|+||+.+|+.+-..-       .-++..|+.++++.+-.        | ..|.|..  
T Consensus       224 ~~~~i~~~A-~~~~pVLI~GE~GTGKe~lA~~IH~~S-------~r~~~pfv~inC~~l~e~lleseLFG~~~gaftga~  295 (526)
T TIGR02329       224 VRALVRLYA-RSDATVLILGESGTGKELVAQAIHQLS-------GRRDFPFVAINCGAIAESLLEAELFGYEEGAFTGAR  295 (526)
T ss_pred             HHHHHHHHh-CCCCcEEEECCCCcCHHHHHHHHHHhc-------CcCCCCEEEeccccCChhHHHHHhcCCccccccccc
Confidence            333444444 367799999999999999999886531       12456899999887632        1 0111110  


Q ss_pred             --HHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-----CCCC----ceEEEEE
Q 003038          284 --RVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-----IGEN----ARFWLMG  351 (854)
Q Consensus       284 --rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-----~~g~----g~l~lIg  351 (854)
                        .-..+++.+    .+| .||||||+.+ ....                 ..+.++|..     -++.    -++++|+
T Consensus       296 ~~~~~Gl~e~A----~gG-TLfLdeI~~Lp~~~Q-----------------~~Ll~~L~~~~~~r~g~~~~~~~dvRiIa  353 (526)
T TIGR02329       296 RGGRTGLIEAA----HRG-TLFLDEIGEMPLPLQ-----------------TRLLRVLEEREVVRVGGTEPVPVDVRVVA  353 (526)
T ss_pred             ccccccchhhc----CCc-eEEecChHhCCHHHH-----------------HHHHHHHhcCcEEecCCCceeeecceEEe
Confidence              011222222    123 5999999999 4322                 234444421     0111    1469999


Q ss_pred             ecCHHHHHHhhccCCchhh-h-hccCCCCCCCchHH
Q 003038          352 IATFQSYMRCKSGHPSLET-L-WSLHPLTIPAGSLS  385 (854)
Q Consensus       352 atT~~ey~k~~~~~pale~-~-~~~~~v~i~~~sl~  385 (854)
                      +|+.+--..  .....|.. + ++|..++|.=|.|.
T Consensus       354 at~~~l~~~--v~~g~fr~dL~~rL~~~~I~lPPLR  387 (526)
T TIGR02329       354 ATHCALTTA--VQQGRFRRDLFYRLSILRIALPPLR  387 (526)
T ss_pred             ccCCCHHHH--hhhcchhHHHHHhcCCcEEeCCCch
Confidence            998654322  23344443 1 36666666555543

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]

Probab=96.44  E-value=0.0019  Score=75.01  Aligned_cols=147  Identities=18%  Similarity=0.243  Sum_probs=91.6

Q ss_pred             HhhcCcccccHHHHHHHHHHHHHhhcCCCc-ccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHH----HhCCCCce
Q 003038          614 NALEKKVPWQKDTVYDIANTVLKCRSGTMR-RKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARL----VFGSHNNF  688 (854)
Q Consensus       614 ~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~-~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~----lfg~~~~~  688 (854)
                      .-+.-.|+|+..+..+||-++...   ..+ +.++    .+-|....+|++|.||+||+..-|-.++.    +|-....-
T Consensus       445 aSiaPsIyGh~~VK~AvAlaLfGG---v~kn~~~k----hkvRGDinvLL~GDPGTaKSQFLKY~eK~s~RAV~tTGqGA  517 (854)
T KOG0477|consen  445 ASIAPSIYGHEDVKRAVALALFGG---VPKNPGGK----HKVRGDINVLLLGDPGTAKSQFLKYAEKTSPRAVFTTGQGA  517 (854)
T ss_pred             HhhCchhhchHHHHHHHHHHHhcC---CccCCCCC----ceeccceeEEEecCCCccHHHHHHHHHhcCcceeEeccCCc
Confidence            344556899999999999998763   322 1110    11255569999999999999998877753    33221111


Q ss_pred             EEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCC-Cc
Q 003038          689 VSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSS-GD  767 (854)
Q Consensus       689 i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~-G~  767 (854)
                      -.+.++.|.       .++.+.+-|     ..   =.+|+--.-..|-+|||+|||..+=...+-.+||.-.|.-++ |-
T Consensus       518 SavGLTa~v-------~KdPvtrEW-----TL---EaGALVLADkGvClIDEFDKMndqDRtSIHEAMEQQSISISKAGI  582 (854)
T KOG0477|consen  518 SAVGLTAYV-------RKDPVTREW-----TL---EAGALVLADKGVCLIDEFDKMNDQDRTSIHEAMEQQSISISKAGI  582 (854)
T ss_pred             cccceeEEE-------eeCCcccee-----ee---ccCeEEEccCceEEeehhhhhcccccchHHHHHHhcchhhhhhhH
Confidence            112222222       233333322     00   011222234579999999999999999999999987776554 44


Q ss_pred             eeec-CCeEEEEecCC
Q 003038          768 EVSL-GDAIVILSCES  782 (854)
Q Consensus       768 ~v~~-~~aIiIlTsn~  782 (854)
                      ..++ ..|-+|.++|.
T Consensus       583 VtsLqArctvIAAanP  598 (854)
T KOG0477|consen  583 VTSLQARCTVIAAANP  598 (854)
T ss_pred             HHHHHhhhhhheecCC
Confidence            4444 36778888885

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=96.44  E-value=0.01  Score=61.31  Aligned_cols=98  Identities=11%  Similarity=0.072  Sum_probs=53.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc---CCCccccccccccCCCCCCchHHHHHHHHHcCCCE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST---RADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHR  734 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~---~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~  734 (854)
                      ...++.||+|+|||++.+.+++.+-.....++-+..+.-...   .........+.+++.....+..   .......++.
T Consensus        19 ~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~apT~~Aa~~L~~~~~~~a~Ti~~~l~~~~~~~~---~~~~~~~~~~   95 (196)
T PF13604_consen   19 RVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLAPTNKAAKELREKTGIEAQTIHSFLYRIPNGDD---EGRPELPKKD   95 (196)
T ss_dssp             SEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHHTS-EEEHHHHTTEECCEEC---CSSCC-TSTS
T ss_pred             eEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEECCcHHHHHHHHHhhCcchhhHHHHHhcCCcccc---cccccCCccc
Confidence            367889999999999999999988766556555544321100   0000000011111100000000   0000024567


Q ss_pred             EEEEecCCCCCHHHHHHHHHhhhc
Q 003038          735 VFLIEDVEQADYCSQKGFKRAIES  758 (854)
Q Consensus       735 ViliDEieka~~~v~~~Ll~~le~  758 (854)
                      ||++||+-.++......|++.+..
T Consensus        96 vliVDEasmv~~~~~~~ll~~~~~  119 (196)
T PF13604_consen   96 VLIVDEASMVDSRQLARLLRLAKK  119 (196)
T ss_dssp             EEEESSGGG-BHHHHHHHHHHS-T
T ss_pred             EEEEecccccCHHHHHHHHHHHHh
Confidence            999999999999999999998875

>PRK14974 cell division protein FtsY; Provisional

Probab=96.42  E-value=0.042  Score=61.53  Aligned_cols=98  Identities=16%  Similarity=0.157  Sum_probs=55.8

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccc--ccccc-C--CCCCCch--HHHHHHHH-
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDS--RNKRS-R--DEQSCSY--IERFAEAV-  728 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~--~~~rl-~--~~~g~g~--~e~L~eav-  728 (854)
                      ...++|.||+|+|||+++..||..+-.....+..+++..|..   ...++.  ...++ +  ....+|.  ...+.+++ 
T Consensus       140 ~~vi~~~G~~GvGKTTtiakLA~~l~~~g~~V~li~~Dt~R~---~a~eqL~~~a~~lgv~v~~~~~g~dp~~v~~~ai~  216 (336)
T PRK14974        140 PVVIVFVGVNGTGKTTTIAKLAYYLKKNGFSVVIAAGDTFRA---GAIEQLEEHAERLGVKVIKHKYGADPAAVAYDAIE  216 (336)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEecCCcCcH---HHHHHHHHHHHHcCCceecccCCCCHHHHHHHHHH
Confidence            358999999999999999999987754444555565554431   000110  00011 0  0111111  12233433 


Q ss_pred             --HcCCCEEEEEecCCCCC--HHHHHHHHHhhh
Q 003038          729 --SNNPHRVFLIEDVEQAD--YCSQKGFKRAIE  757 (854)
Q Consensus       729 --~~~p~~ViliDEieka~--~~v~~~Ll~~le  757 (854)
                        +...+.|||||..-.++  ......|..+.+
T Consensus       217 ~~~~~~~DvVLIDTaGr~~~~~~lm~eL~~i~~  249 (336)
T PRK14974        217 HAKARGIDVVLIDTAGRMHTDANLMDELKKIVR  249 (336)
T ss_pred             HHHhCCCCEEEEECCCccCCcHHHHHHHHHHHH
Confidence              34567899999999985  455566655543

>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=96.42  E-value=0.015  Score=62.99  Aligned_cols=106  Identities=14%  Similarity=0.226  Sum_probs=56.7

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHH--HhCCCCceEEEccccccCcCCCccccc---cccccCCCC------CCchH---
Q 003038          656 EETWLFFQGVDADAKEKIAKELARL--VFGSHNNFVSIALSSFSSTRADSTEDS---RNKRSRDEQ------SCSYI---  721 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~--lfg~~~~~i~id~s~~~~~~~~s~e~~---~~~rl~~~~------g~g~~---  721 (854)
                      +...+.++|+.|+|||.||+.+++.  +-......+-++.+....      ...   .+.+.+...      .....   
T Consensus        18 ~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~------~~~~~~~i~~~l~~~~~~~~~~~~~~~~~   91 (287)
T PF00931_consen   18 EVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPS------LEQLLEQILRQLGEPDSSISDPKDIEELQ   91 (287)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SC------CHHHHHHHHHHHTCC-STSSCCSSHHHHH
T ss_pred             CeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccc------ccccccccccccccccccccccccccccc
Confidence            3568999999999999999999977  434444556666654331      111   111111111      11122   


Q ss_pred             HHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecC
Q 003038          722 ERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       722 e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn  781 (854)
                      +.|.+.++.+ ..+|+||+|+...  ....|...+-.+           -.++-||+||.
T Consensus        92 ~~l~~~L~~~-~~LlVlDdv~~~~--~~~~l~~~~~~~-----------~~~~kilvTTR  137 (287)
T PF00931_consen   92 DQLRELLKDK-RCLLVLDDVWDEE--DLEELREPLPSF-----------SSGSKILVTTR  137 (287)
T ss_dssp             HHHHHHHCCT-SEEEEEEEE-SHH--HH-------HCH-----------HSS-EEEEEES
T ss_pred             ccchhhhccc-cceeeeeeecccc--cccccccccccc-----------ccccccccccc
Confidence            2566666666 7999999998544  333343333210           12456788885

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.

>TIGR00602 rad24 checkpoint protein rad24

Probab=96.41  E-value=0.013  Score=70.57  Aligned_cols=41  Identities=12%  Similarity=0.167  Sum_probs=28.3

Q ss_pred             cHHHHHHHHHHhhcc-----CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSK-----RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       211 r~~ei~~v~~~L~r~-----~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      -++.|..|...|...     .++-.+|+||||+|||++++.+|..+
T Consensus        89 ~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l  134 (637)
T TIGR00602        89 HKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKEL  134 (637)
T ss_pred             cHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            344455555444322     22338999999999999999999765

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=96.41  E-value=0.012  Score=70.76  Aligned_cols=137  Identities=16%  Similarity=0.158  Sum_probs=81.1

Q ss_pred             HHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceE
Q 003038          610 TSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFV  689 (854)
Q Consensus       610 ~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i  689 (854)
                      ..|-+.+.-.|.|++++.++|+-.+.-   |..+.-..+   ..-|...++|+.|.||+||+.|-|-+++..-    .-+
T Consensus       278 ~~l~~SiaPsIyG~e~VKkAilLqLfg---Gv~k~~~~g---~~iRGDInILLvGDPgtaKSqlLk~v~~~aP----r~v  347 (682)
T COG1241         278 DILIKSIAPSIYGHEDVKKAILLQLFG---GVKKNLPDG---TRIRGDIHILLVGDPGTAKSQLLKYVAKLAP----RGV  347 (682)
T ss_pred             HHHHHHhcccccCcHHHHHHHHHHhcC---CCcccCCCC---cccccceeEEEcCCCchhHHHHHHHHHhhCC----ceE
Confidence            345556677899999988877655543   433311100   1125567999999999999999999987651    112


Q ss_pred             EEccccccCcCCCccccccccccCCCC-C-CchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCC
Q 003038          690 SIALSSFSSTRADSTEDSRNKRSRDEQ-S-CSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSS  765 (854)
Q Consensus       690 ~id~s~~~~~~~~s~e~~~~~rl~~~~-g-~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~  765 (854)
                      +.....-+      ...-...-..++. | | +.+  .+|+--.-..|..|||+|||+..-+++|..+||...++-++
T Consensus       348 ytsgkgss------~~GLTAav~rd~~tge~-~Le--aGALVlAD~Gv~cIDEfdKm~~~dr~aihEaMEQQtIsIaK  416 (682)
T COG1241         348 YTSGKGSS------AAGLTAAVVRDKVTGEW-VLE--AGALVLADGGVCCIDEFDKMNEEDRVAIHEAMEQQTISIAK  416 (682)
T ss_pred             EEcccccc------ccCceeEEEEccCCCeE-EEe--CCEEEEecCCEEEEEeccCCChHHHHHHHHHHHhcEeeecc
Confidence            22211101      0000000000100 0 0 000  12233334679999999999999999999999998777543

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.39  E-value=0.0018  Score=65.84  Aligned_cols=64  Identities=14%  Similarity=0.253  Sum_probs=41.4

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCcc
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDL  307 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfidel  307 (854)
                      .+++|+|+||+||||+++.||+++            .+..+|.+.+   +|+.+.++ .++..+++....++- |+.|++
T Consensus         1 ~riiilG~pGaGK~T~A~~La~~~------------~i~hlstgd~---~r~~~~~~-t~lg~~~k~~i~~g~-lv~d~i   63 (178)
T COG0563           1 MRILILGPPGAGKSTLAKKLAKKL------------GLPHLDTGDI---LRAAIAER-TELGEEIKKYIDKGE-LVPDEI   63 (178)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh------------CCcEEcHhHH---hHhhhccC-ChHHHHHHHHHHcCC-ccchHH
Confidence            368999999999999999999873            4555654433   45555555 555555554322222 666665


Q ss_pred             c
Q 003038          308 E  308 (854)
Q Consensus       308 ~  308 (854)
                      .
T Consensus        64 ~   64 (178)
T COG0563          64 V   64 (178)
T ss_pred             H
Confidence            3

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.37  E-value=0.062  Score=62.27  Aligned_cols=69  Identities=12%  Similarity=0.096  Sum_probs=44.0

Q ss_pred             cHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          623 QKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       623 Q~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ++.+++.|...+.....+...+..      ...+...++|+|++|+|||+++..||..+-.....+..+++..|.
T Consensus        67 ~~~~~~~v~~~L~~~l~~~~~~~~------~~~~p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~D~~R  135 (437)
T PRK00771         67 REHVIKIVYEELVKLLGEETEPLV------LPLKPQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAADTYR  135 (437)
T ss_pred             HHHHHHHHHHHHHHHhCCCccccc------cCCCCeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecCCCCC
Confidence            345566666666554332211100      012346899999999999999999998775444566667776664

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]

Probab=96.33  E-value=0.0076  Score=69.02  Aligned_cols=143  Identities=10%  Similarity=0.139  Sum_probs=81.2

Q ss_pred             cHHHHHHHHHHhh--ccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc--------c-chH
Q 003038          211 RNEDVMYVIENLM--SKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH--------M-NRV  279 (854)
Q Consensus       211 r~~ei~~v~~~L~--r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~--------~-~rg  279 (854)
                      +-..++++++...  -++.-+++|.||+||||+-+++++=+.=-+       ++..||.+++++|-.        | .+|
T Consensus       228 ~S~am~~ll~~i~~VA~Sd~tVLi~GETGtGKElvAraIH~~S~R-------~~kPfV~~NCAAlPesLlESELFGHeKG  300 (550)
T COG3604         228 RSPAMRQLLKEIEVVAKSDSTVLIRGETGTGKELVARAIHQLSPR-------RDKPFVKLNCAALPESLLESELFGHEKG  300 (550)
T ss_pred             cCHHHHHHHHHHHHHhcCCCeEEEecCCCccHHHHHHHHHhhCcc-------cCCCceeeeccccchHHHHHHHhccccc
Confidence            4445555544422  257788999999999999999988765222       567899999987743        2 334


Q ss_pred             HHHHHHHHHHHHHHhhhCCCeEEEeCccccc--cccccccccccccchhhhHHHHHHHhhccc---C--CCC----ceEE
Q 003038          280 EVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA--EFRASSSEQVRGYYCSIEHIIMEIGKLVCG---I--GEN----ARFW  348 (854)
Q Consensus       280 e~E~rl~~l~~~~~~~~~~~~ILfidel~~l--~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~---~--~g~----g~l~  348 (854)
                      -|---...=....+-. .+| =||+|||--+  ...                  ..+-+.|..   .  +|+    =+++
T Consensus       301 AFTGA~~~r~GrFElA-dGG-TLFLDEIGelPL~lQ------------------aKLLRvLQegEieRvG~~r~ikVDVR  360 (550)
T COG3604         301 AFTGAINTRRGRFELA-DGG-TLFLDEIGELPLALQ------------------AKLLRVLQEGEIERVGGDRTIKVDVR  360 (550)
T ss_pred             ccccchhccCcceeec-CCC-eEechhhccCCHHHH------------------HHHHHHHhhcceeecCCCceeEEEEE
Confidence            3332221111111111 234 5999999766  221                  123333311   1  221    1699


Q ss_pred             EEEecCHHHHHHhhccCCchhhh--hccCCCCCCCc
Q 003038          349 LMGIATFQSYMRCKSGHPSLETL--WSLHPLTIPAG  382 (854)
Q Consensus       349 lIgatT~~ey~k~~~~~pale~~--~~~~~v~i~~~  382 (854)
                      +|+||+-+=.+.  ..+..|..+  +|+..++|.-|
T Consensus       361 iIAATNRDL~~~--V~~G~FRaDLYyRLsV~Pl~lP  394 (550)
T COG3604         361 VIAATNRDLEEM--VRDGEFRADLYYRLSVFPLELP  394 (550)
T ss_pred             EEeccchhHHHH--HHcCcchhhhhhcccccccCCC
Confidence            999999765443  456666542  46655555433

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.32  E-value=0.016  Score=64.35  Aligned_cols=93  Identities=9%  Similarity=0.127  Sum_probs=60.4

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH--hCCCCceEEEc-cccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV--FGSHNNFVSIA-LSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHR  734 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l--fg~~~~~i~id-~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~  734 (854)
                      .++++.|++|+|||+++++|+..+  +....+++.+. ..++.-.     .+.. ..+......++.+-+..++|.+| .
T Consensus       149 ~~ilI~G~tGSGKTTll~aL~~~~~~~~~~~rivtIEd~~El~~~-----~~~~-v~~~~~~~~~~~~ll~~aLR~~P-D  221 (319)
T PRK13894        149 RNILVIGGTGSGKTTLVNAIINEMVIQDPTERVFIIEDTGEIQCA-----AENY-VQYHTSIDVNMTALLKTTLRMRP-D  221 (319)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhhhhcCCCceEEEEcCCCccccC-----CCCE-EEEecCCCCCHHHHHHHHhcCCC-C
Confidence            479999999999999999999875  23445566553 3333310     0001 11111223366667788888888 5


Q ss_pred             EEEEecCCCCCHHHHHHHHHhhhcCe
Q 003038          735 VFLIEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       735 ViliDEieka~~~v~~~Ll~~le~G~  760 (854)
                      +|++.||-  +++... +++++..|.
T Consensus       222 ~IivGEiR--~~Ea~~-~l~A~~tGh  244 (319)
T PRK13894        222 RILVGEVR--GPEALD-LLMAWNTGH  244 (319)
T ss_pred             EEEEeccC--CHHHHH-HHHHHHcCC
Confidence            57799998  456654 689999874

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=96.31  E-value=0.013  Score=70.30  Aligned_cols=108  Identities=8%  Similarity=0.091  Sum_probs=72.1

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHH--------HHHH
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERF--------AEAV  728 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L--------~eav  728 (854)
                      +|=+++.|+.|+||+.+++.|+.+|- ...+|+.+-.+--            ..+++++-  .....|        ...|
T Consensus        25 ~gGv~i~g~~G~~ks~~~r~l~~llp-~~~p~r~~p~~~t------------~~~L~Gg~--Dl~~~l~~g~~~~~pGll   89 (584)
T PRK13406         25 LGGVVLRARAGPVRDRWLAALRALLP-AGTPLRRLPPGIA------------DDRLLGGL--DLAATLRAGRPVAQRGLL   89 (584)
T ss_pred             cceEEEEcCCCcHHHHHHHHHHHhcC-CCCCcccCCCCCc------------HHHccCCc--hHHhHhhcCCcCCCCCce
Confidence            56789999999999999999999883 2345554433211            11222110  000000        1123


Q ss_pred             HcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecC-CCceeecC-CeEEEEe
Q 003038          729 SNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTS-SGDEVSLG-DAIVILS  779 (854)
Q Consensus       729 ~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~-~G~~v~~~-~aIiIlT  779 (854)
                      ....+.|+|+||+..+++.+++.|+++|++|.++-. .|..+.+. +-++|.|
T Consensus        90 a~Ah~GvL~lDe~n~~~~~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat  142 (584)
T PRK13406         90 AEADGGVLVLAMAERLEPGTAARLAAALDTGEVRLERDGLALRLPARFGLVAL  142 (584)
T ss_pred             eeccCCEEEecCcccCCHHHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEec
Confidence            344568999999999999999999999999999863 56777774 4455555

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.28  E-value=0.075  Score=61.21  Aligned_cols=99  Identities=8%  Similarity=0.103  Sum_probs=56.0

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCcccccc-ccccCCCCCC------chHHHH---
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSR-NKRSRDEQSC------SYIERF---  724 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~-~~rl~~~~g~------g~~e~L---  724 (854)
                      ++.+.++|+|++|+|||+++..||..+-.......-+++..|...   ..+... ..+...-|.+      ......   
T Consensus        98 ~~~~vi~lvG~~GvGKTTtaaKLA~~l~~~G~kV~lV~~D~~R~a---A~eQLk~~a~~~~vp~~~~~~~~dp~~i~~~~  174 (429)
T TIGR01425        98 GKQNVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVCADTFRAG---AFDQLKQNATKARIPFYGSYTESDPVKIASEG  174 (429)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEcCcccchh---HHHHHHHHhhccCCeEEeecCCCCHHHHHHHH
Confidence            345799999999999999999999877544456666676655410   001100 0000110101      111111   


Q ss_pred             HHHHHcCCCEEEEEecCCCCCHH--HHHHHHHhh
Q 003038          725 AEAVSNNPHRVFLIEDVEQADYC--SQKGFKRAI  756 (854)
Q Consensus       725 ~eav~~~p~~ViliDEieka~~~--v~~~Ll~~l  756 (854)
                      .+.++...+.+||+|=.-+.+.+  ....|.++.
T Consensus       175 l~~~~~~~~DvViIDTaGr~~~d~~lm~El~~i~  208 (429)
T TIGR01425       175 VEKFKKENFDIIIVDTSGRHKQEDSLFEEMLQVA  208 (429)
T ss_pred             HHHHHhCCCCEEEEECCCCCcchHHHHHHHHHHh
Confidence            22234467899999998877653  444444443

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.

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.28  E-value=0.037  Score=66.78  Aligned_cols=41  Identities=12%  Similarity=0.131  Sum_probs=29.3

Q ss_pred             HHHHH-HHHHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHc
Q 003038          213 EDVMY-VIENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       213 ~ei~~-v~~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      +.+.. +...+..++-.+ .||+||+|||||++++.+|+.+..
T Consensus        22 e~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c   64 (620)
T PRK14954         22 EHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNC   64 (620)
T ss_pred             HHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCC
Confidence            44333 333344334444 789999999999999999999865

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.24  E-value=0.019  Score=56.85  Aligned_cols=96  Identities=15%  Similarity=0.187  Sum_probs=56.1

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCC-----------------CceEEEccccccCcCCCccccccccc-----c-C
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSH-----------------NNFVSIALSSFSSTRADSTEDSRNKR-----S-R  713 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~-----------------~~~i~id~s~~~~~~~~s~e~~~~~r-----l-~  713 (854)
                      ...+++.|+||+|||++++-||+.|-...                 --|--+|...-        +...+.+     . +
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e~L~~~g~kvgGf~t~EVR~gGkR~GF~Ivdl~tg--------~~~~la~~~~~~~rv   76 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAEKLREKGYKVGGFITPEVREGGKRIGFKIVDLATG--------EEGILARVGFSRPRV   76 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHHHHHhcCceeeeEEeeeeecCCeEeeeEEEEccCC--------ceEEEEEcCCCCccc
Confidence            34789999999999999999998885331                 11122222211        1111111     1 1


Q ss_pred             CCCCC---chHHHHHHHHHc--CCCEEEEEecCCCC---CHHHHHHHHHhhhcCe
Q 003038          714 DEQSC---SYIERFAEAVSN--NPHRVFLIEDVEQA---DYCSQKGFKRAIESGR  760 (854)
Q Consensus       714 ~~~g~---g~~e~L~eav~~--~p~~ViliDEieka---~~~v~~~Ll~~le~G~  760 (854)
                      +.++-   ++.+....++++  ..-.||+||||-+|   .+.+...+-++|+++.
T Consensus        77 GkY~V~v~~le~i~~~al~rA~~~aDvIIIDEIGpMElks~~f~~~ve~vl~~~k  131 (179)
T COG1618          77 GKYGVNVEGLEEIAIPALRRALEEADVIIIDEIGPMELKSKKFREAVEEVLKSGK  131 (179)
T ss_pred             ceEEeeHHHHHHHhHHHHHHHhhcCCEEEEecccchhhccHHHHHHHHHHhcCCC
Confidence            11111   122234556654  22479999999988   4667777888887664

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.23  E-value=0.048  Score=59.37  Aligned_cols=70  Identities=14%  Similarity=0.043  Sum_probs=45.3

Q ss_pred             cHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          623 QKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       623 Q~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +..+...+.+.+.........+-.     ...++...++|+||+|+|||+++.-||..+-.....+.-+++..|.
T Consensus        43 ~~~~~~~~~e~l~~~~~~~~~~~~-----~~~~~~~vi~l~G~~G~GKTTt~akLA~~l~~~g~~V~li~~D~~r  112 (272)
T TIGR00064        43 AELLKEILKEYLKEILKETDLELI-----VEENKPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAGDTFR  112 (272)
T ss_pred             HHHHHHHHHHHHHHHHcccchhhc-----ccCCCCeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEeCCCCC
Confidence            455666666766665443211100     0123456889999999999999999998775555566667776553

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.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=96.20  E-value=0.038  Score=61.81  Aligned_cols=116  Identities=9%  Similarity=0.123  Sum_probs=0.0

Q ss_pred             ccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEE-ccccccC
Q 003038          620 VPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSI-ALSSFSS  698 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~i-d~s~~~~  698 (854)
                      .+.+.+...-+..+|..                    ...+++.|++|+|||++.++|...+ ....+++.+ |-.|+.-
T Consensus       143 ~~~~~~~~~~L~~~v~~--------------------~~nili~G~tgSGKTTll~aL~~~i-p~~~ri~tiEd~~El~l  201 (332)
T PRK13900        143 LLAEKKIKEFLEHAVIS--------------------KKNIIISGGTSTGKTTFTNAALREI-PAIERLITVEDAREIVL  201 (332)
T ss_pred             hhhhHHHHHHHHHHHHc--------------------CCcEEEECCCCCCHHHHHHHHHhhC-CCCCeEEEecCCCcccc


Q ss_pred             cCCCccccccccccCCCCCC-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCe
Q 003038          699 TRADSTEDSRNKRSRDEQSC-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~g~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~  760 (854)
                      ......-.....+...+.+. .+.+-+..++|.+| .+|++.|+-  +.++... ++++..|.
T Consensus       202 ~~~~n~~~~~~~~~~~~~~~~~~~~ll~~~LR~~P-D~IivGEiR--~~ea~~~-l~a~~tGh  260 (332)
T PRK13900        202 SNHPNRVHLLASKGGQGRAKVTTQDLIEACLRLRP-DRIIVGELR--GAEAFSF-LRAINTGH  260 (332)
T ss_pred             ccCCCEEEEEecCCCCCcCcCcHHHHHHHHhccCC-CeEEEEecC--CHHHHHH-HHHHHcCC

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.19  E-value=0.035  Score=63.29  Aligned_cols=96  Identities=10%  Similarity=0.117  Sum_probs=54.4

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhC----CCCceEEEccccccCcCCCccccc-cccccCC-CC--CCchHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFG----SHNNFVSIALSSFSSTRADSTEDS-RNKRSRD-EQ--SCSYIERFAEAVS  729 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg----~~~~~i~id~s~~~~~~~~s~e~~-~~~rl~~-~~--g~g~~e~L~eav~  729 (854)
                      ..++|+||+|+|||+++.-||..+--    ....+.-+++..|...   +.+.. ...+..+ |.  .+.+ +.+..++.
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~a---a~eQL~~~a~~lgvpv~~~~~~-~~l~~~L~  250 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIG---AKKQIQTYGDIMGIPVKAIESF-KDLKEEIT  250 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHH---HHHHHHHHhhcCCcceEeeCcH-HHHHHHHH
Confidence            58999999999999999999976531    1234444444444310   00110 1111111 11  1122 23444443


Q ss_pred             -cCCCEEEEEecCCCCCHHHH--HHHHHhhh
Q 003038          730 -NNPHRVFLIEDVEQADYCSQ--KGFKRAIE  757 (854)
Q Consensus       730 -~~p~~ViliDEieka~~~v~--~~Ll~~le  757 (854)
                       ...+.+|+||.+.+.+.+..  ..+.+.++
T Consensus       251 ~~~~~DlVLIDTaGr~~~~~~~l~el~~~l~  281 (388)
T PRK12723        251 QSKDFDLVLVDTIGKSPKDFMKLAEMKELLN  281 (388)
T ss_pred             HhCCCCEEEEcCCCCCccCHHHHHHHHHHHH
Confidence             35689999999999987643  34555555

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=96.18  E-value=0.052  Score=60.23  Aligned_cols=90  Identities=14%  Similarity=0.094  Sum_probs=52.6

Q ss_pred             HHHHHHHhhccCcCCc-eeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHH
Q 003038          215 VMYVIENLMSKRKRNF-VVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVR  293 (854)
Q Consensus       215 i~~v~~~L~r~~k~n~-vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~  293 (854)
                      ++.+...+.+++-.+. +++||+|+|||++++.+|+.+.....+..--+  ++.+...  ..... .++ .++++.+.+.
T Consensus        13 ~~~l~~~~~~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D--~~~~~~~--~~~~i-~v~-~ir~~~~~~~   86 (313)
T PRK05564         13 KNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVD--IIEFKPI--NKKSI-GVD-DIRNIIEEVN   86 (313)
T ss_pred             HHHHHHHHHcCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCC--eEEeccc--cCCCC-CHH-HHHHHHHHHh
Confidence            4555666665555555 79999999999999999998865432221112  2222110  01100 011 2556666554


Q ss_pred             hhh--CCCeEEEeCccccc
Q 003038          294 SCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       294 ~~~--~~~~ILfidel~~l  310 (854)
                      ...  ++.=|++||+.+.+
T Consensus        87 ~~p~~~~~kv~iI~~ad~m  105 (313)
T PRK05564         87 KKPYEGDKKVIIIYNSEKM  105 (313)
T ss_pred             cCcccCCceEEEEechhhc
Confidence            321  44568999999888

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=96.17  E-value=0.0063  Score=65.09  Aligned_cols=64  Identities=14%  Similarity=0.098  Sum_probs=44.1

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      .-++||..|-++-.-.+...|+.-             -.-..+||.||+|+|||.+|-++++.| |+.-+|..+-.|+
T Consensus        38 ~g~vGQ~~AReAagiivdlik~Kk-------------maGravLlaGppgtGKTAlAlaisqEL-G~kvPFcpmvgSE  101 (456)
T KOG1942|consen   38 AGFVGQENAREAAGIIVDLIKSKK-------------MAGRAVLLAGPPGTGKTALALAISQEL-GPKVPFCPMVGSE  101 (456)
T ss_pred             cccccchhhhhhhhHHHHHHHhhh-------------ccCcEEEEecCCCCchhHHHHHHHHHh-CCCCCcccccchh
Confidence            457999887655443333333310             011278999999999999999999999 7777776665554

>PLN02165 adenylate isopentenyltransferase

Probab=96.13  E-value=0.0062  Score=67.56  Aligned_cols=47  Identities=13%  Similarity=0.141  Sum_probs=34.6

Q ss_pred             CCCCCCcHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          205 VSLDPIRNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       205 g~ldpvr~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      .+|-|-|+++-..-...+..+++..++|+||+|+|||+++..||.++
T Consensus        21 ~~~~~~~~~~~~~~~~~~~~~~g~iivIiGPTGSGKStLA~~LA~~l   67 (334)
T PLN02165         21 RKLPPPRSVVTMTSVAMEQNCKDKVVVIMGATGSGKSRLSVDLATRF   67 (334)
T ss_pred             ccCCCCcccccccccccccCCCCCEEEEECCCCCcHHHHHHHHHHHc
Confidence            34555555554444444455667789999999999999999999885

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.13  E-value=0.059  Score=61.15  Aligned_cols=97  Identities=8%  Similarity=0.035  Sum_probs=58.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCcccccc-ccccCCCCCC-chH-HHHHHHHHc----
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSR-NKRSRDEQSC-SYI-ERFAEAVSN----  730 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~-~~rl~~~~g~-g~~-e~L~eav~~----  730 (854)
                      ..++|.||+|+|||+++..||..+.+....+.-+++..|..   .+.+... .....+-+.+ .+. ..+.+++..    
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI~aDt~Ri---aAvEQLk~yae~lgipv~v~~d~~~L~~aL~~lk~~  318 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRI---GTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFKEE  318 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEEecCCcch---HHHHHHHHHhhhcCCcEEecCCHHHHHHHHHHHHhc
Confidence            58999999999999999999998876665666666655531   0001100 0000111111 111 244455532    


Q ss_pred             CCCEEEEEecCCCCCHH--HHHHHHHhhh
Q 003038          731 NPHRVFLIEDVEQADYC--SQKGFKRAIE  757 (854)
Q Consensus       731 ~p~~ViliDEieka~~~--v~~~Ll~~le  757 (854)
                      ..+.+||||-.-..+.+  ....|.++++
T Consensus       319 ~~~DvVLIDTaGRs~kd~~lm~EL~~~lk  347 (436)
T PRK11889        319 ARVDYILIDTAGKNYRASETVEEMIETMG  347 (436)
T ss_pred             cCCCEEEEeCccccCcCHHHHHHHHHHHh
Confidence            35799999999888744  4555666665

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.12  E-value=0.021  Score=63.52  Aligned_cols=93  Identities=10%  Similarity=0.211  Sum_probs=59.1

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHh--CCCCceEEEc-cccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVF--GSHNNFVSIA-LSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHR  734 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lf--g~~~~~i~id-~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~  734 (854)
                      ..+++.|++|+|||++.++|...+.  ....+++.+. -.|+.-.     ....+ .+....+..+.+-+..++|.+|. 
T Consensus       145 ~nilI~G~tGSGKTTll~aL~~~i~~~~~~~rivtiEd~~El~~~-----~~n~v-~l~~~~~~~~~~lv~~aLR~~PD-  217 (323)
T PRK13833        145 LNIVISGGTGSGKTTLANAVIAEIVASAPEDRLVILEDTAEIQCA-----AENAV-ALHTSDTVDMARLLKSTMRLRPD-  217 (323)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHhcCCCCceEEEecCCcccccC-----CCCEE-EeccCCCcCHHHHHHHHhCCCCC-
Confidence            3689999999999999999999874  2334666654 3333200     00111 11112233566677788888885 


Q ss_pred             EEEEecCCCCCHHHHHHHHHhhhcCe
Q 003038          735 VFLIEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       735 ViliDEieka~~~v~~~Ll~~le~G~  760 (854)
                      +|++-||-  +++... +++++..|.
T Consensus       218 ~IivGEiR--g~ea~~-~l~a~~tGh  240 (323)
T PRK13833        218 RIIVGEVR--DGAALT-LLKAWNTGH  240 (323)
T ss_pred             EEEEeecC--CHHHHH-HHHHHcCCC
Confidence            55699998  446654 688888774

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=96.12  E-value=0.01  Score=70.41  Aligned_cols=86  Identities=10%  Similarity=0.146  Sum_probs=59.3

Q ss_pred             cHHHHHHHH-HHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHH
Q 003038          211 RNEDVMYVI-ENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIK  289 (854)
Q Consensus       211 r~~ei~~v~-~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~  289 (854)
                      ++.|+--+. +-.-|..|+=.+|.||||-|||++|+-+|.-          .|..++.++.+.=++  -..+++|+..++
T Consensus       309 ~~ke~~~~~~~~s~RP~kKilLL~GppGlGKTTLAHViAkq----------aGYsVvEINASDeRt--~~~v~~kI~~av  376 (877)
T KOG1969|consen  309 TEKEVLDMELDPSKRPPKKILLLCGPPGLGKTTLAHVIAKQ----------AGYSVVEINASDERT--APMVKEKIENAV  376 (877)
T ss_pred             chhhhhhcccCccCCCccceEEeecCCCCChhHHHHHHHHh----------cCceEEEeccccccc--HHHHHHHHHHHH
Confidence            555544333 3334457778899999999999999988865          688999998875543  344666766554


Q ss_pred             HHHHhh-h-CCCeEEEeCccc
Q 003038          290 NLVRSC-L-GRGIVLNLGDLE  308 (854)
Q Consensus       290 ~~~~~~-~-~~~~ILfidel~  308 (854)
                      .-=.-. . ++|+-|+||||+
T Consensus       377 q~~s~l~adsrP~CLViDEID  397 (877)
T KOG1969|consen  377 QNHSVLDADSRPVCLVIDEID  397 (877)
T ss_pred             hhccccccCCCcceEEEeccc
Confidence            432211 0 468889999994

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=96.11  E-value=0.012  Score=74.39  Aligned_cols=113  Identities=18%  Similarity=0.209  Sum_probs=77.3

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccC-CCCCC-chHH-HHHHHHHcCCCE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSR-DEQSC-SYIE-RFAEAVSNNPHR  734 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~-~~~g~-g~~e-~L~eav~~~p~~  734 (854)
                      -.+|+.||+.+|||.|.+-||+..   +..||||+-.+.++.     .++ +-... ...|. .|.| .|.+|+|+.-  
T Consensus       889 fP~LiQGpTSSGKTSMI~yla~~t---ghkfVRINNHEHTdl-----qeY-iGTyvTdd~G~lsFkEGvLVeAlR~Gy--  957 (4600)
T COG5271         889 FPLLIQGPTSSGKTSMILYLARET---GHKFVRINNHEHTDL-----QEY-IGTYVTDDDGSLSFKEGVLVEALRRGY--  957 (4600)
T ss_pred             CcEEEecCCCCCcchHHHHHHHHh---CccEEEecCcccchH-----HHH-hhceeecCCCceeeehhHHHHHHhcCc--
Confidence            368999999999999999999987   579999998766621     011 00011 22332 4555 7999998754  


Q ss_pred             EEEEecCCCCCHHHHHHHHHhhhcCeE-ecCCCcee--ecCCeEEEEecC
Q 003038          735 VFLIEDVEQADYCSQKGFKRAIESGRI-VTSSGDEV--SLGDAIVILSCE  781 (854)
Q Consensus       735 ViliDEieka~~~v~~~Ll~~le~G~l-~d~~G~~v--~~~~aIiIlTsn  781 (854)
                      -|++||..-|+.+|..+|-+.+|+.|- --+.-.+|  .-.|-.+..|-|
T Consensus       958 WIVLDELNLApTDVLEaLNRLLDDNRelfIPETqevV~PHp~F~lFATQN 1007 (4600)
T COG5271         958 WIVLDELNLAPTDVLEALNRLLDDNRELFIPETQEVVVPHPNFRLFATQN 1007 (4600)
T ss_pred             EEEeeccccCcHHHHHHHHHhhccccceecCCcceeeccCCCeeEEeecC
Confidence            688999999999999999999997542 22333333  233444444544

>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=96.10  E-value=0.0054  Score=57.54  Aligned_cols=32  Identities=28%  Similarity=0.453  Sum_probs=26.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      .+++.||+|+|||++|+.||+.+     .+..++++.
T Consensus         1 vI~I~G~~gsGKST~a~~La~~~-----~~~~i~~d~   32 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAERL-----GFPVISMDD   32 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH-----TCEEEEEHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH-----CCeEEEecc
Confidence            37899999999999999999987     355566665

...

>PRK08118 topology modulation protein; Reviewed

Probab=96.09  E-value=0.009  Score=60.13  Aligned_cols=32  Identities=13%  Similarity=0.269  Sum_probs=26.4

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccc
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSI  270 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~  270 (854)
                      .++++|+||+|||++++.|+.++          +..++++|.
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l----------~~~~~~lD~   34 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKL----------NIPVHHLDA   34 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh----------CCCceecch
Confidence            58999999999999999999874          456666663

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.09  E-value=0.042  Score=66.46  Aligned_cols=92  Identities=10%  Similarity=0.101  Sum_probs=53.6

Q ss_pred             HHHHHHHHHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCCC---------------cccCCceEEEccccccccc
Q 003038          213 EDVMYVIENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDVP---------------EALRDVKCLPLSISSFRHM  276 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~vp---------------~~L~~~~~~~l~~~~l~~~  276 (854)
                      .-++.+...+..++-.+ .+|+||+|+|||++++.+|..+......               .......++.++.+.-.  
T Consensus        24 ~~~~~L~~~i~~~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n~~~ld~~~~~--  101 (614)
T PRK14971         24 ALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSYNIHELDAASNN--  101 (614)
T ss_pred             HHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCCceEEecccccC--
Confidence            33444555555444445 5899999999999999999988632210               11122344444433111  


Q ss_pred             chHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          277 NRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       277 ~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                      ..    .-++++++.+....  ++.=|++|||+|.+
T Consensus       102 ~v----d~Ir~li~~~~~~P~~~~~KVvIIdea~~L  133 (614)
T PRK14971        102 SV----DDIRNLIEQVRIPPQIGKYKIYIIDEVHML  133 (614)
T ss_pred             CH----HHHHHHHHHHhhCcccCCcEEEEEECcccC
Confidence            11    23455565555321  33458999999999

>PRK06696 uridine kinase; Validated

Probab=96.08  E-value=0.013  Score=61.59  Aligned_cols=59  Identities=19%  Similarity=0.300  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          624 KDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       624 ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +..+.+|+..|.....               .....+.+.|++|+|||++|+.|++.|-......+.+.|..|.
T Consensus         4 ~~~~~~la~~~~~~~~---------------~~~~iI~I~G~sgsGKSTlA~~L~~~l~~~g~~v~~~~~Ddf~   62 (223)
T PRK06696          4 KQLIKELAEHILTLNL---------------TRPLRVAIDGITASGKTTFADELAEEIKKRGRPVIRASIDDFH   62 (223)
T ss_pred             HHHHHHHHHHHHHhCC---------------CCceEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEecccccc
Confidence            4577888888876432               2235899999999999999999999985434567777777776

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=96.07  E-value=0.0092  Score=65.69  Aligned_cols=45  Identities=20%  Similarity=0.369  Sum_probs=32.2

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCC-cccCCceEEEcccc
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVP-EALRDVKCLPLSIS  271 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp-~~L~~~~~~~l~~~  271 (854)
                      ..+.++++||||+||||+|-|+|+.+-. +|| -.+.+-.||++++.
T Consensus        64 aGrgiLi~GppgTGKTAlA~gIa~eLG~-dvPF~~isgsEiYS~E~k  109 (450)
T COG1224          64 AGRGILIVGPPGTGKTALAMGIARELGE-DVPFVAISGSEIYSLEVK  109 (450)
T ss_pred             cccEEEEECCCCCcHHHHHHHHHHHhCC-CCCceeeccceeeeeccc
Confidence            5678999999999999999999998633 344 34444444444443

>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=96.04  E-value=0.0064  Score=57.04  Aligned_cols=31  Identities=3%  Similarity=0.202  Sum_probs=25.9

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccc
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSI  270 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~  270 (854)
                      ++|+|+||+|||++++.||+++          |..++++|-
T Consensus         2 I~I~G~~gsGKST~a~~La~~~----------~~~~i~~d~   32 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERL----------GFPVISMDD   32 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH----------TCEEEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH----------CCeEEEecc
Confidence            5799999999999999999986          556666655

...

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=95.98  E-value=0.041  Score=57.46  Aligned_cols=99  Identities=14%  Similarity=0.220  Sum_probs=57.6

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCC-----CceEEEccc-cccCcCCCccccccccccCC-CCCCchHHHHHHHHHcC
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSH-----NNFVSIALS-SFSSTRADSTEDSRNKRSRD-EQSCSYIERFAEAVSNN  731 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~-----~~~i~id~s-~~~~~~~~s~e~~~~~rl~~-~~g~g~~e~L~eav~~~  731 (854)
                      ..|+.||||||||++-|.||+.+-..-     ....-+|-+ +.. ......-.|...+-.+ -.++--.+-+-.+++..
T Consensus       139 ntLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiDersEIa-g~~~gvpq~~~g~R~dVld~cpk~~gmmmaIrsm  217 (308)
T COG3854         139 NTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEIA-GCLNGVPQHGRGRRMDVLDPCPKAEGMMMAIRSM  217 (308)
T ss_pred             eeEEecCCCCChHHHHHHHHHHhhccccccCCceEEEEeccchhh-ccccCCchhhhhhhhhhcccchHHHHHHHHHHhc
Confidence            358999999999999999999885432     233444422 111 0000000111111000 00000112467899998


Q ss_pred             CCEEEEEecCCCCCHHHHHHHHHhhhcCe
Q 003038          732 PHRVFLIEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       732 p~~ViliDEieka~~~v~~~Ll~~le~G~  760 (854)
                      -..|+++|||-...  --.+++.++..|.
T Consensus       218 ~PEViIvDEIGt~~--d~~A~~ta~~~GV  244 (308)
T COG3854         218 SPEVIIVDEIGTEE--DALAILTALHAGV  244 (308)
T ss_pred             CCcEEEEeccccHH--HHHHHHHHHhcCc
Confidence            88999999998543  4467888888773

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=95.96  E-value=0.0087  Score=69.36  Aligned_cols=144  Identities=10%  Similarity=0.118  Sum_probs=85.3

Q ss_pred             cHHHHHHHHHHhhcc--CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc--------c-chH
Q 003038          211 RNEDVMYVIENLMSK--RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH--------M-NRV  279 (854)
Q Consensus       211 r~~ei~~v~~~L~r~--~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~--------~-~rg  279 (854)
                      ....+.++++...|-  +-.+++|+||+|+||+-+|+++=..=.+       ++..||+++++++-.        | -+|
T Consensus       250 ~S~~m~~~~~~akr~A~tdstVLi~GESGTGKElfA~~IH~~S~R-------~~~PFIaiNCaAiPe~LlESELFGye~G  322 (560)
T COG3829         250 ESPAMLRVLELAKRIAKTDSTVLILGESGTGKELFARAIHNLSPR-------ANGPFIAINCAAIPETLLESELFGYEKG  322 (560)
T ss_pred             CCHHHHHHHHHHHhhcCCCCcEEEecCCCccHHHHHHHHHhcCcc-------cCCCeEEEecccCCHHHHHHHHhCcCCc
Confidence            667777777765443  6668999999999999999876543211       567899999987631        2 233


Q ss_pred             HHHHH----HHHHHHHHHhhhCCCeEEEeCccccccccccccccccccchhhhHHHHHHHhhcc--c--C-CC----Cce
Q 003038          280 EVEQR----VEEIKNLVRSCLGRGIVLNLGDLEWAEFRASSSEQVRGYYCSIEHIIMEIGKLVC--G--I-GE----NAR  346 (854)
Q Consensus       280 e~E~r----l~~l~~~~~~~~~~~~ILfidel~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ll~--~--~-~g----~g~  346 (854)
                      -|---    =+.+|+.+.    +| =||+|||-.+.-                +....+-+.|.  .  . +|    .-+
T Consensus       323 AFTGA~~~GK~GlfE~A~----gG-TLFLDEIgempl----------------~LQaKLLRVLQEkei~rvG~t~~~~vD  381 (560)
T COG3829         323 AFTGASKGGKPGLFELAN----GG-TLFLDEIGEMPL----------------PLQAKLLRVLQEKEIERVGGTKPIPVD  381 (560)
T ss_pred             cccccccCCCCcceeecc----CC-eEEehhhccCCH----------------HHHHHHHHHHhhceEEecCCCCceeeE
Confidence            33211    223555543    23 499999966611                12223444441  1  1 11    127


Q ss_pred             EEEEEecCHHHHHHhhccCCchhhh--hccCCCCCCCchH
Q 003038          347 FWLMGIATFQSYMRCKSGHPSLETL--WSLHPLTIPAGSL  384 (854)
Q Consensus       347 l~lIgatT~~ey~k~~~~~pale~~--~~~~~v~i~~~sl  384 (854)
                      |++|+||+-+-=. . ..+..|.++  +|+..++|+=|.|
T Consensus       382 VRIIAATN~nL~~-~-i~~G~FReDLYYRLNV~~i~iPPL  419 (560)
T COG3829         382 VRIIAATNRNLEK-M-IAEGTFREDLYYRLNVIPITIPPL  419 (560)
T ss_pred             EEEEeccCcCHHH-H-HhcCcchhhheeeeceeeecCCCc
Confidence            9999999743211 1 234556543  5887777776654

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

Probab=95.96  E-value=0.016  Score=60.44  Aligned_cols=96  Identities=16%  Similarity=0.156  Sum_probs=54.2

Q ss_pred             CCcHHHHHHHHHHhhc-cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHH--HHHHH
Q 003038          209 PIRNEDVMYVIENLMS-KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVE--VEQRV  285 (854)
Q Consensus       209 pvr~~ei~~v~~~L~r-~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge--~E~rl  285 (854)
                      -|..|+...-++++.+ +.-.|.++.||||+|||+-+..||+++.-....+     -++.|+.+.    .||-  +-.++
T Consensus        29 IVGNe~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke-----~vLELNASd----eRGIDvVRn~I   99 (333)
T KOG0991|consen   29 IVGNEDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELLGDSYKE-----AVLELNASD----ERGIDVVRNKI   99 (333)
T ss_pred             hhCCHHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhh-----HhhhccCcc----ccccHHHHHHH
Confidence            3444554444455554 4667999999999999999999998865322111     244454442    2331  12232


Q ss_pred             HHHHHH-HHhhhCCCeEEEeCccccc--ccc
Q 003038          286 EEIKNL-VRSCLGRGIVLNLGDLEWA--EFR  313 (854)
Q Consensus       286 ~~l~~~-~~~~~~~~~ILfidel~~l--~~~  313 (854)
                      |..-.. |.--.|.-=|+.+||.+.+  |+.
T Consensus       100 K~FAQ~kv~lp~grhKIiILDEADSMT~gAQ  130 (333)
T KOG0991|consen  100 KMFAQKKVTLPPGRHKIIILDEADSMTAGAQ  130 (333)
T ss_pred             HHHHHhhccCCCCceeEEEeeccchhhhHHH
Confidence            221111 0000034468899999888  544

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.92  E-value=0.11  Score=59.47  Aligned_cols=95  Identities=14%  Similarity=0.169  Sum_probs=55.8

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH-hCCCCceEEEccccccCcCCCcccccccccc---CCCCCCch--HHHHHHHHHcC
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV-FGSHNNFVSIALSSFSSTRADSTEDSRNKRS---RDEQSCSY--IERFAEAVSNN  731 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l-fg~~~~~i~id~s~~~~~~~~s~e~~~~~rl---~~~~g~g~--~e~L~eav~~~  731 (854)
                      ..++|.||+|+|||+++..||..+ +.......-+++..|...   +  ...+.+.   .+-+.+..  ...+.+.++..
T Consensus       224 ~vi~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Lit~Dt~R~a---A--~eQLk~yAe~lgvp~~~~~~~~~l~~~l~~~  298 (432)
T PRK12724        224 KVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDNYRIA---A--IEQLKRYADTMGMPFYPVKDIKKFKETLARD  298 (432)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEecccchhhh---H--HHHHHHHHHhcCCCeeehHHHHHHHHHHHhC
Confidence            478999999999999999999754 444445555666655420   0  0111111   11111111  12566667777


Q ss_pred             CCEEEEEecCCCCC--HHHHHHHHHhhh
Q 003038          732 PHRVFLIEDVEQAD--YCSQKGFKRAIE  757 (854)
Q Consensus       732 p~~ViliDEieka~--~~v~~~Ll~~le  757 (854)
                      .+.+||||=.-..+  ......|...++
T Consensus       299 ~~D~VLIDTaGr~~rd~~~l~eL~~~~~  326 (432)
T PRK12724        299 GSELILIDTAGYSHRNLEQLERMQSFYS  326 (432)
T ss_pred             CCCEEEEeCCCCCccCHHHHHHHHHHHH
Confidence            88999999555443  445555555554

>PRK10867 signal recognition particle protein; Provisional

Probab=95.91  E-value=0.11  Score=60.06  Aligned_cols=88  Identities=14%  Similarity=0.213  Sum_probs=51.9

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCC-CCceEEEccccccCcCCCcccccc--ccc--c--CC-CCCCchHH---H
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGS-HNNFVSIALSSFSSTRADSTEDSR--NKR--S--RD-EQSCSYIE---R  723 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-~~~~i~id~s~~~~~~~~s~e~~~--~~r--l--~~-~~g~g~~e---~  723 (854)
                      ++..+++|+||+|+|||+++--||..+-.. ...+..+++..|....   .++..  ..+  .  .. +.+....+   .
T Consensus        98 ~~p~vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV~~D~~R~aa---~eQL~~~a~~~gv~v~~~~~~~dp~~i~~~  174 (433)
T PRK10867         98 KPPTVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAADVYRPAA---IEQLKTLGEQIGVPVFPSGDGQDPVDIAKA  174 (433)
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEEEccccchHH---HHHHHHHHhhcCCeEEecCCCCCHHHHHHH
Confidence            345799999999999999999999877544 4556667776665210   00000  000  0  00 11111112   2


Q ss_pred             HHHHHHcCCCEEEEEecCCCCC
Q 003038          724 FAEAVSNNPHRVFLIEDVEQAD  745 (854)
Q Consensus       724 L~eav~~~p~~ViliDEieka~  745 (854)
                      ..+..+...+.+|++|=.-+.+
T Consensus       175 a~~~a~~~~~DvVIIDTaGrl~  196 (433)
T PRK10867        175 ALEEAKENGYDVVIVDTAGRLH  196 (433)
T ss_pred             HHHHHHhcCCCEEEEeCCCCcc
Confidence            2233455678999999998875

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=95.91  E-value=0.019  Score=55.85  Aligned_cols=24  Identities=13%  Similarity=0.090  Sum_probs=21.4

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHc
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ++|+|+||+|||+++..++.....
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~   25 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIAT   25 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHh
Confidence            578999999999999999887754

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.

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=95.90  E-value=0.078  Score=58.43  Aligned_cols=96  Identities=15%  Similarity=0.171  Sum_probs=59.1

Q ss_pred             HHHHHHHHHhh-ccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCCCccc--------------CCceEEEccccccccc
Q 003038          213 EDVMYVIENLM-SKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDVPEAL--------------RDVKCLPLSISSFRHM  276 (854)
Q Consensus       213 ~ei~~v~~~L~-r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~vp~~L--------------~~~~~~~l~~~~l~~~  276 (854)
                      +.+.++..-.. ..+-.+ .+|+||||+|||+++..+|..+..-.....-              ....|+.++.+.....
T Consensus         8 ~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~   87 (325)
T COG0470           8 EAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKI   87 (325)
T ss_pred             hHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecccccCCC
Confidence            33444444433 444556 8999999999999999999988743322111              1235666665544332


Q ss_pred             chHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc
Q 003038          277 NRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       277 ~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l  310 (854)
                      .  -..+.++++.+......  ++.-|++|||++.+
T Consensus        88 ~--i~~~~vr~~~~~~~~~~~~~~~kviiidead~m  121 (325)
T COG0470          88 D--IIVEQVRELAEFLSESPLEGGYKVVIIDEADKL  121 (325)
T ss_pred             c--chHHHHHHHHHHhccCCCCCCceEEEeCcHHHH
Confidence            1  23445666655554432  34678999999888

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.87  E-value=0.03  Score=61.79  Aligned_cols=93  Identities=13%  Similarity=0.171  Sum_probs=59.7

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhC--CCCceEEEcc-ccccCcCCCccccccccccCCCCCC-chHHHHHHHHHcCCC
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFG--SHNNFVSIAL-SSFSSTRADSTEDSRNKRSRDEQSC-SYIERFAEAVSNNPH  733 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg--~~~~~i~id~-s~~~~~~~~s~e~~~~~rl~~~~g~-g~~e~L~eav~~~p~  733 (854)
                      +.+++.||+|+|||+++++|...+-.  ...+++.+.- .|+.-.     .+. ...+....+. ++.+-+..++|.+| 
T Consensus       133 ~~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd~~El~~~-----~~~-~v~~~~~~~~~~~~~~l~~aLR~~p-  205 (299)
T TIGR02782       133 KNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTRELQCA-----APN-VVQLRTSDDAISMTRLLKATLRLRP-  205 (299)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECCchhhcCC-----CCC-EEEEEecCCCCCHHHHHHHHhcCCC-
Confidence            47899999999999999999988743  2455666642 232200     001 1111111222 56667888888888 


Q ss_pred             EEEEEecCCCCCHHHHHHHHHhhhcCe
Q 003038          734 RVFLIEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       734 ~ViliDEieka~~~v~~~Ll~~le~G~  760 (854)
                      .+|++.||-  +++... +++++..|.
T Consensus       206 D~iivGEiR--~~ea~~-~l~a~~tGh  229 (299)
T TIGR02782       206 DRIIVGEVR--GGEALD-LLKAWNTGH  229 (299)
T ss_pred             CEEEEeccC--CHHHHH-HHHHHHcCC
Confidence            456699998  466654 589998874

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>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=95.85  E-value=0.025  Score=56.26  Aligned_cols=66  Identities=21%  Similarity=0.319  Sum_probs=47.9

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc----------chHHHHHHHHHHHHHHHhhhCCC
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM----------NRVEVEQRVEEIKNLVRSCLGRG  299 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~----------~rge~E~rl~~l~~~~~~~~~~~  299 (854)
                      +.|+|-||+|||+|+++|.+++..       .|.+++-||...+..+          .|.|.-.|+.++-..+...   |
T Consensus         5 IwltGlsGsGKtTlA~~L~~~L~~-------~g~~~~~LDgD~lR~~l~~dl~fs~~dR~e~~rr~~~~A~ll~~~---G   74 (156)
T PF01583_consen    5 IWLTGLSGSGKTTLARALERRLFA-------RGIKVYLLDGDNLRHGLNADLGFSKEDREENIRRIAEVAKLLADQ---G   74 (156)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHHHH-------TTS-EEEEEHHHHCTTTTTT--SSHHHHHHHHHHHHHHHHHHHHT---T
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH-------cCCcEEEecCcchhhccCCCCCCCHHHHHHHHHHHHHHHHHHHhC---C
Confidence            678999999999999999999876       4678888988777653          3455556666665555553   6


Q ss_pred             eEEEeC
Q 003038          300 IVLNLG  305 (854)
Q Consensus       300 ~ILfid  305 (854)
                      +|+.+.
T Consensus        75 ~ivIva   80 (156)
T PF01583_consen   75 IIVIVA   80 (156)
T ss_dssp             SEEEEE
T ss_pred             CeEEEe
Confidence            666655

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 ....

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=95.85  E-value=0.032  Score=63.33  Aligned_cols=144  Identities=13%  Similarity=0.111  Sum_probs=81.0

Q ss_pred             ccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCC
Q 003038          622 WQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRA  701 (854)
Q Consensus       622 GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~  701 (854)
                      -|..+...|..++...                 . ...+++.||.|+|||++.++|-..+-.....++...-+... +..
T Consensus         5 eQ~~~~~~v~~~~~~~-----------------~-~~~~fv~G~~GtGKs~l~~~i~~~~~~~~~~~~~~a~tg~A-A~~   65 (364)
T PF05970_consen    5 EQRRVFDTVIEAIENE-----------------E-GLNFFVTGPAGTGKSFLIKAIIDYLRSRGKKVLVTAPTGIA-AFN   65 (364)
T ss_pred             HHHHHHHHHHHHHHcc-----------------C-CcEEEEEcCCCCChhHHHHHHHHHhccccceEEEecchHHH-HHh
Confidence            3777878877776541                 1 24788899999999999999998875544444333222111 000


Q ss_pred             C--ccccccccccC-CCCCCchH-----HHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCC
Q 003038          702 D--STEDSRNKRSR-DEQSCSYI-----ERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGD  773 (854)
Q Consensus       702 ~--s~e~~~~~rl~-~~~g~g~~-----e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~  773 (854)
                      .  ..--|+...+. ........     ..+.+.++  .-.||+||||-.++..++..+-+.|.+=  ..+......|..
T Consensus        66 i~~G~T~hs~f~i~~~~~~~~~~~~~~~~~~~~~l~--~~~~lIiDEism~~~~~l~~i~~~lr~i--~~~~~~~~pFGG  141 (364)
T PF05970_consen   66 IPGGRTIHSFFGIPINNNEKSQCKISKNSRLRERLR--KADVLIIDEISMVSADMLDAIDRRLRDI--RKSKDSDKPFGG  141 (364)
T ss_pred             ccCCcchHHhcCccccccccccccccccchhhhhhh--hheeeecccccchhHHHHHHHHHhhhhh--hcccchhhhcCc
Confidence            0  00123333322 11111100     11222222  2369999999999999999887777641  111002467888


Q ss_pred             eEEEEecCCCCCCCCC
Q 003038          774 AIVILSCESFSSRSRA  789 (854)
Q Consensus       774 aIiIlTsn~f~~~s~~  789 (854)
                      ..+||. ..|-..++.
T Consensus       142 ~~vil~-GDf~QlpPV  156 (364)
T PF05970_consen  142 KQVILF-GDFLQLPPV  156 (364)
T ss_pred             ceEEee-hhhhhcCCC
Confidence            888884 445444333

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=95.84  E-value=0.023  Score=64.74  Aligned_cols=85  Identities=21%  Similarity=0.277  Sum_probs=48.7

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCC--ceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCE
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHN--NFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHR  734 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~--~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~  734 (854)
                      -.+++++||+|.|||.|..++.........  .++.+....|.       .+. +.-+..    +..+.+.+..   ...
T Consensus       113 ~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se~f~-------~~~-v~a~~~----~~~~~Fk~~y---~~d  177 (408)
T COG0593         113 YNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFT-------NDF-VKALRD----NEMEKFKEKY---SLD  177 (408)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccHHHHH-------HHH-HHHHHh----hhHHHHHHhh---ccC
Confidence            457999999999999999999988865544  34444333332       000 000000    1112222222   357


Q ss_pred             EEEEecCCCCCH--HHHHHHHHhh
Q 003038          735 VFLIEDVEQADY--CSQKGFKRAI  756 (854)
Q Consensus       735 ViliDEieka~~--~v~~~Ll~~l  756 (854)
                      +++||+|+....  ..|..|...|
T Consensus       178 lllIDDiq~l~gk~~~qeefFh~F  201 (408)
T COG0593         178 LLLIDDIQFLAGKERTQEEFFHTF  201 (408)
T ss_pred             eeeechHhHhcCChhHHHHHHHHH
Confidence            999999997543  3455555444

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=95.84  E-value=0.086  Score=54.48  Aligned_cols=37  Identities=16%  Similarity=0.150  Sum_probs=27.2

Q ss_pred             HHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          216 MYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       216 ~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      +.+-.+|. ...+-.+|.|+||+|||+++..++..+..
T Consensus         8 ~a~~~~l~-~~~~~~~l~G~aGtGKT~~l~~~~~~~~~   44 (196)
T PF13604_consen    8 EAVRAILT-SGDRVSVLQGPAGTGKTTLLKALAEALEA   44 (196)
T ss_dssp             HHHHHHHH-CTCSEEEEEESTTSTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHh-cCCeEEEEEECCCCCHHHHHHHHHHHHHh
Confidence            33333444 34555777899999999999999888766

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=95.84  E-value=0.039  Score=65.64  Aligned_cols=57  Identities=11%  Similarity=0.086  Sum_probs=39.9

Q ss_pred             cHHHHHHHHHHhhc--cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc
Q 003038          211 RNEDVMYVIENLMS--KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR  274 (854)
Q Consensus       211 r~~ei~~v~~~L~r--~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~  274 (854)
                      ...-++++++-+.+  ....+++|+||+|+||+.+|+++-..-..       .+..|+.++++.+-
T Consensus       209 ~s~~~~~~~~~~~~~A~~~~pvlI~GE~GtGK~~lA~aiH~~s~r-------~~~pfv~inca~~~  267 (520)
T PRK10820        209 VSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHLRSPR-------GKKPFLALNCASIP  267 (520)
T ss_pred             CCHHHHHHHHHHHHHhCCCCCEEEECCCCccHHHHHHHHHHhCCC-------CCCCeEEeccccCC
Confidence            55555555555432  36778999999999999999997543211       34578899988763

>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=95.84  E-value=0.066  Score=58.13  Aligned_cols=104  Identities=19%  Similarity=0.310  Sum_probs=65.4

Q ss_pred             ccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc
Q 003038          620 VPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST  699 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~  699 (854)
                      ++=-++|+..|++..+-.+                .|.|++|+.|..|+||++++| ||-.+.+  ..+..+.++     
T Consensus        10 lVlf~~ai~hi~ri~RvL~----------------~~~Gh~LLvG~~GsGr~sl~r-Laa~i~~--~~~~~i~~~-----   65 (268)
T PF12780_consen   10 LVLFDEAIEHIARISRVLS----------------QPRGHALLVGVGGSGRQSLAR-LAAFICG--YEVFQIEIT-----   65 (268)
T ss_dssp             ----HHHHHHHHHHHHHHC----------------STTEEEEEECTTTSCHHHHHH-HHHHHTT--EEEE-TTTS-----
T ss_pred             eeeHHHHHHHHHHHHHHHc----------------CCCCCeEEecCCCccHHHHHH-HHHHHhc--cceEEEEee-----
Confidence            3445677777777655432                467899999999999999999 5555532  223333222     


Q ss_pred             CCCccccccccccCCCCCCchH---HHHHHHHH----cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEec
Q 003038          700 RADSTEDSRNKRSRDEQSCSYI---ERFAEAVS----NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVT  763 (854)
Q Consensus       700 ~~~s~e~~~~~rl~~~~g~g~~---e~L~eav~----~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d  763 (854)
                                      .+|+..   +.|..++.    ++...|++|+|-+-.+......+-..|..|.+.+
T Consensus        66 ----------------~~y~~~~f~~dLk~~~~~ag~~~~~~vfll~d~qi~~~~fLe~in~LL~sGeip~  120 (268)
T PF12780_consen   66 ----------------KGYSIKDFKEDLKKALQKAGIKGKPTVFLLTDSQIVDESFLEDINSLLSSGEIPN  120 (268)
T ss_dssp             ----------------TTTHHHHHHHHHHHHHHHHHCS-S-EEEEEECCCSSSCHHHHHHHHHHHCSS-TT
T ss_pred             ----------------CCcCHHHHHHHHHHHHHHHhccCCCeEEEecCcccchHhHHHHHHHHHhCCCCCC
Confidence                            234332   34444433    5667899999988888888888888888887763

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>PHA00729 NTP-binding motif containing protein

Probab=95.83  E-value=0.02  Score=60.23  Aligned_cols=25  Identities=28%  Similarity=0.276  Sum_probs=22.8

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHh
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVF  682 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lf  682 (854)
                      ..+++.|++|+|||.+|.+||+.+.
T Consensus        18 ~nIlItG~pGvGKT~LA~aLa~~l~   42 (226)
T PHA00729         18 VSAVIFGKQGSGKTTYALKVARDVF   42 (226)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3789999999999999999999873

>TIGR00368 Mg chelatase-related protein

Probab=95.83  E-value=0.016  Score=68.15  Aligned_cols=39  Identities=8%  Similarity=0.025  Sum_probs=31.9

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      ..+.+.+-+++-.. ...|++|+||||+|||++++.++..
T Consensus       196 Gq~~~~~al~~aa~-~g~~vlliG~pGsGKTtlar~l~~l  234 (499)
T TIGR00368       196 GQQHAKRALEIAAA-GGHNLLLFGPPGSGKTMLASRLQGI  234 (499)
T ss_pred             CcHHHHhhhhhhcc-CCCEEEEEecCCCCHHHHHHHHhcc
Confidence            56677777777663 6679999999999999999988754

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=95.76  E-value=0.036  Score=62.29  Aligned_cols=93  Identities=12%  Similarity=0.214  Sum_probs=58.9

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc-cccccCcCCCccccccccccC-C--C--C-CCchHHHHHHHHH
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA-LSSFSSTRADSTEDSRNKRSR-D--E--Q-SCSYIERFAEAVS  729 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id-~s~~~~~~~~s~e~~~~~rl~-~--~--~-g~g~~e~L~eav~  729 (854)
                      ...+++.||+|+|||++.++|...+ ....+++.+. ..|+.-.     ....+ ++. .  +  . +..+.+-+..++|
T Consensus       162 ~~nilI~G~tGSGKTTll~aLl~~i-~~~~rivtiEd~~El~l~-----~~~~v-~l~~~~~~~~~~~~t~~~ll~~~LR  234 (344)
T PRK13851        162 RLTMLLCGPTGSGKTTMSKTLISAI-PPQERLITIEDTLELVIP-----HENHV-RLLYSKNGAGLGAVTAEHLLQASLR  234 (344)
T ss_pred             CCeEEEECCCCccHHHHHHHHHccc-CCCCCEEEECCCccccCC-----CCCEE-EEEeeccccCcCccCHHHHHHHHhc
Confidence            3479999999999999999999887 4455666653 3333210     01111 111 1  1  1 1245556777888


Q ss_pred             cCCCEEEEEecCCCCCHHHHHHHHHhhhcCe
Q 003038          730 NNPHRVFLIEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       730 ~~p~~ViliDEieka~~~v~~~Ll~~le~G~  760 (854)
                      .+| .+|++-|+-  +.+... +++++..|.
T Consensus       235 ~~p-D~IivGEiR--~~ea~~-~l~a~~tGh  261 (344)
T PRK13851        235 MRP-DRILLGEMR--DDAAWA-YLSEVVSGH  261 (344)
T ss_pred             CCC-CeEEEEeeC--cHHHHH-HHHHHHhCC
Confidence            888 457789998  566665 677887764

>PHA02774 E1; Provisional

Probab=95.75  E-value=0.04  Score=65.01  Aligned_cols=94  Identities=12%  Similarity=0.218  Sum_probs=56.4

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      ..++|+||+|+|||.+|..|++.+-|.--.|  ++-.          ..+.            .+.|.+      -.|++
T Consensus       435 nciv~~GPP~TGKS~fa~sL~~~L~G~vi~f--vN~~----------s~Fw------------Lqpl~d------~ki~v  484 (613)
T PHA02774        435 NCLVIYGPPDTGKSMFCMSLIKFLKGKVISF--VNSK----------SHFW------------LQPLAD------AKIAL  484 (613)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCEEEE--EECc----------cccc------------cchhcc------CCEEE
Confidence            3799999999999999999999985432222  3311          0111            111221      36999


Q ss_pred             EecCCCC-CHHHHHHHHHhhhcCeEe-c-CCCceeecCCeEEEEecC
Q 003038          738 IEDVEQA-DYCSQKGFKRAIESGRIV-T-SSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       738 iDEieka-~~~v~~~Ll~~le~G~l~-d-~~G~~v~~~~aIiIlTsn  781 (854)
                      |||+-.. -..+...|+.+|+-..+. | .+-..+..+..=+|+|||
T Consensus       485 lDD~t~~~w~y~d~~Lrn~LdG~~v~lD~Khk~~~q~k~pPlIITSN  531 (613)
T PHA02774        485 LDDATHPCWDYIDTYLRNALDGNPVSIDCKHKAPVQIKCPPLLITSN  531 (613)
T ss_pred             EecCcchHHHHHHHHHHHHcCCCcceeeecccCcccccCCCEEEecC
Confidence            9999332 233444666666644222 2 123445566677888898

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

Probab=95.73  E-value=0.0091  Score=59.98  Aligned_cols=63  Identities=10%  Similarity=0.118  Sum_probs=39.6

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      +++|-++.++.+...+....               .+....++++|++|+|||.+.+++.+.+-.....++.+++..+
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~---------------~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~~~~~~~~~~   63 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQ---------------SGSPRNLLLTGESGSGKTSLLRALLDRLAERGGYVISINCDDS   63 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTS---------------S-----EEE-B-TTSSHHHHHHHHHHHHHHHT--EEEEEEETT
T ss_pred             CCCCHHHHHHHHHHHHHHHH---------------cCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEEEecc
Confidence            35788888888888875111               1233589999999999999999888877554434777777766

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=95.72  E-value=0.1  Score=58.44  Aligned_cols=136  Identities=7%  Similarity=-0.051  Sum_probs=73.5

Q ss_pred             HHHHHHhhccCcCCc-eeecCCCCCHHHHHHHHHHHHHcCCCCcc----------------cCCceEEEcccccccccch
Q 003038          216 MYVIENLMSKRKRNF-VVVGECLASIEGVVRGVIDKIEKGDVPEA----------------LRDVKCLPLSISSFRHMNR  278 (854)
Q Consensus       216 ~~v~~~L~r~~k~n~-vLvGe~GvGKta~v~~la~~i~~~~vp~~----------------L~~~~~~~l~~~~l~~~~r  278 (854)
                      +.+...+..++-.+. +|+||+|+||+++++.+|+.+...+....                ..+..++..+-..    ..
T Consensus        16 ~~L~~~~~~~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~i~~~~~~----i~   91 (329)
T PRK08058         16 KMLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVHLVAPDGQS----IK   91 (329)
T ss_pred             HHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEecccccc----CC
Confidence            344444444455555 89999999999999999999875431110                1122333222110    01


Q ss_pred             HHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhc-ccCCCCceEEEEEecC
Q 003038          279 VEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CGIGENARFWLMGIAT  354 (854)
Q Consensus       279 ge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~~~g~g~l~lIgatT  354 (854)
                         =+.++++++.+....  ++.=|++|||++.+ ..                 +...+-+.| .|. +  ...+|.+|+
T Consensus        92 ---id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~-----------------a~NaLLK~LEEPp-~--~~~~Il~t~  148 (329)
T PRK08058         92 ---KDQIRYLKEEFSKSGVESNKKVYIIEHADKMTAS-----------------AANSLLKFLEEPS-G--GTTAILLTE  148 (329)
T ss_pred             ---HHHHHHHHHHHhhCCcccCceEEEeehHhhhCHH-----------------HHHHHHHHhcCCC-C--CceEEEEeC
Confidence               123445555544211  34458999999988 43                 122334444 221 2  366666555


Q ss_pred             HHHHHHhhccCCchhhhhccCCCCCCCchHH
Q 003038          355 FQSYMRCKSGHPSLETLWSLHPLTIPAGSLS  385 (854)
Q Consensus       355 ~~ey~k~~~~~pale~~~~~~~v~i~~~sl~  385 (854)
                      ...  +   --|++.+  |-+.|.++.++-.
T Consensus       149 ~~~--~---ll~TIrS--Rc~~i~~~~~~~~  172 (329)
T PRK08058        149 NKH--Q---ILPTILS--RCQVVEFRPLPPE  172 (329)
T ss_pred             ChH--h---CcHHHHh--hceeeeCCCCCHH
Confidence            211  2   3467777  7777777665543

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=95.67  E-value=0.045  Score=60.62  Aligned_cols=92  Identities=11%  Similarity=0.159  Sum_probs=57.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc-cccccCcCCCccccccccccC-C----CC-CCchHHHHHHHHHc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA-LSSFSSTRADSTEDSRNKRSR-D----EQ-SCSYIERFAEAVSN  730 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id-~s~~~~~~~~s~e~~~~~rl~-~----~~-g~g~~e~L~eav~~  730 (854)
                      ..++|.||+|+|||++.++|...+ ......+.++ ..++...     ....+ .+. .    +. ...+.+.+..++|.
T Consensus       145 ~~ili~G~tGsGKTTll~al~~~~-~~~~~iv~ied~~El~~~-----~~~~~-~l~~~~~~~~~~~~~~~~~l~~~Lr~  217 (308)
T TIGR02788       145 KNIIISGGTGSGKTTFLKSLVDEI-PKDERIITIEDTREIFLP-----HPNYV-HLFYSKGGQGLAKVTPKDLLQSCLRM  217 (308)
T ss_pred             CEEEEECCCCCCHHHHHHHHHccC-CccccEEEEcCccccCCC-----CCCEE-EEEecCCCCCcCccCHHHHHHHHhcC
Confidence            489999999999999999999876 4445566664 2222210     00111 011 0    11 12455567777887


Q ss_pred             CCCEEEEEecCCCCCHHHHHHHHHhhhcCe
Q 003038          731 NPHRVFLIEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       731 ~p~~ViliDEieka~~~v~~~Ll~~le~G~  760 (854)
                      +| .+|++||+--  .++.. +++++..|.
T Consensus       218 ~p-d~ii~gE~r~--~e~~~-~l~a~~~g~  243 (308)
T TIGR02788       218 RP-DRIILGELRG--DEAFD-FIRAVNTGH  243 (308)
T ss_pred             CC-CeEEEeccCC--HHHHH-HHHHHhcCC
Confidence            77 5678999994  66654 577777663

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=95.67  E-value=0.011  Score=69.50  Aligned_cols=44  Identities=9%  Similarity=0.215  Sum_probs=37.0

Q ss_pred             cHHHHHHHHHHh------hccCcCCceeecCCCCCHHHHHHHHHHHHHcC
Q 003038          211 RNEDVMYVIENL------MSKRKRNFVVVGECLASIEGVVRGVIDKIEKG  254 (854)
Q Consensus       211 r~~ei~~v~~~L------~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~  254 (854)
                      -++.++++++.|      ...+++-.+|+||||+|||++|+.|+..+..-
T Consensus        81 lee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~le~~  130 (644)
T PRK15455         81 MEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLMERV  130 (644)
T ss_pred             cHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHHHhC
Confidence            788899999998      22356678899999999999999999977654

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.66  E-value=0.0095  Score=57.93  Aligned_cols=44  Identities=14%  Similarity=0.263  Sum_probs=30.1

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHcC-----------CCCcccCCceEEEcccccc
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEKG-----------DVPEALRDVKCLPLSISSF  273 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~~-----------~vp~~L~~~~~~~l~~~~l  273 (854)
                      ++|+||+|+|||++++.|++.+..+           .-+..+.+...+-++...|
T Consensus         2 i~i~GpsGsGKstl~~~L~~~~~~~~~~~v~~tTr~p~~~e~~g~~~~~v~~~~~   56 (137)
T cd00071           2 IVLSGPSGVGKSTLLKRLLEEFDPNFGFSVSHTTRKPRPGEVDGVDYHFVSKEEF   56 (137)
T ss_pred             EEEECCCCCCHHHHHHHHHhcCCccceecccccccCCCCCccCCceeEEeCHHHH
Confidence            5789999999999999999875321           1123455666666654444

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.

>PRK04296 thymidine kinase; Provisional

Probab=95.65  E-value=0.02  Score=58.88  Aligned_cols=24  Identities=8%  Similarity=-0.061  Sum_probs=21.2

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHc
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      .+++||||+|||+++-+++.+...
T Consensus         5 ~litG~~GsGKTT~~l~~~~~~~~   28 (190)
T PRK04296          5 EFIYGAMNSGKSTELLQRAYNYEE   28 (190)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHH
Confidence            578999999999999999988754

>TIGR00959 ffh signal recognition particle protein

Probab=95.65  E-value=0.23  Score=57.53  Aligned_cols=42  Identities=14%  Similarity=0.218  Sum_probs=33.4

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHh-CCCCceEEEcccccc
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVF-GSHNNFVSIALSSFS  697 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lf-g~~~~~i~id~s~~~  697 (854)
                      +...++|.|++|+|||++|.-||..+. ....+...+++..|.
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV~~D~~R  140 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACDLYR  140 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEEeccccc
Confidence            346999999999999999999999875 234566777777665

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.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=95.63  E-value=0.031  Score=55.65  Aligned_cols=69  Identities=13%  Similarity=0.144  Sum_probs=0.0

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccc----------cccccc-chHHHHHHHHHHHHHHH
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSI----------SSFRHM-NRVEVEQRVEEIKNLVR  293 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~----------~~l~~~-~rge~E~rl~~l~~~~~  293 (854)
                      ..+.+++|+|+||+|||++++.||+++          +..++..|.          ..+... ....|.+....++..+.
T Consensus         2 ~~~~~i~l~G~~GsGKstla~~La~~l----------~~~~~d~d~~~~~~~g~~~~~~~~~~g~~~~~~~~~~~~~~l~   71 (175)
T PRK00131          2 LKGPNIVLIGFMGAGKSTIGRLLAKRL----------GYDFIDTDHLIEARAGKSIPEIFEEEGEAAFRELEEEVLAELL   71 (175)
T ss_pred             CCCCeEEEEcCCCCCHHHHHHHHHHHh----------CCCEEEChHHHHHHcCCCHHHHHHHHCHHHHHHHHHHHHHHHH


Q ss_pred             hhhCCCeEEEeC
Q 003038          294 SCLGRGIVLNLG  305 (854)
Q Consensus       294 ~~~~~~~ILfid  305 (854)
                      ..  .++||..+
T Consensus        72 ~~--~~~vi~~g   81 (175)
T PRK00131         72 AR--HNLVISTG   81 (175)
T ss_pred             hc--CCCEEEeC

>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=95.62  E-value=0.029  Score=54.09  Aligned_cols=62  Identities=8%  Similarity=0.026  Sum_probs=0.0

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccc------------ccccccchHHHHHHHHHHHHHHHhhhC
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSI------------SSFRHMNRVEVEQRVEEIKNLVRSCLG  297 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~------------~~l~~~~rge~E~rl~~l~~~~~~~~~  297 (854)
                      ++++|+||+|||++++.++..          .+..+++.|.            ..........+.+.+.+.+....+. +
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~----------~~~~~i~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-g   70 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKR----------LGAVVISQDEIRRRLAGEDPPSPSDYIEAEERAYQILNAAIRKALRN-G   70 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH----------STEEEEEHHHHHHHHCCSSSGCCCCCHHHHHHHHHHHHHHHHHHHHT-T
T ss_pred             EEEECCCCCCHHHHHHHHHHH----------CCCEEEeHHHHHHHHcccccccchhHHHHHHHHHHHHHHHHHHHHHc-C


Q ss_pred             CCeEE
Q 003038          298 RGIVL  302 (854)
Q Consensus       298 ~~~IL  302 (854)
                      .++||
T Consensus        71 ~~~vv   75 (143)
T PF13671_consen   71 NSVVV   75 (143)
T ss_dssp             -EEEE
T ss_pred             CCcee

...

>KOG1808 consensus AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=95.62  E-value=0.027  Score=73.71  Aligned_cols=89  Identities=20%  Similarity=0.265  Sum_probs=65.5

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccC-CCCCC-chHH-HHHHHHHcCCCEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSR-DEQSC-SYIE-RFAEAVSNNPHRV  735 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~-~~~g~-g~~e-~L~eav~~~p~~V  735 (854)
                      .+||.||+++|||.+++.||+..   ..++++|+-.+.++.      ..-+.+.. ...|. .+.+ .|.+|+++  ...
T Consensus       442 pillqG~tssGKtsii~~la~~~---g~~~vrinnhehtd~------qeyig~y~~~~~g~l~freg~LV~Alr~--G~~  510 (1856)
T KOG1808|consen  442 PILLQGPTSSGKTSIIKELARAT---GKNIVRINNHEHTDL------QEYIGTYVADDNGDLVFREGVLVQALRN--GDW  510 (1856)
T ss_pred             CeEEecCcCcCchhHHHHHHHHh---ccCceehhccccchH------HHHHHhhhcCCCCCeeeehhHHHHHHHh--CCE
Confidence            58999999999999999999988   468899887655521      00111111 12222 3333 57777776  458


Q ss_pred             EEEecCCCCCHHHHHHHHHhhhc
Q 003038          736 FLIEDVEQADYCSQKGFKRAIES  758 (854)
Q Consensus       736 iliDEieka~~~v~~~Ll~~le~  758 (854)
                      +++||++-++.+++++|.+.+++
T Consensus       511 ~vlD~lnla~~dvL~aLnrlldd  533 (1856)
T KOG1808|consen  511 IVLDELNLAPHDVLEALNRLLDD  533 (1856)
T ss_pred             EEeccccccchHHHHHHHhhhhh
Confidence            99999999999999999999997

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=95.60  E-value=0.026  Score=60.40  Aligned_cols=24  Identities=8%  Similarity=0.135  Sum_probs=21.8

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHc
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ++|+|.||+|||++++.|+..+..
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l~~   25 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKLSE   25 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHH
Confidence            589999999999999999998754

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=95.59  E-value=0.016  Score=59.18  Aligned_cols=39  Identities=8%  Similarity=0.067  Sum_probs=31.8

Q ss_pred             HHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          213 EDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      +++...+....+ .+.+++++||+|+|||++.+.++..+.
T Consensus        12 ~~~~~~l~~~v~-~g~~i~I~G~tGSGKTTll~aL~~~i~   50 (186)
T cd01130          12 PLQAAYLWLAVE-ARKNILISGGTGSGKTTLLNALLAFIP   50 (186)
T ss_pred             HHHHHHHHHHHh-CCCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            456667776665 577899999999999999999997764

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.59  E-value=0.099  Score=60.51  Aligned_cols=97  Identities=18%  Similarity=0.149  Sum_probs=55.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHh--CCCCceEEEccccccCcCCCccccc-cccccCCCCCC-chH-HHHHHHHHc-C
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVF--GSHNNFVSIALSSFSSTRADSTEDS-RNKRSRDEQSC-SYI-ERFAEAVSN-N  731 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lf--g~~~~~i~id~s~~~~~~~~s~e~~-~~~rl~~~~g~-g~~-e~L~eav~~-~  731 (854)
                      ..++|.||+|+|||+++..||..+-  .....+..+++..|...   ..+.. ...+..+-+.+ .+. +.+...+++ .
T Consensus       222 ~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~~r~~---a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~~~  298 (424)
T PRK05703        222 GVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIG---AVEQLKTYAKIMGIPVEVVYDPKELAKALEQLR  298 (424)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCccHHH---HHHHHHHHHHHhCCceEccCCHHhHHHHHHHhC
Confidence            4899999999999999999987653  33456666776655310   00000 00111110111 111 245555543 4


Q ss_pred             CCEEEEEecCCCC--CHHHHHHHHHhhh
Q 003038          732 PHRVFLIEDVEQA--DYCSQKGFKRAIE  757 (854)
Q Consensus       732 p~~ViliDEieka--~~~v~~~Ll~~le  757 (854)
                      .+.+||||-.-..  +......|.+.++
T Consensus       299 ~~DlVlIDt~G~~~~d~~~~~~L~~ll~  326 (424)
T PRK05703        299 DCDVILIDTAGRSQRDKRLIEELKALIE  326 (424)
T ss_pred             CCCEEEEeCCCCCCCCHHHHHHHHHHHh
Confidence            6899999977654  4445566777776

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=95.56  E-value=0.11  Score=56.74  Aligned_cols=127  Identities=13%  Similarity=0.077  Sum_probs=72.7

Q ss_pred             HHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHh---CC---C
Q 003038          612 LCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVF---GS---H  685 (854)
Q Consensus       612 L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lf---g~---~  685 (854)
                      +......+.||...|...+...-...    ..|++       .| ...+|++|++|.|||++++...+.--   +.   .
T Consensus        28 I~~i~~~rWIgY~~A~~~L~~L~~Ll----~~P~~-------~R-mp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~   95 (302)
T PF05621_consen   28 IAYIRADRWIGYPRAKEALDRLEELL----EYPKR-------HR-MPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAER   95 (302)
T ss_pred             HHHHhcCCeecCHHHHHHHHHHHHHH----hCCcc-------cC-CCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCcc
Confidence            33344689999998876655443322    23321       12 24799999999999999999987441   11   1


Q ss_pred             CceEEEccccccCcCCCccccccccc----cCCCCCC----chHH-HHHHHHHcCCCEEEEEecCCCC---CHHHHHHHH
Q 003038          686 NNFVSIALSSFSSTRADSTEDSRNKR----SRDEQSC----SYIE-RFAEAVSNNPHRVFLIEDVEQA---DYCSQKGFK  753 (854)
Q Consensus       686 ~~~i~id~s~~~~~~~~s~e~~~~~r----l~~~~g~----g~~e-~L~eav~~~p~~ViliDEieka---~~~v~~~Ll  753 (854)
                      -+++.+.|..-.+      +......    +..|...    .-.+ +..+.++...-++++||||+.+   ...-|..++
T Consensus        96 ~PVv~vq~P~~p~------~~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~L  169 (302)
T PF05621_consen   96 IPVVYVQMPPEPD------ERRFYSAILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSYRKQREFL  169 (302)
T ss_pred             ccEEEEecCCCCC------hHHHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccHHHHHHHH
Confidence            2466666653331      2211111    1112111    1112 4557788888899999999974   333344444


Q ss_pred             Hhh
Q 003038          754 RAI  756 (854)
Q Consensus       754 ~~l  756 (854)
                      .+|
T Consensus       170 n~L  172 (302)
T PF05621_consen  170 NAL  172 (302)
T ss_pred             HHH
Confidence            444

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=95.55  E-value=0.066  Score=58.13  Aligned_cols=83  Identities=12%  Similarity=0.123  Sum_probs=60.3

Q ss_pred             HHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHH
Q 003038          214 DVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVR  293 (854)
Q Consensus       214 ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~  293 (854)
                      -|-|+..||.. .+-|.+|||.+|+||.++++-.| -|         .+..++.+.+..  .-...+|.+-||.++..+-
T Consensus        19 hi~ri~RvL~~-~~Gh~LLvG~~GsGr~sl~rLaa-~i---------~~~~~~~i~~~~--~y~~~~f~~dLk~~~~~ag   85 (268)
T PF12780_consen   19 HIARISRVLSQ-PRGHALLVGVGGSGRQSLARLAA-FI---------CGYEVFQIEITK--GYSIKDFKEDLKKALQKAG   85 (268)
T ss_dssp             HHHHHHHHHCS-TTEEEEEECTTTSCHHHHHHHHH-HH---------TTEEEE-TTTST--TTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcC-CCCCeEEecCCCccHHHHHHHHH-HH---------hccceEEEEeeC--CcCHHHHHHHHHHHHHHHh
Confidence            46778888874 66889999999999999998444 33         578899888653  1146788888988887765


Q ss_pred             hhhCCCeEEEeCccccc
Q 003038          294 SCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       294 ~~~~~~~ILfidel~~l  310 (854)
                      -. ++++++++.|-+-.
T Consensus        86 ~~-~~~~vfll~d~qi~  101 (268)
T PF12780_consen   86 IK-GKPTVFLLTDSQIV  101 (268)
T ss_dssp             CS--S-EEEEEECCCSS
T ss_pred             cc-CCCeEEEecCcccc
Confidence            43 67899999885544

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=95.54  E-value=0.017  Score=58.30  Aligned_cols=25  Identities=16%  Similarity=0.262  Sum_probs=22.4

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      .+.++|.|+||+|||++++.|+.+.
T Consensus         2 ~~~i~l~G~~gsGKst~a~~l~~~~   26 (175)
T cd00227           2 GRIIILNGGSSAGKSSIARALQSVL   26 (175)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhh
Confidence            4578999999999999999999874

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK06217 hypothetical protein; Validated

Probab=95.54  E-value=0.028  Score=57.26  Aligned_cols=56  Identities=11%  Similarity=0.150  Sum_probs=38.6

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccc-ccc----cchHHHHHHHHHHHHHHHh
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISS-FRH----MNRVEVEQRVEEIKNLVRS  294 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~-l~~----~~rge~E~rl~~l~~~~~~  294 (854)
                      +++|+|.||+|||++++.|+.++          |..++++|--. ...    ..++..+.++..+.+.+..
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l----------~~~~~~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   63 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERL----------DIPHLDTDDYFWLPTDPPFTTKRPPEERLRLLLEDLRP   63 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc----------CCcEEEcCceeeccCCCCccccCCHHHHHHHHHHHHhc
Confidence            48999999999999999999874          45566665211 111    1355667777777776643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	854
1qvr_A	854	Crystal Structure Analysis Of Clpb Length = 854		1e-05
4hse_A	397	Crystal Structure Of Clpb Nbd1 In Complex With Guan		1e-05
3pxg_A	468	Structure Of Meca121 And Clpc1-485 Complex Length =		1e-05
3pxi_A	758	Structure Of Meca108:clpc Length = 758		1e-05
1jbk_A	195	Crystal Structure Of The First Nucelotide Binding D		4e-04

>pdb|1QVR|A Chain A, Crystal Structure Analysis Of Clpb Length = 854

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 2/69 (2%)
Query: 207 LDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVK 264
           LDP+  R+E++  VI+ L+ + K N V++GE       +V G+  +I KGDVPE L+  +
Sbjct: 169 LDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKR 228
Query: 265 CLPLSISSF 273
            + L + S 
Sbjct: 229 IVSLQMGSL 237

>pdb|4HSE|A Chain A, Crystal Structure Of Clpb Nbd1 In Complex With Guanidinium Chloride And Adp Length = 397

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 2/69 (2%)
Query: 207 LDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVK 264
           LDP+  R+E++  VI+ L+ + K N V++GE       +V G+  +I KGDVPE L+  +
Sbjct: 32  LDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKR 91
Query: 265 CLPLSISSF 273
            + L + S 
Sbjct: 92  IVSLQMGSL 100

>pdb|3PXG|A Chain A, Structure Of Meca121 And Clpc1-485 Complex Length = 468

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/153 (27%), Positives = 72/153 (47%), Gaps = 10/153 (6%)
Query: 146 SRVMREAGFSSTQVKSNVEQAV-SLEICSQSTPVSSNKSKESNVLVLSQTASATKVSKPR 204
           +RV+   G S  + +  V Q + S E  S +   +SN    +N   L   A         
Sbjct: 121 ARVLNNLGVSLNKARQQVLQLLGSNETGSSAAGTNSN----ANTPTLDSLARDLTAIAKE 176
Query: 205 VSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRD 262
            SLDP+  R++++  VIE L  + K N V++GE       +  G+  +I   +VPE LRD
Sbjct: 177 DSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRD 236
Query: 263 VKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSC 295
            + + L + +     R E E R++++ + +R  
Sbjct: 237 KRVMTLDMGT---KYRGEFEDRLKKVMDEIRQA 266

>pdb|3PXI|A Chain A, Structure Of Meca108:clpc Length = 758

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/153 (27%), Positives = 72/153 (47%), Gaps = 10/153 (6%)
Query: 146 SRVMREAGFSSTQVKSNVEQAV-SLEICSQSTPVSSNKSKESNVLVLSQTASATKVSKPR 204
           +RV+   G S  + +  V Q + S E  S +   +SN    +N   L   A         
Sbjct: 121 ARVLNNLGVSLNKARQQVLQLLGSNETGSSAAGTNSN----ANTPTLDSLARDLTAIAKE 176
Query: 205 VSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRD 262
            SLDP+  R++++  VIE L  + K N V++GE       +  G+  +I   +VPE LRD
Sbjct: 177 DSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRD 236
Query: 263 VKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSC 295
            + + L + +     R E E R++++ + +R  
Sbjct: 237 KRVMTLDMGT---KYRGEFEDRLKKVMDEIRQA 266

>pdb|1JBK|A Chain A, Crystal Structure Of The First Nucelotide Binding Domain Of Clpb Length = 195

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 27/88 (30%), Positives = 47/88 (53%), Gaps = 4/88 (4%)
Query: 207 LDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVK 264
           LDP+  R+E++   I+ L  + K N V++GE       +V G+  +I  G+VPE L+  +
Sbjct: 21  LDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRR 80
Query: 265 CLPLSISSF--RHMNRVEVEQRVEEIKN 290
            L L + +       R E E+R++ + N
Sbjct: 81  VLALDMGALVAGAKYRGEFEERLKGVLN 108

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	854
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	1e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	1e-09
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	2e-09
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	4e-08
3zri_A	171	CLPB protein, CLPV; chaperone, HSP100 proteins, AA	2e-07
1khy_A	148	CLPB protein; alpha helix, chaperone; 1.95A {Esche	1e-06
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	4e-06
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	6e-06

>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* Length = 758

 Score = 64.2 bits (157), Expect = 1e-10
 Identities = 63/289 (21%), Positives = 105/289 (36%), Gaps = 66/289 (22%)

Query: 12  LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALEL 71
           L  E    +  A   AR   H  +T  H+   +LA    LL         +P   +ALE 
Sbjct: 2   LNQELELSLNMAFARAREHRHEFMTVEHL---LLA----LLS--------NPSAREALEA 46

Query: 72  CFNVALNRL--------PASTSTPMLGGHCQFPTISNALVAAFKRAQAH-QRRGSIENQQ 122
           C +V L  L          +T         +    + +     +RA  H Q  G  E   
Sbjct: 47  C-SVDLVALRQELEAFIEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRNE--- 102

Query: 123 QPLLAVKIELEQLIISILDDPS--VSRVMREAGFSSTQVKSNVEQAVSLEICSQS----- 175
                  +    ++++I  +     + ++R+   S   V + +      +  +QS     
Sbjct: 103 -------VTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHGTRKDEPTQSSDPGS 155

Query: 176 TPVSSNKSKESNVLV-----LSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKR 228
            P S  ++     L      L+Q A           +DP+  R +++   I+ L  +RK 
Sbjct: 156 QPNSEEQAGGEERLENFTTNLNQLARVGG-------IDPLIGREKELERAIQVLCRRRKN 208

Query: 229 NFVVVGECLASIEGV-----VRGVIDKIEKGDVPEALRDVKCLPLSISS 272
           N ++VGE      GV       G+  +I +GDVPE + D     L I S
Sbjct: 209 NPLLVGE-----SGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGS 252

>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 = 61.0 bits (147), Expect = 1e-09
 Identities = 96/622 (15%), Positives = 206/622 (33%), Gaps = 157/622 (25%)

Query: 118 IENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAV--SLEI---- 171
           +++  + +L+ K E++ +I+S     +VS  +R      ++ +  V++ V   L I    
Sbjct: 38  VQDMPKSILS-KEEIDHIIMS---KDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKF 93

Query: 172 --------CSQSTPVSSNKSKESNVLVLSQTASATKVSKPRVSLDPIRNEDVMYVIENLM 223
                     Q + ++    ++ + L           +K  VS    R +  + + + L+
Sbjct: 94  LMSPIKTEQRQPSMMTRMYIEQRDRL----YNDNQVFAKYNVS----RLQPYLKLRQALL 145

Query: 224 SKRKRNFVVV------GE-CLASIEGVVR--GVIDKIEKG---------DVPEAL----- 260
             R    V++      G+  +A    V     V  K++           + PE +     
Sbjct: 146 ELRPAKNVLIDGVLGSGKTWVAL--DVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQ 203

Query: 261 ---RDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRS-----CLGRGIVL-NLGDLE-WA 310
                +     S S      ++ +     E++ L++S     CL   +VL N+ + + W 
Sbjct: 204 KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL---LVLLNVQNAKAWN 260

Query: 311 EF----------RASS-SEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYM 359
            F          R    ++ +     +  HI ++       +  +    +  +     Y+
Sbjct: 261 AFNLSCKILLTTRFKQVTDFLSAATTT--HISLD--HHSMTLTPDE---VKSL--LLKYL 311

Query: 360 RCKSGHPSLETLWSLHPLTIP--AGSLSLSLITTD--SDLQSQSTSKKAESGVSWLLFEG 415
            C+      E L + +P  +   A S+   L T D    +     +   ES ++ L    
Sbjct: 312 DCRPQDLPREVL-TTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVL---E 367

Query: 416 EEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPA-WLQQYKNEKKATLSNNDKD 474
             E ++       S  F            ++  PT  L   W    K++    ++   K 
Sbjct: 368 PAEYRK--MFDRLSV-FPP----------SAHIPTILLSLIWFDVIKSDVMVVVNKLHKY 414

Query: 475 SGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYD------QQYPNFHKT 528
           S    L +K         K+   S  ++         +     Y         Y N  KT
Sbjct: 415 S----LVEKQP-------KESTISIPSIYLELKVKLEN----EYALHRSIVDHY-NIPKT 458

Query: 529 HRDWAVVEPKQS--WREH---HFLFSHEASDKSTSEPSLRLYIPEHKD---LKQPLSSNR 580
                ++ P     +  H   H L + E  ++ T      +++    D   L+Q +   R
Sbjct: 459 FDSDDLIPPYLDQYFYSHIGHH-LKNIEHPERMTLFR--MVFL----DFRFLEQKI---R 508

Query: 581 NSTPNSTSSSDIM----EMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLK 636
           + +    +S  I+    ++++   +   N      L NA+   +P        I   ++ 
Sbjct: 509 HDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLP-------KIEENLIC 561

Query: 637 CRSGTMRRKGKFKDHSEVKEET 658
            +   + R     +   + EE 
Sbjct: 562 SKYTDLLRIALMAEDEAIFEEA 583

>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 = 45.2 bits (106), Expect = 1e-04
 Identities = 52/384 (13%), Positives = 112/384 (29%), Gaps = 74/384 (19%)

Query: 417 EENKQLTCCADCSAKFEAEARSLQSSSCN--SDSPTSSLPAWLQQYKNEKKATLSNNDKD 474
           E  +      D  + FE     + +  C    D P S L       K E    + + D  
Sbjct: 10  ETGEHQYQYKDILSVFEDAF--VDNFDCKDVQDMPKSILS------KEEIDHIIMSKDAV 61

Query: 475 SGVR----DLCKKWNSI----CNSIHKQPY-YSERTLTFSSASPSSSTSGFSYDQQYPNF 525
           SG       L  K   +       + +  Y +    +      PS  T  +   +     
Sbjct: 62  SGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRD---- 117

Query: 526 HKTHRDWAVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDL---KQPLSSN--R 580
            + + D  V       R   +L   +A  +     ++ +       L   K  ++ +   
Sbjct: 118 -RLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI----DGVLGSGKTWVALDVCL 172

Query: 581 NSTPNSTSSSDI--MEMEYVHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCR 638
           +          I  + ++  +  + +  E L  L   ++     + D     +N  L+  
Sbjct: 173 SYKVQCKMDFKIFWLNLKNCNSPETV-LEMLQKLLYQIDPNWTSRSDH---SSNIKLRIH 228

Query: 639 SGTMRRKGKFKDHS---------EVKE-ETWLFFQGVDADAKEKI-----AKELARLVFG 683
           S     +   K             V+  + W  F     +   KI      K++   +  
Sbjct: 229 SIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAF-----NLSCKILLTTRFKQVTDFLSA 283

Query: 684 SHNNFVSIALSSFSSTRADSTE---DSRNKRSRD--EQSCS----YIERFAEAVSNNPHR 734
           +    +S+   S + T  +         + R +D   +  +     +   AE++ +    
Sbjct: 284 ATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT 343

Query: 735 VFLIEDVEQADYCSQKGFKRAIES 758
               ++ +  +          IES
Sbjct: 344 ---WDNWKHVNC---DKLTTIIES 361

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis} Length = 758

 Score = 60.7 bits (148), Expect = 1e-09
 Identities = 60/298 (20%), Positives = 113/298 (37%), Gaps = 57/298 (19%)

Query: 12  LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALEL 71
            T  A  V+  A   A R GH  +   H+   ++    G+   A LQ+    L  + ++ 
Sbjct: 6   FTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKA-LQALG--LGSEKIQK 62

Query: 72  CFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIE 131
                + R    + T         P     +  +   A+                   + 
Sbjct: 63  EVESLIGRGQEMSQTIHYT-----PRAKKVIELSMDEARKLGHS-------------YVG 104

Query: 132 LEQLIISILDDPS--VSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKESNVL 189
            E +++ ++ +     +RV+   G S  + +  V Q +      ++   ++  +  +N  
Sbjct: 105 TEHILLGLIREGEGVAARVLNNLGVSLNKARQQVLQLLGSN---ETGSSAAGTNSNANTP 161

Query: 190 VLSQ-----TASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEG 242
            L       TA A +       LDP+  R++++  VIE L  + K N V++GE      G
Sbjct: 162 TLDSLARDLTAIAKE-DS----LDPVIGRSKEIQRVIEVLSRRTKNNPVLIGE-----PG 211

Query: 243 V-----VRGVIDKIEKGDVPEALRDVKCLPLSI-SSFRHMNRVEVEQR----VEEIKN 290
           V       G+  +I   +VPE LRD + + L + + +R     E E R    ++EI+ 
Sbjct: 212 VGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMGTKYRG----EFEDRLKKVMDEIRQ 265

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis} Length = 468

 Score = 59.9 bits (146), Expect = 2e-09
 Identities = 54/265 (20%), Positives = 99/265 (37%), Gaps = 48/265 (18%)

Query: 12  LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALEL 71
            T  A  V+  A   A R GH  +   H+   ++    G+   A LQ+    L  + ++ 
Sbjct: 6   FTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKA-LQALG--LGSEKIQK 62

Query: 72  CFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIE 131
                + R    + T         P     +  +   A+              L    + 
Sbjct: 63  EVESLIGRGQEMSQTIHYT-----PRAKKVIELSMDEARK-------------LGHSYVG 104

Query: 132 LEQLIISILDDPS--VSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKESNVL 189
            E +++ ++ +     +RV+   G S  + +  V Q +      ++   ++  +  +N  
Sbjct: 105 TEHILLGLIREGEGVAARVLNNLGVSLNKARQQVLQLLGSN---ETGSSAAGTNSNANTP 161

Query: 190 VLSQ-----TASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEG 242
            L       TA A +       LDP+  R++++  VIE L  + K N V++GE      G
Sbjct: 162 TLDSLARDLTAIAKE-DS----LDPVIGRSKEIQRVIEVLSRRTKNNPVLIGE-----PG 211

Query: 243 V-----VRGVIDKIEKGDVPEALRD 262
           V       G+  +I   +VPE LRD
Sbjct: 212 VGKTAIAEGLAQQIINNEVPEILRD 236

>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 Length = 854

 Score = 56.4 bits (137), Expect = 4e-08
 Identities = 59/269 (21%), Positives = 103/269 (38%), Gaps = 54/269 (20%)

Query: 12  LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALEL 71
            T  A   + QA  LA+R  H  +   H+   +L     L      ++ + P   KAL+ 
Sbjct: 6   WTQAAREALAQAQVLAQRMKHQAIDLPHLWAVLLKDERSLAWRLLEKAGADP---KALKE 62

Query: 72  CFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIE 131
                L RLP        G       +++ L  A  RA+                   + 
Sbjct: 63  LQERELARLPKVE-----GAEVG-QYLTSRLSGALNRAEGLMEELKDR---------YVA 107

Query: 132 LEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAVSLEICSQSTPVSSNKSKESNVLV- 190
           ++ L++++ +                     ++ A+  E+    T  + +     N L  
Sbjct: 108 VDTLVLALAEAT-----------PGLPGLEALKGALK-ELRGGRTVQTEHAESTYNALEQ 155

Query: 191 ----LSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGV- 243
               L++ A+  K       LDP+  R+E++  VI+ L+ + K N V++GE      GV 
Sbjct: 156 YGIDLTRLAAEGK-------LDPVIGRDEEIRRVIQILLRRTKNNPVLIGE-----PGVG 203

Query: 244 ----VRGVIDKIEKGDVPEALRDVKCLPL 268
               V G+  +I KGDVPE L+  + + L
Sbjct: 204 KTAIVEGLAQRIVKGDVPEGLKGKRIVSL 232

>3zri_A CLPB protein, CLPV; chaperone, HSP100 proteins, AAA+ proteins, T6SS, secretion,; 1.80A {Vibrio cholerae} PDB: 3zrj_A Length = 171

 Score = 51.1 bits (122), Expect = 2e-07
 Identities = 28/168 (16%), Positives = 55/168 (32%), Gaps = 29/168 (17%)

Query: 12  LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALEL 71
           L A++   ++QA +L   R H +VT  H  + +L      +R    Q+         ++ 
Sbjct: 25  LNAQSKLALEQAASLCIERQHPEVTLEHYLDVLLDNPLSDVRLVLKQAGLEV---DQVKQ 81

Query: 72  CFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIE 131
                 +R     + P           S  LV   + A       S E +Q      ++ 
Sbjct: 82  AIASTYSREQVLDTYPAF---------SPLLVELLQEAWLL---SSTELEQA-----ELR 124

Query: 132 LEQLIISILDDPS---VSRVMRE-AGFSSTQVKSNVEQAVSLEICSQS 175
              + ++ L         +++    G +   +K +        I S S
Sbjct: 125 SGAIFLAALTRADRYLSFKLISLFEGINRENLKKHFA-----MILSDS 167

>1khy_A CLPB protein; alpha helix, chaperone; 1.95A {Escherichia coli} SCOP: a.174.1.1 Length = 148

 Score = 48.0 bits (115), Expect = 1e-06
 Identities = 33/163 (20%), Positives = 58/163 (35%), Gaps = 33/163 (20%)

Query: 12  LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALEL 71
           LT +    +  A +LA    +  + PLH+ + +L    G +      +  +      L  
Sbjct: 6   LTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINA---GQLRT 62

Query: 72  CFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAH-QRRG----SIENQQQPLL 126
             N ALNRLP         G       S  LV          Q+RG    S E       
Sbjct: 63  DINQALNRLPQVE------GTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSEL------ 110

Query: 127 AVKIELEQLIISILDDPS-VSRVMREAGFSSTQVKSNVEQAVS 168
                    +++ L+    ++ +++ AG +     +N+ QA+ 
Sbjct: 111 --------FVLAALESRGTLADILKAAGAT----TANITQAIE 141

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum} Length = 187

 Score = 47.4 bits (113), Expect = 4e-06
 Identities = 28/103 (27%), Positives = 55/103 (53%), Gaps = 12/103 (11%)

Query: 207 LDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVK 264
           LDP+  R+ ++   I+ L  + K N +++G+       +V G+  KI +GDVP++L+  K
Sbjct: 21  LDPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRK 80

Query: 265 CLPLSISS------FRHMNRVEVEQRVEEIKNLVRSCLGRGIV 301
            + L +SS      +R     + E+R++ I   V+   G+ ++
Sbjct: 81  LVSLDLSSLIAGAKYRG----DFEERLKSILKEVQDAEGQVVM 119

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20 Length = 195

 Score = 46.9 bits (112), Expect = 6e-06
 Identities = 29/103 (28%), Positives = 52/103 (50%), Gaps = 12/103 (11%)

Query: 207 LDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVK 264
           LDP+  R+E++   I+ L  + K N V++GE       +V G+  +I  G+VPE L+  +
Sbjct: 21  LDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRR 80

Query: 265 CLPLSISS------FRHMNRVEVEQRVEEIKNLVRSCLGRGIV 301
            L L + +      +R     E E+R++ + N +    G  I+
Sbjct: 81  VLALDMGALVAGAKYRG----EFEERLKGVLNDLAKQEGNVIL 119

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	854
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	100.0
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	100.0
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	100.0
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	100.0
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.85
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.83
3fh2_A	146	Probable ATP-dependent protease (heat shock prote;	99.82
3fes_A	145	ATP-dependent CLP endopeptidase; alpha-helical bun	99.8
2y1q_A	150	CLPC N-domain, negative regulator of genetic compe	99.79
1khy_A	148	CLPB protein; alpha helix, chaperone; 1.95A {Esche	99.79
3zri_A	171	CLPB protein, CLPV; chaperone, HSP100 proteins, AA	99.74
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.71
1k6k_A	143	ATP-dependent CLP protease ATP-binding subunit CLP	99.69
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.69
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.67
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.52
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.49
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	99.45
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.44
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	99.41
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	99.41
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	99.39
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	99.39
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.33
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.32
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	99.31
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.23
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.22
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.21
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.18
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.18
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.18
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.17
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	99.15
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.14
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.12
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.12
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.1
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.1
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.1
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.08
3co5_A	143	Putative two-component system transcriptional RES	99.08
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.07
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	99.06
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	99.06
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	99.04
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.04
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.04
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.01
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	99.01
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.0
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.0
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.99
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	98.98
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	98.98
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	98.98
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	98.96
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	98.95
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	98.94
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.93
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	98.93
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	98.92
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.92
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.92
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	98.92
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	98.9
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	98.9
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.89
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	98.88
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.87
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	98.87
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	98.87
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	98.87
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	98.86
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	98.86
3pvs_A	447	Replication-associated recombination protein A; ma	98.85
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.85
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.85
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	98.84
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.83
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.83
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.82
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.82
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.82
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.81
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	98.8
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.77
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.75
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	98.74
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	98.74
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	98.74
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	98.74
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	98.73
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	98.72
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	98.7
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.7
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	98.69
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.69
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.69
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	98.66
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.65
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	98.64
3pvs_A	447	Replication-associated recombination protein A; ma	98.64
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.64
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	98.63
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.63
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	98.62
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	98.6
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.59
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.56
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.53
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.52
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.49
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.49
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	98.47
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.44
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	98.44
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.42
3co5_A	143	Putative two-component system transcriptional RES	98.41
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.41
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	98.39
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.38
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.38
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.36
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.35
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.34
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	98.32
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	98.32
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.32
3bos_A	242	Putative DNA replication factor; P-loop containing	98.32
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	98.31
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	98.31
3fh2_A	146	Probable ATP-dependent protease (heat shock prote;	98.3
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	98.29
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.29
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.28
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.27
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.27
3fes_A	145	ATP-dependent CLP endopeptidase; alpha-helical bun	98.26
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.24
3f8t_A	506	Predicted ATPase involved in replication control,	98.23
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	98.22
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	98.21
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	98.17
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	98.17
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.15
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.11
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.1
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.1
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.1
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	98.1
2y1q_A	150	CLPC N-domain, negative regulator of genetic compe	98.09
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.09
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	98.07
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.05
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	98.04
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.03
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	98.01
3bos_A	242	Putative DNA replication factor; P-loop containing	97.93
2r44_A	331	Uncharacterized protein; putative ATPase, structur	97.87
2qgz_A	308	Helicase loader, putative primosome component; str	97.87
1k6k_A	143	ATP-dependent CLP protease ATP-binding subunit CLP	97.85
2fna_A	357	Conserved hypothetical protein; structural genomic	97.81
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	97.8
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	97.72
1khy_A	148	CLPB protein; alpha helix, chaperone; 1.95A {Esche	97.71
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.68
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	97.65
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.65
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.64
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.63
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.6
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.56
1tue_A	212	Replication protein E1; helicase, replication, E1E	97.48
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	97.41
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	97.34
2qgz_A	308	Helicase loader, putative primosome component; str	97.28
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	97.14
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	97.13
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	97.06
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.05
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	97.04
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	97.01
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	97.0
3zri_A	171	CLPB protein, CLPV; chaperone, HSP100 proteins, AA	96.99
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	96.97
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.93
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	96.93
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	96.87
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	96.86
2fna_A	357	Conserved hypothetical protein; structural genomic	96.84
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	96.83
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	96.82
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	96.81
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.72
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	96.68
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	96.66
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	96.63
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	96.58
2eyu_A	261	Twitching motility protein PILT; pilus retraction	96.57
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	96.54
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.41
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	96.33
2ewv_A	372	Twitching motility protein PILT; pilus retraction	96.29
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	96.19
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	95.9
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	95.86
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	95.76
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	95.76
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	95.69
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	95.65
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	95.65
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	95.61
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.57
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	95.33
3ice_A	422	Transcription termination factor RHO; transcriptio	95.24
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.22
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	95.22
1p9r_A	418	General secretion pathway protein E; bacterial typ	95.19
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	95.15
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	95.14
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	95.07
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	95.0
1tue_A	212	Replication protein E1; helicase, replication, E1E	95.0
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	94.98
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	94.92
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	94.88
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	94.85
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	94.82
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	94.79
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	94.77
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	94.77
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	94.73
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	94.73
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	94.65
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	94.64
1via_A	175	Shikimate kinase; structural genomics, transferase	94.63
2xxa_A	433	Signal recognition particle protein; protein trans	94.62
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	94.61
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	94.61
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	94.56
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	94.55
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	94.52
4a74_A	231	DNA repair and recombination protein RADA; hydrola	94.51
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	94.48
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	94.41
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	94.4
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	94.35
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	94.33
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	94.27
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	94.26
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	94.22
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	94.19
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	94.15
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	94.12
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	94.11
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	94.09
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	94.09
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	94.07
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	94.06
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	94.02
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	94.02
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	93.99
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	93.99
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	93.99
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	93.96
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	93.95
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	93.94
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	93.82
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	93.82
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	93.76
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	93.75
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	93.69
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	93.68
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	93.68
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	93.64
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	93.63
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	93.59
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	93.56
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	93.56
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	93.55
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	93.54
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	93.54
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	93.5
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	93.49
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	93.49
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	93.41
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	93.39
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	93.36
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	93.36
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	93.33
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	93.29
2cvh_A	220	DNA repair and recombination protein RADB; filamen	93.27
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	93.26
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	93.23
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	93.2
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	93.17
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	93.11
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	93.1
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	93.1
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	93.08
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	93.06
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	93.05
2og2_A	359	Putative signal recognition particle receptor; nuc	93.04
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	93.03
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	92.98
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	92.96
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	92.95
1xp8_A	366	RECA protein, recombinase A; recombination, radior	92.94
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	92.92
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	92.92
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	92.91
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	92.9
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	92.87
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	92.84
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	92.84
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	92.83
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	92.83
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	92.82
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	92.81
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	92.8
1via_A	175	Shikimate kinase; structural genomics, transferase	92.8
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	92.8
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	92.77
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	92.76
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	92.74
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	92.72
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	92.72
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	92.69
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	92.66
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	92.66
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	92.65
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	92.63
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	92.62
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	92.62
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	92.62
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	92.61
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	92.52
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	92.51
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	92.47
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	92.46
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	92.45
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	92.44
2xxa_A	433	Signal recognition particle protein; protein trans	92.43
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	92.41
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	92.39
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	92.39
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	92.38
2z43_A	324	DNA repair and recombination protein RADA; archaea	92.37
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	92.29
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	92.29
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	92.29
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	92.28
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	92.25
1xp8_A	366	RECA protein, recombinase A; recombination, radior	92.22
1u94_A	356	RECA protein, recombinase A; homologous recombinat	92.2
1u94_A	356	RECA protein, recombinase A; homologous recombinat	92.19
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	92.18
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	92.17
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	92.14
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	92.11
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	92.1
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	92.08
2vli_A	183	Antibiotic resistance protein; transferase, tunica	92.08
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	92.08
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	92.08
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	92.04
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	92.03
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	92.02
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	91.99
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	91.97
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	91.95
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	91.91
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	91.9
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	91.87
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	91.85
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	91.83
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	91.81
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	91.77
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	91.75
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	91.74
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	91.72
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	91.67
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	91.62
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	91.58
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	91.56
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	91.55
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	91.5
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	91.5
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	91.49
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	91.47
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	91.45
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	91.38
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	91.36
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	91.35
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	91.32
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	91.29
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	91.28
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	91.27
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	91.27
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	91.21
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	91.15
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	91.13
3l0o_A	427	Transcription termination factor RHO; helicase, RH	91.13
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	91.08
2fh5_B	214	SR-beta, signal recognition particle receptor beta	91.08
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	91.07
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	91.06
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	91.03
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	91.01
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	91.0
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	90.91
2ged_A	193	SR-beta, signal recognition particle receptor beta	90.9
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	90.85
2vli_A	183	Antibiotic resistance protein; transferase, tunica	90.83
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	90.81
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	90.81
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	90.73
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	90.72
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	90.69
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	90.69
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	90.67
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	90.65
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	90.65
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	90.62
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	90.62
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	90.53
2hf9_A	226	Probable hydrogenase nickel incorporation protein	90.53
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	90.47
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	90.4
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	90.38
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	90.37
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	90.34
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	90.33
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	90.31
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	90.31
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	90.27
2r6a_A	454	DNAB helicase, replicative helicase; replication,	90.25
2z43_A	324	DNA repair and recombination protein RADA; archaea	90.24
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	90.22
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	90.18
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	90.18
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	90.17
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	90.11
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	90.08
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	90.07
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	90.04
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	90.02
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	89.97
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	89.95
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	89.93
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	89.87
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	89.81
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	89.78
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	89.76
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	89.68
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	89.67
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	89.66
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	89.62
3io5_A	333	Recombination and repair protein; storage dimer, i	89.62
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	89.57
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	89.57
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	89.54
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	89.53
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	89.52
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	89.52
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	89.43
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	89.37
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	89.34
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	89.32
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	89.23
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	89.16
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	89.15
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	89.11
3b6e_A	216	Interferon-induced helicase C domain-containing P;	89.08
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	89.05
1nrj_B	218	SR-beta, signal recognition particle receptor beta	89.0
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	88.96
1nrj_B	218	SR-beta, signal recognition particle receptor beta	88.89
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	88.89
2wji_A	165	Ferrous iron transport protein B homolog; membrane	88.87
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	88.84
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	88.83
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	88.8
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	88.78
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	88.72
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	88.72
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	88.69
3kta_A	182	Chromosome segregation protein SMC; structural mai	88.63
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	88.6
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	88.58
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	88.55
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	88.54
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	88.52
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	88.52
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	88.38
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	88.37
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	88.36
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	88.35
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	88.34

>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=100.00  E-value=8.1e-71  Score=679.67  Aligned_cols=646  Identities=20%  Similarity=0.269  Sum_probs=448.2

Q ss_pred             chHHhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCCCCC
Q 003038            7 TIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTST   86 (854)
Q Consensus         7 ~~~~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~~~~   86 (854)
                      |++++||+.++++|+.|+++|+++||.+|+|||||++||.++++.+.++|.++|+++   +.|+..++..+.++|...++
T Consensus         1 ~~~~~~t~~a~~al~~A~~~A~~~~h~~i~~eHLLlaLl~~~~~~~~~iL~~~gvd~---~~l~~~l~~~l~~~p~~~~~   77 (854)
T 1qvr_A            1 MNLERWTQAAREALAQAQVLAQRMKHQAIDLPHLWAVLLKDERSLAWRLLEKAGADP---KALKELQERELARLPKVEGA   77 (854)
T ss_dssp             ---CCSCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHCCSSSSHHHHHHHTTSSCH---HHHHHHHHHHHHTSCCCCGG
T ss_pred             CChhhhCHHHHHHHHHHHHHHHHcCCCCccHHHHHHHHHhCCCcHHHHHHHHcCCCH---HHHHHHHHHHHhhCCCCCCC
Confidence            467899999999999999999999999999999999999999999999999999986   89999999999998875421


Q ss_pred             CCCCCCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCChHHHHHHHhCCCHHHHHHHHHHH
Q 003038           87 PMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQA  166 (854)
Q Consensus        87 ~~~~~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~~~~~iL~~~Gi~~~~l~~~v~~~  166 (854)
                      +  +.++++|.+.++|+.|...|..+    +.+         +|+++|||+||++++...       ++...++..+.+ 
T Consensus        78 ~--~~~~~S~~~~~vL~~A~~~a~~~----g~~---------~I~~ehlLlall~~~~~~-------~~~~~~~~~~~~-  134 (854)
T 1qvr_A           78 E--VGQYLTSRLSGALNRAEGLMEEL----KDR---------YVAVDTLVLALAEATPGL-------PGLEALKGALKE-  134 (854)
T ss_dssp             G--TTCEECHHHHHHHHHHHHHHHTT----TCS---------SCCHHHHHHHHHHHSTTS-------CCHHHHHHHHTS-
T ss_pred             C--CCCCCCHHHHHHHHHHHHHHHHc----CCc---------EeeHHHHHHHHHhccccc-------CCHHHHHHHHHH-
Confidence            1  12334555555444444444432    223         599999999999875321       788888777653 


Q ss_pred             hhhhhccCCCCCCCCCcccccccccccccccccccCCCCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHH
Q 003038          167 VSLEICSQSTPVSSNKSKESNVLVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVV  244 (854)
Q Consensus       167 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v  244 (854)
                      +++    ........  .....+.+.+|+.+++..++.|++||+  |++++++++++|.+++++|++|+||||||||++|
T Consensus       135 ~~~----~~~~~~~~--~~~~~~~l~~~~~~l~~~~r~~~ld~viGr~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~la  208 (854)
T 1qvr_A          135 LRG----GRTVQTEH--AESTYNALEQYGIDLTRLAAEGKLDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIV  208 (854)
T ss_dssp             SCS----CCSSCSSC--CCCCCSHHHHHEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHH
T ss_pred             hcc----cccccccc--ccccchhHHHHHHhHHHHHhcCCCcccCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHH
Confidence            221    11111111  111245688999999988889999997  9999999999999999999999999999999999


Q ss_pred             HHHHHHHHcCCCCcccCCceEEEccccccccc--chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-ccccccccccc
Q 003038          245 RGVIDKIEKGDVPEALRDVKCLPLSISSFRHM--NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVR  321 (854)
Q Consensus       245 ~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~--~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~  321 (854)
                      +++|.++..+++|..|++.+++.++++.+.++  ++|+++++++.+++.+... ++++||||||+|++ +.+...     
T Consensus       209 ~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~g~~~~g~~~~~l~~~~~~~~~~-~~~~iL~IDEi~~l~~~~~~~-----  282 (854)
T 1qvr_A          209 EGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQS-QGEVILFIDELHTVVGAGKAE-----  282 (854)
T ss_dssp             HHHHHHHHHTCSCTTSTTCEEEEECC-----------CHHHHHHHHHHHHHTT-CSSEEEEECCC---------------
T ss_pred             HHHHHHHhcCCCchhhcCCeEEEeehHHhhccCccchHHHHHHHHHHHHHHhc-CCCeEEEEecHHHHhccCCcc-----
Confidence            99999999999999999999999999999865  9999999999999999875 56899999999999 776532     


Q ss_pred             ccchhhhHHHHHHHhhccc--CCCCceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHHHhh----------
Q 003038          322 GYYCSIEHIIMEIGKLVCG--IGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLI----------  389 (854)
Q Consensus       322 ~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~al~----------  389 (854)
                              +.+++.++|++  .++  .+++||+||..+|++ +..+|+|.+  ||+.|.|++++......          
T Consensus       283 --------g~~~~~~~L~~~l~~~--~i~~I~at~~~~~~~-~~~d~aL~r--Rf~~i~l~~p~~~e~~~iL~~~~~~~~  349 (854)
T 1qvr_A          283 --------GAVDAGNMLKPALARG--ELRLIGATTLDEYRE-IEKDPALER--RFQPVYVDEPTVEETISILRGLKEKYE  349 (854)
T ss_dssp             -----------------HHHHHTT--CCCEEEEECHHHHHH-HTTCTTTCS--CCCCEEECCCCHHHHHHHHHHHHHHHH
T ss_pred             --------chHHHHHHHHHHHhCC--CeEEEEecCchHHhh-hccCHHHHh--CCceEEeCCCCHHHHHHHHHhhhhhhh
Confidence                    34567777765  344  699999999999999 899999999  99999999987543221          


Q ss_pred             ------cccch------hhhccccCCcCCCcccccccchhhhhhhcccccchhhhHHHHhhhhcccCCCCCCCCCChHHH
Q 003038          390 ------TTDSD------LQSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWL  457 (854)
Q Consensus       390 ------~~~s~------~~~~~~~~~~~pdkaidlld~a~~~~~~~c~~~~~~~~e~e~~~~~~~~~~~~~~~~~lp~~l  457 (854)
                            +.+..      +..+|++++++|||+++++|+|++.+.+.                          ..+.|.+|
T Consensus       350 ~~~~~~i~~~al~~~~~ls~r~i~~~~lp~kai~lldea~a~~~~~--------------------------~~~~p~~l  403 (854)
T 1qvr_A          350 VHHGVRISDSAIIAAATLSHRYITERRLPDKAIDLIDEAAARLRMA--------------------------LESAPEEI  403 (854)
T ss_dssp             HHTTCEECHHHHHHHHHHHHHHCCSSCTHHHHHHHHHHHHHHHHHT--------------------------TTTHHHHH
T ss_pred             hhcCCCCCHHHHHHHHHHHhhhcccccChHHHHHHHHHHHHHHHhh--------------------------ccCCchhH
Confidence                  12221      33478999999999999999998774321                          11345555


Q ss_pred             HhhHHHHh-------hcccCCCccc-----------ch-----hhHHHHHHHHhhhcccCcccccc--ccccccCCCCCC
Q 003038          458 QQYKNEKK-------ATLSNNDKDS-----------GV-----RDLCKKWNSICNSIHKQPYYSER--TLTFSSASPSSS  512 (854)
Q Consensus       458 ~~~~~~~~-------~~~~~~d~~~-----------~~-----~~L~~~w~~~~~~~~~~~~~~~~--~~~~~s~~~~s~  512 (854)
                      +.++....       .+....+..+           ..     ..+..+|+..+..++.....++.  .+++.       
T Consensus       404 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------  476 (854)
T 1qvr_A          404 DALERKKLQLEIEREALKKEKDPDSQERLKAIEAEIAKLTEEIAKLRAEWEREREILRKLREAQHRLDEVRRE-------  476 (854)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCSSHHHHSCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------
T ss_pred             HHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh-------
Confidence            54442221       1110000000           00     16788898887655431111100  00000       


Q ss_pred             CCcccccccCcchhhhhhhhhccccccchhccccccccccccCCCCCcccccccccccccccccccCCCCCCCCCCcccc
Q 003038          513 TSGFSYDQQYPNFHKTHRDWAVVEPKQSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNSTSSSDI  592 (854)
Q Consensus       513 ~~~~~~~~~~~~l~~~~~~~~~~~~~~p~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~  592 (854)
                      ..  ..+. ..++.....- .  ....|...+ ++...+...                 ...+++.      ..++.+++
T Consensus       477 ~~--~~~~-~~~~~~~~~~-~--~~~~~~~~~-~~~~~~~~~-----------------~~~~~~~------~~v~~~~l  526 (854)
T 1qvr_A          477 IE--LAER-QYDLNRAAEL-R--YGELPKLEA-EVEALSEKL-----------------RGARFVR------LEVTEEDI  526 (854)
T ss_dssp             HH--HHTT-TTCHHHHHHH-H--TTHHHHHHH-HHHHHHHHS-----------------SSCSSCC------SEECHHHH
T ss_pred             HH--HHHh-cccHHHHHHH-h--hhhhHHHHH-HHHHHHhhh-----------------ccccccc------CCcCHHHH
Confidence            00  0000 1111111100 0  001111111 110000000                 0000111      22344445


Q ss_pred             ccc--hhh----hhhhhhhHHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCC
Q 003038          593 MEM--EYV----HKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVD  666 (854)
Q Consensus       593 ~~v--~~~----~~~~~~~~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~  666 (854)
                      ..+  +|+    .++.+.+.+++..|++.|.++|+||++++..|..+|.+.++|+.+++         +|.+++||+||+
T Consensus       527 ~~~v~~~~~ip~~~~~~~~~~~l~~l~~~l~~~viG~~~a~~~l~~~i~~~~~g~~~~~---------~p~~~vLl~Gp~  597 (854)
T 1qvr_A          527 AEIVSRWTGIPVSKLLEGEREKLLRLEEELHKRVVGQDEAIRAVADAIRRARAGLKDPN---------RPIGSFLFLGPT  597 (854)
T ss_dssp             HHHHHTTSSCHHHHTTCCHHHHHHSHHHHHHHHSCSCHHHHHHHHHHHHHHGGGCSCSS---------SCSEEEEEBSCS
T ss_pred             HHHHHHHhCCChHhhcHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHHHHHhcccCCCC---------CCceEEEEECCC
Confidence            444  554    34556677888899999999999999999999999999999998864         788899999999


Q ss_pred             CchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccC-CCCCC-chHH--HHHHHHHcCCCEEEEEecCC
Q 003038          667 ADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSR-DEQSC-SYIE--RFAEAVSNNPHRVFLIEDVE  742 (854)
Q Consensus       667 GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~-~~~g~-g~~e--~L~eav~~~p~~ViliDEie  742 (854)
                      |||||++|++||+.+|++..+|+++||++|.       +.+..++++ .+++| ||.+  .|+++++.+|++|||||||+
T Consensus       598 GtGKT~lA~~la~~~~~~~~~~i~i~~~~~~-------~~~~~s~l~g~~~~~~G~~~~g~l~~~~~~~~~~vl~lDEi~  670 (854)
T 1qvr_A          598 GVGKTELAKTLAATLFDTEEAMIRIDMTEYM-------EKHAVSRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDEIE  670 (854)
T ss_dssp             SSSHHHHHHHHHHHHHSSGGGEEEECTTTCC-------SSGGGGGC--------------CHHHHHHHCSSEEEEESSGG
T ss_pred             CCCHHHHHHHHHHHhcCCCCcEEEEechhcc-------chhHHHHHcCCCCCCcCccccchHHHHHHhCCCeEEEEeccc
Confidence            9999999999999999999999999999998       667777777 46677 8875  79999999999999999999


Q ss_pred             CCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCC
Q 003038          743 QADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       743 ka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      ++++++|+.|+++|++|+++|+.|+.++|+|+|||||||.
T Consensus       671 ~l~~~~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~tsn~  710 (854)
T 1qvr_A          671 KAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNL  710 (854)
T ss_dssp             GSCHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCT
T ss_pred             ccCHHHHHHHHHHhccCceECCCCCEeccCCeEEEEecCc
Confidence            9999999999999999999999999999999999999995

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=100.00  E-value=6.1e-70  Score=664.38  Aligned_cols=596  Identities=20%  Similarity=0.304  Sum_probs=426.9

Q ss_pred             chHHhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCCCCC
Q 003038            7 TIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTST   86 (854)
Q Consensus         7 ~~~~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~~~~   86 (854)
                      ||+++||+.++++|..|+++|+++||++|+|||||++||.++++.+.++|.++|+|+   +.|+..++..+.+.|...+ 
T Consensus         1 mm~~~~t~~a~~~l~~A~~~A~~~~h~~i~~eHlLlaLl~~~~~~~~~iL~~~gvd~---~~l~~~l~~~l~~~~~~~~-   76 (758)
T 3pxi_A            1 MMFGRFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGS---EKIQKEVESLIGRGQEMSQ-   76 (758)
T ss_dssp             --CCCBCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHSCCSHHHHHHHHHTCCH---HHHHHHHHTTSCCCCTTCS-
T ss_pred             CchhhhCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhccCcHHHHHHHHcCCCH---HHHHHHHHHHhccCCCCCC-
Confidence            478999999999999999999999999999999999999999999999999999986   8999999988887765421 


Q ss_pred             CCCCCCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC--hHHHHHHHhCCCHHHHHHHHH
Q 003038           87 PMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP--SVSRVMREAGFSSTQVKSNVE  164 (854)
Q Consensus        87 ~~~~~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~--~~~~iL~~~Gi~~~~l~~~v~  164 (854)
                          .+++++.+.++|+.|..+|..++    .+         +|+++|||+||++++  .+.++|+++|++.+.++..+.
T Consensus        77 ----~~~~s~~~~~vl~~A~~~A~~~~----~~---------~I~~ehlLlall~~~~~~a~~~L~~~gv~~~~l~~~i~  139 (758)
T 3pxi_A           77 ----TIHYTPRAKKVIELSMDEARKLG----HS---------YVGTEHILLGLIREGEGVAARVLNNLGVSLNKARQQVL  139 (758)
T ss_dssp             ----SCEECHHHHHHHHHHHHHHHTTT----CS---------SBCHHHHHHHHHHTCCSHHHHHHHHTTCCHHHHHHHHH
T ss_pred             ----CCCCCHHHHHHHHHHHHHHHHcC----CC---------cccHHHHHHHHHhcCCcHHHHHHHHcCCCHHHHHHHHH
Confidence                34466777766666666665432    13         599999999999975  578999999999999998887


Q ss_pred             HHhhhhhccCCCCCC-CCCcccccccccccccccccccCCCCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCHH
Q 003038          165 QAVSLEICSQSTPVS-SNKSKESNVLVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIE  241 (854)
Q Consensus       165 ~~l~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKt  241 (854)
                      +.+..    ...... .........+.+.+|+.+++..++.|++||+  |++++++++++|.|++++|++|+||||||||
T Consensus       140 ~~~~~----~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~ld~iiG~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT  215 (758)
T 3pxi_A          140 QLLGS----NETGSSAAGTNSNANTPTLDSLARDLTAIAKEDSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKT  215 (758)
T ss_dssp             TTCCC----CCTTC-----CCSTHHHHHHSSCCBHHHHTTSSCSCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTH
T ss_pred             HHhcC----CcccccccccccchhhhHHHHHHHHHHHHHhhCCCCCccCchHHHHHHHHHHhCCCCCCeEEECCCCCCHH
Confidence            53321    111000 0001111245688999999998889999998  9999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCcccccccccccccccc
Q 003038          242 GVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWAEFRASSSEQVR  321 (854)
Q Consensus       242 a~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l~~~~~~~~~~~  321 (854)
                      ++|++||+++.++++|..+.+++++.+++   ...|+|+||.+++.+++++...  +++|||||       +        
T Consensus       216 ~la~~la~~l~~~~~p~~l~~~~~~~~~~---g~~~~G~~e~~l~~~~~~~~~~--~~~iLfiD-------~--------  275 (758)
T 3pxi_A          216 AIAEGLAQQIINNEVPEILRDKRVMTLDM---GTKYRGEFEDRLKKVMDEIRQA--GNIILFID-------A--------  275 (758)
T ss_dssp             HHHHHHHHHHHSSCSCTTTSSCCEECC-------------CTTHHHHHHHHHTC--CCCEEEEC-------C--------
T ss_pred             HHHHHHHHHHhcCCCChhhcCCeEEEecc---cccccchHHHHHHHHHHHHHhc--CCEEEEEc-------C--------
Confidence            99999999999999999999999999998   4449999999999999999975  68999999       1        


Q ss_pred             ccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHHHhh------------
Q 003038          322 GYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLI------------  389 (854)
Q Consensus       322 ~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~al~------------  389 (854)
                               .+++.++|.+...+|.+++||+||..+|+++++.+|+|.|  ||+.|.|+.|+......            
T Consensus       276 ---------~~~~~~~L~~~l~~~~v~~I~at~~~~~~~~~~~d~al~r--Rf~~i~v~~p~~~~~~~il~~~~~~~~~~  344 (758)
T 3pxi_A          276 ---------AIDASNILKPSLARGELQCIGATTLDEYRKYIEKDAALER--RFQPIQVDQPSVDESIQILQGLRDRYEAH  344 (758)
T ss_dssp             -----------------CCCTTSSSCEEEEECCTTTTHHHHTTCSHHHH--SEEEEECCCCCHHHHHHHHHHTTTTSGGG
T ss_pred             ---------chhHHHHHHHHHhcCCEEEEeCCChHHHHHHhhccHHHHh--hCcEEEeCCCCHHHHHHHHHHHHHHHHHh
Confidence                     1345566755333447999999999999999999999999  88999999887544221            


Q ss_pred             ----cccch------hhhccccCCcCCCcccccccchhhhhhhcccccchhhhHHHHhhhhcccCCCCCCCCCChHHHHh
Q 003038          390 ----TTDSD------LQSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWLQQ  459 (854)
Q Consensus       390 ----~~~s~------~~~~~~~~~~~pdkaidlld~a~~~~~~~c~~~~~~~~e~e~~~~~~~~~~~~~~~~~lp~~l~~  459 (854)
                          +.+.+      +..+|++++++||++++++|+|++.+.+..            ...+.       ....+...+..
T Consensus       345 ~~~~i~~~al~~~~~~s~~~i~~~~~p~~ai~ll~~a~~~~~~~~------------~~~p~-------~~~~l~~~~~~  405 (758)
T 3pxi_A          345 HRVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDEAGSKVRLRS------------FTTPP-------NLKELEQKLDE  405 (758)
T ss_dssp             SSCSCCHHHHHHHHHHHHHSSCCSCTTHHHHHHHHHHHHHHHHHT------------TC--C-------CTHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHHhhcccccCcCCcHHHHHHHHHHHHHHhhc------------cCCCc-------chhhHHHHHHH
Confidence                11111      234799999999999999999877633211            00000       00112233333


Q ss_pred             hHHHHhhcccCCCcccchhhHHHHHHHHhhhcccCccccccccccccCCCCCCCCcccccccCcchhhhhhhhhcccccc
Q 003038          460 YKNEKKATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHKTHRDWAVVEPKQ  539 (854)
Q Consensus       460 ~~~~~~~~~~~~d~~~~~~~L~~~w~~~~~~~~~~~~~~~~~~~~~s~~~~s~~~~~~~~~~~~~l~~~~~~~~~~~~~~  539 (854)
                      ++.+........+.+... .|+.++..++..+                                  ......|.-..   
T Consensus       406 ~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~l----------------------------------~~~~~~~~~~~---  447 (758)
T 3pxi_A          406 VRKEKDAAVQSQEFEKAA-SLRDTEQRLREQV----------------------------------EDTKKSWKEKQ---  447 (758)
T ss_dssp             HHHHHHHHHHHCCSHHHH-HHHHHHHHHHHHH----------------------------------HHHHSGGGHHH---
T ss_pred             HHHHHHHHHhCcCHHHHH-HHHHHHHHHHHHH----------------------------------HHHHHHHHHhh---
Confidence            332221110000100000 2222222221111                                  00000111000   


Q ss_pred             chhccccccccccccCCCCCcccccccccccccccccccCCCCCCCCCCccccccc--hhh----hhhhhhhHHHHHHHH
Q 003038          540 SWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNSTSSSDIMEM--EYV----HKFKELNSENLTSLC  613 (854)
Q Consensus       540 p~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~~~v--~~~----~~~~~~~~e~l~~L~  613 (854)
                                                        . ..      ...++.+++..+  +|+    .++.+.+.+.+..|+
T Consensus       448 ----------------------------------~-~~------~~~v~~~~i~~~v~~~~~ip~~~~~~~~~~~l~~l~  486 (758)
T 3pxi_A          448 ----------------------------------G-QE------NSEVTVDDIAMVVSSWTGVPVSKIAQTETDKLLNME  486 (758)
T ss_dssp             ----------------------------------H-CC---------CCTHHHHHHHHTTC-------CHHHHSCC-CHH
T ss_pred             ----------------------------------c-cc------CcccCHHHHHHHHHHHhCCChHHhhHHHHHHHHHHH
Confidence                                              0 00      011222223332  332    345556667788899


Q ss_pred             HhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcc
Q 003038          614 NALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIAL  693 (854)
Q Consensus       614 ~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~  693 (854)
                      +.|.++|+||++++..|..++.+.+.|+.++.         +|.+++||+||+|||||++|++||+.+|+++.+|+++||
T Consensus       487 ~~l~~~viGq~~a~~~l~~~i~~~~~~~~~~~---------~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i~~  557 (758)
T 3pxi_A          487 NILHSRVIGQDEAVVAVAKAVRRARAGLKDPK---------RPIGSFIFLGPTGVGKTELARALAESIFGDEESMIRIDM  557 (758)
T ss_dssp             HHHHTTSCSCHHHHHHHHHHHHHHTTTCSCTT---------SCSEEEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEEEG
T ss_pred             HHHhCcCcChHHHHHHHHHHHHHHHcccCCCC---------CCceEEEEECCCCCCHHHHHHHHHHHhcCCCcceEEEec
Confidence            99999999999999999999999999998764         788899999999999999999999999999999999999


Q ss_pred             ccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCC
Q 003038          694 SSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGD  773 (854)
Q Consensus       694 s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~  773 (854)
                      ++|.       +.+..+          ...+++++++.|++||||||||++++++|+.|+++|++|++++..|+.+++.|
T Consensus       558 s~~~-------~~~~~~----------~~~l~~~~~~~~~~vl~lDEi~~~~~~~~~~Ll~~le~g~~~~~~g~~~~~~~  620 (758)
T 3pxi_A          558 SEYM-------EKHSTS----------GGQLTEKVRRKPYSVVLLDAIEKAHPDVFNILLQVLEDGRLTDSKGRTVDFRN  620 (758)
T ss_dssp             GGGC-------SSCCCC-------------CHHHHHHCSSSEEEEECGGGSCHHHHHHHHHHHHHSBCC-----CCBCTT
T ss_pred             hhcc-------cccccc----------cchhhHHHHhCCCeEEEEeCccccCHHHHHHHHHHhccCeEEcCCCCEeccCC
Confidence            9998       444322          12468899999999999999999999999999999999999999999999999


Q ss_pred             eEEEEecCC
Q 003038          774 AIVILSCES  782 (854)
Q Consensus       774 aIiIlTsn~  782 (854)
                      ++||+|||.
T Consensus       621 ~~iI~ttn~  629 (758)
T 3pxi_A          621 TILIMTSNV  629 (758)
T ss_dssp             CEEEEEESS
T ss_pred             eEEEEeCCC
Confidence            999999994

>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=100.00  E-value=2.1e-67  Score=642.24  Aligned_cols=569  Identities=16%  Similarity=0.231  Sum_probs=437.4

Q ss_pred             hhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhcc-CCCCCCCCCCC
Q 003038           12 LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNR-LPASTSTPMLG   90 (854)
Q Consensus        12 fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~r-lp~~~~~~~~~   90 (854)
                      ||++++++|..|+++|+++||.+|+|||||++||.++  .+.++|.++|+++   +.|+..++..+.+ +|...++...+
T Consensus         2 ~t~~a~~~l~~A~~~A~~~~h~~i~~eHLLlaLl~~~--~~~~iL~~~gvd~---~~l~~~l~~~l~~~~p~~~~~~~~~   76 (758)
T 1r6b_X            2 LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNP--SAREALEACSVDL---VALRQELEAFIEQTTPVLPASEEER   76 (758)
T ss_dssp             BCHHHHHHHHHHHHHHHHTTBSEECHHHHHHHHTTSH--HHHHHHHHTTCCH---HHHHHHHHHHHHHHSCBCCCSSSCC
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCCccHHHHHHHHHcCc--HHHHHHHHcCCCH---HHHHHHHHHHHhccCCCCCCccccC
Confidence            9999999999999999999999999999999999864  5889999999986   8999999999987 77643210012


Q ss_pred             CCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC--hHHHHHHHhCCCHHHHHHHHHHHhh
Q 003038           91 GHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP--SVSRVMREAGFSSTQVKSNVEQAVS  168 (854)
Q Consensus        91 ~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~--~~~~iL~~~Gi~~~~l~~~v~~~l~  168 (854)
                      .++++|.+.++|+.|...|...++    +         +|+++|||+||++++  .+.++|+++|++...+...+.+...
T Consensus        77 ~~~~s~~~~~vl~~A~~~a~~~~~----~---------~I~~ehlLlall~~~~~~a~~~L~~~gi~~~~l~~~i~~~~~  143 (758)
T 1r6b_X           77 DTQPTLSFQRVLQRAVFHVQSSGR----N---------EVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHGTR  143 (758)
T ss_dssp             CCEECHHHHHHHHHHHHHHHHHTC----S---------SBCHHHHHHHHTTCTTCHHHHHHHHTTCCHHHHHHHHHTC--
T ss_pred             CCCcCHHHHHHHHHHHHHHHHcCC----C---------EeeHHHHHHHHhccccchHHHHHHHcCCCHHHHHHHHHHhhc
Confidence            345677777777777777766531    3         599999999999875  4789999999999998877654221


Q ss_pred             hhh--ccCC-CCCCCCCcccccccccccccccccccCCCCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCHHHH
Q 003038          169 LEI--CSQS-TPVSSNKSKESNVLVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGV  243 (854)
Q Consensus       169 ~~~--~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~  243 (854)
                      ...  .+.. .............+.+.+|+.+++..++.|++||+  |++++++++++|.+++++|++|+||||||||++
T Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~d~~iGr~~~i~~l~~~l~~~~~~~vlL~G~~GtGKT~l  223 (758)
T 1r6b_X          144 KDEPTQSSDPGSQPNSEEQAGGEERLENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAI  223 (758)
T ss_dssp             -------------------------CCSSSCBHHHHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHH
T ss_pred             cccccccccccccccccccccchhHHHHHhHhHHHHHhcCCCCCccCCHHHHHHHHHHHhccCCCCeEEEcCCCCCHHHH
Confidence            100  0000 00000001111245688999999988889999998  999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCCCCcccCCceEEEccccccccc--chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccc
Q 003038          244 VRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM--NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQV  320 (854)
Q Consensus       244 v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~--~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~  320 (854)
                      |++++.++..+.+|..+.+++++.++++.+.++  ++|+++++++.+++.+...  +++||||||+|++ +.+...    
T Consensus       224 a~~la~~l~~~~v~~~~~~~~~~~~~~~~l~~~~~~~g~~e~~l~~~~~~~~~~--~~~iL~IDEi~~l~~~~~~~----  297 (758)
T 1r6b_X          224 AEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQD--TNSILFIDEIHTIIGAGAAS----  297 (758)
T ss_dssp             HHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSSS--SCEEEEETTTTTTTTSCCSS----
T ss_pred             HHHHHHHHHhCCCChhhcCCEEEEEcHHHHhccccccchHHHHHHHHHHHHHhc--CCeEEEEechHHHhhcCCCC----
Confidence            999999999999999999999999999999865  9999999999999999875  5899999999999 776532    


Q ss_pred             cccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHHHhh-----------
Q 003038          321 RGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLI-----------  389 (854)
Q Consensus       321 ~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~al~-----------  389 (854)
                              .+.+++.++|++...++.+++||+||..+|.+++..||+|.+  ||+.|.|++|+......           
T Consensus       298 --------~~~~~~~~~L~~~l~~~~~~~I~at~~~~~~~~~~~d~aL~~--Rf~~i~v~~p~~~e~~~il~~l~~~~~~  367 (758)
T 1r6b_X          298 --------GGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALAR--RFQKIDITEPSIEETVQIINGLKPKYEA  367 (758)
T ss_dssp             --------SCHHHHHHHHSSCSSSCCCEEEEEECHHHHHCCCCCTTSSGG--GEEEEECCCCCHHHHHHHHHHHHHHHHH
T ss_pred             --------cchHHHHHHHHHHHhCCCeEEEEEeCchHHhhhhhcCHHHHh--CceEEEcCCCCHHHHHHHHHHHHHHHHH
Confidence                    134678888876333347999999999999999999999999  88899999988654321           


Q ss_pred             -----cccch------hhhccccCCcCCCcccccccchhhhhhhcccccchhhhHHHHhhhhcccCCCCCCCCCChHHHH
Q 003038          390 -----TTDSD------LQSQSTSKKAESGVSWLLFEGEEENKQLTCCADCSAKFEAEARSLQSSSCNSDSPTSSLPAWLQ  458 (854)
Q Consensus       390 -----~~~s~------~~~~~~~~~~~pdkaidlld~a~~~~~~~c~~~~~~~~e~e~~~~~~~~~~~~~~~~~lp~~l~  458 (854)
                           +.+.+      +..+|+.++++||++++++|+|++...+                     .         |.   
T Consensus       368 ~~~v~~~~~al~~~~~~s~~~i~~~~lp~~~i~lld~a~~~~~~---------------------~---------~~---  414 (758)
T 1r6b_X          368 HHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARL---------------------M---------PV---  414 (758)
T ss_dssp             HHTCCCCHHHHHHHHHHHHHHCTTSCTTHHHHHHHHHHHHHHHH---------------------S---------SS---
T ss_pred             hcCCCCCHHHHHHHHHHhhhhcccccCchHHHHHHHHHHHHHhc---------------------c---------cc---
Confidence                 11111      1235666666666666666655332100                     0         00   


Q ss_pred             hhHHHHhhcccCCCcccchhhHHHHHHHHhhhcccCccccccccccccCCCCCCCCcccccccCcchhhhhhhhhccccc
Q 003038          459 QYKNEKKATLSNNDKDSGVRDLCKKWNSICNSIHKQPYYSERTLTFSSASPSSSTSGFSYDQQYPNFHKTHRDWAVVEPK  538 (854)
Q Consensus       459 ~~~~~~~~~~~~~d~~~~~~~L~~~w~~~~~~~~~~~~~~~~~~~~~s~~~~s~~~~~~~~~~~~~l~~~~~~~~~~~~~  538 (854)
                                                            .. ..         ..+.       ..++......|.    .
T Consensus       415 --------------------------------------~~-~~---------~~v~-------~~di~~~~~~~~----~  435 (758)
T 1r6b_X          415 --------------------------------------SK-RK---------KTVN-------VADIESVVARIA----R  435 (758)
T ss_dssp             --------------------------------------CC-CC---------CSCC-------HHHHHHHHHHHS----C
T ss_pred             --------------------------------------cc-cC---------CccC-------HHHHHHHHHHhc----C
Confidence                                                  00 00         0000       011111111111    1


Q ss_pred             cchhccccccccccccCCCCCcccccccccccccccccccCCCCCCCCCCccccccchhhhhhhhhhHHHHHHHHHhhcC
Q 003038          539 QSWREHHFLFSHEASDKSTSEPSLRLYIPEHKDLKQPLSSNRNSTPNSTSSSDIMEMEYVHKFKELNSENLTSLCNALEK  618 (854)
Q Consensus       539 ~p~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~~~v~~~~~~~~~~~e~l~~L~~~L~~  618 (854)
                      +|+                                                         .++...+.+.+..|++.|.+
T Consensus       436 ip~---------------------------------------------------------~~~~~~~~~~l~~l~~~l~~  458 (758)
T 1r6b_X          436 IPE---------------------------------------------------------KSVSQSDRDTLKNLGDRLKM  458 (758)
T ss_dssp             CCC---------------------------------------------------------CCSSSSHHHHHHHHHHHHTT
T ss_pred             CCc---------------------------------------------------------cccchhHHHHHHHHHHHHHh
Confidence            111                                                         11122355678899999999


Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      +|+||++++..|..++...++|+.+++         +|.+++||+||+|||||++|++||+.+   ..+|+++||++|. 
T Consensus       459 ~v~g~~~~~~~l~~~i~~~~~g~~~~~---------~p~~~~ll~G~~GtGKT~la~~la~~l---~~~~~~i~~s~~~-  525 (758)
T 1r6b_X          459 LVFGQDKAIEALTEAIKMARAGLGHEH---------KPVGSFLFAGPTGVGKTEVTVQLSKAL---GIELLRFDMSEYM-  525 (758)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTCSCTT---------SCSEEEEEECSTTSSHHHHHHHHHHHH---TCEEEEEEGGGCS-
T ss_pred             hccCHHHHHHHHHHHHHHHhcccCCCC---------CCceEEEEECCCCCcHHHHHHHHHHHh---cCCEEEEechhhc-
Confidence            999999999999999999999998764         788999999999999999999999998   3689999999999 


Q ss_pred             cCCCccccccccccC-CCCCC-chHH--HHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCe
Q 003038          699 TRADSTEDSRNKRSR-DEQSC-SYIE--RFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDA  774 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~-~~~g~-g~~e--~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~a  774 (854)
                            +.|.+++++ .++|| ||.+  .+++++++.|++||||||||++++++++.|+++||+|+++|..|+.++|+|+
T Consensus       526 ------~~~~~~~l~g~~~g~~g~~~~~~l~~~~~~~~~~vl~lDEi~~~~~~~~~~Ll~~le~~~~~~~~g~~~~~~~~  599 (758)
T 1r6b_X          526 ------ERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNV  599 (758)
T ss_dssp             ------SSSCCSSSCCCCSCSHHHHHTTHHHHHHHHCSSEEEEEETGGGSCHHHHHHHHHHHHHSEEEETTTEEEECTTE
T ss_pred             ------chhhHhhhcCCCCCCcCccccchHHHHHHhCCCcEEEEeCccccCHHHHHHHHHHhcCcEEEcCCCCEEecCCe
Confidence                  778888888 46778 8876  7899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecCC
Q 003038          775 IVILSCES  782 (854)
Q Consensus       775 IiIlTsn~  782 (854)
                      +||+|||.
T Consensus       600 ~iI~tsN~  607 (758)
T 1r6b_X          600 VLVMTTNA  607 (758)
T ss_dssp             EEEEEECS
T ss_pred             EEEEecCc
Confidence            99999985

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=100.00  E-value=2.7e-47  Score=440.13  Aligned_cols=357  Identities=19%  Similarity=0.277  Sum_probs=276.3

Q ss_pred             chHHhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCCCCC
Q 003038            7 TIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTST   86 (854)
Q Consensus         7 ~~~~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~~~~   86 (854)
                      ||+++||+.++++|+.|+++|+++||++|+|||||++||.++++.+.++|.++|+|+   +.|+..++..+.+.|...+ 
T Consensus         1 mm~~~ft~~a~~al~~A~~~A~~~~h~~v~~eHLLlaLl~~~~~~~~~iL~~~gvd~---~~l~~~l~~~l~~~~~~~~-   76 (468)
T 3pxg_A            1 MMFGRFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGS---EKIQKEVESLIGRGQEMSQ-   76 (468)
T ss_dssp             --CCCBCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHSCCSHHHHHHHHHTCCH---HHHHHHHHTTSCCCCTTCS-
T ss_pred             CcchhhCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhccCcHHHHHHHHcCCCH---HHHHHHHHHHhcccCCCCC-
Confidence            478999999999999999999999999999999999999999999999999999986   8999999988877664321 


Q ss_pred             CCCCCCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC--hHHHHHHHhCCCHHHHHHHHH
Q 003038           87 PMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP--SVSRVMREAGFSSTQVKSNVE  164 (854)
Q Consensus        87 ~~~~~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~--~~~~iL~~~Gi~~~~l~~~v~  164 (854)
                          .++++|.+.++|+.|..+|..+    +.+         +|+++|||+||++++  .+.++|.++|++.+.++..+.
T Consensus        77 ----~~~~S~~~~~vL~~A~~~A~~~----g~~---------~I~teHLLlaLl~~~~~~a~~iL~~~gv~~~~l~~~i~  139 (468)
T 3pxg_A           77 ----TIHYTPRAKKVIELSMDEARKL----GHS---------YVGTEHILLGLIREGEGVAARVLNNLGVSLNKARQQVL  139 (468)
T ss_dssp             ----SCEECHHHHHHHHHHHHHHHTT----TCS---------SBCHHHHHHHHHHTCCSHHHHHHHHTTCCHHHHHHHHH
T ss_pred             ----CCCCCHHHHHHHHHHHHHHHHc----CCC---------eecHHHHHHHHHhcccchHHHHHHHcCCCHHHHHHHHH
Confidence                2345666666666655555433    213         599999999999975  578999999999999998887


Q ss_pred             HHhhhhhccCCCCCC-CCCcccccccccccccccccccCCCCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCHH
Q 003038          165 QAVSLEICSQSTPVS-SNKSKESNVLVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIE  241 (854)
Q Consensus       165 ~~l~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKt  241 (854)
                      +.+..    ...... .........+++.+|+.+++..++.|++||+  |+++|++++++|.|++++||+|+||||||||
T Consensus       140 ~~~~~----~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~r~~~ld~iiGr~~~i~~l~~~l~r~~~~~~LL~G~pG~GKT  215 (468)
T 3pxg_A          140 QLLGS----NETGSSAAGTNSNANTPTLDSLARDLTAIAKEDSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKT  215 (468)
T ss_dssp             TTCCC----CCTTC-----CCSTHHHHHHSSCCBHHHHTTSSCSCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTH
T ss_pred             HHhcc----CcccccccCcCCccCchHHHHHHHHHHHHHhcCCCCCccCcHHHHHHHHHHHhccCCCCeEEECCCCCCHH
Confidence            53321    111000 0001111245688999999998889999998  9999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCcccccccccccccccc
Q 003038          242 GVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWAEFRASSSEQVR  321 (854)
Q Consensus       242 a~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l~~~~~~~~~~~  321 (854)
                      ++|+++|.++..+++|..+.+..|+.++++   +.|+|+|+.+++.++++++..  +++|||||       +        
T Consensus       216 ~la~~la~~l~~~~~p~~l~~~~~~~l~~~---~~~~g~~e~~~~~~~~~~~~~--~~~iLfiD-------~--------  275 (468)
T 3pxg_A          216 AIAEGLAQQIINNEVPEILRDKRVMTLDMG---TKYRGEFEDRLKKVMDEIRQA--GNIILFID-------A--------  275 (468)
T ss_dssp             HHHHHHHHHHHSSCSCTTTSSCCEECC-------------CTTHHHHHHHHHTC--CCCEEEEC-------C--------
T ss_pred             HHHHHHHHHHHhCCCChhhcCCeEEEeeCC---ccccchHHHHHHHHHHHHHhc--CCeEEEEe-------C--------
Confidence            999999999999999999999999999998   669999999999999999975  68999999       1        


Q ss_pred             ccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHHHhh------------
Q 003038          322 GYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLI------------  389 (854)
Q Consensus       322 ~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~al~------------  389 (854)
                               .+++.++|.+...+|.++|||+||..+|+++++.+|+|.+  ||+.|.|++|+......            
T Consensus       276 ---------~~~a~~~L~~~L~~g~v~vI~at~~~e~~~~~~~~~al~~--Rf~~i~v~~p~~e~~~~iL~~~~~~~~~~  344 (468)
T 3pxg_A          276 ---------AIDASNILKPSLARGELQCIGATTLDEYRKYIEKDAALER--RFQPIQVDQPSVDESIQILQGLRDRYEAH  344 (468)
T ss_dssp             -----------------CCCTTSSSCEEEEECCTTTTHHHHTTCSHHHH--SEEEEECCCCCHHHHHHHHHHTTTTSGGG
T ss_pred             ---------chhHHHHHHHhhcCCCEEEEecCCHHHHHHHhhcCHHHHH--hCccceeCCCCHHHHHHHHHHHHHHHHHh
Confidence                     1356677766333447999999999999999999999999  99999999987554321            


Q ss_pred             ----cccch------hhhccccCCcCCCcccccccchhhh
Q 003038          390 ----TTDSD------LQSQSTSKKAESGVSWLLFEGEEEN  419 (854)
Q Consensus       390 ----~~~s~------~~~~~~~~~~~pdkaidlld~a~~~  419 (854)
                          +.+.+      +..+|+.++++||++++++|+|++.
T Consensus       345 ~~~~i~~~al~~l~~~s~~~~~~~~lp~~ai~ll~~a~~~  384 (468)
T 3pxg_A          345 HRVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDEAGSK  384 (468)
T ss_dssp             SSCSCCHHHHHHHHHHHHHSSCCSCTTHHHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHHHHHHhccCcCCcHHHHHHHHHHHH
Confidence                11111      3357999999999999999998766

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=99.85  E-value=3.9e-21  Score=208.53  Aligned_cols=163  Identities=23%  Similarity=0.375  Sum_probs=145.0

Q ss_pred             hhHHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhC
Q 003038          604 LNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFG  683 (854)
Q Consensus       604 ~~~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg  683 (854)
                      .+.+.+..|++.|.++++||+.++..|..++.+.+.|+.++.         +|.+++||+||+|+|||++|++||+.++.
T Consensus         3 ~~~~~l~~l~~~l~~~i~G~~~~~~~l~~~i~~~~~~~~~~~---------~~~~~~ll~G~~GtGKt~la~~la~~~~~   73 (311)
T 4fcw_A            3 GEREKLLRLEEELHKRVVGQDEAIRAVADAIRRARAGLKDPN---------RPIGSFLFLGPTGVGKTELAKTLAATLFD   73 (311)
T ss_dssp             HHHHHHHTHHHHHHTTCCSCHHHHHHHHHHHHHHHHTCSCTT---------SCSEEEEEESCSSSSHHHHHHHHHHHHHS
T ss_pred             cHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhcCCCCCC---------CCceEEEEECCCCcCHHHHHHHHHHHHcC
Confidence            467889999999999999999999999999999999988764         78889999999999999999999999998


Q ss_pred             CCCceEEEccccccCcCCCccccccccccCC-CCCC-chHH--HHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcC
Q 003038          684 SHNNFVSIALSSFSSTRADSTEDSRNKRSRD-EQSC-SYIE--RFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESG  759 (854)
Q Consensus       684 ~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~-~~g~-g~~e--~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G  759 (854)
                      ...+|+.++|+.+.       +.....++++ ++++ |+..  .+.++++..|++||||||||++++.+|+.|+++|++|
T Consensus        74 ~~~~~~~~~~~~~~-------~~~~~~~l~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEi~~l~~~~~~~Ll~~le~~  146 (311)
T 4fcw_A           74 TEEAMIRIDMTEYM-------EKHAVSRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDAIEKAHPDVFNILLQMLDDG  146 (311)
T ss_dssp             CGGGEEEEEGGGCC-------STTHHHHHHCCCTTSTTTTTCCHHHHHHHHCSSEEEEEETGGGSCHHHHHHHHHHHHHS
T ss_pred             CCcceEEeeccccc-------ccccHHHhcCCCCccccccccchHHHHHHhCCCeEEEEeChhhcCHHHHHHHHHHHhcC
Confidence            88899999999887       3443444442 3444 5554  7899999999999999999999999999999999999


Q ss_pred             eEecCCCceeecCCeEEEEecCC
Q 003038          760 RIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       760 ~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      .+++..|+.++++++|||+|||.
T Consensus       147 ~~~~~~~~~~~~~~~iiI~ttn~  169 (311)
T 4fcw_A          147 RLTDSHGRTVDFRNTVIIMTSNL  169 (311)
T ss_dssp             EEECTTSCEEECTTEEEEEEEST
T ss_pred             EEEcCCCCEEECCCcEEEEeccc
Confidence            99999999999999999999986

>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=99.83  E-value=6.1e-20  Score=221.64  Aligned_cols=151  Identities=13%  Similarity=0.128  Sum_probs=109.9

Q ss_pred             HHHHHHHHHH-hhc---------cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHH
Q 003038          212 NEDVMYVIEN-LMS---------KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEV  281 (854)
Q Consensus       212 ~~ei~~v~~~-L~r---------~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~  281 (854)
                      -++|+.+++. |..         +-.+.++|+||||||||.+|+++|..          .+++++.++...+.+.|.|+.
T Consensus       213 ~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~e----------lg~~~~~v~~~~l~sk~~ges  282 (806)
T 3cf2_A          213 LAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE----------TGAFFFLINGPEIMSKLAGES  282 (806)
T ss_dssp             HHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTT----------TTCEEEEEEHHHHHSSCTTHH
T ss_pred             HHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHH----------hCCeEEEEEhHHhhcccchHH
Confidence            4567777765 322         23567999999999999999999965          378999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHH
Q 003038          282 EQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMR  360 (854)
Q Consensus       282 E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k  360 (854)
                      |+++++++..++..  .|+|||||||+.| ..+....+.      .....+..+-.++.....++.+.+||||+..+   
T Consensus       283 e~~lr~lF~~A~~~--~PsIIfIDEiDal~~~r~~~~~~------~~~riv~~LL~~mdg~~~~~~V~VIaaTN~~d---  351 (806)
T 3cf2_A          283 ESNLRKAFEEAEKN--APAIIFIDELDAIAPKREKTHGE------VERRIVSQLLTLMDGLKQRAHVIVMAATNRPN---  351 (806)
T ss_dssp             HHHHHHHHHHHTTS--CSEEEEEESGGGTCCTTTTCCCT------THHHHHHHHHTHHHHCCGGGCEEEEEECSSTT---
T ss_pred             HHHHHHHHHHHHHc--CCeEEEEehhcccccccCCCCCh------HHHHHHHHHHHHHhcccccCCEEEEEecCChh---
Confidence            99999999999986  7999999999999 554322111      11234444444442212233699999998654   


Q ss_pred             hhccCCchhhhhcc-CCCCCCCchHH
Q 003038          361 CKSGHPSLETLWSL-HPLTIPAGSLS  385 (854)
Q Consensus       361 ~~~~~pale~~~~~-~~v~i~~~sl~  385 (854)
                        ..||+|.|--|| +.|.|+.|+..
T Consensus       352 --~LD~ALrR~GRFd~~I~i~~Pd~~  375 (806)
T 3cf2_A          352 --SIDPALRRFGRFDREVDIGIPDAT  375 (806)
T ss_dssp             --TSCTTTTSTTSSCEEEECCCCCHH
T ss_pred             --hcCHHHhCCcccceEEecCCCCHH
Confidence              579999885566 34566655543

>3fh2_A Probable ATP-dependent protease (heat shock prote; struct genomics, PSI2, MCSG, protein structure initiative; 1.60A {Corynebacterium glutamicum}

Probab=99.82  E-value=1.5e-19  Score=175.94  Aligned_cols=140  Identities=16%  Similarity=0.165  Sum_probs=120.1

Q ss_pred             chHHhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCCCCC
Q 003038            7 TIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTST   86 (854)
Q Consensus         7 ~~~~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~~~~   86 (854)
                      +|+++||++++++|+.|+++|+++||.+|+|||||++|+.++++.+.++|.++|+++   +.++..++..+.+.|...+ 
T Consensus         2 ~m~~~~t~~~~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~~~~~iL~~~gv~~---~~l~~~l~~~l~~~~~~~~-   77 (146)
T 3fh2_A            2 AMFERFTDRARRVIVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKALESMGISL---DAVRQEVEEIIGQGSQPTT-   77 (146)
T ss_dssp             GGGGGBCHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHCCSHHHHHHHHTTCCH---HHHHHHHHHHHCCCSCCCC-
T ss_pred             chhhhcCHHHHHHHHHHHHHHHHcCCCCchHHHHHHHHHhCCCChHHHHHHHcCCCH---HHHHHHHHHHhccCCCCCc-
Confidence            578999999999999999999999999999999999999999999999999999987   8999999999998886432 


Q ss_pred             CCCCCCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC--hHHHHHHHhCCCHHHHHHHHH
Q 003038           87 PMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP--SVSRVMREAGFSSTQVKSNVE  164 (854)
Q Consensus        87 ~~~~~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~--~~~~iL~~~Gi~~~~l~~~v~  164 (854)
                         ++++++|.+.++|+.|...|...+    ++         +|+++|||+||++++  .+.++|+++|++.+.++..+.
T Consensus        78 ---~~~~~s~~~~~vL~~A~~~a~~~~----~~---------~i~~eHlLlall~~~~~~a~~iL~~~gv~~~~l~~~l~  141 (146)
T 3fh2_A           78 ---GHIPFTPRAKKVLELSLREGLQMG----HK---------YIGTEFLLLGLIREGEGVAAQVLVKLGADLPRVRQQVI  141 (146)
T ss_dssp             ---SCCCBCHHHHHHHHHHHHHHHHTT----CS---------SBCHHHHHHHHHHHCSSHHHHHHHHHTCCHHHHHHHHH
T ss_pred             ---CCCcCCHHHHHHHHHHHHHHHHcC----CC---------cCcHHHHHHHHHhCCCcHHHHHHHHcCCCHHHHHHHHH
Confidence               234567777777777777776542    23         599999999999864  689999999999999999887


Q ss_pred             HH
Q 003038          165 QA  166 (854)
Q Consensus       165 ~~  166 (854)
                      +.
T Consensus       142 ~~  143 (146)
T 3fh2_A          142 QL  143 (146)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>3fes_A ATP-dependent CLP endopeptidase; alpha-helical bundles, structural genomics, PSI-2, protein S initiative; HET: PG4 EPE; 1.82A {Clostridium difficile}

Probab=99.80  E-value=2.2e-19  Score=174.62  Aligned_cols=138  Identities=15%  Similarity=0.115  Sum_probs=117.0

Q ss_pred             chHHhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCCCCC
Q 003038            7 TIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTST   86 (854)
Q Consensus         7 ~~~~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~~~~   86 (854)
                      .++++||++++++|+.|+++|+++||.+|+|||||++||.++++.+.++|.++|+|+   +.++..++..+.+.|. .+ 
T Consensus         3 ~~~~~~T~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~~~~~iL~~~gvd~---~~l~~~l~~~l~~~~~-~~-   77 (145)
T 3fes_A            3 ANFNRFTQRAKKAIDLAFESAKSLGHNIVGSEHILLGLLREEEGIAAKVLSKVGFTE---AYLEGKIVDMEGKGEE-IS-   77 (145)
T ss_dssp             -CCCCBCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHCSSHHHHHHHHHTCCH---HHHHHHHHHHHCCCSC-CC-
T ss_pred             CcccccCHHHHHHHHHHHHHHHHcCCCCccHHHHHHHHHhCCCChHHHHHHHcCCCH---HHHHHHHHHHHhcCCC-CC-
Confidence            356899999999999999999999999999999999999999999999999999987   8999999999998886 21 


Q ss_pred             CCCCCCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC--hHHHHHHHhCCCHHHHHHHHH
Q 003038           87 PMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP--SVSRVMREAGFSSTQVKSNVE  164 (854)
Q Consensus        87 ~~~~~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~--~~~~iL~~~Gi~~~~l~~~v~  164 (854)
                         ++++++|.+.++|+.|...|...+    ++         +|+++|||+||++++  .+.++|+++|++.+.++..+.
T Consensus        78 ---~~~~~s~~~~~vl~~A~~~A~~~~----~~---------~v~~eHlLlAll~~~~~~a~~iL~~~gv~~~~l~~~i~  141 (145)
T 3fes_A           78 ---EDIVLSPRSKQILELSGMFANKLK----TN---------YIGTEHILLAIIQEGEGIANKILNYAGVNDRTLAQLTI  141 (145)
T ss_dssp             ---SCCEECHHHHHHHHHHHHHHHHTT----CS---------SBCHHHHHHHHHHHCCHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             ---CCCCCCHHHHHHHHHHHHHHHHcC----CC---------cccHHHHHHHHHhCCCcHHHHHHHHcCCCHHHHHHHHH
Confidence               234466776666666666666542    23         599999999999875  478999999999999998887


Q ss_pred             H
Q 003038          165 Q  165 (854)
Q Consensus       165 ~  165 (854)
                      +
T Consensus       142 ~  142 (145)
T 3fes_A          142 D  142 (145)
T ss_dssp             H
T ss_pred             H
Confidence            5

>2y1q_A CLPC N-domain, negative regulator of genetic competence CLPC/MEC; transcription, proteolysis; 1.50A {Bacillus subtilis} PDB: 2y1r_A* 2k77_A

Probab=99.79  E-value=5.1e-19  Score=172.52  Aligned_cols=139  Identities=15%  Similarity=0.199  Sum_probs=112.3

Q ss_pred             chHHhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCCCCC
Q 003038            7 TIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTST   86 (854)
Q Consensus         7 ~~~~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~~~~   86 (854)
                      |++++||++++++|..|+++|+++||.+|+|||||++||.++++.+.++|.++|+|+   +.++..++..+.+.|...+ 
T Consensus         1 M~~~~~t~~~~~al~~A~~~A~~~~h~~i~~eHlLlaLl~~~~~~~~~iL~~~g~~~---~~l~~~l~~~l~~~~~~~~-   76 (150)
T 2y1q_A            1 MMFGRFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGS---EKIQKEVESLIGRAQEMSQ-   76 (150)
T ss_dssp             ---CCBCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHCSSHHHHHHHHTTCCH---HHHHHHHHHHHCCC------
T ss_pred             CcchhhCHHHHHHHHHHHHHHHHcCCCCccHHHHHHHHHhCCCCHHHHHHHHcCCCH---HHHHHHHHHHhccCCcccc-
Confidence            467899999999999999999999999999999999999999999999999999987   8999999999998876432 


Q ss_pred             CCCCCCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC--hHHHHHHHhCCCHHHHHHHHH
Q 003038           87 PMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP--SVSRVMREAGFSSTQVKSNVE  164 (854)
Q Consensus        87 ~~~~~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~--~~~~iL~~~Gi~~~~l~~~v~  164 (854)
                          .+++++.+.++|+.|...|...    +.+         +|+++|||+||++++  .+.++|+++|++.+.++..+.
T Consensus        77 ----~~~~s~~~~~vL~~A~~~A~~~----~~~---------~i~~ehlLlall~~~~~~a~~~L~~~gi~~~~l~~~i~  139 (150)
T 2y1q_A           77 ----TIHYTPRAKKVIELSMDEARKL----GHS---------YVGTEHILLGLIREGEGVAARVLNNLGVSLNKARQQVL  139 (150)
T ss_dssp             ----CCEECHHHHHHHHHHHHHHHHT----TCS---------SBCHHHHHHHHHHHCCSHHHHHHHHTTCCHHHHHHHHH
T ss_pred             ----cCCCCHHHHHHHHHHHHHHHHc----CCC---------eecHHHHHHHHHhCCCcHHHHHHHHcCCCHHHHHHHHH
Confidence                2345666666666666666553    223         599999999999764  457999999999999998887


Q ss_pred             HH
Q 003038          165 QA  166 (854)
Q Consensus       165 ~~  166 (854)
                      +.
T Consensus       140 ~~  141 (150)
T 2y1q_A          140 QL  141 (150)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

>1khy_A CLPB protein; alpha helix, chaperone; 1.95A {Escherichia coli} SCOP: a.174.1.1

Probab=99.79  E-value=1.1e-18  Score=169.60  Aligned_cols=141  Identities=22%  Similarity=0.277  Sum_probs=113.4

Q ss_pred             chHHhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCCCCC
Q 003038            7 TIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTST   86 (854)
Q Consensus         7 ~~~~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~~~~   86 (854)
                      |++++||++++++|+.|+++|+++||.+|+|||||++||.++++.+.++|.++|+++   +.++..++..+.++|...++
T Consensus         1 M~~~~~t~~~~~~l~~A~~~A~~~~~~~i~~eHlLlaLl~~~~~~~~~iL~~~g~~~---~~l~~~l~~~l~~~p~~~~~   77 (148)
T 1khy_A            1 MRLDRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINA---GQLRTDINQALNRLPQVEGT   77 (148)
T ss_dssp             ---CCBCHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHTCTTCSHHHHHHHHTCCH---HHHHHHHHHHHTTSCCC---
T ss_pred             CChhhhhHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHcCCCchHHHHHHHcCCCH---HHHHHHHHHHHHhCCCCCCC
Confidence            467899999999999999999999999999999999999999999999999999986   89999999999998876431


Q ss_pred             CCCCCCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC-hHHHHHHHhCCCHHHHHHHHHH
Q 003038           87 PMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP-SVSRVMREAGFSSTQVKSNVEQ  165 (854)
Q Consensus        87 ~~~~~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~-~~~~iL~~~Gi~~~~l~~~v~~  165 (854)
                      +  +.+++++.+.++|+.|...|...+    ++         +|+++|||+||+++. .+.++|+.+|++.+.++..+.+
T Consensus        78 ~--~~~~~s~~~~~vl~~A~~~a~~~~----~~---------~i~~ehlLlall~~~~~~~~~L~~~gi~~~~l~~~l~~  142 (148)
T 1khy_A           78 G--GDVQPSQDLVRVLNLCDKLAQKRG----DN---------FISSELFVLAALESRGTLADILKAAGATTANITQAIEQ  142 (148)
T ss_dssp             ------CBCHHHHHHHHHHHHHHHHHT----CS---------SBCHHHHHHHHHTSCHHHHHHHHHTTCCHHHHHHHHHC
T ss_pred             C--CCcCcCHHHHHHHHHHHHHHHHcC----CC---------eecHHHHHHHHHcCCcHHHHHHHHcCCCHHHHHHHHHH
Confidence            1  123456666666666666665542    23         599999999999643 5789999999999999887763

>3zri_A CLPB protein, CLPV; chaperone, HSP100 proteins, AAA+ proteins, T6SS, secretion,; 1.80A {Vibrio cholerae} PDB: 3zrj_A

Probab=99.74  E-value=1e-17  Score=167.17  Aligned_cols=140  Identities=14%  Similarity=0.115  Sum_probs=109.0

Q ss_pred             CccchHHhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCC
Q 003038            4 GGCTIQQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPAS   83 (854)
Q Consensus         4 ~~~~~~~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~   83 (854)
                      .+.+++++||++++++|+.|+++|+++||++|+|||||++||.++++.+.++|.++|+|+   +.|+..++ .++++|..
T Consensus        17 ~l~~~~~kfT~~a~~aL~~A~~~A~~~~h~~I~~EHLLlaLL~~~~~~a~~iL~~~gvd~---~~l~~~l~-~l~~~p~~   92 (171)
T 3zri_A           17 ELPTLIAKLNAQSKLALEQAASLCIERQHPEVTLEHYLDVLLDNPLSDVRLVLKQAGLEV---DQVKQAIA-STYSREQV   92 (171)
T ss_dssp             CHHHHHHHBCHHHHHHHHHHHHHHHHHTCSEECHHHHHHHHTTCTTSHHHHHHHHTTCCH---HHHHHHHH-HHSCCCCC
T ss_pred             hHHHHHHHcCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHccCcHHHHHHHHcCCCH---HHHHHHHH-HHhcCCCC
Confidence            456799999999999999999999999999999999999999999999999999999987   89999999 99998864


Q ss_pred             CCCCCCCCCccChhHHHHHHHHHHHHH-HHhhhCCcccccccccccccCHHHHHHHhccCChHHHHH----HH-hCCCHH
Q 003038           84 TSTPMLGGHCQFPTISNALVAAFKRAQ-AHQRRGSIENQQQPLLAVKIELEQLIISILDDPSVSRVM----RE-AGFSST  157 (854)
Q Consensus        84 ~~~~~~~~~~~~p~~s~~L~~al~~A~-~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~~~~~iL----~~-~Gi~~~  157 (854)
                      .+    +.++++|.+.++|+.|..+|. .+    +++         +|+++|||+||++++ ..+++    .. ..|+.+
T Consensus        93 ~~----~~~~~S~~l~~vL~~A~~~A~l~~----gd~---------~I~teHLLLALl~~~-~~~~~~~~~~~l~~i~~~  154 (171)
T 3zri_A           93 LD----TYPAFSPLLVELLQEAWLLSSTEL----EQA---------ELRSGAIFLAALTRA-DRYLSFKLISLFEGINRE  154 (171)
T ss_dssp             CS----SCCEECHHHHHHHHHHHHHHHTTT----CCS---------SBCHHHHHHHHHHTH-HHHSCHHHHHHTTTSCHH
T ss_pred             CC----CCCCcCHHHHHHHHHHHHHHHHHc----CCC---------EEcHHHHHHHHHhCh-hhhHHHHhhHHHHcCCHH
Confidence            32    223445555555555555554 33    324         599999999999986 22222    22 257788


Q ss_pred             HHHHHHHH
Q 003038          158 QVKSNVEQ  165 (854)
Q Consensus       158 ~l~~~v~~  165 (854)
                      .++..+..
T Consensus       155 ~L~~~~~~  162 (171)
T 3zri_A          155 NLKKHFAM  162 (171)
T ss_dssp             HHHHTHHH
T ss_pred             HHHHHHHH
Confidence            77766543

>1k6k_A ATP-dependent CLP protease ATP-binding subunit CLPA; chaperone, ATPase, adaptor binding, X-RAY, structure, N-domain, hydrolase; 1.80A {Escherichia coli} SCOP: a.174.1.1 PDB: 1r6c_X 1r6o_A* 1r6q_A* 1mg9_B* 1lzw_B* 1mbx_A* 1mbv_A 1mbu_A*

Probab=99.69  E-value=9.2e-17  Score=155.25  Aligned_cols=135  Identities=16%  Similarity=0.192  Sum_probs=105.9

Q ss_pred             hhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccC-CCCCCCCCCC
Q 003038           12 LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRL-PASTSTPMLG   90 (854)
Q Consensus        12 fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rl-p~~~~~~~~~   90 (854)
                      ||++++++|+.|+++|+++||.+|+|||||++||.+++  +.++|.++|+++   +.++..++..+.+. |...+.+..+
T Consensus         2 ~t~~~~~~l~~A~~~A~~~~~~~i~~eHlLlaLl~~~~--~~~iL~~~g~~~---~~l~~~l~~~l~~~~p~~~~~~~~~   76 (143)
T 1k6k_A            2 LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPS--AREALEACSVDL---VALRQELEAFIEQTTPVLPASEEER   76 (143)
T ss_dssp             BCHHHHHHHHHHHHHHHHHTBSEECHHHHHHHHTTCHH--HHHHHHHTTCCH---HHHHHHHHHHHHHHSCBCCSSCSCC
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHcCch--HHHHHHHcCCCH---HHHHHHHHHHHHhcCCCCCCCCCCC
Confidence            89999999999999999999999999999999998763  899999999986   78999999999886 7643101001


Q ss_pred             CCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC--hHHHHHHHhCCCHHHHHHHHH
Q 003038           91 GHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP--SVSRVMREAGFSSTQVKSNVE  164 (854)
Q Consensus        91 ~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~--~~~~iL~~~Gi~~~~l~~~v~  164 (854)
                      .    |.+++.+.++++.|+.++++.+++         +|+++|||+||++++  .+.++|+++|++.+.++..+.
T Consensus        77 ~----~~~s~~~~~~l~~A~~~A~~~~~~---------~i~~ehLLlall~~~~~~~~~iL~~~gi~~~~l~~~i~  139 (143)
T 1k6k_A           77 D----TQPTLSFQRVLQRAVFHVQSSGRN---------EVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFIS  139 (143)
T ss_dssp             S----CEECHHHHHHHHHHHHHHHSSSCS---------CBCHHHHHHHHTTCTTSHHHHHHHHTTCCHHHHHHHHH
T ss_pred             C----CCCCHHHHHHHHHHHHHHHHcCCC---------ccCHHHHHHHHHhCcCcHHHHHHHHcCCCHHHHHHHHH
Confidence            2    334444555555555554432223         599999999999865  478999999999999987665

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.69  E-value=1.7e-17  Score=164.70  Aligned_cols=177  Identities=21%  Similarity=0.322  Sum_probs=140.3

Q ss_pred             ccccccccccccCCCCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEE
Q 003038          190 VLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLP  267 (854)
Q Consensus       190 ~~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~  267 (854)
                      .+.++..++....+...++.+  |+++++++++.|.++..++++|+||||+|||++++.++..+.....|..+.+..++.
T Consensus         4 ~l~~~~~~l~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~~   83 (187)
T 2p65_A            4 ALEKYSRDLTALARAGKLDPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVS   83 (187)
T ss_dssp             CTTTTEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEEE
T ss_pred             HHHHHHHHHHHHHhccccchhhcchHHHHHHHHHHhCCCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEEE
Confidence            355565565554445667765  999999999999988889999999999999999999999999888888888999999


Q ss_pred             ccccccccc--chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc--CC
Q 003038          268 LSISSFRHM--NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IG  342 (854)
Q Consensus       268 l~~~~l~~~--~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~  342 (854)
                      +++..+..+  +.|.++..+..++..+... +++.||||||+|++ +.+... .           ...++.++|..  ..
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~vl~iDe~~~l~~~~~~~-~-----------~~~~~~~~l~~~~~~  150 (187)
T 2p65_A           84 LDLSSLIAGAKYRGDFEERLKSILKEVQDA-EGQVVMFIDEIHTVVGAGAVA-E-----------GALDAGNILKPMLAR  150 (187)
T ss_dssp             ECHHHHHHHCCSHHHHHHHHHHHHHHHHHT-TTSEEEEETTGGGGSSSSSSC-T-----------TSCCTHHHHHHHHHT
T ss_pred             EeHHHhhcCCCchhHHHHHHHHHHHHHHhc-CCceEEEEeCHHHhccccccc-c-----------cchHHHHHHHHHHhc
Confidence            998887653  8899999999999998875 67899999999999 654311 0           00122233321  22


Q ss_pred             CCceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCch
Q 003038          343 ENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGS  383 (854)
Q Consensus       343 g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~s  383 (854)
                      +  .+.+|++|+..++.+.+..+|+|.+  ||+.|.|+.|+
T Consensus       151 ~--~~~ii~~~~~~~~~~~~~~~~~l~~--R~~~i~i~~p~  187 (187)
T 2p65_A          151 G--ELRCIGATTVSEYRQFIEKDKALER--RFQQILVEQPS  187 (187)
T ss_dssp             T--CSCEEEEECHHHHHHHTTTCHHHHH--HEEEEECCSCC
T ss_pred             C--CeeEEEecCHHHHHHHHhccHHHHH--hcCcccCCCCC
Confidence            3  5999999999999988889999999  88888888763

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.67  E-value=4.1e-17  Score=162.00  Aligned_cols=168  Identities=21%  Similarity=0.324  Sum_probs=133.0

Q ss_pred             CCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc--cchH
Q 003038          204 RVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH--MNRV  279 (854)
Q Consensus       204 ~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~--~~rg  279 (854)
                      ...++++  |+++++++++.|.++..++++|+||||+|||++++.++..+.....|..+.+..++.+++..+..  .+.|
T Consensus        18 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (195)
T 1jbk_A           18 QGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRG   97 (195)
T ss_dssp             TTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHH
T ss_pred             hccccccccchHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEeeHHHHhccCCccc
Confidence            4556665  99999999999998888999999999999999999999999998888888899999999988874  3889


Q ss_pred             HHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHH
Q 003038          280 EVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSY  358 (854)
Q Consensus       280 e~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey  358 (854)
                      +++..+++++..+... ++++||||||++++ +.+......         ....-+..++.  .+  .+.+|++|+...+
T Consensus        98 ~~~~~~~~~~~~~~~~-~~~~vl~iDe~~~l~~~~~~~~~~---------~~~~~l~~~~~--~~--~~~~i~~~~~~~~  163 (195)
T 1jbk_A           98 EFEERLKGVLNDLAKQ-EGNVILFIDELHTMVGAGKADGAM---------DAGNMLKPALA--RG--ELHCVGATTLDEY  163 (195)
T ss_dssp             HHHHHHHHHHHHHHHS-TTTEEEEEETGGGGTT------CC---------CCHHHHHHHHH--TT--SCCEEEEECHHHH
T ss_pred             cHHHHHHHHHHHHhhc-CCCeEEEEeCHHHHhccCcccchH---------HHHHHHHHhhc--cC--CeEEEEeCCHHHH
Confidence            9999999999988765 56899999999999 654221000         01111222222  23  5999999999999


Q ss_pred             HHhhccCCchhhhhccCCCCCCCchHHHH
Q 003038          359 MRCKSGHPSLETLWSLHPLTIPAGSLSLS  387 (854)
Q Consensus       359 ~k~~~~~pale~~~~~~~v~i~~~sl~~a  387 (854)
                      ...+..+|+|.+  ||+.+.++.++....
T Consensus       164 ~~~~~~~~~l~~--r~~~i~~~~p~~~~~  190 (195)
T 1jbk_A          164 RQYIEKDAALER--RFQKVFVAEPSVEDT  190 (195)
T ss_dssp             HHHTTTCHHHHT--TEEEEECCCCCHHHH
T ss_pred             HHHHhcCHHHHH--HhceeecCCCCHHHH
Confidence            998889999999  888888888876653

>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=99.52  E-value=4.6e-15  Score=165.20  Aligned_cols=146  Identities=15%  Similarity=0.203  Sum_probs=96.7

Q ss_pred             HHHHHHhhcCcccccHHHHHHHHHHHHHh----hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC
Q 003038          609 LTSLCNALEKKVPWQKDTVYDIANTVLKC----RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS  684 (854)
Q Consensus       609 l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~----rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~  684 (854)
                      ...|.+.|.+.|+||++++..|..++...    +.+.....       ...+...+||+||+|+|||++|++||+.+   
T Consensus         6 ~~~l~~~l~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~-------~~~~~~~vll~GppGtGKT~la~~ia~~~---   75 (363)
T 3hws_A            6 PHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNG-------VELGKSNILLIGPTGSGKTLLAETLARLL---   75 (363)
T ss_dssp             HHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHTTSCSSS-------CCCCCCCEEEECCTTSSHHHHHHHHHHHT---
T ss_pred             HHHHHHHHHhhccCHHHHHHHHHHHHHHHHhhhcccccccc-------ccCCCCeEEEECCCCCCHHHHHHHHHHHc---
Confidence            34677888889999999999999988533    33332211       11345689999999999999999999988   


Q ss_pred             CCceEEEccccccCcCCCccccccccccCCCCCC-chH--HHHHHHHHc-------CCCEEEEEecCCCCCHH-------
Q 003038          685 HNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSC-SYI--ERFAEAVSN-------NPHRVFLIEDVEQADYC-------  747 (854)
Q Consensus       685 ~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~~--e~L~eav~~-------~p~~ViliDEieka~~~-------  747 (854)
                      ..+|+.++++.+..                 .+| |+.  ..+.+++..       .+.+||||||||++++.       
T Consensus        76 ~~~~~~~~~~~l~~-----------------~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l~~~~~~~~~~  138 (363)
T 3hws_A           76 DVPFTMADATTLTE-----------------AGYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRKSDNPSIT  138 (363)
T ss_dssp             TCCEEEEEHHHHTT-----------------CHHHHHHHTHHHHHHHHHTTTCHHHHHHCEEEEECHHHHCCCSSCC---
T ss_pred             CCCEEEechHHhcc-----------------cccccccHHHHHHHHHHHhhhhHHhcCCcEEEEeChhhhcccccccccc
Confidence            46899999886541                 112 332  134444433       35679999999999987       


Q ss_pred             -------HHHHHHHhhhcCeE---ecCCCceeecCCeEEEEecCC
Q 003038          748 -------SQKGFKRAIESGRI---VTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       748 -------v~~~Ll~~le~G~l---~d~~G~~v~~~~aIiIlTsn~  782 (854)
                             +|+.|+++|| |.+   .+..|+.+++.++++|+|||.
T Consensus       139 ~~~~~~~~~~~Ll~~le-g~~~~~~~~~~~~~~~~~~~~i~tsn~  182 (363)
T 3hws_A          139 RDVSGEGVQQALLKLIE-GTVAAVPPQGGRKHPQQEFLQVDTSKI  182 (363)
T ss_dssp             CHHHHHHHHHHHHHHHH-CC----------------CCCCCTTSS
T ss_pred             cccchHHHHHHHHHHhc-CceeeccCccccccCCCceEEEECCCc
Confidence                   9999999999 653   455667666666666655553

>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=99.49  E-value=2e-14  Score=160.67  Aligned_cols=153  Identities=11%  Similarity=0.137  Sum_probs=97.8

Q ss_pred             HHHHHHhhcCcccccHHHHHHHHHHH----HHhhcCC-------CcccCCCc-CCcccCcceeEEEecCCCchHHHHHHH
Q 003038          609 LTSLCNALEKKVPWQKDTVYDIANTV----LKCRSGT-------MRRKGKFK-DHSEVKEETWLFFQGVDADAKEKIAKE  676 (854)
Q Consensus       609 l~~L~~~L~~~V~GQ~~av~~Ia~~v----~~~rsgl-------~~~~~~~~-~~~~~kp~~~lLf~Gp~GvGKt~lAr~  676 (854)
                      ++.|++.|.+.|+||++++..|..+|    .+.+.|+       .++.++.. .....++..++||+||+|+|||++|++
T Consensus        12 ~~~l~~~L~~~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~   91 (376)
T 1um8_A           12 PKELKAVLDNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQT   91 (376)
T ss_dssp             HHHHHHHHHTTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHH
T ss_pred             HHHHHHHHhhHccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHH
Confidence            56889999999999999999999998    4555544       11110000 000013456899999999999999999


Q ss_pred             HHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCC-chH--HHHHHHH-------HcCCCEEEEEecCCCCCH
Q 003038          677 LARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSC-SYI--ERFAEAV-------SNNPHRVFLIEDVEQADY  746 (854)
Q Consensus       677 LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~~--e~L~eav-------~~~p~~ViliDEieka~~  746 (854)
                      ||+.+   ..+|+.++++.+..       .          +| |+.  ..+.+.+       ...+++|||||||+++++
T Consensus        92 la~~l---~~~~~~~~~~~~~~-------~----------~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~  151 (376)
T 1um8_A           92 LAKHL---DIPIAISDATSLTE-------A----------GYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISR  151 (376)
T ss_dssp             HHHHT---TCCEEEEEGGGCC-------------------------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC--
T ss_pred             HHHHh---CCCEEEecchhhhh-------c----------CcCCccHHHHHHHHHhhccchhhhcCCeEEEEcCHHHHhh
Confidence            99988   35789999886651       0          11 111  1233332       334678999999999999


Q ss_pred             H--------------HHHHHHHhhhcCeE--ecCCCce--------eecCCeEEEEecC
Q 003038          747 C--------------SQKGFKRAIESGRI--VTSSGDE--------VSLGDAIVILSCE  781 (854)
Q Consensus       747 ~--------------v~~~Ll~~le~G~l--~d~~G~~--------v~~~~aIiIlTsn  781 (854)
                      .              +|+.|+++|+++.+  .+..|+.        +..+|.+||+|+|
T Consensus       152 ~~~~~~~~~~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~  210 (376)
T 1um8_A          152 LSENRSITRDVSGEGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGA  210 (376)
T ss_dssp             ------------CHHHHHHHHHHHHCCEEC---------------CEECTTCEEEEEEC
T ss_pred             hcCCCceecccchHHHHHHHHHHhhccceecccccccccCCcceEEEecCCeEEEecCC
Confidence            8              99999999998854  4445555        4445666666665

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.45  E-value=2.8e-13  Score=151.59  Aligned_cols=141  Identities=13%  Similarity=0.134  Sum_probs=104.5

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..+.++|+||||||||.+|+++|...          ++.|+.++.+.+.++|.||.|++++++|..++..  .|+|||||
T Consensus       181 ~prGvLL~GPPGTGKTllAkAiA~e~----------~~~f~~v~~s~l~sk~vGese~~vr~lF~~Ar~~--aP~IIFiD  248 (405)
T 4b4t_J          181 QPKGVILYGPPGTGKTLLARAVAHHT----------DCKFIRVSGAELVQKYIGEGSRMVRELFVMAREH--APSIIFMD  248 (405)
T ss_dssp             CCCCEEEESCSSSSHHHHHHHHHHHH----------TCEEEEEEGGGGSCSSTTHHHHHHHHHHHHHHHT--CSEEEEEE
T ss_pred             CCCceEEeCCCCCCHHHHHHHHHHhh----------CCCceEEEhHHhhccccchHHHHHHHHHHHHHHh--CCceEeee
Confidence            56899999999999999999999874          7799999999999999999999999999999986  79999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCch
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGS  383 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~s  383 (854)
                      ||+.+ ..+..++.+.   ...+....+.+-+.+....+++.+.+||||+..+     ..||||-|--|| ..|.|+-|+
T Consensus       249 EiDai~~~R~~~~~~~---~~~~~~~l~~lL~~lDg~~~~~~V~vIaATNrpd-----~LDpAllRpGRfD~~I~i~lPd  320 (405)
T 4b4t_J          249 EIDSIGSTRVEGSGGG---DSEVQRTMLELLNQLDGFETSKNIKIIMATNRLD-----ILDPALLRPGRIDRKIEFPPPS  320 (405)
T ss_dssp             SSSCCTTSCSCSSSGG---GGHHHHHHHHHHHHHHTTTCCCCEEEEEEESCSS-----SSCHHHHSTTSSCCEEECCCCC
T ss_pred             cchhhccCCCCCCCCC---cHHHHHHHHHHHHhhhccCCCCCeEEEeccCChh-----hCCHhHcCCCcCceEEEcCCcC
Confidence            99999 5543221110   1112233333333332212233699999999655     579999875566 456666665


Q ss_pred             HHH
Q 003038          384 LSL  386 (854)
Q Consensus       384 l~~  386 (854)
                      ...
T Consensus       321 ~~~  323 (405)
T 4b4t_J          321 VAA  323 (405)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>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=99.44  E-value=2.4e-13  Score=146.57  Aligned_cols=152  Identities=16%  Similarity=0.246  Sum_probs=107.3

Q ss_pred             HHHHHHhhcCcccccHHHHHHHHHHHHH--hhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC
Q 003038          609 LTSLCNALEKKVPWQKDTVYDIANTVLK--CRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN  686 (854)
Q Consensus       609 l~~L~~~L~~~V~GQ~~av~~Ia~~v~~--~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~  686 (854)
                      ...|.+.|.+.|+||++++..|..++..  .+.++..+.+      ..++...+||+||+|+|||++|++||+.+   ..
T Consensus         6 ~~~l~~~l~~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~------~~~~~~~vll~G~~GtGKT~la~~la~~l---~~   76 (310)
T 1ofh_A            6 PREIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLR------HEVTPKNILMIGPTGVGKTEIARRLAKLA---NA   76 (310)
T ss_dssp             HHHHHHHHHTTCCSCHHHHHHHHHHHHHHHHTTSSCHHHH------HHCCCCCEEEECCTTSSHHHHHHHHHHHH---TC
T ss_pred             HHHHHHHHhhhcCChHHHHHHHHHHHHHHHhhhhhccccc------ccCCCceEEEECCCCCCHHHHHHHHHHHh---CC
Confidence            3578889999999999999999999876  3333332110      01234589999999999999999999988   35


Q ss_pred             ceEEEccccccCcCCCccccccccccCCCCCCchHHHHHH----HHHc-CCCEEEEEecCCCCCHHH------------H
Q 003038          687 NFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAE----AVSN-NPHRVFLIEDVEQADYCS------------Q  749 (854)
Q Consensus       687 ~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~e----av~~-~p~~ViliDEieka~~~v------------~  749 (854)
                      .++.++++.+...      .+     .+....+....+.+    .+.. ++++||||||||++++..            +
T Consensus        77 ~~~~i~~~~~~~~------~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~  145 (310)
T 1ofh_A           77 PFIKVEATKFTEV------GY-----VGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQ  145 (310)
T ss_dssp             CEEEEEGGGGSSC------CS-----GGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSSHHHHHHHH
T ss_pred             CEEEEcchhcccC------Cc-----cCccHHHHHHHHHHHhhHHHhhccCCCEEEEEChhhcCccccccccchhHHHHH
Confidence            7999999877621      00     00000011111211    1111 246899999999998775            9


Q ss_pred             HHHHHhhhcCeEecCCCceeecCCeEEEEecC
Q 003038          750 KGFKRAIESGRIVTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       750 ~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn  781 (854)
                      +.|+++|+++.+....| .++..+.+||+++|
T Consensus       146 ~~Ll~~le~~~~~~~~~-~~~~~~~~~i~~~~  176 (310)
T 1ofh_A          146 RDLLPLVEGSTVSTKHG-MVKTDHILFIASGA  176 (310)
T ss_dssp             HHHHHHHHCCEEEETTE-EEECTTCEEEEEEC
T ss_pred             HHHHHHhcCCeEecccc-cccCCcEEEEEcCC
Confidence            99999999998887665 67788999999875

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.41  E-value=6.7e-13  Score=149.00  Aligned_cols=141  Identities=10%  Similarity=0.069  Sum_probs=102.5

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      -++.++|+||||||||.+|+++|...          ++.|+.++.+.|.++|.||.|++++.+|..++..  .|+|||||
T Consensus       215 ~prGvLLyGPPGTGKTlLAkAiA~e~----------~~~fi~v~~s~l~sk~vGesek~ir~lF~~Ar~~--aP~IIfiD  282 (437)
T 4b4t_I          215 PPKGVILYGAPGTGKTLLAKAVANQT----------SATFLRIVGSELIQKYLGDGPRLCRQIFKVAGEN--APSIVFID  282 (437)
T ss_dssp             CCSEEEEESSTTTTHHHHHHHHHHHH----------TCEEEEEESGGGCCSSSSHHHHHHHHHHHHHHHT--CSEEEEEE
T ss_pred             CCCCCceECCCCchHHHHHHHHHHHh----------CCCEEEEEHHHhhhccCchHHHHHHHHHHHHHhc--CCcEEEEe
Confidence            56889999999999999999999884          6799999999999999999999999999999986  79999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCch
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGS  383 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~s  383 (854)
                      |++.+ ..+...+.+.   ...+....+.+-+.+.....++.+.+||||+.-+     ..||||-|--|| ..|.|+-|+
T Consensus       283 EiDai~~~R~~~~~~~---~~~~~~~l~~LL~~lDg~~~~~~ViVIaATNrpd-----~LDpALlRpGRfD~~I~v~lPd  354 (437)
T 4b4t_I          283 EIDAIGTKRYDSNSGG---EREIQRTMLELLNQLDGFDDRGDVKVIMATNKIE-----TLDPALIRPGRIDRKILFENPD  354 (437)
T ss_dssp             EESSSSCCCSCSSCSS---CCHHHHHHHHHHHHHHHCCCSSSEEEEEEESCST-----TCCTTSSCTTTEEEEECCCCCC
T ss_pred             hhhhhcccCCCCCCCc---cHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCChh-----hcCHHHhcCCceeEEEEcCCcC
Confidence            99999 5543221111   1112223333333332212233699999998765     589999884445 235565555


Q ss_pred             HHH
Q 003038          384 LSL  386 (854)
Q Consensus       384 l~~  386 (854)
                      ...
T Consensus       355 ~~~  357 (437)
T 4b4t_I          355 LST  357 (437)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.41  E-value=7.3e-13  Score=150.23  Aligned_cols=141  Identities=12%  Similarity=0.077  Sum_probs=103.6

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      -.+.++|+||||||||.+|+++|...          ++.|+.++.+.+.++|.|+.+..++.+|..++..  .|+|||||
T Consensus       214 ~prGvLL~GPPGtGKTllAkAiA~e~----------~~~~~~v~~s~l~sk~~Gese~~ir~~F~~A~~~--~P~IifiD  281 (437)
T 4b4t_L          214 PPKGVLLYGPPGTGKTLLAKAVAATI----------GANFIFSPASGIVDKYIGESARIIREMFAYAKEH--EPCIIFMD  281 (437)
T ss_dssp             CCCEEEEESCTTSSHHHHHHHHHHHH----------TCEEEEEEGGGTCCSSSSHHHHHHHHHHHHHHHS--CSEEEEEE
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh----------CCCEEEEehhhhccccchHHHHHHHHHHHHHHhc--CCceeeee
Confidence            46889999999999999999999884          6799999999999999999999999999999986  79999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCch
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGS  383 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~s  383 (854)
                      |++.+ ..+......   ....+....+.+-+.+....+.+.+.+||||+.-+     ..||||-|.-|| ..|.|+-|+
T Consensus       282 EiDai~~~R~~~~~~---~~~~~~~~l~~lL~~lDg~~~~~~vivI~ATNrp~-----~LDpAllRpGRfD~~I~i~lPd  353 (437)
T 4b4t_L          282 EVDAIGGRRFSEGTS---ADREIQRTLMELLTQMDGFDNLGQTKIIMATNRPD-----TLDPALLRPGRLDRKVEIPLPN  353 (437)
T ss_dssp             CCCSSSCCCSSSCCS---STTHHHHHHHHHHHHHHSSSCTTSSEEEEEESSTT-----SSCTTTTSTTSEEEEECCCCCC
T ss_pred             cccccccccccCCCC---cchHHHHHHHHHHHHhhcccCCCCeEEEEecCCch-----hhCHHHhCCCccceeeecCCcC
Confidence            99999 554322111   01112223333333332212233699999998654     579999885456 356666665


Q ss_pred             HHH
Q 003038          384 LSL  386 (854)
Q Consensus       384 l~~  386 (854)
                      ...
T Consensus       354 ~~~  356 (437)
T 4b4t_L          354 EAG  356 (437)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.39  E-value=7.3e-13  Score=150.12  Aligned_cols=141  Identities=13%  Similarity=0.119  Sum_probs=103.3

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      -++.++|+||||||||.+|+++|...          ++.|+.++.+.|.++|.|+.|++++.+|..++..  .|+|||||
T Consensus       214 ~prGvLLyGPPGTGKTllAkAiA~e~----------~~~f~~v~~s~l~~~~vGese~~ir~lF~~A~~~--aP~IifiD  281 (434)
T 4b4t_M          214 APKGALMYGPPGTGKTLLARACAAQT----------NATFLKLAAPQLVQMYIGEGAKLVRDAFALAKEK--APTIIFID  281 (434)
T ss_dssp             CCCEEEEESCTTSSHHHHHHHHHHHH----------TCEEEEEEGGGGCSSCSSHHHHHHHHHHHHHHHH--CSEEEEEE
T ss_pred             CCCeeEEECcCCCCHHHHHHHHHHHh----------CCCEEEEehhhhhhcccchHHHHHHHHHHHHHhc--CCeEEeec
Confidence            46889999999999999999999874          6799999999999999999999999999999987  79999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCch
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGS  383 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~s  383 (854)
                      |++.+ ..+.....+   ....+....+.+-+.+....+++.+.+||||+.-+     .-||||-|--|| ..|.|+-|+
T Consensus       282 EiDal~~~R~~~~~~---~~~~~~~~~~~lL~~ldg~~~~~~ViVIaaTNrp~-----~LD~AllRpGRfD~~I~i~lPd  353 (434)
T 4b4t_M          282 ELDAIGTKRFDSEKS---GDREVQRTMLELLNQLDGFSSDDRVKVLAATNRVD-----VLDPALLRSGRLDRKIEFPLPS  353 (434)
T ss_dssp             CTHHHHCCCSSGGGG---TTHHHHHHHHHHHHHHTTSCSSCSSEEEEECSSCC-----CCCTTTCSTTSEEEEEECCCCC
T ss_pred             chhhhhhccCCCCCC---CchHHHHHHHHHHHHhhccCCCCCEEEEEeCCCch-----hcCHhHhcCCceeEEEEeCCcC
Confidence            99999 554322111   01112223333333332212334699999998654     579999774456 345566555


Q ss_pred             HHH
Q 003038          384 LSL  386 (854)
Q Consensus       384 l~~  386 (854)
                      ...
T Consensus       354 ~~~  356 (434)
T 4b4t_M          354 EDS  356 (434)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.39  E-value=1.3e-12  Score=148.01  Aligned_cols=141  Identities=11%  Similarity=0.115  Sum_probs=101.8

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEe
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      +-.+.++|+||||||||.+|+++|...          ++.|+.++.+.|.++|.|+.|++++++|..++..  .|+||||
T Consensus       241 ~pprGILLyGPPGTGKTlLAkAiA~e~----------~~~fi~vs~s~L~sk~vGesek~ir~lF~~Ar~~--aP~IIfi  308 (467)
T 4b4t_H          241 DPPKGILLYGPPGTGKTLCARAVANRT----------DATFIRVIGSELVQKYVGEGARMVRELFEMARTK--KACIIFF  308 (467)
T ss_dssp             CCCSEEEECSCTTSSHHHHHHHHHHHH----------TCEEEEEEGGGGCCCSSSHHHHHHHHHHHHHHHT--CSEEEEE
T ss_pred             CCCCceEeeCCCCCcHHHHHHHHHhcc----------CCCeEEEEhHHhhcccCCHHHHHHHHHHHHHHhc--CCceEee
Confidence            367899999999999999999999884          6799999999999999999999999999999986  7999999


Q ss_pred             Cccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCc
Q 003038          305 GDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAG  382 (854)
Q Consensus       305 del~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~  382 (854)
                      ||++.+ ..+.....+.   ...+....+.+-+.+....+++.+.+||||+.-+     ..||||-|-=|| ..|.|+-|
T Consensus       309 DEiDai~~~R~~~~~~~---~~~~~~~l~~lL~~lDg~~~~~~ViVIaATNrpd-----~LDpALlRpGRFD~~I~i~lP  380 (467)
T 4b4t_H          309 DEIDAVGGARFDDGAGG---DNEVQRTMLELITQLDGFDPRGNIKVMFATNRPN-----TLDPALLRPGRIDRKVEFSLP  380 (467)
T ss_dssp             ECCTTTSBCCSSSSCGG---GGHHHHHHHHHHHHHHSSCCTTTEEEEEECSCTT-----SBCHHHHSTTTCCEEECCCCC
T ss_pred             cccccccccccCcCCCc---cHHHHHHHHHHHHHhhccCCCCcEEEEeCCCCcc-----cCChhhhccccccEEEEeCCc
Confidence            999999 6543321110   1111222222222232212233699999998654     579999873344 34555555


Q ss_pred             hHH
Q 003038          383 SLS  385 (854)
Q Consensus       383 sl~  385 (854)
                      +..
T Consensus       381 d~~  383 (467)
T 4b4t_H          381 DLE  383 (467)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            543

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.33  E-value=5.1e-12  Score=136.58  Aligned_cols=139  Identities=16%  Similarity=0.180  Sum_probs=102.4

Q ss_pred             hHHHHHHHHHhhcCcccccHHHHHHHHHHHHHh-------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHH
Q 003038          605 NSENLTSLCNALEKKVPWQKDTVYDIANTVLKC-------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKEL  677 (854)
Q Consensus       605 ~~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~-------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~L  677 (854)
                      +...+..+.+.|.+.|+||++++..|...+...       +.|+..+          ++...+||+||+|+|||.+|+++
T Consensus        18 ~~~~~~~~~~~l~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~----------~~~~~vll~G~~GtGKT~la~~l   87 (309)
T 3syl_A           18 EGSGAKEVLEELDRELIGLKPVKDRIRETAALLLVERARQKLGLAHE----------TPTLHMSFTGNPGTGKTTVALKM   87 (309)
T ss_dssp             HHTTHHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSS----------CCCCEEEEEECTTSSHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHccChHHHHHHHHHHHHHHHhHHHHHHcCCCCC----------CCCceEEEECCCCCCHHHHHHHH
Confidence            344567788888889999999999998777543       2444432          45568999999999999999999


Q ss_pred             HHHHhCC----CCceEEEccccccCcCCCccccccccccCCCCCCchHH-HHHHHHHcCCCEEEEEecCCCC--------
Q 003038          678 ARLVFGS----HNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIE-RFAEAVSNNPHRVFLIEDVEQA--------  744 (854)
Q Consensus       678 A~~lfg~----~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e-~L~eav~~~p~~ViliDEieka--------  744 (854)
                      |+.+...    ...++.++++.+.       ...     .     |... .+.+.+.....+||||||||.+        
T Consensus        88 a~~l~~~~~~~~~~~~~~~~~~l~-------~~~-----~-----g~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~  150 (309)
T 3syl_A           88 AGLLHRLGYVRKGHLVSVTRDDLV-------GQY-----I-----GHTAPKTKEVLKRAMGGVLFIDEAYYLYRPDNERD  150 (309)
T ss_dssp             HHHHHHTTSSSSCCEEEECGGGTC-------CSS-----T-----TCHHHHHHHHHHHHTTSEEEEETGGGSCCCC---C
T ss_pred             HHHHHhcCCcCCCcEEEEcHHHhh-------hhc-----c-----cccHHHHHHHHHhcCCCEEEEEChhhhccCCCccc
Confidence            9988543    2368888876554       111     1     2222 4455555556789999999966        


Q ss_pred             -CHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecC
Q 003038          745 -DYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       745 -~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn  781 (854)
                       ++.+++.|++.|+++.           .+.+||+|+|
T Consensus       151 ~~~~~~~~Ll~~l~~~~-----------~~~~~i~~~~  177 (309)
T 3syl_A          151 YGQEAIEILLQVMENNR-----------DDLVVILAGY  177 (309)
T ss_dssp             CTHHHHHHHHHHHHHCT-----------TTCEEEEEEC
T ss_pred             ccHHHHHHHHHHHhcCC-----------CCEEEEEeCC
Confidence             9999999999999752           4678899886

>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=99.32  E-value=1.7e-12  Score=137.59  Aligned_cols=142  Identities=13%  Similarity=0.180  Sum_probs=96.3

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++||+.++..+...+.....                ...++||+||+|+|||.+|++|++.+.....+|+.++|+.+.
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~----------------~~~~vll~G~~GtGKt~la~~i~~~~~~~~~~~~~v~~~~~~   69 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAP----------------LDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALN   69 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTT----------------SCSCEEEECCTTSCHHHHHHHHHHTSTTTTSCEEEEEGGGSC
T ss_pred             ccceeCCHHHHHHHHHHHHHhC----------------CCCCEEEECCCCCcHHHHHHHHHHhcCccCCCeEEEecCCCC
Confidence            3578999999998888776532                124789999999999999999999887666789999999875


Q ss_pred             CcCCCccccccccccCCC-CC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCe
Q 003038          698 STRADSTEDSRNKRSRDE-QS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDA  774 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~-~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~a  774 (854)
                             .......+.+. .+ + |......+.+......+||||||+++++++|+.|+++|++|.+....+....-.+.
T Consensus        70 -------~~~~~~~l~g~~~~~~~g~~~~~~~~l~~a~~~~l~lDEi~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~  142 (265)
T 2bjv_A           70 -------ENLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPMMVQEKLLRVIEYGELERVGGSQPLQVNV  142 (265)
T ss_dssp             -------HHHHHHHHHCCC---------CCCCHHHHTTTSEEEEESGGGSCHHHHHHHHHHHHHCEECCCCC--CEECCC
T ss_pred             -------hhHHHHHhcCCcccccccccccccchhhhcCCcEEEEechHhcCHHHHHHHHHHHHhCCeecCCCcccccCCe
Confidence                   22111111110 00 1 11110111233345689999999999999999999999999987654444445678


Q ss_pred             EEEEecCC
Q 003038          775 IVILSCES  782 (854)
Q Consensus       775 IiIlTsn~  782 (854)
                      .||+|||.
T Consensus       143 ~iI~atn~  150 (265)
T 2bjv_A          143 RLVCATNA  150 (265)
T ss_dssp             EEEEEESS
T ss_pred             EEEEecCc
Confidence            89999984

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.31  E-value=4.8e-12  Score=143.30  Aligned_cols=135  Identities=14%  Similarity=0.162  Sum_probs=99.7

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      -++.++|+||||||||.+|+++|...          ++.|+.++.+.+.++|.|+.|.+++++|..++..  .|+|||||
T Consensus       205 ~prGiLL~GPPGtGKT~lakAiA~~~----------~~~~~~v~~~~l~~~~~Ge~e~~ir~lF~~A~~~--aP~IifiD  272 (428)
T 4b4t_K          205 PPRGVLLYGPPGTGKTMLVKAVANST----------KAAFIRVNGSEFVHKYLGEGPRMVRDVFRLAREN--APSIIFID  272 (428)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHHHH----------TCEEEEEEGGGTCCSSCSHHHHHHHHHHHHHHHT--CSEEEEEE
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHh----------CCCeEEEecchhhccccchhHHHHHHHHHHHHHc--CCCeeech
Confidence            46679999999999999999999874          6799999999999999999999999999999986  79999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccC-CCCCC
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLH-PLTIP  380 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~-~v~i~  380 (854)
                      |++.+ ..+.....+.   ..........+-+.+....+.+.+.+||||+..+     .-||||-|--||. .|.+|
T Consensus       273 EiD~i~~~R~~~~~~~---~~~~~r~l~~lL~~ldg~~~~~~v~vI~aTN~~~-----~LD~AllRpGRfd~~I~~p  341 (428)
T 4b4t_K          273 EVDSIATKRFDAQTGS---DREVQRILIELLTQMDGFDQSTNVKVIMATNRAD-----TLDPALLRPGRLDRKIEFP  341 (428)
T ss_dssp             CTHHHHCSCSSSCSCC---CCHHHHHHHHHHHHHHHSCSSCSEEEEEEESCSS-----SCCHHHHSSSSEEEEEECC
T ss_pred             hhhhhhccccCCCCCC---ChHHHHHHHHHHHHhhCCCCCCCEEEEEecCChh-----hcChhhhcCCcceEEEEcC
Confidence            99999 5543221110   1112234444444442211223599999998654     5799998854553 45554

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.23  E-value=2.2e-11  Score=131.61  Aligned_cols=137  Identities=10%  Similarity=0.046  Sum_probs=84.3

Q ss_pred             HHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCc
Q 003038          624 KDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADS  703 (854)
Q Consensus       624 ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s  703 (854)
                      +..+..++..+.+....+...          ++...+||+||+|||||.+|++||+.+   ..+|++++++++.      
T Consensus        13 ~~~~~~~~~~~~k~~l~~~~~----------~~p~~lLl~GppGtGKT~la~aiA~~l---~~~~i~v~~~~l~------   73 (293)
T 3t15_A           13 PAFMDKLVVHITKNFLKLPNI----------KVPLILGIWGGKGQGKSFQCELVFRKM---GINPIMMSAGELE------   73 (293)
T ss_dssp             HHHHHHHHHHHHHTTSCCTTC----------CCCSEEEEEECTTSCHHHHHHHHHHHH---TCCCEEEEHHHHH------
T ss_pred             HHHHHHHHHHHHHHHHhcCCC----------CCCeEEEEECCCCCCHHHHHHHHHHHh---CCCEEEEeHHHhh------
Confidence            445556666666654433221          333467889999999999999999998   4689999988665      


Q ss_pred             cccccccccCCCCCCchHHHHHHH----HHcCCCEEEEEecCCCCCH-------------HHHHHHHHhhhcCeEecCC-
Q 003038          704 TEDSRNKRSRDEQSCSYIERFAEA----VSNNPHRVFLIEDVEQADY-------------CSQKGFKRAIESGRIVTSS-  765 (854)
Q Consensus       704 ~e~~~~~rl~~~~g~g~~e~L~ea----v~~~p~~ViliDEieka~~-------------~v~~~Ll~~le~G~l~d~~-  765 (854)
                       ...     .+ ...++...+.+.    ++..+.+||||||||++.+             .+++.|++.|+........ 
T Consensus        74 -~~~-----~g-~~~~~i~~~f~~a~~~~~~~~~~vl~iDEiD~~~~~~~~~~~~~~~~~~v~~~Ll~~ld~~~~~~~~~  146 (293)
T 3t15_A           74 -SGN-----AG-EPAKLIRQRYREAAEIIRKGNMCCLFINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPG  146 (293)
T ss_dssp             -CC---------HHHHHHHHHHHHHHHHHTTSSCCCEEEECCC--------------CHHHHHHHHHHHHHCCC------
T ss_pred             -hcc-----Cc-hhHHHHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCCCCccccchHHHHHHHHHHHhcccccccccc
Confidence             111     00 000122222222    2566789999999998876             4779999999976654322 


Q ss_pred             -CceeecCCeEEEEecCCCCCC
Q 003038          766 -GDEVSLGDAIVILSCESFSSR  786 (854)
Q Consensus       766 -G~~v~~~~aIiIlTsn~f~~~  786 (854)
                       +.....++.+||+|||..+..
T Consensus       147 ~~~~~~~~~v~vI~ttN~~~~l  168 (293)
T 3t15_A          147 MYNKQENARVPIIVTGNDFSTL  168 (293)
T ss_dssp             -----CCCCCCEEEECSSCCC-
T ss_pred             ccccccCCCcEEEEecCCcccC
Confidence             245667899999999965443

>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=99.22  E-value=4e-11  Score=131.25  Aligned_cols=135  Identities=12%  Similarity=0.134  Sum_probs=97.6

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGD  306 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfide  306 (854)
                      .++++|+||||+|||.+++++|...          +..++.++.+.+.+.+.|+.+..++.++..++..  .+.||||||
T Consensus        51 ~~~vLl~GppGtGKT~la~aia~~~----------~~~~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~~--~~~vl~iDE  118 (322)
T 3eie_A           51 TSGILLYGPPGTGKSYLAKAVATEA----------NSTFFSVSSSDLVSKWMGESEKLVKQLFAMAREN--KPSIIFIDQ  118 (322)
T ss_dssp             CCEEEEECSSSSCHHHHHHHHHHHH----------TCEEEEEEHHHHHTTTGGGHHHHHHHHHHHHHHT--SSEEEEEEC
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHH----------CCCEEEEchHHHhhcccchHHHHHHHHHHHHHhc--CCeEEEech
Confidence            4679999999999999999999874          5689999999999999999999999999999975  689999999


Q ss_pred             cccc-cccccccccccccchhhhHHHHHHHhhccc-CCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCch
Q 003038          307 LEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGS  383 (854)
Q Consensus       307 l~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~s  383 (854)
                      |+.+ .......      ....+.....+-..+.. ....+.+.+||+|+...     ..+|+|.+  || ..+.|+.|+
T Consensus       119 id~l~~~~~~~~------~~~~~~~~~~ll~~l~~~~~~~~~v~vi~atn~~~-----~ld~al~~--Rf~~~i~~~~p~  185 (322)
T 3eie_A          119 VDALTGTRGEGE------SEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPW-----QLDSAIRR--RFERRIYIPLPD  185 (322)
T ss_dssp             GGGGSCC------------CCTHHHHHHHHHHHGGGGTSCCCEEEEEEESCGG-----GSCHHHHH--HCCEEEECCCCC
T ss_pred             hhhhhccCCCCc------chHHHHHHHHHHHHhccccccCCceEEEEecCChh-----hCCHHHHc--ccCeEEEeCCCC
Confidence            9999 5432210      01122333444444422 11223699999998543     46899999  77 345566565


Q ss_pred             HHH
Q 003038          384 LSL  386 (854)
Q Consensus       384 l~~  386 (854)
                      ...
T Consensus       186 ~~~  188 (322)
T 3eie_A          186 LAA  188 (322)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>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=99.21  E-value=9.2e-12  Score=150.60  Aligned_cols=141  Identities=14%  Similarity=0.141  Sum_probs=96.6

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEe
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      +..+.++|+||||+|||.+|+++|..          .+..|++++.+.+.++|.||.|+.++++|+.+++.  .|+||||
T Consensus       509 ~~~~gvLl~GPPGtGKT~lAkaiA~e----------~~~~f~~v~~~~l~s~~vGese~~vr~lF~~Ar~~--~P~Iifi  576 (806)
T 3cf2_A          509 TPSKGVLFYGPPGCGKTLLAKAIANE----------CQANFISIKGPELLTMWFGESEANVREIFDKARQA--APCVLFF  576 (806)
T ss_dssp             CCCSCCEEESSTTSSHHHHHHHHHHT----------TTCEEEECCHHHHHTTTCSSCHHHHHHHHHHHHTT--CSEEEEC
T ss_pred             CCCceEEEecCCCCCchHHHHHHHHH----------hCCceEEeccchhhccccchHHHHHHHHHHHHHHc--CCceeec
Confidence            35567999999999999999999976          47799999999999999999999999999999986  7999999


Q ss_pred             Cccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCc
Q 003038          305 GDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAG  382 (854)
Q Consensus       305 del~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~  382 (854)
                      |||+.+ ..+.....+   .....+..+.++-..+..-.++..+.+||||+..+     ..||||-|--|| ..|.|+-|
T Consensus       577 DEiDsl~~~R~~~~~~---~~~~~~rv~~~lL~~mdg~~~~~~V~vi~aTN~p~-----~lD~AllRpgRfd~~i~v~lP  648 (806)
T 3cf2_A          577 DELDSIAKARGGNIGD---GGGAADRVINQILTEMDGMSTKKNVFIIGATNRPD-----IIDPAILRPGRLDQLIYIPLP  648 (806)
T ss_dssp             SCGGGCC-----------------CHHHHHHHHHHHSSCSSSSEEEECC-CCSS-----SSCHHHHSTTTSCCEEEC---
T ss_pred             hhhhHHhhccCCCCCC---CchHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCch-----hCCHhHcCCCcceEEEEECCc
Confidence            999999 654321000   01122345555544452212223699999998654     579999885566 34556655


Q ss_pred             hHH
Q 003038          383 SLS  385 (854)
Q Consensus       383 sl~  385 (854)
                      +..
T Consensus       649 d~~  651 (806)
T 3cf2_A          649 DEK  651 (806)
T ss_dssp             --C
T ss_pred             CHH
Confidence            533

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.18  E-value=2.1e-11  Score=132.60  Aligned_cols=142  Identities=11%  Similarity=0.128  Sum_probs=97.6

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++|++.++..+...+.+..                +...++||+||+|+|||.+|++|+........+|+.++|+.+.
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a----------------~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~~~v~v~~~~~~   65 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVA----------------PSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALN   65 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHC----------------STTSCEEEESCTTSCHHHHHHHHHHHSSCSSSCCCEEECSSCC
T ss_pred             CCcEECCHHHHHHHHHHHHHh----------------CCCCcEEEECCCCchHHHHHHHHHHhCcccCCCeEEEeCCCCC
Confidence            458999999999988887752                1234789999999999999999999876667889999998765


Q ss_pred             CcCCCccccccccccCCC-CC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCe
Q 003038          698 STRADSTEDSRNKRSRDE-QS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDA  774 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~-~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~a  774 (854)
                             +....+.+.+. .| + |........+......+||||||+.+++++|..|+++|+++.+..-.+....-.++
T Consensus        66 -------~~l~~~~lfg~~~g~~tg~~~~~~g~~~~a~~g~L~LDEi~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~  138 (304)
T 1ojl_A           66 -------ESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDV  138 (304)
T ss_dssp             -------HHHHHHHHTCCCSSCCC---CCCCCHHHHHTTSEEEEESCTTCCHHHHHHHHHHHHSSBCCBTTBCCCCBCCC
T ss_pred             -------hHHHHHHhcCccccccCchhhhhcCHHHhcCCCEEEEeccccCCHHHHHHHHHHHhcCEeeecCCcccccCCe
Confidence                   21111111110 00 0 11000011112223579999999999999999999999999887544433334577


Q ss_pred             EEEEecCC
Q 003038          775 IVILSCES  782 (854)
Q Consensus       775 IiIlTsn~  782 (854)
                      .||++||.
T Consensus       139 riI~atn~  146 (304)
T 1ojl_A          139 RLIAATHR  146 (304)
T ss_dssp             EEEEEESS
T ss_pred             EEEEecCc
Confidence            89998884

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.18  E-value=5.2e-11  Score=133.76  Aligned_cols=151  Identities=11%  Similarity=0.065  Sum_probs=98.9

Q ss_pred             cHHHHHHHHHHhh------------ccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccch
Q 003038          211 RNEDVMYVIENLM------------SKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNR  278 (854)
Q Consensus       211 r~~ei~~v~~~L~------------r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~r  278 (854)
                      .++.++.+.+.+.            +...++++|+||||||||++|+++|.+          .+..|+.++.+.+...|.
T Consensus       120 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~----------~~~~~~~v~~~~l~~~~~  189 (389)
T 3vfd_A          120 QDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAE----------SNATFFNISAASLTSKYV  189 (389)
T ss_dssp             CHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHH----------TTCEEEEECSCCC-----
T ss_pred             HHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHh----------hcCcEEEeeHHHhhcccc
Confidence            6666777777662            234589999999999999999999987          367999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecCH
Q 003038          279 VEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIATF  355 (854)
Q Consensus       279 ge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT~  355 (854)
                      |+++..++.++..++..  .+.||||||||.+ .....+.      ..........+-..+..  ....+++.+||+|+.
T Consensus       190 g~~~~~~~~~~~~a~~~--~~~il~iDEid~l~~~~~~~~------~~~~~~~~~~ll~~l~~~~~~~~~~v~vI~atn~  261 (389)
T 3vfd_A          190 GEGEKLVRALFAVAREL--QPSIIFIDQVDSLLCERREGE------HDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNR  261 (389)
T ss_dssp             --CHHHHHHHHHHHHHS--SSEEEEEETGGGGC--------------CTHHHHHHHHHHHHHHHC-----CEEEEEEESC
T ss_pred             chHHHHHHHHHHHHHhc--CCeEEEEECchhhcccCCCcc------chHHHHHHHHHHHHhhcccccCCCCEEEEEecCC
Confidence            99999999999999875  6889999999999 5432210      00111222233333311  111236999999986


Q ss_pred             HHHHHhhccCCchhhhhccC-CCCCCCchHHH
Q 003038          356 QSYMRCKSGHPSLETLWSLH-PLTIPAGSLSL  386 (854)
Q Consensus       356 ~ey~k~~~~~pale~~~~~~-~v~i~~~sl~~  386 (854)
                      .+     ..+++|.+  ||+ .|.|+.++...
T Consensus       262 ~~-----~l~~~l~~--R~~~~i~i~~p~~~~  286 (389)
T 3vfd_A          262 PQ-----ELDEAVLR--RFIKRVYVSLPNEET  286 (389)
T ss_dssp             GG-----GCCHHHHT--TCCEEEECCCCCHHH
T ss_pred             ch-----hcCHHHHc--CcceEEEcCCcCHHH
Confidence            43     56899999  775 57777766554

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.18  E-value=7.2e-11  Score=129.40  Aligned_cols=136  Identities=13%  Similarity=0.128  Sum_probs=98.7

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGD  306 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfide  306 (854)
                      .++++|+||||+|||++++++|..+         .+..++.++...+...+.|+.++.++.++..++..  .++||||||
T Consensus        45 ~~~iLL~GppGtGKT~la~ala~~~---------~~~~~~~i~~~~l~~~~~g~~~~~~~~lf~~a~~~--~~~vl~iDE  113 (322)
T 1xwi_A           45 WRGILLFGPPGTGKSYLAKAVATEA---------NNSTFFSISSSDLVSKWLGESEKLVKNLFQLAREN--KPSIIFIDE  113 (322)
T ss_dssp             CSEEEEESSSSSCHHHHHHHHHHHT---------TSCEEEEEECCSSCCSSCCSCHHHHHHHHHHHHHT--SSEEEEEET
T ss_pred             CceEEEECCCCccHHHHHHHHHHHc---------CCCcEEEEEhHHHHhhhhhHHHHHHHHHHHHHHhc--CCcEEEeec
Confidence            4689999999999999999999874         35689999999999889999999999999999875  689999999


Q ss_pred             cccc-cccccccccccccchhhhHHHHHHHhhccc-CCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCch
Q 003038          307 LEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGS  383 (854)
Q Consensus       307 l~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~s  383 (854)
                      ++.+ .......      ..........+-..+.. ....+.+.+||+|+...     ..+|+|.|  || ..+.|+.|+
T Consensus       114 id~l~~~~~~~~------~~~~~~~~~~ll~~ld~~~~~~~~v~vI~atn~~~-----~ld~al~r--Rf~~~i~i~~P~  180 (322)
T 1xwi_A          114 IDSLCGSRSENE------SEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPW-----VLDSAIRR--RFEKRIYIPLPE  180 (322)
T ss_dssp             TTGGGCCSSSCC------TTHHHHHHHHHHHHHHCSSSCCTTEEEEEEESCTT-----TSCHHHHH--TCCEEEECCCCC
T ss_pred             HHHhcccccccc------chHHHHHHHHHHHHHhcccccCCCEEEEEecCCcc-----cCCHHHHh--hcCeEEEeCCcC
Confidence            9999 5443211      01112233333333321 11123699999998653     46899999  77 456666665


Q ss_pred             HHH
Q 003038          384 LSL  386 (854)
Q Consensus       384 l~~  386 (854)
                      ...
T Consensus       181 ~~~  183 (322)
T 1xwi_A          181 PHA  183 (322)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.17  E-value=4.3e-11  Score=115.51  Aligned_cols=114  Identities=7%  Similarity=0.029  Sum_probs=83.6

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +.++|++.++..+...+.+...                ...++||+||+|+|||.+|++|++.......+|+ ++++.+.
T Consensus         1 ~~iiG~s~~~~~~~~~~~~~a~----------------~~~~vll~G~~GtGKt~lA~~i~~~~~~~~~~~v-~~~~~~~   63 (145)
T 3n70_A            1 VELIGRSEWINQYRRRLQQLSE----------------TDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFV-YRELTPD   63 (145)
T ss_dssp             ---CCSSHHHHHHHHHHHHHTT----------------CCSCEEEESSTTSSHHHHHHHHHHSSTTTTSCCE-EEECCTT
T ss_pred             CCceeCCHHHHHHHHHHHHHhC----------------CCCCEEEECCCCCCHHHHHHHHHHhCCccCCCEE-EECCCCC
Confidence            3579999999999988877521                2347899999999999999999998766677899 9998665


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEE
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVI  777 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiI  777 (854)
                             +..           .    +.+.+......++||||||.+++++|..|+++|+..           -.+..||
T Consensus        64 -------~~~-----------~----~~~~~~~a~~g~l~ldei~~l~~~~q~~Ll~~l~~~-----------~~~~~~I  110 (145)
T 3n70_A           64 -------NAP-----------Q----LNDFIALAQGGTLVLSHPEHLTREQQYHLVQLQSQE-----------HRPFRLI  110 (145)
T ss_dssp             -------TSS-----------C----HHHHHHHHTTSCEEEECGGGSCHHHHHHHHHHHHSS-----------SCSSCEE
T ss_pred             -------cch-----------h----hhcHHHHcCCcEEEEcChHHCCHHHHHHHHHHHhhc-----------CCCEEEE
Confidence                   110           0    112222224579999999999999999999999431           1244588


Q ss_pred             EecC
Q 003038          778 LSCE  781 (854)
Q Consensus       778 lTsn  781 (854)
                      +|||
T Consensus       111 ~~t~  114 (145)
T 3n70_A          111 GIGD  114 (145)
T ss_dssp             EEES
T ss_pred             EECC
Confidence            8886

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=99.15  E-value=6.4e-11  Score=136.96  Aligned_cols=144  Identities=13%  Similarity=0.125  Sum_probs=99.7

Q ss_pred             HHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC
Q 003038          606 SENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH  685 (854)
Q Consensus       606 ~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~  685 (854)
                      .+.+..|...|.+.|+||++++..+..++..                    .+.+||+||||+|||.+|++||..+ +..
T Consensus        10 ~~~~~~l~~~l~~~ivGq~~~i~~l~~al~~--------------------~~~VLL~GpPGtGKT~LAraLa~~l-~~~   68 (500)
T 3nbx_X           10 AERISRLSSSLEKGLYERSHAIRLCLLAALS--------------------GESVFLLGPPGIAKSLIARRLKFAF-QNA   68 (500)
T ss_dssp             HHHHHHHHHHHHTTCSSCHHHHHHHHHHHHH--------------------TCEEEEECCSSSSHHHHHHHGGGGB-SSC
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHhc--------------------CCeeEeecCchHHHHHHHHHHHHHH-hhh
Confidence            4677899999999999999999887766653                    2378999999999999999999977 444


Q ss_pred             CceEEEccccccCcCCCccccccccccCCC-CCCchH-HHHHHHHHcC---CCEEEEEecCCCCCHHHHHHHHHhhhcCe
Q 003038          686 NNFVSIALSSFSSTRADSTEDSRNKRSRDE-QSCSYI-ERFAEAVSNN---PHRVFLIEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       686 ~~~i~id~s~~~~~~~~s~e~~~~~rl~~~-~g~g~~-e~L~eav~~~---p~~ViliDEieka~~~v~~~Ll~~le~G~  760 (854)
                      ..|..+.+...+ .          ..+.+. .++... ....+.....   ..+|+|||||+++++.+|+.|+++|++|.
T Consensus        69 ~~f~~~~~~~~t-~----------~dL~G~~~~~~~~~~g~~~~~~~g~l~~~~IL~IDEI~r~~~~~q~~LL~~lee~~  137 (500)
T 3nbx_X           69 RAFEYLMTRFST-P----------EEVFGPLSIQALKDEGRYERLTSGYLPEAEIVFLDEIWKAGPAILNTLLTAINERQ  137 (500)
T ss_dssp             CEEEEECCTTCC-H----------HHHHCCBC----------CBCCTTSGGGCSEEEEESGGGCCHHHHHHHHHHHHSSE
T ss_pred             hHHHHHHHhcCC-H----------HHhcCcccHHHHhhchhHHhhhccCCCcceeeeHHhHhhhcHHHHHHHHHHHHHHh
Confidence            556666554211 0          000000 000000 0000000011   14699999999999999999999999999


Q ss_pred             EecCCCceeecCCeEEEEecCC
Q 003038          761 IVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       761 l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      ++. .|....+..-++|++||.
T Consensus       138 v~i-~G~~~~~~~~~iI~ATN~  158 (500)
T 3nbx_X          138 FRN-GAHVEKIPMRLLVAASNE  158 (500)
T ss_dssp             EEC-SSSEEECCCCEEEEEESS
T ss_pred             ccC-CCCcCCcchhhhhhcccc
Confidence            986 566777777778999983

>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=99.14  E-value=1e-10  Score=129.90  Aligned_cols=136  Identities=12%  Similarity=0.131  Sum_probs=93.8

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..++++|+||||||||++|+++|..+          +..++.++...+...+.|+.+..++.++..++..  .++|||||
T Consensus        83 ~~~~iLL~GppGtGKT~la~ala~~~----------~~~~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~~--~~~vl~iD  150 (355)
T 2qp9_X           83 PTSGILLYGPPGTGKSYLAKAVATEA----------NSTFFSVSSSDLVSKWMGESEKLVKQLFAMAREN--KPSIIFID  150 (355)
T ss_dssp             CCCCEEEECSTTSCHHHHHHHHHHHH----------TCEEEEEEHHHHHSCC---CHHHHHHHHHHHHHT--SSEEEEEE
T ss_pred             CCceEEEECCCCCcHHHHHHHHHHHh----------CCCEEEeeHHHHhhhhcchHHHHHHHHHHHHHHc--CCeEEEEe
Confidence            35689999999999999999999885          5689999999998889999999999999999875  68999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhccc-CCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCc
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAG  382 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~  382 (854)
                      |++.+ ..+....      ..........+-..+.. ......+.+||+|+..+     ..+|+|.|  || ..+.|+.|
T Consensus       151 Eid~l~~~r~~~~------~~~~~~~~~~ll~~l~~~~~~~~~v~vI~atn~~~-----~ld~al~r--Rf~~~i~i~~P  217 (355)
T 2qp9_X          151 QVDALTGTRGEGE------SEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPW-----QLDSAIRR--RFERRIYIPLP  217 (355)
T ss_dssp             CGGGGTC------------CTHHHHHHHHHHHHHHHCC---CCEEEEEEESCGG-----GSCHHHHH--TCCEEEECCCC
T ss_pred             chHhhcccCCCCc------chHHHHHHHHHHHHhhcccccCCCeEEEeecCCcc-----cCCHHHHc--ccCEEEEeCCc
Confidence            99999 5432210      01112233333333321 11122599999998654     46899998  77 45566666


Q ss_pred             hHHH
Q 003038          383 SLSL  386 (854)
Q Consensus       383 sl~~  386 (854)
                      +...
T Consensus       218 ~~~~  221 (355)
T 2qp9_X          218 DLAA  221 (355)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            6544

>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=99.12  E-value=1.9e-10  Score=130.59  Aligned_cols=80  Identities=18%  Similarity=0.253  Sum_probs=59.9

Q ss_pred             HHHHHhhcCcccccHHHHHHHHHHHHHh--hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc
Q 003038          610 TSLCNALEKKVPWQKDTVYDIANTVLKC--RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN  687 (854)
Q Consensus       610 ~~L~~~L~~~V~GQ~~av~~Ia~~v~~~--rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~  687 (854)
                      +.+.+.|.+.|+||++++..|..++...  |.++...-+      ...+...+||+||+|+|||++|++||+.+   ...
T Consensus         7 ~~i~~~Ld~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~------~~~~~~~iLl~GppGtGKT~lar~lA~~l---~~~   77 (444)
T 1g41_A            7 REIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLR------HEVTPKNILMIGPTGVGKTEIARRLAKLA---NAP   77 (444)
T ss_dssp             HHHHHHHHTTCCSCHHHHHHHHHHHHHHHHHHHSCTTTT------TTCCCCCEEEECCTTSSHHHHHHHHHHHT---TCC
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhhccccccc------cccCCceEEEEcCCCCCHHHHHHHHHHHc---CCC
Confidence            4688889999999999999999998543  222211100      01234579999999999999999999998   458


Q ss_pred             eEEEccccccC
Q 003038          688 FVSIALSSFSS  698 (854)
Q Consensus       688 ~i~id~s~~~~  698 (854)
                      |+.++++.+..
T Consensus        78 ~~~v~~~~~~~   88 (444)
T 1g41_A           78 FIKVEATKFTE   88 (444)
T ss_dssp             EEEEEGGGGC-
T ss_pred             ceeecchhhcc
Confidence            99999887653

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.12  E-value=3.5e-10  Score=120.79  Aligned_cols=153  Identities=10%  Similarity=0.076  Sum_probs=106.7

Q ss_pred             cHHHHHHHHHHhhc-------------cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccc
Q 003038          211 RNEDVMYVIENLMS-------------KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMN  277 (854)
Q Consensus       211 r~~ei~~v~~~L~r-------------~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~  277 (854)
                      .++.++++.+.+..             +..++++|+||||+|||++++++|..+          +..++.++...+...+
T Consensus        22 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~----------~~~~~~v~~~~~~~~~   91 (285)
T 3h4m_A           22 LEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATET----------NATFIRVVGSELVKKF   91 (285)
T ss_dssp             CHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHT----------TCEEEEEEGGGGCCCS
T ss_pred             HHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHh----------CCCEEEEehHHHHHhc
Confidence            66666766666543             467789999999999999999999874          5689999999998889


Q ss_pred             hHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcc---cCCCCceEEEEEec
Q 003038          278 RVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVC---GIGENARFWLMGIA  353 (854)
Q Consensus       278 rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~---~~~g~g~l~lIgat  353 (854)
                      .|+.+..+..++..++..  .+.||||||++.+ ........+.      .......+..++.   ....++.+.+|++|
T Consensus        92 ~~~~~~~~~~~~~~~~~~--~~~vl~iDEid~l~~~~~~~~~~~------~~~~~~~l~~ll~~~~~~~~~~~~~vI~tt  163 (285)
T 3h4m_A           92 IGEGASLVKDIFKLAKEK--APSIIFIDEIDAIAAKRTDALTGG------DREVQRTLMQLLAEMDGFDARGDVKIIGAT  163 (285)
T ss_dssp             TTHHHHHHHHHHHHHHHT--CSEEEEEETTHHHHBCCSSSCCGG------GGHHHHHHHHHHHHHHTTCSSSSEEEEEEC
T ss_pred             cchHHHHHHHHHHHHHHc--CCeEEEEECHHHhcccCccccCCc------cHHHHHHHHHHHHHhhCCCCCCCEEEEEeC
Confidence            999999999999999875  6899999999999 5433211000      0012223334442   11122369999999


Q ss_pred             CHHHHHHhhccCCchhhhhcc-CCCCCCCchHHH
Q 003038          354 TFQSYMRCKSGHPSLETLWSL-HPLTIPAGSLSL  386 (854)
Q Consensus       354 T~~ey~k~~~~~pale~~~~~-~~v~i~~~sl~~  386 (854)
                      +..+     ..+|++.+.-|| ..+.++.++...
T Consensus       164 n~~~-----~l~~~l~~~~Rf~~~i~~~~p~~~~  192 (285)
T 3h4m_A          164 NRPD-----ILDPAILRPGRFDRIIEVPAPDEKG  192 (285)
T ss_dssp             SCGG-----GBCHHHHSTTSEEEEEECCCCCHHH
T ss_pred             CCch-----hcCHHHcCCCcCCeEEEECCCCHHH
Confidence            8653     357888763344 256666666544

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.10  E-value=2.6e-10  Score=123.21  Aligned_cols=142  Identities=9%  Similarity=0.060  Sum_probs=104.0

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEe
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      +...|++|+||||||||++++.+|..+....   .+.+..++.++...+...+.|+.+.++.+++..+.     +.||||
T Consensus        65 ~~~~~vll~G~~GtGKT~la~~la~~l~~~~---~~~~~~~~~~~~~~l~~~~~g~~~~~~~~~~~~~~-----~~vl~i  136 (309)
T 3syl_A           65 TPTLHMSFTGNPGTGKTTVALKMAGLLHRLG---YVRKGHLVSVTRDDLVGQYIGHTAPKTKEVLKRAM-----GGVLFI  136 (309)
T ss_dssp             CCCCEEEEEECTTSSHHHHHHHHHHHHHHTT---SSSSCCEEEECGGGTCCSSTTCHHHHHHHHHHHHT-----TSEEEE
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHHHhcC---CcCCCcEEEEcHHHhhhhcccccHHHHHHHHHhcC-----CCEEEE
Confidence            3455799999999999999999999886532   23456899999999988888988888888877653     459999


Q ss_pred             Cccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCc
Q 003038          305 GDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAG  382 (854)
Q Consensus       305 del~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~  382 (854)
                      ||++.+ ..+....      +.  ......+-+++.....  .+.+|++|+...+..++..+|+|.+  || +.|.++.+
T Consensus       137 DEid~l~~~~~~~~------~~--~~~~~~Ll~~l~~~~~--~~~~i~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~~  204 (309)
T 3syl_A          137 DEAYYLYRPDNERD------YG--QEAIEILLQVMENNRD--DLVVILAGYADRMENFFQSNPGFRS--RIAHHIEFPDY  204 (309)
T ss_dssp             ETGGGSCCCC---C------CT--HHHHHHHHHHHHHCTT--TCEEEEEECHHHHHHHHHHSTTHHH--HEEEEEEECCC
T ss_pred             EChhhhccCCCccc------cc--HHHHHHHHHHHhcCCC--CEEEEEeCChHHHHHHHhhCHHHHH--hCCeEEEcCCc
Confidence            999999 5432110      00  0233344444432222  5999999999888888888999999  77 88888887


Q ss_pred             hHHH
Q 003038          383 SLSL  386 (854)
Q Consensus       383 sl~~  386 (854)
                      +...
T Consensus       205 ~~~~  208 (309)
T 3syl_A          205 SDEE  208 (309)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            7544

>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=99.10  E-value=4.5e-11  Score=140.10  Aligned_cols=147  Identities=13%  Similarity=0.231  Sum_probs=93.4

Q ss_pred             HhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcc
Q 003038          614 NALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIAL  693 (854)
Q Consensus       614 ~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~  693 (854)
                      +.|.+.++|++++...+...+.........            +...++|+||+|+|||++|++||..+   ...++++++
T Consensus        77 ~~l~~di~G~~~vk~~i~~~~~l~~~~~~~------------~g~~vll~Gp~GtGKTtlar~ia~~l---~~~~~~i~~  141 (543)
T 3m6a_A           77 RLLDEEHHGLEKVKERILEYLAVQKLTKSL------------KGPILCLAGPPGVGKTSLAKSIAKSL---GRKFVRISL  141 (543)
T ss_dssp             GTHHHHCSSCHHHHHHHHHHHHHHHHSSSC------------CSCEEEEESSSSSSHHHHHHHHHHHH---TCEEEEECC
T ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHhcccC------------CCCEEEEECCCCCCHHHHHHHHHHhc---CCCeEEEEe
Confidence            445577999999999998777654432221            23489999999999999999999998   457889988


Q ss_pred             ccccCcCCCccccccccccCCCCCC-chHH-HHHHHHHcC--CCEEEEEecCCCCCHH----HHHHHHHhhhcCe---Ee
Q 003038          694 SSFSSTRADSTEDSRNKRSRDEQSC-SYIE-RFAEAVSNN--PHRVFLIEDVEQADYC----SQKGFKRAIESGR---IV  762 (854)
Q Consensus       694 s~~~~~~~~s~e~~~~~rl~~~~g~-g~~e-~L~eav~~~--p~~ViliDEieka~~~----v~~~Ll~~le~G~---l~  762 (854)
                      +.+..       .......  ...| |+.. .+...+...  ...|+|||||++++++    .++.|+++|+++.   +.
T Consensus       142 ~~~~~-------~~~~~g~--~~~~ig~~~~~~~~~~~~a~~~~~vl~lDEid~l~~~~~~~~~~~LL~~ld~~~~~~~~  212 (543)
T 3m6a_A          142 GGVRD-------ESEIRGH--RRTYVGAMPGRIIQGMKKAGKLNPVFLLDEIDKMSSDFRGDPSSAMLEVLDPEQNSSFS  212 (543)
T ss_dssp             CC-----------------------------CHHHHHHTTCSSSEEEEEEESSSCC---------CCGGGTCTTTTTBCC
T ss_pred             cccch-------hhhhhhH--HHHHhccCchHHHHHHHHhhccCCEEEEhhhhhhhhhhccCHHHHHHHHHhhhhcceee
Confidence            76541       1110000  0011 2221 122222222  3349999999999988    5699999998764   44


Q ss_pred             cC-CCceeecCCeEEEEecCCCC
Q 003038          763 TS-SGDEVSLGDAIVILSCESFS  784 (854)
Q Consensus       763 d~-~G~~v~~~~aIiIlTsn~f~  784 (854)
                      +. .+..+++++++||+|+|..+
T Consensus       213 ~~~~~~~~~~~~v~iI~ttN~~~  235 (543)
T 3m6a_A          213 DHYIEETFDLSKVLFIATANNLA  235 (543)
T ss_dssp             CSSSCCCCBCSSCEEEEECSSTT
T ss_pred             cccCCeeecccceEEEeccCccc
Confidence            42 35778899999999999754

>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=99.10  E-value=3.7e-10  Score=125.40  Aligned_cols=151  Identities=15%  Similarity=0.100  Sum_probs=104.5

Q ss_pred             cHHHHHHHHHHhh------------ccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccch
Q 003038          211 RNEDVMYVIENLM------------SKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNR  278 (854)
Q Consensus       211 r~~ei~~v~~~L~------------r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~r  278 (854)
                      .++.++.+.+.+.            .+..++++|+||||||||++++++|..+          +..++.++.+.+...+.
T Consensus        89 ~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~----------~~~~~~i~~~~l~~~~~  158 (357)
T 3d8b_A           89 VEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQS----------GATFFSISASSLTSKWV  158 (357)
T ss_dssp             CHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHT----------TCEEEEEEGGGGCCSST
T ss_pred             hHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHc----------CCeEEEEehHHhhcccc
Confidence            5566666666553            2457789999999999999999999873          56899999999998899


Q ss_pred             HHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecCH
Q 003038          279 VEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIATF  355 (854)
Q Consensus       279 ge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT~  355 (854)
                      |+.+..++.++..++..  .+.||||||++.+ .....+..      .........+-..+..  ....+.+.+||+|+.
T Consensus       159 g~~~~~~~~~~~~a~~~--~~~vl~iDEid~l~~~~~~~~~------~~~~~~~~~lL~~l~~~~~~~~~~v~vI~atn~  230 (357)
T 3d8b_A          159 GEGEKMVRALFAVARCQ--QPAVIFIDEIDSLLSQRGDGEH------ESSRRIKTEFLVQLDGATTSSEDRILVVGATNR  230 (357)
T ss_dssp             THHHHHHHHHHHHHHHT--CSEEEEEETHHHHTBC------------CHHHHHHHHHHHHHHC----CCCCEEEEEEESC
T ss_pred             chHHHHHHHHHHHHHhc--CCeEEEEeCchhhhccCCCCcc------hHHHHHHHHHHHHHhcccccCCCCEEEEEecCC
Confidence            99999999999998865  6899999999999 54322100      0111222233333321  111236999999987


Q ss_pred             HHHHHhhccCCchhhhhccC-CCCCCCchHHH
Q 003038          356 QSYMRCKSGHPSLETLWSLH-PLTIPAGSLSL  386 (854)
Q Consensus       356 ~ey~k~~~~~pale~~~~~~-~v~i~~~sl~~  386 (854)
                      ..     ..+++|.+  ||. .+.|+.++...
T Consensus       231 ~~-----~l~~~l~~--Rf~~~i~i~~p~~~~  255 (357)
T 3d8b_A          231 PQ-----EIDEAARR--RLVKRLYIPLPEASA  255 (357)
T ss_dssp             GG-----GBCHHHHT--TCCEEEECCCCCHHH
T ss_pred             hh-----hCCHHHHh--hCceEEEeCCcCHHH
Confidence            43     46889988  775 45666665544

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.08  E-value=5.6e-10  Score=122.30  Aligned_cols=127  Identities=12%  Similarity=0.122  Sum_probs=94.1

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++||+.++..+...+...+..             .++...+||+||+|+|||.+|++||+.+   ...|+.++++.+.
T Consensus        29 ~~iiG~~~~~~~l~~~l~~~~~~-------------~~~~~~vll~G~~GtGKT~la~~ia~~~---~~~~~~~~~~~~~   92 (338)
T 3pfi_A           29 DGYIGQESIKKNLNVFIAAAKKR-------------NECLDHILFSGPAGLGKTTLANIISYEM---SANIKTTAAPMIE   92 (338)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHT-------------TSCCCCEEEECSTTSSHHHHHHHHHHHT---TCCEEEEEGGGCC
T ss_pred             HHhCChHHHHHHHHHHHHHHHhc-------------CCCCCeEEEECcCCCCHHHHHHHHHHHh---CCCeEEecchhcc
Confidence            35899999999999998876431             1334578999999999999999999987   3468888776443


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHc-CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecC-------CCcee
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSN-NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTS-------SGDEV  769 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~-~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~-------~G~~v  769 (854)
                             .               ...+...+.. ....|||||||+.+++.+|+.|+++|+++.+.--       ....+
T Consensus        93 -------~---------------~~~~~~~~~~~~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~  150 (338)
T 3pfi_A           93 -------K---------------SGDLAAILTNLSEGDILFIDEIHRLSPAIEEVLYPAMEDYRLDIIIGSGPAAQTIKI  150 (338)
T ss_dssp             -------S---------------HHHHHHHHHTCCTTCEEEEETGGGCCHHHHHHHHHHHHTSCC---------CCCCCC
T ss_pred             -------c---------------hhHHHHHHHhccCCCEEEEechhhcCHHHHHHHHHHHHhccchhhcccCccccceec
Confidence                   0               1123344433 5678999999999999999999999999875421       22334


Q ss_pred             ecCCeEEEEecCC
Q 003038          770 SLGDAIVILSCES  782 (854)
Q Consensus       770 ~~~~aIiIlTsn~  782 (854)
                      ++.+.+||++||.
T Consensus       151 ~~~~~~~i~atn~  163 (338)
T 3pfi_A          151 DLPKFTLIGATTR  163 (338)
T ss_dssp             CCCCCEEEEEESC
T ss_pred             CCCCeEEEEeCCC
Confidence            5567899999986

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.08  E-value=5.2e-11  Score=114.74  Aligned_cols=110  Identities=18%  Similarity=0.172  Sum_probs=81.6

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .++|+++++..+...+.+...                ...++||+||+|+|||.+|++|+....    +|+.++++.+. 
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~----------------~~~~vll~G~~GtGKt~lA~~i~~~~~----~~~~~~~~~~~-   63 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAK----------------RTSPVFLTGEAGSPFETVARYFHKNGT----PWVSPARVEYL-   63 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHT----------------CSSCEEEEEETTCCHHHHHGGGCCTTS----CEECCSSTTHH-
T ss_pred             CceeCCHHHHHHHHHHHHHhC----------------CCCcEEEECCCCccHHHHHHHHHHhCC----CeEEechhhCC-
Confidence            478999999999888876521                123689999999999999999988652    78888887554 


Q ss_pred             cCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEE
Q 003038          699 TRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVIL  778 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIl  778 (854)
                            +..                +.+.+......++|||||+.++++.|..|+++|+++.          -.++.||+
T Consensus        64 ------~~~----------------~~~~~~~a~~~~l~lDei~~l~~~~q~~Ll~~l~~~~----------~~~~~iI~  111 (143)
T 3co5_A           64 ------IDM----------------PMELLQKAEGGVLYVGDIAQYSRNIQTGITFIIGKAE----------RCRVRVIA  111 (143)
T ss_dssp             ------HHC----------------HHHHHHHTTTSEEEEEECTTCCHHHHHHHHHHHHHHT----------TTTCEEEE
T ss_pred             ------hHh----------------hhhHHHhCCCCeEEEeChHHCCHHHHHHHHHHHHhCC----------CCCEEEEE
Confidence                  111                1222333446799999999999999999999999863          24567888


Q ss_pred             ecC
Q 003038          779 SCE  781 (854)
Q Consensus       779 Tsn  781 (854)
                      |||
T Consensus       112 ~tn  114 (143)
T 3co5_A          112 SCS  114 (143)
T ss_dssp             EEE
T ss_pred             ecC
Confidence            887

>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=99.07  E-value=3.3e-10  Score=129.59  Aligned_cols=137  Identities=13%  Similarity=0.132  Sum_probs=90.7

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..++++|+||||||||++|+++|..+         .+..|+.++.+.+...+.|+.+..++.++..++..  .+.|||||
T Consensus       166 ~~~~vLL~GppGtGKT~lA~aia~~~---------~~~~~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~~--~~~vl~iD  234 (444)
T 2zan_A          166 PWRGILLFGPPGTGKSYLAKAVATEA---------NNSTFFSISSSDLVSKWLGESEKLVKNLFQLAREN--KPSIIFID  234 (444)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHHHC---------CSSEEEEECCC---------CCCTHHHHHHHHHHS--CSEEEEES
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHc---------CCCCEEEEeHHHHHhhhcchHHHHHHHHHHHHHHc--CCeEEEEe
Confidence            45789999999999999999999874         35689999999999889999999999999999875  68999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhccc-CCCCceEEEEEecCHHHHHHhhccCCchhhhhccC-CCCCCCc
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGENARFWLMGIATFQSYMRCKSGHPSLETLWSLH-PLTIPAG  382 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~-~v~i~~~  382 (854)
                      ||+.+ ..+.....      .........+-..+.. ....+.+.+||+|+...     ..+|+|.|  ||. .+.|+.|
T Consensus       235 Eid~l~~~~~~~~~------~~~~~~~~~lL~~l~~~~~~~~~v~vI~atn~~~-----~ld~al~r--Rf~~~i~i~~P  301 (444)
T 2zan_A          235 EIDSLCGSRSENES------EAARRIKTEFLVQMQGVGVDNDGILVLGATNIPW-----VLDSAIRR--RFEKRIYIPLP  301 (444)
T ss_dssp             CTTTTCCCSSCCCC------GGGHHHHHHHHTTTTCSSCCCSSCEEEEEESCGG-----GSCHHHHT--TCCEEEECCCC
T ss_pred             chHhhccCCCCccc------cHHHHHHHHHHHHHhCcccCCCCEEEEecCCCcc-----ccCHHHHh--hcceEEEeCCc
Confidence            99999 54332111      1112233333333321 11123699999998653     47899999  774 5666666


Q ss_pred             hHHH
Q 003038          383 SLSL  386 (854)
Q Consensus       383 sl~~  386 (854)
                      +...
T Consensus       302 ~~~~  305 (444)
T 2zan_A          302 EAHA  305 (444)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            5443

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.06  E-value=7.4e-10  Score=123.93  Aligned_cols=130  Identities=8%  Similarity=0.107  Sum_probs=92.1

Q ss_pred             CcccccHHHHHHHHHHHHH--------hhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceE
Q 003038          618 KKVPWQKDTVYDIANTVLK--------CRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFV  689 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~--------~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i  689 (854)
                      ..|.|.++++..|..+|..        .+.|+..             ..-+||+||||||||.+|+++|..+   ..+|+
T Consensus       148 ~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~-------------prGvLL~GPPGTGKTllAkAiA~e~---~~~f~  211 (405)
T 4b4t_J          148 DMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQ-------------PKGVILYGPPGTGKTLLARAVAHHT---DCKFI  211 (405)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCC-------------CCCEEEESCSSSSHHHHHHHHHHHH---TCEEE
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCC-------------CCceEEeCCCCCCHHHHHHHHHHhh---CCCce
Confidence            4588999999999988864        2334433             2357899999999999999999988   46899


Q ss_pred             EEccccccCcCCCccccccccccCCCCCCchHH----HHHHHHHcCCCEEEEEecCCCCCH-----------H---HHHH
Q 003038          690 SIALSSFSSTRADSTEDSRNKRSRDEQSCSYIE----RFAEAVSNNPHRVFLIEDVEQADY-----------C---SQKG  751 (854)
Q Consensus       690 ~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e----~L~eav~~~p~~ViliDEieka~~-----------~---v~~~  751 (854)
                      .++++++.       .++.          |-.+    .+++..+.+..+||||||||..-+           .   +.+.
T Consensus       212 ~v~~s~l~-------sk~v----------Gese~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~  274 (405)
T 4b4t_J          212 RVSGAELV-------QKYI----------GEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLE  274 (405)
T ss_dssp             EEEGGGGS-------CSST----------THHHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHH
T ss_pred             EEEhHHhh-------cccc----------chHHHHHHHHHHHHHHhCCceEeeecchhhccCCCCCCCCCcHHHHHHHHH
Confidence            99988765       1110          3322    566777777789999999997632           2   4556


Q ss_pred             HHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCCCC
Q 003038          752 FKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRA  789 (854)
Q Consensus       752 Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~  789 (854)
                      ||..||.-         -.-.+.+||+|||.-+....+
T Consensus       275 lL~~lDg~---------~~~~~V~vIaATNrpd~LDpA  303 (405)
T 4b4t_J          275 LLNQLDGF---------ETSKNIKIIMATNRLDILDPA  303 (405)
T ss_dssp             HHHHHHTT---------TCCCCEEEEEEESCSSSSCHH
T ss_pred             HHHhhhcc---------CCCCCeEEEeccCChhhCCHh
Confidence            66666621         123567899999976555443

>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=99.06  E-value=5.3e-10  Score=123.01  Aligned_cols=133  Identities=8%  Similarity=0.132  Sum_probs=85.2

Q ss_pred             ccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc
Q 003038          620 VPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST  699 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~  699 (854)
                      .+||++++..+..++...                 +....+||+||+|+|||++|+++|+.+++....- ...|..+..+
T Consensus         4 ~pw~~~~~~~l~~~i~~~-----------------~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~-~~~c~~c~~c   65 (334)
T 1a5t_A            4 YPWLRPDFEKLVASYQAG-----------------RGHHALLIQALPGMGDDALIYALSRYLLCQQPQG-HKSCGHCRGC   65 (334)
T ss_dssp             CGGGHHHHHHHHHHHHTT-----------------CCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBT-TBCCSCSHHH
T ss_pred             CCchHHHHHHHHHHHHcC-----------------CcceeEEEECCCCchHHHHHHHHHHHHhCCCCCC-CCCCCCCHHH
Confidence            589999999999888753                 2345799999999999999999999997643210 0000100000


Q ss_pred             CCCccccc-cccccCCC----CCCchHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCce
Q 003038          700 RADSTEDS-RNKRSRDE----QSCSYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDE  768 (854)
Q Consensus       700 ~~~s~e~~-~~~rl~~~----~g~g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~  768 (854)
                      .......| .+.. +.+    ...+..+  .+.+.+...|    ++||+|||+|+++...+|.|++.||+.         
T Consensus        66 ~~~~~~~~~d~~~-~~~~~~~~~~~i~~ir~l~~~~~~~~~~~~~kvviIdead~l~~~a~naLLk~lEep---------  135 (334)
T 1a5t_A           66 QLMQAGTHPDYYT-LAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEP---------  135 (334)
T ss_dssp             HHHHHTCCTTEEE-ECCCTTCSSBCHHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSC---------
T ss_pred             HHHhcCCCCCEEE-EeccccCCCCCHHHHHHHHHHHhhccccCCcEEEEECchhhcCHHHHHHHHHHhcCC---------
Confidence            00000000 0000 111    1123332  4555555444    799999999999999999999999973         


Q ss_pred             eecCCeEEEEecCC
Q 003038          769 VSLGDAIVILSCES  782 (854)
Q Consensus       769 v~~~~aIiIlTsn~  782 (854)
                        -.+++|||+||.
T Consensus       136 --~~~~~~Il~t~~  147 (334)
T 1a5t_A          136 --PAETWFFLATRE  147 (334)
T ss_dssp             --CTTEEEEEEESC
T ss_pred             --CCCeEEEEEeCC
Confidence              257889999874

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.04  E-value=2.7e-09  Score=121.04  Aligned_cols=130  Identities=12%  Similarity=0.148  Sum_probs=92.0

Q ss_pred             CcccccHHHHHHHHHHHHHh--------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceE
Q 003038          618 KKVPWQKDTVYDIANTVLKC--------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFV  689 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~--------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i  689 (854)
                      ..|.|.++++..|..+|..-        +.|+.             |..-+||+||||||||.+|++||..+   ..+|+
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~-------------~prGvLL~GPPGtGKTllAkAiA~e~---~~~~~  244 (437)
T 4b4t_L          181 DGIGGLTEQIRELREVIELPLKNPEIFQRVGIK-------------PPKGVLLYGPPGTGKTLLAKAVAATI---GANFI  244 (437)
T ss_dssp             GGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCC-------------CCCEEEEESCTTSSHHHHHHHHHHHH---TCEEE
T ss_pred             hHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCC-------------CCCeEEEECCCCCcHHHHHHHHHHHh---CCCEE
Confidence            45789999999999888642        23443             33457899999999999999999998   46899


Q ss_pred             EEccccccCcCCCccccccccccCCCCCCchHH----HHHHHHHcCCCEEEEEecCCCCC-----------HH---HHHH
Q 003038          690 SIALSSFSSTRADSTEDSRNKRSRDEQSCSYIE----RFAEAVSNNPHRVFLIEDVEQAD-----------YC---SQKG  751 (854)
Q Consensus       690 ~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e----~L~eav~~~p~~ViliDEieka~-----------~~---v~~~  751 (854)
                      .++++++.       .++.          |-.+    .++...+.+..+||||||||..-           ..   +.+.
T Consensus       245 ~v~~s~l~-------sk~~----------Gese~~ir~~F~~A~~~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~  307 (437)
T 4b4t_L          245 FSPASGIV-------DKYI----------GESARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLME  307 (437)
T ss_dssp             EEEGGGTC-------CSSS----------SHHHHHHHHHHHHHHHSCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHH
T ss_pred             EEehhhhc-------cccc----------hHHHHHHHHHHHHHHhcCCceeeeecccccccccccCCCCcchHHHHHHHH
Confidence            99988765       1111          2222    45666677778999999999652           22   4556


Q ss_pred             HHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCCCC
Q 003038          752 FKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRA  789 (854)
Q Consensus       752 Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~  789 (854)
                      ||..|+.-         -+..+.+||+|||..+....+
T Consensus       308 lL~~lDg~---------~~~~~vivI~ATNrp~~LDpA  336 (437)
T 4b4t_L          308 LLTQMDGF---------DNLGQTKIIMATNRPDTLDPA  336 (437)
T ss_dssp             HHHHHHSS---------SCTTSSEEEEEESSTTSSCTT
T ss_pred             HHHHhhcc---------cCCCCeEEEEecCCchhhCHH
Confidence            77777631         123578999999976665544

>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=99.04  E-value=7.1e-10  Score=127.42  Aligned_cols=140  Identities=11%  Similarity=0.087  Sum_probs=96.3

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGD  306 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfide  306 (854)
                      .++++|+||||+|||++++++|...          ++.|+.++.+.+...+.|..+.+++.++..++..  .|+||||||
T Consensus        49 p~gvLL~GppGtGKT~Laraia~~~----------~~~f~~is~~~~~~~~~g~~~~~~r~lf~~A~~~--~p~ILfIDE  116 (476)
T 2ce7_A           49 PKGILLVGPPGTGKTLLARAVAGEA----------NVPFFHISGSDFVELFVGVGAARVRDLFAQAKAH--APCIVFIDE  116 (476)
T ss_dssp             CSEEEEECCTTSSHHHHHHHHHHHH----------TCCEEEEEGGGTTTCCTTHHHHHHHHHHHHHHHT--CSEEEEEET
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHc----------CCCeeeCCHHHHHHHHhcccHHHHHHHHHHHHhc--CCCEEEEec
Confidence            4679999999999999999999864          5679999999999889999999999999999875  699999999


Q ss_pred             cccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccC-CCCCCCchH
Q 003038          307 LEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLH-PLTIPAGSL  384 (854)
Q Consensus       307 l~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~-~v~i~~~sl  384 (854)
                      ++.+ ..+..+..+.   ....+.....+-..+.....+..+.+|++|+..+     ..||++-|..||. .|.|+.|++
T Consensus       117 id~l~~~r~~~~~g~---~~~~~~~l~~LL~~ld~~~~~~~viVIaaTn~~~-----~Ld~allR~gRFd~~i~i~~Pd~  188 (476)
T 2ce7_A          117 IDAVGRHRGAGLGGG---HDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPD-----ILDPALLRPGRFDKKIVVDPPDM  188 (476)
T ss_dssp             GGGTCCC------------CHHHHHHHHHHHHHHHSCGGGTEEEEEEESCGG-----GSCGGGGSTTSSCEEEECCCCCH
T ss_pred             hhhhhhhcccccCcC---cHHHHHHHHHHHHHHhccCCCCCEEEEEecCChh-----hhchhhcccCcceeEeecCCCCH
Confidence            9999 5432110000   0001122222222221111122599999998754     3688988766775 566666665


Q ss_pred             HH
Q 003038          385 SL  386 (854)
Q Consensus       385 ~~  386 (854)
                      ..
T Consensus       189 ~~  190 (476)
T 2ce7_A          189 LG  190 (476)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=99.04  E-value=6.4e-10  Score=128.51  Aligned_cols=153  Identities=12%  Similarity=0.095  Sum_probs=109.1

Q ss_pred             cHHHHHHHHHHhhc-------------cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccc
Q 003038          211 RNEDVMYVIENLMS-------------KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMN  277 (854)
Q Consensus       211 r~~ei~~v~~~L~r-------------~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~  277 (854)
                      .++.++++.+.+.+             +..++++|+||||+|||.++++++...          +..|+.++.+.+.+.+
T Consensus       209 ~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~----------~~~fv~vn~~~l~~~~  278 (489)
T 3hu3_A          209 CRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET----------GAFFFLINGPEIMSKL  278 (489)
T ss_dssp             CHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHC----------SSEEEEEEHHHHHTSC
T ss_pred             HHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHh----------CCCEEEEEchHhhhhh
Confidence            56666666666543             456789999999999999999999873          5789999999999889


Q ss_pred             hHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHH
Q 003038          278 RVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQ  356 (854)
Q Consensus       278 rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~  356 (854)
                      .|+.+..++.++..+...  .+.|||||||+.+ ..+.....      .........+-++|.....++.+.+|+||+..
T Consensus       279 ~g~~~~~~~~~f~~A~~~--~p~iLfLDEId~l~~~~~~~~~------~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~  350 (489)
T 3hu3_A          279 AGESESNLRKAFEEAEKN--APAIIFIDELDAIAPKREKTHG------EVERRIVSQLLTLMDGLKQRAHVIVMAATNRP  350 (489)
T ss_dssp             TTHHHHHHHHHHHHHHHT--CSEEEEEESHHHHCBCTTSCCC------HHHHHHHHHHHHHHHHSCTTSCEEEEEEESCG
T ss_pred             cchhHHHHHHHHHHHHhc--CCcEEEecchhhhccccccccc------hHHHHHHHHHHHHhhccccCCceEEEEecCCc
Confidence            999999999999999875  6899999999999 54332100      01112334444444321122369999999876


Q ss_pred             HHHHhhccCCchhhhhccC-CCCCCCchHHH
Q 003038          357 SYMRCKSGHPSLETLWSLH-PLTIPAGSLSL  386 (854)
Q Consensus       357 ey~k~~~~~pale~~~~~~-~v~i~~~sl~~  386 (854)
                      +     ..+|+|.+.-+|. .|.|+.|+...
T Consensus       351 ~-----~Ld~al~r~gRf~~~i~i~~P~~~e  376 (489)
T 3hu3_A          351 N-----SIDPALRRFGRFDREVDIGIPDATG  376 (489)
T ss_dssp             G-----GBCGGGGSTTSSCEEEECCCCCHHH
T ss_pred             c-----ccCHHHhCCCcCceEEEeCCCCHHH
Confidence            3     4678998744453 25666665544

>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=99.01  E-value=6.1e-10  Score=120.65  Aligned_cols=142  Identities=15%  Similarity=0.167  Sum_probs=97.3

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEe
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      +..++++|+||||+|||++++++|..+          +..++.++...+...+.|+.+.+++.++..+...  .++||||
T Consensus        47 ~~~~~vLL~Gp~GtGKT~la~ala~~~----------~~~~i~v~~~~l~~~~~g~~~~~~~~~f~~a~~~--~p~il~i  114 (301)
T 3cf0_A           47 TPSKGVLFYGPPGCGKTLLAKAIANEC----------QANFISIKGPELLTMWFGESEANVREIFDKARQA--APCVLFF  114 (301)
T ss_dssp             CCCSEEEEECSSSSSHHHHHHHHHHHT----------TCEEEEECHHHHHHHHHTTCTTHHHHHHHHHHHT--CSEEEEE
T ss_pred             CCCceEEEECCCCcCHHHHHHHHHHHh----------CCCEEEEEhHHHHhhhcCchHHHHHHHHHHHHhc--CCeEEEE
Confidence            356789999999999999999999864          4689999998888888999999999999999875  6899999


Q ss_pred             Cccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCc
Q 003038          305 GDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAG  382 (854)
Q Consensus       305 del~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~  382 (854)
                      ||++.+ ...........+   ..+.....+-..+........+.+||+|+..+     ..+|++-|.-|| ..+.|+.|
T Consensus       115 DEid~l~~~~~~~~~~~~~---~~~~~~~~lL~~l~~~~~~~~v~vi~atn~~~-----~ld~al~r~gRf~~~i~i~~p  186 (301)
T 3cf0_A          115 DELDSIAKARGGNIGDGGG---AADRVINQILTEMDGMSTKKNVFIIGATNRPD-----IIDPAILRPGRLDQLIYIPLP  186 (301)
T ss_dssp             CSTTHHHHHHTTTTCCSSC---SCCHHHHHHHHHHHSSCTTSSEEEEEEESCGG-----GSCGGGGSTTSSCEEEECCCC
T ss_pred             EChHHHhhccCCCcCCcch---HHHHHHHHHHHHhhcccCCCCEEEEEecCCcc-----ccChHHhcCCccceEEecCCc
Confidence            999999 443211000000   11123344444442211123599999998764     368888763344 24556655


Q ss_pred             hHHH
Q 003038          383 SLSL  386 (854)
Q Consensus       383 sl~~  386 (854)
                      +...
T Consensus       187 ~~~~  190 (301)
T 3cf0_A          187 DEKS  190 (301)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            5443

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.01  E-value=3.3e-09  Score=119.17  Aligned_cols=130  Identities=14%  Similarity=0.168  Sum_probs=91.1

Q ss_pred             CcccccHHHHHHHHHHHHHh--------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceE
Q 003038          618 KKVPWQKDTVYDIANTVLKC--------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFV  689 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~--------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i  689 (854)
                      ..|.|.++++..|...|..-        +.|+.             |..-+||+||||||||.+|++||..+   ..+|+
T Consensus       182 ~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~-------------~prGvLLyGPPGTGKTlLAkAiA~e~---~~~fi  245 (437)
T 4b4t_I          182 SDIGGLESQIQEIKESVELPLTHPELYEEMGIK-------------PPKGVILYGAPGTGKTLLAKAVANQT---SATFL  245 (437)
T ss_dssp             GGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCC-------------CCSEEEEESSTTTTHHHHHHHHHHHH---TCEEE
T ss_pred             eecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCC-------------CCCCCceECCCCchHHHHHHHHHHHh---CCCEE
Confidence            45789999999999988642        23433             23358999999999999999999988   46899


Q ss_pred             EEccccccCcCCCccccccccccCCCCCCchHH----HHHHHHHcCCCEEEEEecCCCCC-----------HH---HHHH
Q 003038          690 SIALSSFSSTRADSTEDSRNKRSRDEQSCSYIE----RFAEAVSNNPHRVFLIEDVEQAD-----------YC---SQKG  751 (854)
Q Consensus       690 ~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e----~L~eav~~~p~~ViliDEieka~-----------~~---v~~~  751 (854)
                      .++++++.       .++          .|-.+    .+++..+++..+||||||||..-           ..   +.+.
T Consensus       246 ~v~~s~l~-------sk~----------vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~  308 (437)
T 4b4t_I          246 RIVGSELI-------QKY----------LGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLE  308 (437)
T ss_dssp             EEESGGGC-------CSS----------SSHHHHHHHHHHHHHHHTCSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHH
T ss_pred             EEEHHHhh-------hcc----------CchHHHHHHHHHHHHHhcCCcEEEEehhhhhcccCCCCCCCccHHHHHHHHH
Confidence            99988765       111          13333    46666777777999999999652           23   3445


Q ss_pred             HHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCCCC
Q 003038          752 FKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRA  789 (854)
Q Consensus       752 Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~  789 (854)
                      ||..||.-         -.-.+.+||+|||.-+....+
T Consensus       309 LL~~lDg~---------~~~~~ViVIaATNrpd~LDpA  337 (437)
T 4b4t_I          309 LLNQLDGF---------DDRGDVKVIMATNKIETLDPA  337 (437)
T ss_dssp             HHHHHHHC---------CCSSSEEEEEEESCSTTCCTT
T ss_pred             HHHHhhCc---------CCCCCEEEEEeCCChhhcCHH
Confidence            55555521         123578999999976666555

>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=99.00  E-value=1.7e-09  Score=113.65  Aligned_cols=143  Identities=12%  Similarity=0.091  Sum_probs=87.9

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEe
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      +..++++|+||||+|||++++++|..+          +..++.++.+.+...+.|+.+..++.++..+...  .+.||||
T Consensus        37 ~~~~~vll~G~~GtGKT~la~~la~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~--~~~vl~i  104 (262)
T 2qz4_A           37 KVPKGALLLGPPGCGKTLLAKAVATEA----------QVPFLAMAGAEFVEVIGGLGAARVRSLFKEARAR--APCIVYI  104 (262)
T ss_dssp             CCCCEEEEESCTTSSHHHHHHHHHHHH----------TCCEEEEETTTTSSSSTTHHHHHHHHHHHHHHHT--CSEEEEE
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHh----------CCCEEEechHHHHhhccChhHHHHHHHHHHHHhc--CCeEEEE
Confidence            345778999999999999999999875          4578999998888888899999999999998875  6899999


Q ss_pred             Cccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCc
Q 003038          305 GDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAG  382 (854)
Q Consensus       305 del~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~  382 (854)
                      ||++.+ ........+....  ........+-+.+........+.+|++|+..+     ..++++.+.-|| ..+.|+.|
T Consensus       105 Deid~l~~~~~~~~~~~~~~--~~~~~l~~ll~~~~~~~~~~~~~vi~~tn~~~-----~ld~~l~~~~R~~~~i~i~~p  177 (262)
T 2qz4_A          105 DEIDAVGKKRSTTMSGFSNT--EEEQTLNQLLVEMDGMGTTDHVIVLASTNRAD-----ILDGALMRPGRLDRHVFIDLP  177 (262)
T ss_dssp             ECC---------------------CHHHHHHHHHHHTCCTTCCEEEEEEESCGG-----GGGSGGGSTTSCCEEEECCSC
T ss_pred             eCcchhhccccccccCccch--hHHHHHHHHHHHhhCcCCCCCEEEEecCCChh-----hcCHHHhcCCcCCeEEEeCCc
Confidence            999999 5432110000000  00011122222221111123699999998654     346777652233 34456555


Q ss_pred             hHHH
Q 003038          383 SLSL  386 (854)
Q Consensus       383 sl~~  386 (854)
                      +...
T Consensus       178 ~~~~  181 (262)
T 2qz4_A          178 TLQE  181 (262)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            5544

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=99.00  E-value=2.3e-09  Score=117.21  Aligned_cols=143  Identities=14%  Similarity=0.196  Sum_probs=97.7

Q ss_pred             HHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC
Q 003038          607 ENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN  686 (854)
Q Consensus       607 e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~  686 (854)
                      +.+..+...+...|+||++++..+..++..                    ...+||+||+|+|||.+|++||+.+   ..
T Consensus        16 ~~~~~~~~~~~~~i~g~~~~~~~l~~~l~~--------------------~~~vll~G~pGtGKT~la~~la~~~---~~   72 (331)
T 2r44_A           16 NKIKEVIDEVGKVVVGQKYMINRLLIGICT--------------------GGHILLEGVPGLAKTLSVNTLAKTM---DL   72 (331)
T ss_dssp             HHHHHHHHHHTTTCCSCHHHHHHHHHHHHH--------------------TCCEEEESCCCHHHHHHHHHHHHHT---TC
T ss_pred             HHHHHHHHHhccceeCcHHHHHHHHHHHHc--------------------CCeEEEECCCCCcHHHHHHHHHHHh---CC
Confidence            456778888999999999999888777654                    1268999999999999999999987   24


Q ss_pred             ceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCC--CEEEEEecCCCCCHHHHHHHHHhhhcCeEecC
Q 003038          687 NFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNP--HRVFLIEDVEQADYCSQKGFKRAIESGRIVTS  764 (854)
Q Consensus       687 ~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p--~~ViliDEieka~~~v~~~Ll~~le~G~l~d~  764 (854)
                      .+++++++.....     ..........+....+.      .+..+  ..|+|||||+++++.+++.|+++|+++.++. 
T Consensus        73 ~~~~i~~~~~~~~-----~~l~g~~~~~~~~~~~~------~~~g~l~~~vl~iDEi~~~~~~~~~~Ll~~l~~~~~~~-  140 (331)
T 2r44_A           73 DFHRIQFTPDLLP-----SDLIGTMIYNQHKGNFE------VKKGPVFSNFILADEVNRSPAKVQSALLECMQEKQVTI-  140 (331)
T ss_dssp             CEEEEECCTTCCH-----HHHHEEEEEETTTTEEE------EEECTTCSSEEEEETGGGSCHHHHHHHHHHHHHSEEEE-
T ss_pred             CeEEEecCCCCCh-----hhcCCceeecCCCCceE------eccCcccccEEEEEccccCCHHHHHHHHHHHhcCceee-
Confidence            6777776422210     00000000000000000      00111  3799999999999999999999999999886 


Q ss_pred             CCceeecC-CeEEEEecCCCC
Q 003038          765 SGDEVSLG-DAIVILSCESFS  784 (854)
Q Consensus       765 ~G~~v~~~-~aIiIlTsn~f~  784 (854)
                      .|..+.+. +.+||.|+|..+
T Consensus       141 ~g~~~~~~~~~~viat~np~~  161 (331)
T 2r44_A          141 GDTTYPLDNPFLVLATQNPVE  161 (331)
T ss_dssp             TTEEEECCSSCEEEEEECTTC
T ss_pred             CCEEEECCCCEEEEEecCCCc
Confidence            46666654 567777888544

>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=98.99  E-value=2.7e-09  Score=115.85  Aligned_cols=127  Identities=11%  Similarity=0.076  Sum_probs=92.7

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++|++.++..+...+.....+             .++...+||+||+|+|||.+|+++++.+   ..+|+.++++.+.
T Consensus        12 ~~~ig~~~~~~~l~~~l~~~~~~-------------~~~~~~vll~G~~GtGKT~la~~i~~~~---~~~~~~~~~~~~~   75 (324)
T 1hqc_A           12 DEYIGQERLKQKLRVYLEAAKAR-------------KEPLEHLLLFGPPGLGKTTLAHVIAHEL---GVNLRVTSGPAIE   75 (324)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHH-------------CSCCCCCEEECCTTCCCHHHHHHHHHHH---TCCEEEECTTTCC
T ss_pred             HHhhCHHHHHHHHHHHHHHHHcc-------------CCCCCcEEEECCCCCCHHHHHHHHHHHh---CCCEEEEeccccC
Confidence            45899999999998888765321             0233478999999999999999999987   2467777765443


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHc--CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecC--C-----Cce
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSN--NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTS--S-----GDE  768 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~--~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~--~-----G~~  768 (854)
                             .               ...+.+.+..  ....+||||||+.+++..++.|+++++++.+.--  .     .-.
T Consensus        76 -------~---------------~~~l~~~l~~~~~~~~~l~lDEi~~l~~~~~~~L~~~l~~~~~~~v~~~~~~~~~~~  133 (324)
T 1hqc_A           76 -------K---------------PGDLAAILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIR  133 (324)
T ss_dssp             -------S---------------HHHHHHHHTTTCCTTCEEEETTTTSCCHHHHHHHHHHHHHSEEEECCSSSSSCCCEE
T ss_pred             -------C---------------hHHHHHHHHHhccCCCEEEEECCcccccchHHHHHHHHHhhhhHHhccccccccccc
Confidence                   0               1124444544  4568999999999999999999999999876521  1     112


Q ss_pred             eecCCeEEEEecCC
Q 003038          769 VSLGDAIVILSCES  782 (854)
Q Consensus       769 v~~~~aIiIlTsn~  782 (854)
                      ....+.+||++||.
T Consensus       134 ~~~~~~~~i~~t~~  147 (324)
T 1hqc_A          134 LELPRFTLIGATTR  147 (324)
T ss_dssp             EECCCCEEEEEESC
T ss_pred             cCCCCEEEEEeCCC
Confidence            34467889999885

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=98.98  E-value=1.5e-09  Score=116.75  Aligned_cols=135  Identities=10%  Similarity=0.050  Sum_probs=92.8

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..++++|+||||+|||++++.+|...          +..++.++.+.+...+.|+.+.+++.++..+...  .+.|||||
T Consensus        53 ~~~~vll~Gp~GtGKT~la~~la~~~----------~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~--~~~vl~iD  120 (297)
T 3b9p_A           53 PAKGLLLFGPPGNGKTLLARAVATEC----------SATFLNISAASLTSKYVGDGEKLVRALFAVARHM--QPSIIFID  120 (297)
T ss_dssp             CCSEEEEESSSSSCHHHHHHHHHHHT----------TCEEEEEESTTTSSSSCSCHHHHHHHHHHHHHHT--CSEEEEEE
T ss_pred             CCCeEEEECcCCCCHHHHHHHHHHHh----------CCCeEEeeHHHHhhcccchHHHHHHHHHHHHHHc--CCcEEEec
Confidence            45789999999999999999999874          5689999999888888999999999999998875  68999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhc-cc-C-CCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCC
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CG-I-GENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIP  380 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~-~-~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~  380 (854)
                      |++.+ ........      .........+-..+ .. . ...+.+.+|++|+..+     ..+|++.+  || +.+.++
T Consensus       121 Eid~l~~~~~~~~~------~~~~~~~~~ll~~l~~~~~~~~~~~v~vi~~tn~~~-----~l~~~l~~--R~~~~i~~~  187 (297)
T 3b9p_A          121 EVDSLLSERSSSEH------EASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQ-----ELDEAALR--RFTKRVYVS  187 (297)
T ss_dssp             TGGGTSBCC-----------CCSHHHHHHHHHHHHHCC------CEEEEEEESCGG-----GBCHHHHH--HCCEEEECC
T ss_pred             cHHHhccccccCcc------hHHHHHHHHHHHHHhcccccCCCCcEEEEeecCChh-----hCCHHHHh--hCCeEEEeC
Confidence            99999 54332100      00112222333333 11 1 1112599999998654     46888888  55 345555


Q ss_pred             CchHH
Q 003038          381 AGSLS  385 (854)
Q Consensus       381 ~~sl~  385 (854)
                      .|+..
T Consensus       188 ~p~~~  192 (297)
T 3b9p_A          188 LPDEQ  192 (297)
T ss_dssp             CCCHH
T ss_pred             CcCHH
Confidence            55443

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.98  E-value=2.1e-09  Score=121.77  Aligned_cols=130  Identities=10%  Similarity=0.090  Sum_probs=89.8

Q ss_pred             CcccccHHHHHHHHHHHHHh--------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceE
Q 003038          618 KKVPWQKDTVYDIANTVLKC--------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFV  689 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~--------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i  689 (854)
                      ..|.|.++++..|...|...        +.|+.             |..-+||+||||||||.+|++||..+   ..+|+
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~-------------~prGvLLyGPPGTGKTllAkAiA~e~---~~~f~  244 (434)
T 4b4t_M          181 SDVGGLDKQIEELVEAIVLPMKRADKFKDMGIR-------------APKGALMYGPPGTGKTLLARACAAQT---NATFL  244 (434)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCC-------------CCCEEEEESCTTSSHHHHHHHHHHHH---TCEEE
T ss_pred             HhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCC-------------CCCeeEEECcCCCCHHHHHHHHHHHh---CCCEE
Confidence            46789999999998887542        23433             23357899999999999999999998   46899


Q ss_pred             EEccccccCcCCCccccccccccCCCCCCchHH----HHHHHHHcCCCEEEEEecCCCC-----------CHH---HHHH
Q 003038          690 SIALSSFSSTRADSTEDSRNKRSRDEQSCSYIE----RFAEAVSNNPHRVFLIEDVEQA-----------DYC---SQKG  751 (854)
Q Consensus       690 ~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e----~L~eav~~~p~~ViliDEieka-----------~~~---v~~~  751 (854)
                      .++++++.       .++          .|-.+    .++...+.+..+||||||||..           +..   +.+.
T Consensus       245 ~v~~s~l~-------~~~----------vGese~~ir~lF~~A~~~aP~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~  307 (434)
T 4b4t_M          245 KLAAPQLV-------QMY----------IGEGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLE  307 (434)
T ss_dssp             EEEGGGGC-------SSC----------SSHHHHHHHHHHHHHHHHCSEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHH
T ss_pred             EEehhhhh-------hcc----------cchHHHHHHHHHHHHHhcCCeEEeecchhhhhhccCCCCCCCchHHHHHHHH
Confidence            99988765       111          13333    4566666666799999999953           122   3455


Q ss_pred             HHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCCCC
Q 003038          752 FKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRA  789 (854)
Q Consensus       752 Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~  789 (854)
                      ||..|+.-         -+-.+.+||+|||..+....+
T Consensus       308 lL~~ldg~---------~~~~~ViVIaaTNrp~~LD~A  336 (434)
T 4b4t_M          308 LLNQLDGF---------SSDDRVKVLAATNRVDVLDPA  336 (434)
T ss_dssp             HHHHHTTS---------CSSCSSEEEEECSSCCCCCTT
T ss_pred             HHHHhhcc---------CCCCCEEEEEeCCCchhcCHh
Confidence            66666521         012467899999976666555

>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=98.98  E-value=2.2e-09  Score=116.67  Aligned_cols=112  Identities=15%  Similarity=0.258  Sum_probs=80.3

Q ss_pred             ccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhC---CCCceEEEccccccC
Q 003038          622 WQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFG---SHNNFVSIALSSFSS  698 (854)
Q Consensus       622 GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg---~~~~~i~id~s~~~~  698 (854)
                      ||++++..+...|...                 + ...+||+||+|+|||++|++||+....   ....|+.++.+.   
T Consensus         1 g~~~~~~~L~~~i~~~-----------------~-~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~---   59 (305)
T 2gno_A            1 GAKDQLETLKRIIEKS-----------------E-GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEG---   59 (305)
T ss_dssp             ---CHHHHHHHHHHTC-----------------S-SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSS---
T ss_pred             ChHHHHHHHHHHHHCC-----------------C-CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCc---
Confidence            8999999999888752                 2 358999999999999999999986311   123444444321   


Q ss_pred             cCCCccccccccccCCCCCCchHH--HHHHHHHcCC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecC
Q 003038          699 TRADSTEDSRNKRSRDEQSCSYIE--RFAEAVSNNP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLG  772 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~g~g~~e--~L~eav~~~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~  772 (854)
                                       ...+..+  .+.+.+...|    ++||+|||+|+++...+|.|+++||+.           -.
T Consensus        60 -----------------~~~~id~ir~li~~~~~~p~~~~~kvviIdead~lt~~a~naLLk~LEep-----------~~  111 (305)
T 2gno_A           60 -----------------ENIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMTQQAANAFLKALEEP-----------PE  111 (305)
T ss_dssp             -----------------SCBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBCHHHHHHTHHHHHSC-----------CT
T ss_pred             -----------------CCCCHHHHHHHHHHHhhccccCCceEEEeccHHHhCHHHHHHHHHHHhCC-----------CC
Confidence                             0013332  4666666665    689999999999999999999999974           25


Q ss_pred             CeEEEEecCC
Q 003038          773 DAIVILSCES  782 (854)
Q Consensus       773 ~aIiIlTsn~  782 (854)
                      +++|||+|+.
T Consensus       112 ~t~fIl~t~~  121 (305)
T 2gno_A          112 YAVIVLNTRR  121 (305)
T ss_dssp             TEEEEEEESC
T ss_pred             CeEEEEEECC
Confidence            7889998864

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.96  E-value=3.5e-09  Score=120.07  Aligned_cols=130  Identities=12%  Similarity=0.121  Sum_probs=90.6

Q ss_pred             CcccccHHHHHHHHHHHHH--------hhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceE
Q 003038          618 KKVPWQKDTVYDIANTVLK--------CRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFV  689 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~--------~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i  689 (854)
                      ..|.|.++++..|.+.|..        .+.|+..             ..-+||+||||||||.+|++||..+   ..+|+
T Consensus       209 ~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~p-------------prGILLyGPPGTGKTlLAkAiA~e~---~~~fi  272 (467)
T 4b4t_H          209 SDVGGCKDQIEKLREVVELPLLSPERFATLGIDP-------------PKGILLYGPPGTGKTLCARAVANRT---DATFI  272 (467)
T ss_dssp             SSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCC-------------CSEEEECSCTTSSHHHHHHHHHHHH---TCEEE
T ss_pred             HHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCC-------------CCceEeeCCCCCcHHHHHHHHHhcc---CCCeE
Confidence            4688999999999888754        1334433             3357899999999999999999998   46899


Q ss_pred             EEccccccCcCCCccccccccccCCCCCCchHH----HHHHHHHcCCCEEEEEecCCCCC-----------HH---HHHH
Q 003038          690 SIALSSFSSTRADSTEDSRNKRSRDEQSCSYIE----RFAEAVSNNPHRVFLIEDVEQAD-----------YC---SQKG  751 (854)
Q Consensus       690 ~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e----~L~eav~~~p~~ViliDEieka~-----------~~---v~~~  751 (854)
                      .++++++.       .++          .|..+    .++...+.+..+||||||||..-           ..   +.+.
T Consensus       273 ~vs~s~L~-------sk~----------vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~  335 (467)
T 4b4t_H          273 RVIGSELV-------QKY----------VGEGARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLE  335 (467)
T ss_dssp             EEEGGGGC-------CCS----------SSHHHHHHHHHHHHHHHTCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHH
T ss_pred             EEEhHHhh-------ccc----------CCHHHHHHHHHHHHHHhcCCceEeecccccccccccCcCCCccHHHHHHHHH
Confidence            99988765       111          13333    45666677777999999999762           12   4455


Q ss_pred             HHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCCCC
Q 003038          752 FKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRA  789 (854)
Q Consensus       752 Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~  789 (854)
                      ||..|+..         -...+.+||+|||..+....+
T Consensus       336 lL~~lDg~---------~~~~~ViVIaATNrpd~LDpA  364 (467)
T 4b4t_H          336 LITQLDGF---------DPRGNIKVMFATNRPNTLDPA  364 (467)
T ss_dssp             HHHHHHSS---------CCTTTEEEEEECSCTTSBCHH
T ss_pred             HHHHhhcc---------CCCCcEEEEeCCCCcccCChh
Confidence            66666521         123578899999975555433

>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=98.95  E-value=2.2e-09  Score=117.27  Aligned_cols=136  Identities=12%  Similarity=0.082  Sum_probs=90.9

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+|+++++..|...|.....   .+....   ...+|...+||+||+|+|||.+|+++|+.+   ..+|+.++++++.
T Consensus        18 ~di~G~~~~~~~l~~~i~~~~~---~~~~~~---~~~~~~~~vLl~GppGtGKT~la~aia~~~---~~~~~~v~~~~l~   88 (322)
T 3eie_A           18 EDVAGLEGAKEALKEAVILPVK---FPHLFK---GNRKPTSGILLYGPPGTGKSYLAKAVATEA---NSTFFSVSSSDLV   88 (322)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHH---CGGGCC---TTCCCCCEEEEECSSSSCHHHHHHHHHHHH---TCEEEEEEHHHHH
T ss_pred             HHhcChHHHHHHHHHHHHHHHh---CHHHHh---cCCCCCCeEEEECCCCCcHHHHHHHHHHHH---CCCEEEEchHHHh
Confidence            4589999999999998854321   110000   001345679999999999999999999987   4678999887654


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCH-----------HHHHHHHHhhhcCeEecCCC
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADY-----------CSQKGFKRAIESGRIVTSSG  766 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~-----------~v~~~Ll~~le~G~l~d~~G  766 (854)
                             ....     + ........+.+..+....+||||||||.+.+           .+++.|+..|+.-.      
T Consensus        89 -------~~~~-----g-~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~------  149 (322)
T 3eie_A           89 -------SKWM-----G-ESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVG------  149 (322)
T ss_dssp             -------TTTG-----G-GHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGG------
T ss_pred             -------hccc-----c-hHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhcccc------
Confidence                   1110     0 0001222566666777789999999998754           56788888887311      


Q ss_pred             ceeecCCeEEEEecCCC
Q 003038          767 DEVSLGDAIVILSCESF  783 (854)
Q Consensus       767 ~~v~~~~aIiIlTsn~f  783 (854)
                        -.-.+.+||.|||..
T Consensus       150 --~~~~~v~vi~atn~~  164 (322)
T 3eie_A          150 --NDSQGVLVLGATNIP  164 (322)
T ss_dssp             --TSCCCEEEEEEESCG
T ss_pred             --ccCCceEEEEecCCh
Confidence              122467888899863

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.94  E-value=2.3e-09  Score=121.31  Aligned_cols=130  Identities=14%  Similarity=0.099  Sum_probs=91.4

Q ss_pred             CcccccHHHHHHHHHHHHHh--------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceE
Q 003038          618 KKVPWQKDTVYDIANTVLKC--------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFV  689 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~--------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i  689 (854)
                      ..|.|.++++..|...|...        +.|+..             ..-+||+||||||||.+|++||..+   ..+|+
T Consensus       172 ~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~-------------prGiLL~GPPGtGKT~lakAiA~~~---~~~~~  235 (428)
T 4b4t_K          172 ADVGGLDMQKQEIREAVELPLVQADLYEQIGIDP-------------PRGVLLYGPPGTGKTMLVKAVANST---KAAFI  235 (428)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCC-------------CCEEEEESCTTTTHHHHHHHHHHHH---TCEEE
T ss_pred             HHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCC-------------CceEEEECCCCCCHHHHHHHHHHHh---CCCeE
Confidence            46899999999998888642        234432             2358999999999999999999998   46899


Q ss_pred             EEccccccCcCCCccccccccccCCCCCCchHH----HHHHHHHcCCCEEEEEecCCCC-----------CH---HHHHH
Q 003038          690 SIALSSFSSTRADSTEDSRNKRSRDEQSCSYIE----RFAEAVSNNPHRVFLIEDVEQA-----------DY---CSQKG  751 (854)
Q Consensus       690 ~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e----~L~eav~~~p~~ViliDEieka-----------~~---~v~~~  751 (854)
                      .++++++.       .++          .|-.+    .++...+.+..+||||||+|..           +.   .+.+.
T Consensus       236 ~v~~~~l~-------~~~----------~Ge~e~~ir~lF~~A~~~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~  298 (428)
T 4b4t_K          236 RVNGSEFV-------HKY----------LGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIE  298 (428)
T ss_dssp             EEEGGGTC-------CSS----------CSHHHHHHHHHHHHHHHTCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHH
T ss_pred             EEecchhh-------ccc----------cchhHHHHHHHHHHHHHcCCCeeechhhhhhhccccCCCCCCChHHHHHHHH
Confidence            99988765       111          03222    5666677777799999999842           21   35667


Q ss_pred             HHHhhhcCeEecCCCceeecCCeEEEEecCCCCCCCCC
Q 003038          752 FKRAIESGRIVTSSGDEVSLGDAIVILSCESFSSRSRA  789 (854)
Q Consensus       752 Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s~~  789 (854)
                      ||..|+.-         -+..+.+||+|||..+....+
T Consensus       299 lL~~ldg~---------~~~~~v~vI~aTN~~~~LD~A  327 (428)
T 4b4t_K          299 LLTQMDGF---------DQSTNVKVIMATNRADTLDPA  327 (428)
T ss_dssp             HHHHHHHS---------CSSCSEEEEEEESCSSSCCHH
T ss_pred             HHHHhhCC---------CCCCCEEEEEecCChhhcChh
Confidence            77777631         123568999999975554433

>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=3.7e-09  Score=114.42  Aligned_cols=118  Identities=21%  Similarity=0.301  Sum_probs=83.7

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC--CceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH--NNFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~--~~~i~id~s~  695 (854)
                      ..++||++++..+...+...                 + ...+||+||+|+|||++|+++++.+++..  ..++.++++.
T Consensus        25 ~~~~g~~~~~~~l~~~l~~~-----------------~-~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~~~~   86 (327)
T 1iqp_A           25 DDIVGQEHIVKRLKHYVKTG-----------------S-MPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASD   86 (327)
T ss_dssp             TTCCSCHHHHHHHHHHHHHT-----------------C-CCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTC
T ss_pred             HHhhCCHHHHHHHHHHHHcC-----------------C-CCeEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEeeccc
Confidence            45899999999988877652                 1 12499999999999999999999987542  2356665442


Q ss_pred             ccCcCCCccccccccccCCCCCCchHHHHHHHHHc-----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceee
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSN-----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVS  770 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~-----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~  770 (854)
                      ..       ...           ...+.+.+....     ..+.||+|||+|++++..++.|++++++.           
T Consensus        87 ~~-------~~~-----------~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~-----------  137 (327)
T 1iqp_A           87 ER-------GIN-----------VIREKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMF-----------  137 (327)
T ss_dssp             HH-------HHH-----------TTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHT-----------
T ss_pred             cC-------chH-----------HHHHHHHHHHhhCCcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhc-----------
Confidence            21       000           011123333322     45789999999999999999999999963           


Q ss_pred             cCCeEEEEecCC
Q 003038          771 LGDAIVILSCES  782 (854)
Q Consensus       771 ~~~aIiIlTsn~  782 (854)
                      -.+++||++||.
T Consensus       138 ~~~~~~i~~~~~  149 (327)
T 1iqp_A          138 SSNVRFILSCNY  149 (327)
T ss_dssp             TTTEEEEEEESC
T ss_pred             CCCCeEEEEeCC
Confidence            146788998875

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=98.93  E-value=5.9e-09  Score=114.15  Aligned_cols=138  Identities=12%  Similarity=0.070  Sum_probs=90.5

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+|+++++..|..+|.....   .+.-..   ...+|...+||+||+|+|||.+|+++|+.+.  ...|+.++++++.
T Consensus        12 ~di~G~~~~k~~l~~~v~~p~~---~~~~~~---~~~~~~~~iLL~GppGtGKT~la~ala~~~~--~~~~~~i~~~~l~   83 (322)
T 1xwi_A           12 SDVAGLEGAKEALKEAVILPIK---FPHLFT---GKRTPWRGILLFGPPGTGKSYLAKAVATEAN--NSTFFSISSSDLV   83 (322)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHH---CGGGSC---TTCCCCSEEEEESSSSSCHHHHHHHHHHHTT--SCEEEEEECCSSC
T ss_pred             HHhcCHHHHHHHHHHHHHHHHh---CHHHHh---CCCCCCceEEEECCCCccHHHHHHHHHHHcC--CCcEEEEEhHHHH
Confidence            4589999999999988864311   000000   0013445789999999999999999999873  3578889887654


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCC-----------HHHHHHHHHhhhcCeEecCCC
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQAD-----------YCSQKGFKRAIESGRIVTSSG  766 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~-----------~~v~~~Ll~~le~G~l~d~~G  766 (854)
                             ...     .+ ........+.+..+....+||||||||.+.           ..+.+.|+..|+.-       
T Consensus        84 -------~~~-----~g-~~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~-------  143 (322)
T 1xwi_A           84 -------SKW-----LG-ESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGV-------  143 (322)
T ss_dssp             -------CSS-----CC-SCHHHHHHHHHHHHHTSSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCS-------
T ss_pred             -------hhh-----hh-HHHHHHHHHHHHHHhcCCcEEEeecHHHhccccccccchHHHHHHHHHHHHHhcc-------
Confidence                   111     00 000222356666677778999999999872           24667777777631       


Q ss_pred             ceeecCCeEEEEecCCCC
Q 003038          767 DEVSLGDAIVILSCESFS  784 (854)
Q Consensus       767 ~~v~~~~aIiIlTsn~f~  784 (854)
                       ...-.+.+||.+||.-+
T Consensus       144 -~~~~~~v~vI~atn~~~  160 (322)
T 1xwi_A          144 -GVDNDGILVLGATNIPW  160 (322)
T ss_dssp             -SSCCTTEEEEEEESCTT
T ss_pred             -cccCCCEEEEEecCCcc
Confidence             11235788999998643

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=98.92  E-value=3.4e-09  Score=111.62  Aligned_cols=141  Identities=11%  Similarity=0.086  Sum_probs=92.0

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..++++|+||||+|||++++.++...          +..++.++...+...+.|+.+.+++.++..+...  .++|||||
T Consensus        44 ~~~~vll~G~~GtGKT~la~~la~~~----------~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~a~~~--~~~il~iD  111 (257)
T 1lv7_A           44 IPKGVLMVGPPGTGKTLLAKAIAGEA----------KVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKA--APCIIFID  111 (257)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHH----------TCCEEEECSCSSTTSCCCCCHHHHHHHHHHHHTT--CSEEEEET
T ss_pred             CCCeEEEECcCCCCHHHHHHHHHHHc----------CCCEEEEeHHHHHHHhhhhhHHHHHHHHHHHHHc--CCeeehhh
Confidence            35679999999999999999999864          3467888888888778888889999999998764  68999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccC-CCCCCCch
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLH-PLTIPAGS  383 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~-~v~i~~~s  383 (854)
                      |++.+ ........+...   .....+..+-..+....++..+.+|++|+..+     ..+|++.|.-||. .+.|+.|+
T Consensus       112 eid~l~~~~~~~~~~~~~---~~~~~~~~ll~~l~~~~~~~~~~vI~~tn~~~-----~l~~~l~r~~rf~~~i~i~~P~  183 (257)
T 1lv7_A          112 EIDAVGRQRGAGLGGGHD---EREQTLNQMLVEMDGFEGNEGIIVIAATNRPD-----VLDPALLRPGRFDRQVVVGLPD  183 (257)
T ss_dssp             THHHHTCCCSTTSCCTTC---HHHHHHHHHHHHHHTCCSSSCEEEEEEESCTT-----TSCGGGGSTTSSCEEEECCCCC
T ss_pred             hhhhhccCCCCCcCCCch---HHHHHHHHHHHHhhCcccCCCEEEEEeeCCch-----hCCHHHcCCCcCCeEEEeCCCC
Confidence            99999 543221000000   00112222222222111223599999998753     4578886622332 45555555


Q ss_pred             HHH
Q 003038          384 LSL  386 (854)
Q Consensus       384 l~~  386 (854)
                      +..
T Consensus       184 ~~~  186 (257)
T 1lv7_A          184 VRG  186 (257)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.92  E-value=2.9e-09  Score=113.64  Aligned_cols=136  Identities=12%  Similarity=0.152  Sum_probs=88.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCC---CcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGT---MRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl---~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      ..|+|+++++..|...+......-   ....        .++...+||+||+|+|||.+|++||+.+   ...++.++++
T Consensus        17 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~--------~~~~~~~ll~G~~GtGKT~la~~la~~~---~~~~~~v~~~   85 (285)
T 3h4m_A           17 EDIGGLEKQMQEIREVVELPLKHPELFEKVG--------IEPPKGILLYGPPGTGKTLLAKAVATET---NATFIRVVGS   85 (285)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCHHHHHHHC--------CCCCSEEEEESSSSSSHHHHHHHHHHHT---TCEEEEEEGG
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhcC--------CCCCCeEEEECCCCCcHHHHHHHHHHHh---CCCEEEEehH
Confidence            357899999999888875532110   0000        0223468999999999999999999987   4578888877


Q ss_pred             cccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCC-----------CHHHHHHHHHhhhcCeEec
Q 003038          695 SFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQA-----------DYCSQKGFKRAIESGRIVT  763 (854)
Q Consensus       695 ~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka-----------~~~v~~~Ll~~le~G~l~d  763 (854)
                      ++.       ...     . +........+....+....+||||||||.+           +...+..|.+.++...-..
T Consensus        86 ~~~-------~~~-----~-~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~  152 (285)
T 3h4m_A           86 ELV-------KKF-----I-GEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFD  152 (285)
T ss_dssp             GGC-------CCS-----T-THHHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTC
T ss_pred             HHH-------Hhc-----c-chHHHHHHHHHHHHHHcCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCC
Confidence            654       111     0 000012224555566666799999999987           6778888888776421000


Q ss_pred             CCCceeecCCeEEEEecCCC
Q 003038          764 SSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       764 ~~G~~v~~~~aIiIlTsn~f  783 (854)
                            .-.+.+||+|||.-
T Consensus       153 ------~~~~~~vI~ttn~~  166 (285)
T 3h4m_A          153 ------ARGDVKIIGATNRP  166 (285)
T ss_dssp             ------SSSSEEEEEECSCG
T ss_pred             ------CCCCEEEEEeCCCc
Confidence                  11368899999853

>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=98.92  E-value=6.5e-09  Score=109.13  Aligned_cols=138  Identities=13%  Similarity=0.129  Sum_probs=79.6

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +.|+|+++++..|...+...+..-.... .     ..++...+||+||+|+|||++|++||+.+   ..+++.++++.+.
T Consensus         6 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~-~-----g~~~~~~vll~G~~GtGKT~la~~la~~~---~~~~~~~~~~~~~   76 (262)
T 2qz4_A            6 KDVAGMHEAKLEVREFVDYLKSPERFLQ-L-----GAKVPKGALLLGPPGCGKTLLAKAVATEA---QVPFLAMAGAEFV   76 (262)
T ss_dssp             TSSCSCHHHHHHHHHHHHHHHCCC------------CCCCCEEEEESCTTSSHHHHHHHHHHHH---TCCEEEEETTTTS
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHH-c-----CCCCCceEEEECCCCCCHHHHHHHHHHHh---CCCEEEechHHHH
Confidence            5689999999998887765332111000 0     00233468999999999999999999987   3578899888665


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCC------------CHHHHHHHHHhhhcCeEecCC
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQA------------DYCSQKGFKRAIESGRIVTSS  765 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka------------~~~v~~~Ll~~le~G~l~d~~  765 (854)
                             +...      +.+......+.+..+....+||||||||.+            +...+..|.+.++.  + +..
T Consensus        77 -------~~~~------~~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~--~-~~~  140 (262)
T 2qz4_A           77 -------EVIG------GLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVE--M-DGM  140 (262)
T ss_dssp             -------SSST------THHHHHHHHHHHHHHHTCSEEEEEECC-------------------CHHHHHHHHH--H-HTC
T ss_pred             -------hhcc------ChhHHHHHHHHHHHHhcCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHH--h-hCc
Confidence                   1110      000011124455555666799999999998            33344444444432  0 000


Q ss_pred             CceeecCCeEEEEecCCC
Q 003038          766 GDEVSLGDAIVILSCESF  783 (854)
Q Consensus       766 G~~v~~~~aIiIlTsn~f  783 (854)
                         ..-.+.+||+|+|.-
T Consensus       141 ---~~~~~~~vi~~tn~~  155 (262)
T 2qz4_A          141 ---GTTDHVIVLASTNRA  155 (262)
T ss_dssp             ---CTTCCEEEEEEESCG
T ss_pred             ---CCCCCEEEEecCCCh
Confidence               012478899999853

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=98.92  E-value=6.7e-10  Score=120.02  Aligned_cols=136  Identities=13%  Similarity=0.012  Sum_probs=82.7

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhh--CCCeEEE
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCL--GRGIVLN  303 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~--~~~~ILf  303 (854)
                      ..+.++|+||||||||++++++|..+          +..++.++.+.+.+.+.|+.+.++++++..+....  ..++|||
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~~l----------~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~~~~~~~vl~  104 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFRKM----------GINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLF  104 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHHHH----------TCCCEEEEHHHHHCC---HHHHHHHHHHHHHHHHHTTSSCCCEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh----------CCCEEEEeHHHhhhccCchhHHHHHHHHHHHHHHHhcCCCeEEE
Confidence            34567889999999999999999886          67899999999999999999999999999883110  3689999


Q ss_pred             eCccccc-cccccccccccccchhhhHHHHHHHhhccc-C----------CCCceEEEEEecCHHHHHHhhccCCchhhh
Q 003038          304 LGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-I----------GENARFWLMGIATFQSYMRCKSGHPSLETL  371 (854)
Q Consensus       304 idel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~----------~g~g~l~lIgatT~~ey~k~~~~~pale~~  371 (854)
                      ||||+.+ +...+...+ +   -........+-++|.. .          ....++.+|+||+..+     ..+|+|-|.
T Consensus       105 iDEiD~~~~~~~~~~~~-~---~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~-----~ld~al~R~  175 (293)
T 3t15_A          105 INDLDAGAGRMGGTTQY-T---VNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFS-----TLYAPLIRD  175 (293)
T ss_dssp             EECCC------------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCC-----C--CHHHHH
T ss_pred             EechhhhcCCCCCCccc-c---chHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcc-----cCCHHHhCC
Confidence            9999999 532211000 0   0000122344444421 0          0123599999998542     457888764


Q ss_pred             hccCC-CCCC
Q 003038          372 WSLHP-LTIP  380 (854)
Q Consensus       372 ~~~~~-v~i~  380 (854)
                      -||.. +.+|
T Consensus       176 ~R~d~~i~~P  185 (293)
T 3t15_A          176 GRMEKFYWAP  185 (293)
T ss_dssp             HHEEEEEECC
T ss_pred             CCCceeEeCc
Confidence            45532 3444

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=98.90  E-value=1.6e-09  Score=121.71  Aligned_cols=142  Identities=15%  Similarity=0.195  Sum_probs=102.7

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++|+..++..+...+.+..                .....+++.|++|+||+.+|+.|.........+|+.+||+.+.
T Consensus       137 ~~~ig~s~~m~~l~~~i~~~a----------------~~~~~vli~Ge~GtGK~~lAr~ih~~s~r~~~~fv~v~~~~~~  200 (387)
T 1ny5_A          137 EEYVFESPKMKEILEKIKKIS----------------CAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIP  200 (387)
T ss_dssp             CCCCCCSHHHHHHHHHHHHHT----------------TCCSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSC
T ss_pred             hhhhhccHHhhHHHHHHHHhc----------------CCCCCeEEecCCCcCHHHHHHHHHHhcCCCCCCeEEEecCCCC
Confidence            468999999888888887632                1234579999999999999999999887778899999999876


Q ss_pred             CcCCCccccccccccCC-CCC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCe
Q 003038          698 STRADSTEDSRNKRSRD-EQS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDA  774 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~-~~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~a  774 (854)
                             +....+.+.+ ..| + |-...-.+.+......++|||||+.+++.+|..|+++|++|.++.-.|......|+
T Consensus       201 -------~~~~~~elfg~~~g~~tga~~~~~g~~~~a~~gtlfldei~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~  273 (387)
T 1ny5_A          201 -------RDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNV  273 (387)
T ss_dssp             -------HHHHHHHHHCBCTTSSTTCCSCBCCHHHHTTTSEEEEESGGGCCHHHHHHHHHHHHHSEECCBTCCSBEECCC
T ss_pred             -------HHHHHHHhcCCCCCCCCCcccccCCceeeCCCcEEEEcChhhCCHHHHHHHHHHHhcCcEEeCCCCceeeccE
Confidence                   2211111111 000 0 00000011123345689999999999999999999999999998766666667788


Q ss_pred             EEEEecCC
Q 003038          775 IVILSCES  782 (854)
Q Consensus       775 IiIlTsn~  782 (854)
                      .||++||.
T Consensus       274 rii~at~~  281 (387)
T 1ny5_A          274 RILAATNR  281 (387)
T ss_dssp             EEEEEESS
T ss_pred             EEEEeCCC
Confidence            99999984

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=98.90  E-value=2.7e-10  Score=134.85  Aligned_cols=155  Identities=10%  Similarity=0.107  Sum_probs=95.6

Q ss_pred             HHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC
Q 003038          607 ENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN  686 (854)
Q Consensus       607 e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~  686 (854)
                      +.+..|.+.|...|+||++++..|..++..   |..+.. ..   ...+....+||+||||+|||.+|++||+.+..   
T Consensus       284 ~~~~~l~~~l~~~I~G~e~vk~al~~~l~~---g~~~~~-~~---~~~r~~~~vLL~GppGtGKT~LAr~la~~~~r---  353 (595)
T 3f9v_A          284 WIRDRIISSIAPSIYGHWELKEALALALFG---GVPKVL-ED---TRIRGDIHILIIGDPGTAKSQMLQFISRVAPR---  353 (595)
T ss_dssp             TGGGTHHHHTSSTTSCCHHHHHHHTTTTTC---CCCEET-TT---TEECCSCCEEEEESSCCTHHHHHHSSSTTCSC---
T ss_pred             HHHHHHHHhhcchhcChHHHHHHHHHHHhC---CCcccc-cC---CCcCCCcceEEECCCchHHHHHHHHHHHhCCC---
Confidence            345678889999999999988776544332   211100 00   01133448999999999999999999987621   


Q ss_pred             ceEEEccccccCcCCCccccccccccC-CCCCC--chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEec
Q 003038          687 NFVSIALSSFSSTRADSTEDSRNKRSR-DEQSC--SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVT  763 (854)
Q Consensus       687 ~~i~id~s~~~~~~~~s~e~~~~~rl~-~~~g~--g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d  763 (854)
                      .+...+..  ....... .. ...... +....  |.   +.    .....|+|||||+++++++|+.|+++|++|.++-
T Consensus       354 ~~~~~~~~--~~~~~l~-~~-~~~~~~~g~~~~~~G~---l~----~A~~gil~IDEid~l~~~~q~~Ll~~le~~~i~i  422 (595)
T 3f9v_A          354 AVYTTGKG--STAAGLT-AA-VVREKGTGEYYLEAGA---LV----LADGGIAVIDEIDKMRDEDRVAIHEAMEQQTVSI  422 (595)
T ss_dssp             EECCCTTC--STTTTSE-EE-CSSGGGTSSCSEEECH---HH----HHSSSEECCTTTTCCCSHHHHHHHHHHHSSSEEE
T ss_pred             ceecCCCc--ccccccc-ce-eeeccccccccccCCe---eE----ecCCCcEEeehhhhCCHhHhhhhHHHHhCCEEEE
Confidence            11111110  0000000 00 000000 00000  22   22    2245799999999999999999999999999983


Q ss_pred             -CCCceeec-CCeEEEEecCC
Q 003038          764 -SSGDEVSL-GDAIVILSCES  782 (854)
Q Consensus       764 -~~G~~v~~-~~aIiIlTsn~  782 (854)
                       ..|....+ .+++||.|+|.
T Consensus       423 ~~~g~~~~~~~~~~vIaatNp  443 (595)
T 3f9v_A          423 AKAGIVAKLNARAAVIAAGNP  443 (595)
T ss_dssp             ESSSSEEEECCCCEEEEEECC
T ss_pred             ecCCcEEEecCceEEEEEcCC
Confidence             45666666 57899999996

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=98.89  E-value=1e-08  Score=103.52  Aligned_cols=118  Identities=21%  Similarity=0.321  Sum_probs=81.7

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC--CceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH--NNFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~--~~~i~id~s~  695 (854)
                      ..++|+++++..|...+...                 + ...++|+||+|+|||++|+.+++.+.+..  ..++.++++.
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~-----------------~-~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~~   78 (226)
T 2chg_A           17 DEVVGQDEVIQRLKGYVERK-----------------N-IPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASD   78 (226)
T ss_dssp             GGCCSCHHHHHHHHHHHHTT-----------------C-CCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEETTC
T ss_pred             HHHcCcHHHHHHHHHHHhCC-----------------C-CCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEecccc
Confidence            34789999999888877542                 1 12489999999999999999999885432  3455555442


Q ss_pred             ccCcCCCccccccccccCCCCCCchHHHHHHHHH-----cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceee
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVS-----NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVS  770 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~-----~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~  770 (854)
                      ..       ...           ...+.+.....     .....||+|||++++++..++.|++.+++.           
T Consensus        79 ~~-------~~~-----------~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~-----------  129 (226)
T 2chg_A           79 ER-------GID-----------VVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMY-----------  129 (226)
T ss_dssp             TT-------CHH-----------HHHHHHHHHHTSCCSTTCSCEEEEEETGGGSCHHHHHHHHHHHHHT-----------
T ss_pred             cc-------ChH-----------HHHHHHHHHhcccCCCccCceEEEEeChhhcCHHHHHHHHHHHHhc-----------
Confidence            22       000           01112233332     245789999999999999999999999863           


Q ss_pred             cCCeEEEEecCC
Q 003038          771 LGDAIVILSCES  782 (854)
Q Consensus       771 ~~~aIiIlTsn~  782 (854)
                      -.+++||+|||.
T Consensus       130 ~~~~~~i~~~~~  141 (226)
T 2chg_A          130 SKSCRFILSCNY  141 (226)
T ss_dssp             TTTEEEEEEESC
T ss_pred             CCCCeEEEEeCC
Confidence            246778888874

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=98.88  E-value=4.8e-09  Score=117.70  Aligned_cols=134  Identities=11%  Similarity=0.109  Sum_probs=88.7

Q ss_pred             CcccccHHHHHHHHHHHHHhhc--CCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRS--GTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rs--gl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      ..|+||+.++..|...+.....  .+....        ..+...+||+||+|+|||.+|++||+.+   ...|+.++++.
T Consensus       115 ~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~--------~~~~~~vLL~GppGtGKT~la~aia~~~---~~~~~~v~~~~  183 (389)
T 3vfd_A          115 DDIAGQDLAKQALQEIVILPSLRPELFTGL--------RAPARGLLLFGPPGNGKTMLAKAVAAES---NATFFNISAAS  183 (389)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCTTTSCGG--------GCCCSEEEEESSTTSCHHHHHHHHHHHT---TCEEEEECSCC
T ss_pred             HHhCCHHHHHHHHHHHHHHhccCHHHhccc--------CCCCceEEEECCCCCCHHHHHHHHHHhh---cCcEEEeeHHH
Confidence            3589999999999988865322  000000        1234589999999999999999999986   46899999886


Q ss_pred             ccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCC-----------CHHHHHHHHHhhhcCeEecC
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQA-----------DYCSQKGFKRAIESGRIVTS  764 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka-----------~~~v~~~Ll~~le~G~l~d~  764 (854)
                      +.       ..+.      +........+.+..+....+||||||||.+           ...+++.|+..|+...-   
T Consensus       184 l~-------~~~~------g~~~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~---  247 (389)
T 3vfd_A          184 LT-------SKYV------GEGEKLVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQS---  247 (389)
T ss_dssp             C--------------------CHHHHHHHHHHHHHSSSEEEEEETGGGGC--------CTHHHHHHHHHHHHHHHC----
T ss_pred             hh-------cccc------chHHHHHHHHHHHHHhcCCeEEEEECchhhcccCCCccchHHHHHHHHHHHHhhcccc---
Confidence            65       1110      000022234556666677799999999887           56678888888873211   


Q ss_pred             CCceeecCCeEEEEecCC
Q 003038          765 SGDEVSLGDAIVILSCES  782 (854)
Q Consensus       765 ~G~~v~~~~aIiIlTsn~  782 (854)
                          ..-.+.+||.|||.
T Consensus       248 ----~~~~~v~vI~atn~  261 (389)
T 3vfd_A          248 ----AGDDRVLVMGATNR  261 (389)
T ss_dssp             --------CEEEEEEESC
T ss_pred             ----cCCCCEEEEEecCC
Confidence                11246789999985

>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=98.87  E-value=4.2e-09  Score=114.68  Aligned_cols=117  Identities=14%  Similarity=0.149  Sum_probs=85.9

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++||++++..|...+...                 +....+||.||+|+|||.+|++||+.+   ...++.++++.+.
T Consensus        26 ~~ivg~~~~~~~l~~~l~~~-----------------~~~~~~L~~G~~G~GKT~la~~la~~l---~~~~~~i~~~~~~   85 (324)
T 3u61_B           26 DECILPAFDKETFKSITSKG-----------------KIPHIILHSPSPGTGKTTVAKALCHDV---NADMMFVNGSDCK   85 (324)
T ss_dssp             TTSCCCHHHHHHHHHHHHTT-----------------CCCSEEEECSSTTSSHHHHHHHHHHHT---TEEEEEEETTTCC
T ss_pred             HHHhCcHHHHHHHHHHHHcC-----------------CCCeEEEeeCcCCCCHHHHHHHHHHHh---CCCEEEEcccccC
Confidence            46899999999888887731                 223478999999999999999999988   3567888765332


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHcC----CCEEEEEecCCCCC-HHHHHHHHHhhhcCeEecCCCceeecC
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSNN----PHRVFLIEDVEQAD-YCSQKGFKRAIESGRIVTSSGDEVSLG  772 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~----p~~ViliDEieka~-~~v~~~Ll~~le~G~l~d~~G~~v~~~  772 (854)
                             ..            ...+.+.+.....    .++||||||+|.+. .+.++.|++.+++.           -.
T Consensus        86 -------~~------------~i~~~~~~~~~~~~~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~-----------~~  135 (324)
T 3u61_B           86 -------ID------------FVRGPLTNFASAASFDGRQKVIVIDEFDRSGLAESQRHLRSFMEAY-----------SS  135 (324)
T ss_dssp             -------HH------------HHHTHHHHHHHBCCCSSCEEEEEEESCCCGGGHHHHHHHHHHHHHH-----------GG
T ss_pred             -------HH------------HHHHHHHHHHhhcccCCCCeEEEEECCcccCcHHHHHHHHHHHHhC-----------CC
Confidence                   00            0011233333332    46899999999999 99999999999963           14


Q ss_pred             CeEEEEecCCCC
Q 003038          773 DAIVILSCESFS  784 (854)
Q Consensus       773 ~aIiIlTsn~f~  784 (854)
                      +++||+|||...
T Consensus       136 ~~~iI~~~n~~~  147 (324)
T 3u61_B          136 NCSIIITANNID  147 (324)
T ss_dssp             GCEEEEEESSGG
T ss_pred             CcEEEEEeCCcc
Confidence            678999998643

>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=98.87  E-value=9.5e-09  Score=117.45  Aligned_cols=135  Identities=14%  Similarity=0.116  Sum_probs=88.5

Q ss_pred             CcccccHHHHHHHHHHHHHhhc--CCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRS--GTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rs--gl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      ..|+|+++++..|...|.....  .+-...        .+|...+||+||+|+|||.+|++||..+.  ...|+.+++++
T Consensus       134 ~di~G~~~~k~~l~~~v~~p~~~~~~~~~~--------~~~~~~vLL~GppGtGKT~lA~aia~~~~--~~~~~~v~~~~  203 (444)
T 2zan_A          134 SDVAGLEGAKEALKEAVILPIKFPHLFTGK--------RTPWRGILLFGPPGTGKSYLAKAVATEAN--NSTFFSISSSD  203 (444)
T ss_dssp             GGSCSCHHHHHHHHHHHTHHHHCTTTTSGG--------GCCCSEEEEECSTTSSHHHHHHHHHHHCC--SSEEEEECCC-
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHhhcc--------CCCCceEEEECCCCCCHHHHHHHHHHHcC--CCCEEEEeHHH
Confidence            3589999999999988853211  010000        13446789999999999999999999873  35789998876


Q ss_pred             ccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCC-----------HHHHHHHHHhhhcCeEecC
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQAD-----------YCSQKGFKRAIESGRIVTS  764 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~-----------~~v~~~Ll~~le~G~l~d~  764 (854)
                      +.       ...     .+. .......+.+..+....+||||||||.+.           ..+++.|+..|+.-     
T Consensus       204 l~-------~~~-----~g~-~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~-----  265 (444)
T 2zan_A          204 LV-------SKW-----LGE-SEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGV-----  265 (444)
T ss_dssp             ---------------------CCCTHHHHHHHHHHSCSEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCS-----
T ss_pred             HH-------hhh-----cch-HHHHHHHHHHHHHHcCCeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhCc-----
Confidence            54       111     100 01223356666677778999999999883           35777788777642     


Q ss_pred             CCceeecCCeEEEEecCCC
Q 003038          765 SGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       765 ~G~~v~~~~aIiIlTsn~f  783 (854)
                         ...-.+.+||+|||..
T Consensus       266 ---~~~~~~v~vI~atn~~  281 (444)
T 2zan_A          266 ---GVDNDGILVLGATNIP  281 (444)
T ss_dssp             ---SCCCSSCEEEEEESCG
T ss_pred             ---ccCCCCEEEEecCCCc
Confidence               1123578899999863

>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=98.87  E-value=5.1e-09  Score=113.42  Aligned_cols=127  Identities=13%  Similarity=0.127  Sum_probs=88.0

Q ss_pred             cccccHHHHHHHHHHHHHh--------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEE
Q 003038          619 KVPWQKDTVYDIANTVLKC--------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVS  690 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~--------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~  690 (854)
                      .|+|+++++..|...|...        ..|+             ++...+||+||+|+|||.+|++||..+   ..+|+.
T Consensus        16 di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~-------------~~~~~vLL~Gp~GtGKT~la~ala~~~---~~~~i~   79 (301)
T 3cf0_A           16 DIGGLEDVKRELQELVQYPVEHPDKFLKFGM-------------TPSKGVLFYGPPGCGKTLLAKAIANEC---QANFIS   79 (301)
T ss_dssp             GSCSCHHHHHHHHHHHHHHHHCHHHHHHHCC-------------CCCSEEEEECSSSSSHHHHHHHHHHHT---TCEEEE
T ss_pred             HhCCHHHHHHHHHHHHHHHhhCHHHHHHcCC-------------CCCceEEEECCCCcCHHHHHHHHHHHh---CCCEEE
Confidence            4899999999999888652        2222             233478999999999999999999987   368899


Q ss_pred             EccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCH--------------HHHHHHHHhh
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADY--------------CSQKGFKRAI  756 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~--------------~v~~~Ll~~l  756 (854)
                      ++++++.       ...     .+.. ......+.+..+....+||||||||.+.+              .+++.|+..|
T Consensus        80 v~~~~l~-------~~~-----~g~~-~~~~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l  146 (301)
T 3cf0_A           80 IKGPELL-------TMW-----FGES-EANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEM  146 (301)
T ss_dssp             ECHHHHH-------HHH-----HTTC-TTHHHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHH
T ss_pred             EEhHHHH-------hhh-----cCch-HHHHHHHHHHHHhcCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHh
Confidence            9877654       111     1000 01222455555666679999999996543              4678899998


Q ss_pred             hcCeEecCCCceeecCCeEEEEecCCC
Q 003038          757 ESGRIVTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       757 e~G~l~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                      +.-.         .-.+.+||+|||.-
T Consensus       147 ~~~~---------~~~~v~vi~atn~~  164 (301)
T 3cf0_A          147 DGMS---------TKKNVFIIGATNRP  164 (301)
T ss_dssp             HSSC---------TTSSEEEEEEESCG
T ss_pred             hccc---------CCCCEEEEEecCCc
Confidence            8310         12578999999864

>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=98.87  E-value=1e-08  Score=113.85  Aligned_cols=134  Identities=13%  Similarity=0.091  Sum_probs=88.7

Q ss_pred             CcccccHHHHHHHHHHHHHhhc--CCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRS--GTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rs--gl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      ..|+|++.++..|...|.....  .+-...        .++...+||+||+|+|||.+|++||+.+   ...|+.+++++
T Consensus        84 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~--------~~~~~~vLl~GppGtGKT~la~aia~~~---~~~~~~i~~~~  152 (357)
T 3d8b_A           84 EDIAGVEFAKATIKEIVVWPMLRPDIFTGL--------RGPPKGILLFGPPGTGKTLIGKCIASQS---GATFFSISASS  152 (357)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCTTTSCGG--------GSCCSEEEEESSTTSSHHHHHHHHHHHT---TCEEEEEEGGG
T ss_pred             HHhCChHHHHHHHHHHHHHHhhChHhHhhc--------cCCCceEEEECCCCCCHHHHHHHHHHHc---CCeEEEEehHH
Confidence            4589999999999998875211  110000        1334578999999999999999999987   45789999886


Q ss_pred             ccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCC-----------HHHHHHHHHhhhcCeEecC
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQAD-----------YCSQKGFKRAIESGRIVTS  764 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~-----------~~v~~~Ll~~le~G~l~d~  764 (854)
                      +.       ...     . +........+.+..+....+||||||||.+.           ..+++.|+..++.....  
T Consensus       153 l~-------~~~-----~-g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~--  217 (357)
T 3d8b_A          153 LT-------SKW-----V-GEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTS--  217 (357)
T ss_dssp             GC-------CSS-----T-THHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC------
T ss_pred             hh-------ccc-----c-chHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhccccc--
Confidence            65       111     0 0000111245555666778999999998763           35678888888743211  


Q ss_pred             CCceeecCCeEEEEecCC
Q 003038          765 SGDEVSLGDAIVILSCES  782 (854)
Q Consensus       765 ~G~~v~~~~aIiIlTsn~  782 (854)
                           .-.+.+||.|||.
T Consensus       218 -----~~~~v~vI~atn~  230 (357)
T 3d8b_A          218 -----SEDRILVVGATNR  230 (357)
T ss_dssp             -----CCCCEEEEEEESC
T ss_pred             -----CCCCEEEEEecCC
Confidence                 1246788999985

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=98.86  E-value=1.1e-08  Score=109.94  Aligned_cols=135  Identities=10%  Similarity=0.102  Sum_probs=87.5

Q ss_pred             CcccccHHHHHHHHHHHHHhhc--CCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRS--GTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rs--gl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      ..|+|+++++..|...+.....  .+-...        ..+...+||+||+|+|||.+|++||+.+   ...|+.++++.
T Consensus        21 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~--------~~~~~~vll~Gp~GtGKT~la~~la~~~---~~~~~~i~~~~   89 (297)
T 3b9p_A           21 TDIAGQDVAKQALQEMVILPSVRPELFTGL--------RAPAKGLLLFGPPGNGKTLLARAVATEC---SATFLNISAAS   89 (297)
T ss_dssp             GGSCCCHHHHHHHHHHTHHHHHCGGGSCGG--------GCCCSEEEEESSSSSCHHHHHHHHHHHT---TCEEEEEESTT
T ss_pred             HHhCChHHHHHHHHHHHHhhhhCHHHHhcC--------CCCCCeEEEECcCCCCHHHHHHHHHHHh---CCCeEEeeHHH
Confidence            3589999999999888865321  000000        1234578999999999999999999987   35788888876


Q ss_pred             ccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCC-----------CHHHHHHHHHhhhcCeEecC
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQA-----------DYCSQKGFKRAIESGRIVTS  764 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka-----------~~~v~~~Ll~~le~G~l~d~  764 (854)
                      +.       ...     . +.+......+....+....+||||||||.+           ...+++.|+..++.....  
T Consensus        90 l~-------~~~-----~-~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~--  154 (297)
T 3b9p_A           90 LT-------SKY-----V-GDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGN--  154 (297)
T ss_dssp             TS-------SSS-----C-SCHHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHHCC----
T ss_pred             Hh-------hcc-----c-chHHHHHHHHHHHHHHcCCcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhccccc--
Confidence            54       111     0 000011124555556667799999999877           356777888888753221  


Q ss_pred             CCceeecCCeEEEEecCC
Q 003038          765 SGDEVSLGDAIVILSCES  782 (854)
Q Consensus       765 ~G~~v~~~~aIiIlTsn~  782 (854)
                          ..-.+.+||.+||.
T Consensus       155 ----~~~~~v~vi~~tn~  168 (297)
T 3b9p_A          155 ----PDGDRIVVLAATNR  168 (297)
T ss_dssp             --------CEEEEEEESC
T ss_pred             ----CCCCcEEEEeecCC
Confidence                11245788889985

>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=98.86  E-value=5.8e-09  Score=115.73  Aligned_cols=136  Identities=12%  Similarity=0.082  Sum_probs=89.1

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+|+++++..|..+|.....   .+....   ...+|...+||+||+|+|||.+|++||..+   ..+|+.++++++.
T Consensus        51 ~di~G~~~~~~~l~~~v~~~~~---~~~~~~---~~~~~~~~iLL~GppGtGKT~la~ala~~~---~~~~~~v~~~~l~  121 (355)
T 2qp9_X           51 EDVAGLEGAKEALKEAVILPVK---FPHLFK---GNRKPTSGILLYGPPGTGKSYLAKAVATEA---NSTFFSVSSSDLV  121 (355)
T ss_dssp             GGSCCGGGHHHHHHHHTHHHHH---CGGGGC---SSCCCCCCEEEECSTTSCHHHHHHHHHHHH---TCEEEEEEHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHh---CHHHHh---cCCCCCceEEEECCCCCcHHHHHHHHHHHh---CCCEEEeeHHHHh
Confidence            4589999999999988854311   010000   001344578999999999999999999988   4678889887554


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCH-----------HHHHHHHHhhhcCeEecCCC
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADY-----------CSQKGFKRAIESGRIVTSSG  766 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~-----------~v~~~Ll~~le~G~l~d~~G  766 (854)
                             ...     .+ ........+.+..+.+..+||||||||.+.+           .+++.|+..|+.-.      
T Consensus       122 -------~~~-----~g-~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~------  182 (355)
T 2qp9_X          122 -------SKW-----MG-ESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVG------  182 (355)
T ss_dssp             -------SCC---------CHHHHHHHHHHHHHTSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHCC------
T ss_pred             -------hhh-----cc-hHHHHHHHHHHHHHHcCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhccc------
Confidence                   111     00 0001222455666667779999999998863           46788888887311      


Q ss_pred             ceeecCCeEEEEecCCC
Q 003038          767 DEVSLGDAIVILSCESF  783 (854)
Q Consensus       767 ~~v~~~~aIiIlTsn~f  783 (854)
                        -...+.+||.|||.-
T Consensus       183 --~~~~~v~vI~atn~~  197 (355)
T 2qp9_X          183 --NDSQGVLVLGATNIP  197 (355)
T ss_dssp             -----CCEEEEEEESCG
T ss_pred             --ccCCCeEEEeecCCc
Confidence              123568899999853

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=98.85  E-value=5.2e-09  Score=119.70  Aligned_cols=107  Identities=16%  Similarity=0.224  Sum_probs=69.2

Q ss_pred             CcccccHHHH---HHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          618 KKVPWQKDTV---YDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       618 ~~V~GQ~~av---~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      ..|+||++++   ..+...|...                 + ..++||+||+|+|||++|++||+.+   ...|+.++..
T Consensus        26 ~~ivGq~~~~~~~~~L~~~i~~~-----------------~-~~~vLL~GppGtGKTtlAr~ia~~~---~~~f~~l~a~   84 (447)
T 3pvs_A           26 AQYIGQQHLLAAGKPLPRAIEAG-----------------H-LHSMILWGPPGTGKTTLAEVIARYA---NADVERISAV   84 (447)
T ss_dssp             TTCCSCHHHHSTTSHHHHHHHHT-----------------C-CCEEEEECSTTSSHHHHHHHHHHHT---TCEEEEEETT
T ss_pred             HHhCCcHHHHhchHHHHHHHHcC-----------------C-CcEEEEECCCCCcHHHHHHHHHHHh---CCCeEEEEec
Confidence            4589999999   6777777652                 1 2589999999999999999999987   3567777643


Q ss_pred             cccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeE
Q 003038          695 SFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRI  761 (854)
Q Consensus       695 ~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l  761 (854)
                      ...       .. .+.        ...+............|||||||+.++...|+.|++.|++|.+
T Consensus        85 ~~~-------~~-~ir--------~~~~~a~~~~~~~~~~iLfIDEI~~l~~~~q~~LL~~le~~~v  135 (447)
T 3pvs_A           85 TSG-------VK-EIR--------EAIERARQNRNAGRRTILFVDEVHRFNKSQQDAFLPHIEDGTI  135 (447)
T ss_dssp             TCC-------HH-HHH--------HHHHHHHHHHHTTCCEEEEEETTTCC------CCHHHHHTTSC
T ss_pred             cCC-------HH-HHH--------HHHHHHHHhhhcCCCcEEEEeChhhhCHHHHHHHHHHHhcCce
Confidence            211       00 000        0001111112235679999999999999999999999998653

>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=98.85  E-value=1.6e-09  Score=115.19  Aligned_cols=135  Identities=9%  Similarity=0.059  Sum_probs=80.9

Q ss_pred             HhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcc
Q 003038          614 NALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIAL  693 (854)
Q Consensus       614 ~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~  693 (854)
                      ..+...++|+..++..+..........+....        .++...+||+||+|+|||.+|+++|+.+   ..+|+.+++
T Consensus        29 ~~~~~~~i~~~~~~~~i~~~~~~l~~~l~~~~--------~~~~~~vLl~G~~GtGKT~la~~ia~~~---~~~~~~i~~   97 (272)
T 1d2n_A           29 SYIMNGIIKWGDPVTRVLDDGELLVQQTKNSD--------RTPLVSVLLEGPPHSGKTALAAKIAEES---NFPFIKICS   97 (272)
T ss_dssp             TTCTTCCCCCSHHHHHHHHHHHHHHHHHHHCS--------SCSEEEEEEECSTTSSHHHHHHHHHHHH---TCSEEEEEC
T ss_pred             HHHhcCCCCccHHHHHHHHHHHHHHHHHhccC--------CCCCeEEEEECCCCCcHHHHHHHHHHHh---CCCEEEEeC
Confidence            34556789998888777764211111111110        1345689999999999999999999986   356888876


Q ss_pred             ccccCcCCCccccccccccCCCCCC---chHHHHHHHHHcCCCEEEEEecCCCC----------CHHHHHHHHHhhhcCe
Q 003038          694 SSFSSTRADSTEDSRNKRSRDEQSC---SYIERFAEAVSNNPHRVFLIEDVEQA----------DYCSQKGFKRAIESGR  760 (854)
Q Consensus       694 s~~~~~~~~s~e~~~~~rl~~~~g~---g~~e~L~eav~~~p~~ViliDEieka----------~~~v~~~Ll~~le~G~  760 (854)
                      +...               .+....   +....+.+.....+.+||||||||++          ...+++.|...++.- 
T Consensus        98 ~~~~---------------~g~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~~-  161 (272)
T 1d2n_A           98 PDKM---------------IGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKA-  161 (272)
T ss_dssp             GGGC---------------TTCCHHHHHHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCC-
T ss_pred             HHHh---------------cCCchHHHHHHHHHHHHHHHhcCCcEEEEEChhhhhccCCCChhHHHHHHHHHHHHhcCc-
Confidence            5211               100000   11123444445577899999999986          444555555544421 


Q ss_pred             EecCCCceeecCCeEEEEecCC
Q 003038          761 IVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       761 l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                       .      -.-.+.+||.|||.
T Consensus       162 -~------~~~~~~~ii~ttn~  176 (272)
T 1d2n_A          162 -P------PQGRKLLIIGTTSR  176 (272)
T ss_dssp             -C------STTCEEEEEEEESC
T ss_pred             -c------CCCCCEEEEEecCC
Confidence             0      11245678888875

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.85  E-value=6.8e-09  Score=112.10  Aligned_cols=116  Identities=11%  Similarity=0.229  Sum_probs=81.6

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC--CceEEEccccc
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH--NNFVSIALSSF  696 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~--~~~i~id~s~~  696 (854)
                      .++||++++..+...+...                 +.. .++|+||+|+|||++|+.+++.+++..  ..++.++.+..
T Consensus        22 ~~~g~~~~~~~l~~~l~~~-----------------~~~-~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~   83 (323)
T 1sxj_B           22 DIVGNKETIDRLQQIAKDG-----------------NMP-HMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDD   83 (323)
T ss_dssp             GCCSCTHHHHHHHHHHHSC-----------------CCC-CEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSC
T ss_pred             HHHCCHHHHHHHHHHHHcC-----------------CCC-eEEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEecCccc
Confidence            4789999999888886531                 222 399999999999999999999986532  23555554421


Q ss_pred             cCcCCCccccccccccCCCCCCchHHHHHHHHH-------cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          697 SSTRADSTEDSRNKRSRDEQSCSYIERFAEAVS-------NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       697 ~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~-------~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .                   +......+.+.+.       ..++.||+|||+|+++...++.|++.+++.          
T Consensus        84 ~-------------------~~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~----------  134 (323)
T 1sxj_B           84 R-------------------GIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELY----------  134 (323)
T ss_dssp             C-------------------SHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHT----------
T ss_pred             c-------------------ChHHHHHHHHHHHhccccCCCCCceEEEEECcccCCHHHHHHHHHHHhcc----------
Confidence            1                   0011111222222       234789999999999999999999999963          


Q ss_pred             ecCCeEEEEecCC
Q 003038          770 SLGDAIVILSCES  782 (854)
Q Consensus       770 ~~~~aIiIlTsn~  782 (854)
                       -.+++||++||.
T Consensus       135 -~~~~~~il~~~~  146 (323)
T 1sxj_B          135 -SNSTRFAFACNQ  146 (323)
T ss_dssp             -TTTEEEEEEESC
T ss_pred             -CCCceEEEEeCC
Confidence             156788998875

>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=98.84  E-value=1.4e-08  Score=111.70  Aligned_cols=114  Identities=16%  Similarity=0.216  Sum_probs=81.0

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC--ceEEEccccc
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN--NFVSIALSSF  696 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~--~~i~id~s~~  696 (854)
                      .++||++++..|...|...                 + ...++|+||+|+|||++|++||+.+++...  .++.++.+..
T Consensus        26 ~~~g~~~~~~~L~~~i~~g-----------------~-~~~~ll~Gp~G~GKTtla~~la~~l~~~~~~~~~~~~~~~~~   87 (340)
T 1sxj_C           26 EVYGQNEVITTVRKFVDEG-----------------K-LPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDD   87 (340)
T ss_dssp             GCCSCHHHHHHHHHHHHTT-----------------C-CCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSC
T ss_pred             HhcCcHHHHHHHHHHHhcC-----------------C-CceEEEECCCCCCHHHHHHHHHHHHcCCCccceEEEEcCccc
Confidence            4789999999988887642                 1 124899999999999999999999987532  2444443321


Q ss_pred             cCcCCCccccccccccCCCCCCchHH---HHHHHHHc-----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCce
Q 003038          697 SSTRADSTEDSRNKRSRDEQSCSYIE---RFAEAVSN-----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDE  768 (854)
Q Consensus       697 ~~~~~~s~e~~~~~rl~~~~g~g~~e---~L~eav~~-----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~  768 (854)
                      .                     |..+   .+.+....     ..+.|++|||+|+++.+.++.|+++|++.         
T Consensus        88 ~---------------------~~~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~---------  137 (340)
T 1sxj_C           88 R---------------------GIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERY---------  137 (340)
T ss_dssp             C---------------------SHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHT---------
T ss_pred             c---------------------cHHHHHHHHHHHHhhcccCCCCceEEEEeCCCCCCHHHHHHHHHHHhcC---------
Confidence            1                     1111   12222211     23799999999999999999999999974         


Q ss_pred             eecCCeEEEEecCC
Q 003038          769 VSLGDAIVILSCES  782 (854)
Q Consensus       769 v~~~~aIiIlTsn~  782 (854)
                        -.+++||++||.
T Consensus       138 --~~~~~~il~~n~  149 (340)
T 1sxj_C          138 --TKNTRFCVLANY  149 (340)
T ss_dssp             --TTTEEEEEEESC
T ss_pred             --CCCeEEEEEecC
Confidence              146778888875

>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=3.3e-09  Score=114.36  Aligned_cols=117  Identities=21%  Similarity=0.320  Sum_probs=82.1

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC--CceEEEccccc
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH--NNFVSIALSSF  696 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~--~~~i~id~s~~  696 (854)
                      .++||++++..|...+...                 +. .++||+||+|+|||++|+++++.+++..  ..++.++++..
T Consensus        18 ~~~g~~~~~~~l~~~l~~~-----------------~~-~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~   79 (319)
T 2chq_A           18 EVVGQDEVIQRLKGYVERK-----------------NI-PHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDE   79 (319)
T ss_dssp             GSCSCHHHHHHHHTTTTTT-----------------CC-CCEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEETTST
T ss_pred             HHhCCHHHHHHHHHHHhCC-----------------CC-CeEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEeCccc
Confidence            4789999888776665421                 12 2489999999999999999999987653  34677776543


Q ss_pred             cCcCCCccccccccccCCCCCCchHHHHHHHHH-----cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeec
Q 003038          697 SSTRADSTEDSRNKRSRDEQSCSYIERFAEAVS-----NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSL  771 (854)
Q Consensus       697 ~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~-----~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~  771 (854)
                      .       ....           ..+.+.+...     ..++.||+|||+|++++..++.|++++++.           -
T Consensus        80 ~-------~~~~-----------~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~-----------~  130 (319)
T 2chq_A           80 R-------GIDV-----------VRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMY-----------S  130 (319)
T ss_dssp             T-------CTTT-----------SSHHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSS-----------S
T ss_pred             c-------ChHH-----------HHHHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhc-----------C
Confidence            2       0000           0011222221     245789999999999999999999999862           2


Q ss_pred             CCeEEEEecCC
Q 003038          772 GDAIVILSCES  782 (854)
Q Consensus       772 ~~aIiIlTsn~  782 (854)
                      .+++||++||.
T Consensus       131 ~~~~~i~~~~~  141 (319)
T 2chq_A          131 KSCRFILSCNY  141 (319)
T ss_dssp             SSEEEEEEESC
T ss_pred             CCCeEEEEeCC
Confidence            46789998875

>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=98.83  E-value=7.2e-09  Score=113.59  Aligned_cols=129  Identities=15%  Similarity=0.205  Sum_probs=80.6

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC---CCceEEEccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS---HNNFVSIALS  694 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~---~~~~i~id~s  694 (854)
                      ..++||++++..|...+...                 ++ ..++|+||+|+|||++|++||+.+.+.   ...++.++++
T Consensus        37 ~~i~g~~~~~~~l~~~l~~~-----------------~~-~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~   98 (353)
T 1sxj_D           37 DEVTAQDHAVTVLKKTLKSA-----------------NL-PHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNAS   98 (353)
T ss_dssp             TTCCSCCTTHHHHHHHTTCT-----------------TC-CCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSS
T ss_pred             HHhhCCHHHHHHHHHHHhcC-----------------CC-CEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccc
Confidence            45899999988877775431                 11 248999999999999999999998532   3456666655


Q ss_pred             cccCcCCCccccccccccC----CCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceee
Q 003038          695 SFSSTRADSTEDSRNKRSR----DEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVS  770 (854)
Q Consensus       695 ~~~~~~~~s~e~~~~~rl~----~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~  770 (854)
                      ...       ....+...+    .....+............++.||+|||++.+++..++.|+++|+++.          
T Consensus        99 ~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~----------  161 (353)
T 1sxj_D           99 DER-------GISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYS----------  161 (353)
T ss_dssp             SCC-------CHHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTT----------
T ss_pred             ccc-------chHHHHHHHHHHhhhcccccchhhcccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcC----------
Confidence            322       000000000    00000000000000012356899999999999999999999999742          


Q ss_pred             cCCeEEEEecCC
Q 003038          771 LGDAIVILSCES  782 (854)
Q Consensus       771 ~~~aIiIlTsn~  782 (854)
                       .+++||++||.
T Consensus       162 -~~~~~il~~~~  172 (353)
T 1sxj_D          162 -GVTRFCLICNY  172 (353)
T ss_dssp             -TTEEEEEEESC
T ss_pred             -CCceEEEEeCc
Confidence             36778888864

>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=98.82  E-value=1.3e-07  Score=126.96  Aligned_cols=105  Identities=10%  Similarity=0.148  Sum_probs=74.9

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .++--++|+..|++..+-.+                .|.|++|++|+.|+||+.++|..|-.- |  ..+..|.++    
T Consensus      1587 ~LVlF~dai~Hi~RI~Ril~----------------~p~G~~LLvGvgGsGkqSltrLaa~i~-~--~~~fqi~~~---- 1643 (2695)
T 4akg_A         1587 PMVIHESMVDHILRIDRALK----------------QVQGHMMLIGASRTGKTILTRFVAWLN-G--LKIVQPKIH---- 1643 (2695)
T ss_dssp             CCCCCHHHHHHHHHHHHHHH----------------SSSEEEEEECTTTSCHHHHHHHHHHHT-T--CEEECCCCC----
T ss_pred             eeeeHHHHHHHHHHHHHHHc----------------CCCCCEEEECCCCCcHHHHHHHHHHHh-C--CeeEEEEee----
Confidence            57778889988887655543                367899999999999999999776543 2  233333322    


Q ss_pred             cCCCccccccccccCCCCCCchH---HHHHHHH----HcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEec
Q 003038          699 TRADSTEDSRNKRSRDEQSCSYI---ERFAEAV----SNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVT  763 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~g~g~~---e~L~eav----~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d  763 (854)
                                       .+||..   +.|...+    -++...|++|+|-+-.++.+...+-..|.+|.+.+
T Consensus      1644 -----------------~~Y~~~~f~eDLk~l~~~aG~~~~~~vFL~tD~qi~~e~FLE~IN~lL~sGEVP~ 1698 (2695)
T 4akg_A         1644 -----------------RHSNLSDFDMILKKAISDCSLKESRTCLIIDESNILETAFLERMNTLLANADIPD 1698 (2695)
T ss_dssp             -----------------TTCCHHHHHHHHHHHHHHHHHSCCCEEEEEETTTCCSHHHHHHHHHHHHSSSCTT
T ss_pred             -----------------CCCCHHHHHHHHHHHHHHcCCCCCceEEEEeccccccHHHHHHHHHHHccCCCCC
Confidence                             234332   3443333    35778899999999999998888888888887753

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.82  E-value=8.1e-09  Score=101.71  Aligned_cols=119  Identities=14%  Similarity=0.146  Sum_probs=80.3

Q ss_pred             hcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhC-------CCCce
Q 003038          616 LEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFG-------SHNNF  688 (854)
Q Consensus       616 L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg-------~~~~~  688 (854)
                      -...++|+++.+..+...+..                  +....++|+||+|+|||++|+.+++.+..       ....+
T Consensus        20 ~~~~~~g~~~~~~~l~~~l~~------------------~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~   81 (187)
T 2p65_A           20 KLDPVIGRDTEIRRAIQILSR------------------RTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKL   81 (187)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTS------------------SSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEE
T ss_pred             ccchhhcchHHHHHHHHHHhC------------------CCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeE
Confidence            346789999888887776532                  11246799999999999999999998854       23456


Q ss_pred             EEEccccccCcCCCccccccccccCCCCCC-ch----HHHHHHHHHcC-CCEEEEEecCCCCC---------HHHHHHHH
Q 003038          689 VSIALSSFSSTRADSTEDSRNKRSRDEQSC-SY----IERFAEAVSNN-PHRVFLIEDVEQAD---------YCSQKGFK  753 (854)
Q Consensus       689 i~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~----~e~L~eav~~~-p~~ViliDEieka~---------~~v~~~Ll  753 (854)
                      +.++++.+.       ..         ..+ +.    ...+.+.+... ...||+|||++++.         .++++.|+
T Consensus        82 ~~~~~~~~~-------~~---------~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~~l~  145 (187)
T 2p65_A           82 VSLDLSSLI-------AG---------AKYRGDFEERLKSILKEVQDAEGQVVMFIDEIHTVVGAGAVAEGALDAGNILK  145 (187)
T ss_dssp             EEECHHHHH-------HH---------CCSHHHHHHHHHHHHHHHHHTTTSEEEEETTGGGGSSSSSSCTTSCCTHHHHH
T ss_pred             EEEeHHHhh-------cC---------CCchhHHHHHHHHHHHHHHhcCCceEEEEeCHHHhcccccccccchHHHHHHH
Confidence            666654332       00         001 11    11333344333 45799999999987         67889999


Q ss_pred             HhhhcCeEecCCCceeecCCeEEEEecC
Q 003038          754 RAIESGRIVTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       754 ~~le~G~l~d~~G~~v~~~~aIiIlTsn  781 (854)
                      ..++++.             .+||+++|
T Consensus       146 ~~~~~~~-------------~~ii~~~~  160 (187)
T 2p65_A          146 PMLARGE-------------LRCIGATT  160 (187)
T ss_dssp             HHHHTTC-------------SCEEEEEC
T ss_pred             HHHhcCC-------------eeEEEecC
Confidence            9987643             44888876

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.82  E-value=8.2e-09  Score=101.73  Aligned_cols=119  Identities=8%  Similarity=0.144  Sum_probs=80.4

Q ss_pred             hcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhC-------CCCce
Q 003038          616 LEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFG-------SHNNF  688 (854)
Q Consensus       616 L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg-------~~~~~  688 (854)
                      -...++|+++.+..+...+..                  +....++|+||+|+|||.+|+.+++.+..       ....+
T Consensus        20 ~~~~~~g~~~~~~~l~~~l~~------------------~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~   81 (195)
T 1jbk_A           20 KLDPVIGRDEEIRRTIQVLQR------------------RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRV   81 (195)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTS------------------SSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEE
T ss_pred             cccccccchHHHHHHHHHHhc------------------CCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcE
Confidence            346789999988888777543                  11246899999999999999999998854       23556


Q ss_pred             EEEccccccCcCCCccccccccccCCCCCC-chH----HHHHHHH-HcCCCEEEEEecCCCCC--------HHHHHHHHH
Q 003038          689 VSIALSSFSSTRADSTEDSRNKRSRDEQSC-SYI----ERFAEAV-SNNPHRVFLIEDVEQAD--------YCSQKGFKR  754 (854)
Q Consensus       689 i~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~~----e~L~eav-~~~p~~ViliDEieka~--------~~v~~~Ll~  754 (854)
                      +.++++.+..                +..+ |..    ..+.+.+ +.....||+|||+|.+.        ..+++.|+.
T Consensus        82 ~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~l~~  145 (195)
T 1jbk_A           82 LALDMGALVA----------------GAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKP  145 (195)
T ss_dssp             EEECHHHHHT----------------TTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHH
T ss_pred             EEeeHHHHhc----------------cCCccccHHHHHHHHHHHHhhcCCCeEEEEeCHHHHhccCcccchHHHHHHHHH
Confidence            6666654320                0011 111    1233333 34557899999999984        566889988


Q ss_pred             hhhcCeEecCCCceeecCCeEEEEecC
Q 003038          755 AIESGRIVTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       755 ~le~G~l~d~~G~~v~~~~aIiIlTsn  781 (854)
                      .++.+             +.+||+++|
T Consensus       146 ~~~~~-------------~~~~i~~~~  159 (195)
T 1jbk_A          146 ALARG-------------ELHCVGATT  159 (195)
T ss_dssp             HHHTT-------------SCCEEEEEC
T ss_pred             hhccC-------------CeEEEEeCC
Confidence            88764             344788775

>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=98.81  E-value=2.8e-08  Score=109.73  Aligned_cols=136  Identities=15%  Similarity=0.137  Sum_probs=82.9

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++||++++..+...+...+                 ....++|+||+|+|||++|+++|+.+.... ......+..+.
T Consensus        16 ~~~vg~~~~~~~L~~~l~~~~-----------------~~~~~ll~G~~G~GKT~la~~la~~l~~~~-~~~~~~~~~~~   77 (373)
T 1jr3_A           16 ADVVGQEHVLTALANGLSLGR-----------------IHHAYLFSGTRGVGKTSIARLLAKGLNCET-GITATPCGVCD   77 (373)
T ss_dssp             TTSCSCHHHHHHHHHHHHHTC-----------------CCSEEEEESCTTSSHHHHHHHHHHHHSCTT-CSCSSCCSSSH
T ss_pred             hhccCcHHHHHHHHHHHHhCC-----------------CCeEEEEECCCCCCHHHHHHHHHHHhCCCC-CCCCCCCcccH
Confidence            358999999999999886532                 234789999999999999999999985432 11111111100


Q ss_pred             CcCCCccccc-cccccCCC--CCCchHHHHHHHHHcC----CCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceee
Q 003038          698 STRADSTEDS-RNKRSRDE--QSCSYIERFAEAVSNN----PHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVS  770 (854)
Q Consensus       698 ~~~~~s~e~~-~~~rl~~~--~g~g~~e~L~eav~~~----p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~  770 (854)
                      .+.......+ .+..+-..  .+..-...+.+.+...    .+.||+|||+|+++...++.|++.+++.           
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~~-----------  146 (373)
T 1jr3_A           78 NCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEP-----------  146 (373)
T ss_dssp             HHHHHHTSCCSSCEEEETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHHHHHHHHHHHHSC-----------
T ss_pred             HHHHHhccCCCceEEecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhcHHHHHHHHHHHhcC-----------
Confidence            0000000000 00000000  0111122455555543    3689999999999999999999999861           


Q ss_pred             cCCeEEEEecCC
Q 003038          771 LGDAIVILSCES  782 (854)
Q Consensus       771 ~~~aIiIlTsn~  782 (854)
                      -.+++||++|+.
T Consensus       147 ~~~~~~Il~~~~  158 (373)
T 1jr3_A          147 PEHVKFLLATTD  158 (373)
T ss_dssp             CSSEEEEEEESC
T ss_pred             CCceEEEEEeCC
Confidence            246788888864

>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=98.80  E-value=8.6e-10  Score=116.75  Aligned_cols=139  Identities=13%  Similarity=0.085  Sum_probs=89.2

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..++++|+||||+|||++++.+|...          +..++.++...+...+.|+.+.+++.+++.+...  .+.|||||
T Consensus        43 ~~~~vll~G~~GtGKT~la~~la~~~----------~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~a~~~--~~~vl~iD  110 (268)
T 2r62_A           43 IPKGVLLVGPPGTGKTLLAKAVAGEA----------HVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQ--APSIIFID  110 (268)
T ss_dssp             CCSCCCCBCSSCSSHHHHHHHHHHHH----------TCCCCCCCSCTTTTSCSSSCSSSSSTTHHHHHHS--CSCEEEES
T ss_pred             CCceEEEECCCCCcHHHHHHHHHHHh----------CCCEEEechHHHHHhhcchHHHHHHHHHHHHHhc--CCeEEEEe
Confidence            46789999999999999999999875          3356777777777666666667777888888764  57899999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhccc----CCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCC
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG----IGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTI  379 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~----~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i  379 (854)
                      |++.+ .....+........     ....+..||..    ....+.+.+|++|+..+     ..+|++-+.+|| ..+.|
T Consensus       111 Eid~l~~~~~~~~~~~~~~~-----~~~~~~~ll~~l~~~~~~~~~v~vi~ttn~~~-----~ld~~l~r~~Rf~~~i~i  180 (268)
T 2r62_A          111 EIDAIGKSRAAGGVVSGNDE-----REQTLNQLLAEMDGFGSENAPVIVLAATNRPE-----ILDPALMRPGRFDRQVLV  180 (268)
T ss_dssp             CGGGTTC----------CCC-----SCSSTTTTTTTTTCSSCSCSCCEEEECBSCCT-----TSCGGGGSSSSSCCCCBC
T ss_pred             ChhhhcccccccccCCCchh-----HHHHHHHHHHHhhCcccCCCCEEEEEecCCch-----hcCHhHcCCCCCCeEEEe
Confidence            99999 54321100000000     00012234422    11123589999998764     357888886667 45677


Q ss_pred             CCchHHH
Q 003038          380 PAGSLSL  386 (854)
Q Consensus       380 ~~~sl~~  386 (854)
                      +.|+...
T Consensus       181 ~~p~~~~  187 (268)
T 2r62_A          181 DKPDFNG  187 (268)
T ss_dssp             CCCCTTT
T ss_pred             cCcCHHH
Confidence            7666443

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=98.77  E-value=4.7e-08  Score=107.99  Aligned_cols=66  Identities=20%  Similarity=0.173  Sum_probs=50.6

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++||+.++..+...+...+.|.             .+...+||+||+|+|||.+|+++|+.+ +...+++.+++..+.
T Consensus        44 ~~ivG~~~~~~~l~~l~~~~~~~~-------------~~~~~vLl~GppGtGKT~la~~la~~l-~~~~~~~~~~~~~~~  109 (368)
T 3uk6_A           44 QGMVGQLAARRAAGVVLEMIREGK-------------IAGRAVLIAGQPGTGKTAIAMGMAQAL-GPDTPFTAIAGSEIF  109 (368)
T ss_dssp             TTEESCHHHHHHHHHHHHHHHTTC-------------CTTCEEEEEESTTSSHHHHHHHHHHHH-CSSCCEEEEEGGGGS
T ss_pred             hhccChHHHHHHHHHHHHHHHcCC-------------CCCCEEEEECCCCCCHHHHHHHHHHHh-cccCCcccccchhhh
Confidence            468999999888776666655432             223478999999999999999999998 444578888876543

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=98.75  E-value=5.3e-08  Score=99.32  Aligned_cols=134  Identities=19%  Similarity=0.195  Sum_probs=80.4

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++|+++++..|...+...                 +....++|+||+|+|||++++.+++.+.... .++...+..+.
T Consensus        23 ~~~~g~~~~~~~l~~~l~~~-----------------~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~-~~~~~~~~~~~   84 (250)
T 1njg_A           23 ADVVGQEHVLTALANGLSLG-----------------RIHHAYLFSGTRGVGKTSIARLLAKGLNCET-GITATPCGVCD   84 (250)
T ss_dssp             GGCCSCHHHHHHHHHHHHHT-----------------CCCSEEEEECSTTSCHHHHHHHHHHHHHCTT-CSCSSCCSCSH
T ss_pred             HHHhCcHHHHHHHHHHHHcC-----------------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCC-CCCCCCCcccH
Confidence            35899999999998888652                 1224789999999999999999999885322 11111100000


Q ss_pred             CcCCCccccccccccC--CCCCCchHHHHHHHHHc-------CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCce
Q 003038          698 STRADSTEDSRNKRSR--DEQSCSYIERFAEAVSN-------NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDE  768 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~--~~~g~g~~e~L~eav~~-------~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~  768 (854)
                      .....  .......+.  .+......+.+.+.+..       ....||+|||++.+++..++.|++.+++.         
T Consensus        85 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~---------  153 (250)
T 1njg_A           85 NCREI--EQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEP---------  153 (250)
T ss_dssp             HHHHH--HTTCCSSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSC---------
T ss_pred             HHHHH--hccCCcceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcC---------
Confidence            00000  000000000  11111112223333332       23689999999999999999999999852         


Q ss_pred             eecCCeEEEEecCC
Q 003038          769 VSLGDAIVILSCES  782 (854)
Q Consensus       769 v~~~~aIiIlTsn~  782 (854)
                        -.+++||++||.
T Consensus       154 --~~~~~~i~~t~~  165 (250)
T 1njg_A          154 --PEHVKFLLATTD  165 (250)
T ss_dssp             --CTTEEEEEEESC
T ss_pred             --CCceEEEEEeCC
Confidence              246788888864

>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=98.74  E-value=1.4e-08  Score=117.29  Aligned_cols=134  Identities=14%  Similarity=0.126  Sum_probs=89.3

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCC--cccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTM--RRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~--~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      ..|+|++.++..|...|......-.  ..-+       .++...+||+||+|+|||.+|++||..+   ..+|+.+++++
T Consensus       204 ~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g-------~~~~~~vLL~GppGtGKT~lAraia~~~---~~~fv~vn~~~  273 (489)
T 3hu3_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIG-------VKPPRGILLYGPPGTGKTLIARAVANET---GAFFFLINGPE  273 (489)
T ss_dssp             GGCCSCHHHHHHHHHHTHHHHHCHHHHHHHT-------CCCCCEEEEECSTTSSHHHHHHHHHHHC---SSEEEEEEHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHHhhCHHHHHhcC-------CCCCCcEEEECcCCCCHHHHHHHHHHHh---CCCEEEEEchH
Confidence            3589999999999888865311000  0000       1233478999999999999999999987   46899999886


Q ss_pred             ccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCC-----------HHHHHHHHHhhhcCeEecC
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQAD-----------YCSQKGFKRAIESGRIVTS  764 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~-----------~~v~~~Ll~~le~G~l~d~  764 (854)
                      +.       ...     . +...+....+++.......+||||||||.+.           ..+++.|++.|+.-.    
T Consensus       274 l~-------~~~-----~-g~~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~----  336 (489)
T 3hu3_A          274 IM-------SKL-----A-GESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLK----  336 (489)
T ss_dssp             HH-------TSC-----T-THHHHHHHHHHHHHHHTCSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSC----
T ss_pred             hh-------hhh-----c-chhHHHHHHHHHHHHhcCCcEEEecchhhhccccccccchHHHHHHHHHHHHhhccc----
Confidence            65       111     0 0000222234444455566999999996553           378999999998421    


Q ss_pred             CCceeecCCeEEEEecCCC
Q 003038          765 SGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       765 ~G~~v~~~~aIiIlTsn~f  783 (854)
                           .-.+.+||.|||.-
T Consensus       337 -----~~~~v~vIaaTn~~  350 (489)
T 3hu3_A          337 -----QRAHVIVMAATNRP  350 (489)
T ss_dssp             -----TTSCEEEEEEESCG
T ss_pred             -----cCCceEEEEecCCc
Confidence                 12468899999864

>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=98.74  E-value=5.4e-08  Score=111.83  Aligned_cols=134  Identities=12%  Similarity=0.138  Sum_probs=87.3

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +.|+|+++++..|...+...+.-....+ -     ..++...+||+||+|+|||.+|++||..+   ..+|+.++++++.
T Consensus        16 ~di~G~~~~~~~l~e~v~~l~~~~~~~~-~-----g~~~p~gvLL~GppGtGKT~Laraia~~~---~~~f~~is~~~~~   86 (476)
T 2ce7_A           16 KDVGGAEEAIEELKEVVEFLKDPSKFNR-I-----GARMPKGILLVGPPGTGKTLLARAVAGEA---NVPFFHISGSDFV   86 (476)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCTHHHHT-T-----TCCCCSEEEEECCTTSSHHHHHHHHHHHH---TCCEEEEEGGGTT
T ss_pred             HHhCCcHHHHHHHHHHHHHhhChHHHhh-c-----CCCCCCeEEEECCCCCCHHHHHHHHHHHc---CCCeeeCCHHHHH
Confidence            3589999999999888766432100000 0     00122248899999999999999999987   3578999888776


Q ss_pred             CcCCCccccccccccCCCCCCch--HHHHHHHHHcCCCEEEEEecCCCCCH--------------HHHHHHHHhhhcCeE
Q 003038          698 STRADSTEDSRNKRSRDEQSCSY--IERFAEAVSNNPHRVFLIEDVEQADY--------------CSQKGFKRAIESGRI  761 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~--~e~L~eav~~~p~~ViliDEieka~~--------------~v~~~Ll~~le~G~l  761 (854)
                             +.+        .|.|-  ...+.+..+.+..+||||||||.+.+              .+++.|+..|+.  +
T Consensus        87 -------~~~--------~g~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~--~  149 (476)
T 2ce7_A           87 -------ELF--------VGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDG--F  149 (476)
T ss_dssp             -------TCC--------TTHHHHHHHHHHHHHHHTCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHH--S
T ss_pred             -------HHH--------hcccHHHHHHHHHHHHhcCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhc--c
Confidence                   211        01111  11344555556669999999998743              467788888873  1


Q ss_pred             ecCCCceeecCCeEEEEecCCCC
Q 003038          762 VTSSGDEVSLGDAIVILSCESFS  784 (854)
Q Consensus       762 ~d~~G~~v~~~~aIiIlTsn~f~  784 (854)
                      .       .-.+.+||.+||.-+
T Consensus       150 ~-------~~~~viVIaaTn~~~  165 (476)
T 2ce7_A          150 D-------SKEGIIVMAATNRPD  165 (476)
T ss_dssp             C-------GGGTEEEEEEESCGG
T ss_pred             C-------CCCCEEEEEecCChh
Confidence            0       124678999998643

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=98.74  E-value=4.3e-08  Score=103.16  Aligned_cols=137  Identities=16%  Similarity=0.119  Sum_probs=84.9

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+|+++++..|...+...+..-.... .     ..++...++|+||+|+|||++|++||..+   ..+++.++++.+.
T Consensus        12 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~-~-----~~~~~~~vll~G~~GtGKT~la~~la~~~---~~~~~~i~~~~~~   82 (257)
T 1lv7_A           12 ADVAGCDEAKEEVAELVEYLREPSRFQK-L-----GGKIPKGVLMVGPPGTGKTLLAKAIAGEA---KVPFFTISGSDFV   82 (257)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----------CCCCEEEEECCTTSCHHHHHHHHHHHH---TCCEEEECSCSST
T ss_pred             HHhcCcHHHHHHHHHHHHHHhCHHHHHH-c-----CCCCCCeEEEECcCCCCHHHHHHHHHHHc---CCCEEEEeHHHHH
Confidence            4579999999888877654321000000 0     00122358999999999999999999987   3468889887665


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCH--------------HHHHHHHHhhhcCeEec
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADY--------------CSQKGFKRAIESGRIVT  763 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~--------------~v~~~Ll~~le~G~l~d  763 (854)
                             +..     . +.+......+.+..+....+|+||||||.+.+              ..++.++..++.-.   
T Consensus        83 -------~~~-----~-~~~~~~~~~~~~~a~~~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---  146 (257)
T 1lv7_A           83 -------EMF-----V-GVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFE---  146 (257)
T ss_dssp             -------TSC-----C-CCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCC---
T ss_pred             -------HHh-----h-hhhHHHHHHHHHHHHHcCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCcc---
Confidence                   111     0 01111122344555556678999999976532              45566777776311   


Q ss_pred             CCCceeecCCeEEEEecCCCCC
Q 003038          764 SSGDEVSLGDAIVILSCESFSS  785 (854)
Q Consensus       764 ~~G~~v~~~~aIiIlTsn~f~~  785 (854)
                            .-.+.+||.|||..+.
T Consensus       147 ------~~~~~~vI~~tn~~~~  162 (257)
T 1lv7_A          147 ------GNEGIIVIAATNRPDV  162 (257)
T ss_dssp             ------SSSCEEEEEEESCTTT
T ss_pred             ------cCCCEEEEEeeCCchh
Confidence                  1246789999986543

>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=98.74  E-value=4.8e-09  Score=110.98  Aligned_cols=130  Identities=15%  Similarity=0.158  Sum_probs=80.3

Q ss_pred             CcccccHHHHHHHHHHHHHhhc-------CCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRS-------GTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVS  690 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rs-------gl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~  690 (854)
                      ..|+|+++++..|...+...+.       |.             ++...+||+||+|+|||.+|++||+.+.   .+|+.
T Consensus        11 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~-------------~~~~~vll~G~~GtGKT~la~~la~~~~---~~~~~   74 (268)
T 2r62_A           11 KDMAGNEEAKEEVVEIVDFLKYPERYANLGA-------------KIPKGVLLVGPPGTGKTLLAKAVAGEAH---VPFFS   74 (268)
T ss_dssp             TTSSSCTTTHHHHHHHHHHHHCHHHHHHHSC-------------CCCSCCCCBCSSCSSHHHHHHHHHHHHT---CCCCC
T ss_pred             HHhCCcHHHHHHHHHHHHHHHChHHHHHCCC-------------CCCceEEEECCCCCcHHHHHHHHHHHhC---CCEEE
Confidence            4578888888888777654221       11             1122478999999999999999999873   46777


Q ss_pred             EccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHH---------------HHHHHHHh
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYC---------------SQKGFKRA  755 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~---------------v~~~Ll~~  755 (854)
                      ++++.+..       ..     .+ .+......+.+.......+||||||||.+...               .++.|+..
T Consensus        75 v~~~~~~~-------~~-----~~-~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~  141 (268)
T 2r62_A           75 MGGSSFIE-------MF-----VG-LGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAE  141 (268)
T ss_dssp             CCSCTTTT-------SC-----SS-SCSSSSSTTHHHHHHSCSCEEEESCGGGTTC----------CCCSCSSTTTTTTT
T ss_pred             echHHHHH-------hh-----cc-hHHHHHHHHHHHHHhcCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHH
Confidence            87776551       11     00 00000011334444556689999999998653               45556666


Q ss_pred             hhcCeEecCCCceeecCCeEEEEecCCCC
Q 003038          756 IESGRIVTSSGDEVSLGDAIVILSCESFS  784 (854)
Q Consensus       756 le~G~l~d~~G~~v~~~~aIiIlTsn~f~  784 (854)
                      ++.-        .-.-.+.+||.|||.-+
T Consensus       142 l~~~--------~~~~~~v~vi~ttn~~~  162 (268)
T 2r62_A          142 MDGF--------GSENAPVIVLAATNRPE  162 (268)
T ss_dssp             TTCS--------SCSCSCCEEEECBSCCT
T ss_pred             hhCc--------ccCCCCEEEEEecCCch
Confidence            6531        01224578899998644

>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=98.73  E-value=2e-08  Score=110.11  Aligned_cols=50  Identities=12%  Similarity=0.112  Sum_probs=39.4

Q ss_pred             CEEEEEecCCCCCHHHHHHHHHhhhcCeEec-CCCceee-cCCeEEEEecCC
Q 003038          733 HRVFLIEDVEQADYCSQKGFKRAIESGRIVT-SSGDEVS-LGDAIVILSCES  782 (854)
Q Consensus       733 ~~ViliDEieka~~~v~~~Ll~~le~G~l~d-~~G~~v~-~~~aIiIlTsn~  782 (854)
                      ..|||||||+++++.+|+.|+++|++|...- ..|.... -.+.+||.|+|.
T Consensus       145 ~~vl~iDEi~~l~~~~~~~Ll~~le~~~~~~~~~g~~~~~~~~~~li~~~n~  196 (350)
T 1g8p_A          145 RGYLYIDECNLLEDHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNP  196 (350)
T ss_dssp             TEEEEETTGGGSCHHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECS
T ss_pred             CCEEEEeChhhCCHHHHHHHHHHHhcCceEEEecceEEeeCCceEEEEEeCC
Confidence            6899999999999999999999999986432 2333333 347889999984

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=98.72  E-value=1.4e-08  Score=113.38  Aligned_cols=140  Identities=16%  Similarity=0.205  Sum_probs=97.1

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++|+..++..+...+.+...                ....+++.|++|+||+.+|+.+.+.-. ....|+.+||+.+.
T Consensus       129 ~~~ig~s~~~~~~~~~~~~~a~----------------~~~~vli~GesGtGKe~lAr~ih~~s~-r~~~fv~vnc~~~~  191 (368)
T 3dzd_A          129 IEFVGEHPKILEIKRLIPKIAK----------------SKAPVLITGESGTGKEIVARLIHRYSG-RKGAFVDLNCASIP  191 (368)
T ss_dssp             CCCCCCSHHHHHHHHHHHHHHT----------------SCSCEEEECCTTSSHHHHHHHHHHHHC-CCSCEEEEESSSSC
T ss_pred             ccccccchHHHHHHhhhhhhhc----------------cchhheEEeCCCchHHHHHHHHHHhcc-ccCCcEEEEcccCC
Confidence            3578998888888777766422                234688999999999999999998774 34459999999876


Q ss_pred             CcCCCccccccccccCC-CCC-C-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCe
Q 003038          698 STRADSTEDSRNKRSRD-EQS-C-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDA  774 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~-~~g-~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~a  774 (854)
                      .       ....+.+.+ ..| + |....-...+.......+|||||+.+++.+|..|+++|++|.++.-.|...-.-++
T Consensus       192 ~-------~~~~~~lfg~~~g~~tga~~~~~g~~~~a~~gtlfldei~~l~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~  264 (368)
T 3dzd_A          192 Q-------ELAESELFGHEKGAFTGALTRKKGKLELADQGTLFLDEVGELDQRVQAKLLRVLETGSFTRLGGNQKIEVDI  264 (368)
T ss_dssp             T-------TTHHHHHHEECSCSSSSCCCCEECHHHHTTTSEEEEETGGGSCHHHHHHHHHHHHHSEECCBTCCCBEECCC
T ss_pred             h-------HHHHHHhcCccccccCCcccccCChHhhcCCCeEEecChhhCCHHHHHHHHHHHHhCCcccCCCCcceeeee
Confidence            2       221122211 000 0 10000001122334578999999999999999999999999999766655556688


Q ss_pred             EEEEecC
Q 003038          775 IVILSCE  781 (854)
Q Consensus       775 IiIlTsn  781 (854)
                      .||.+||
T Consensus       265 rii~at~  271 (368)
T 3dzd_A          265 RVISATN  271 (368)
T ss_dssp             EEEEEES
T ss_pred             EEEEecC
Confidence            8999887

>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=98.70  E-value=1.7e-08  Score=115.71  Aligned_cols=76  Identities=12%  Similarity=0.049  Sum_probs=64.9

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHH---HhhhCCCeEEE
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLV---RSCLGRGIVLN  303 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~---~~~~~~~~ILf  303 (854)
                      .++++|+||||||||++++++|..+..        ++.|+.++.+.+...+.|+.+. +.+++..+   +..  .|+|||
T Consensus        63 ~~~iLl~GppGtGKT~la~ala~~l~~--------~~~~~~~~~~~~~~~~~~~~~~-~~~~f~~a~~~~~~--~~~il~  131 (456)
T 2c9o_A           63 GRAVLLAGPPGTGKTALALAIAQELGS--------KVPFCPMVGSEVYSTEIKKTEV-LMENFRRAIGLRIK--ETKEVY  131 (456)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHCT--------TSCEEEEEGGGGCCSSSCHHHH-HHHHHHHTEEEEEE--EEEEEE
T ss_pred             CCeEEEECCCcCCHHHHHHHHHHHhCC--------CceEEEEeHHHHHHHhhhhhHH-HHHHHHHHHhhhhc--CCcEEE
Confidence            368999999999999999999988522        3789999999999889999997 99999887   443  689999


Q ss_pred             eCccccc-ccc
Q 003038          304 LGDLEWA-EFR  313 (854)
Q Consensus       304 idel~~l-~~~  313 (854)
                      |||++.+ ..+
T Consensus       132 iDEid~l~~~r  142 (456)
T 2c9o_A          132 EGEVTELTPCE  142 (456)
T ss_dssp             EEEEEEEEEC-
T ss_pred             Eechhhccccc
Confidence            9999999 544

>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=98.70  E-value=1.3e-07  Score=100.25  Aligned_cols=115  Identities=6%  Similarity=0.055  Sum_probs=76.7

Q ss_pred             ccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc-chHHHHHHHHHHHHHHHhhhCCCeEE
Q 003038          224 SKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM-NRVEVEQRVEEIKNLVRSCLGRGIVL  302 (854)
Q Consensus       224 r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~-~rge~E~rl~~l~~~~~~~~~~~~IL  302 (854)
                      ++..++++|+||||+|||++|+.+|...          +..++.++......+ ..++....++.+++.+...  .+.||
T Consensus        61 ~~~~~~vLl~G~~GtGKT~la~~ia~~~----------~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~--~~~vl  128 (272)
T 1d2n_A           61 RTPLVSVLLEGPPHSGKTALAAKIAEES----------NFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKS--QLSCV  128 (272)
T ss_dssp             SCSEEEEEEECSTTSSHHHHHHHHHHHH----------TCSEEEEECGGGCTTCCHHHHHHHHHHHHHHHHTS--SEEEE
T ss_pred             CCCCeEEEEECCCCCcHHHHHHHHHHHh----------CCCEEEEeCHHHhcCCchHHHHHHHHHHHHHHHhc--CCcEE
Confidence            4567789999999999999999999873          456777766544333 4566677888888888754  58899


Q ss_pred             EeCccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecCHHHH
Q 003038          303 NLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIATFQSY  358 (854)
Q Consensus       303 fidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT~~ey  358 (854)
                      ||||++.+ +........ .      ......+..++..  ..+ ..+.+|++|+..+.
T Consensus       129 ~iDEid~l~~~~~~~~~~-~------~~~l~~L~~~~~~~~~~~-~~~~ii~ttn~~~~  179 (272)
T 1d2n_A          129 VVDDIERLLDYVPIGPRF-S------NLVLQALLVLLKKAPPQG-RKLLIIGTTSRKDV  179 (272)
T ss_dssp             EECCHHHHTTCBTTTTBC-C------HHHHHHHHHHTTCCCSTT-CEEEEEEEESCHHH
T ss_pred             EEEChhhhhccCCCChhH-H------HHHHHHHHHHhcCccCCC-CCEEEEEecCChhh
Confidence            99999999 654321000 0      0112223334432  112 26889999987664

>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=98.69  E-value=2.9e-08  Score=113.80  Aligned_cols=98  Identities=15%  Similarity=0.104  Sum_probs=72.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +.|+||++++..+...+...+.|..             |...+||+||||+|||.+|++||+.+ +....|+.++++++.
T Consensus        37 ~~iiG~~~~~~~l~~~~~~~~~~~~-------------~~~~iLl~GppGtGKT~la~ala~~l-~~~~~~~~~~~~~~~  102 (456)
T 2c9o_A           37 SGLVGQENAREACGVIVELIKSKKM-------------AGRAVLLAGPPGTGKTALALAIAQEL-GSKVPFCPMVGSEVY  102 (456)
T ss_dssp             TTEESCHHHHHHHHHHHHHHHTTCC-------------TTCEEEEECCTTSSHHHHHHHHHHHH-CTTSCEEEEEGGGGC
T ss_pred             hhccCHHHHHHHHHHHHHHHHhCCC-------------CCCeEEEECCCcCCHHHHHHHHHHHh-CCCceEEEEeHHHHH
Confidence            6789999999998888877766543             23468999999999999999999997 545789999988665


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHH------cCCCEEEEEecCCCCCH
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVS------NNPHRVFLIEDVEQADY  746 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~------~~p~~ViliDEieka~~  746 (854)
                             .+.          .|-.+.+.+.++      ....+||||||||.+-+
T Consensus       103 -------~~~----------~~~~~~~~~~f~~a~~~~~~~~~il~iDEid~l~~  140 (456)
T 2c9o_A          103 -------STE----------IKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTP  140 (456)
T ss_dssp             -------CSS----------SCHHHHHHHHHHHTEEEEEEEEEEEEEEEEEEEEE
T ss_pred             -------HHh----------hhhhHHHHHHHHHHHhhhhcCCcEEEEechhhccc
Confidence                   111          133333444443      34568999999997753

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.69  E-value=2.3e-08  Score=110.47  Aligned_cols=157  Identities=15%  Similarity=0.183  Sum_probs=95.8

Q ss_pred             cHHHHHHHHHHhhc----cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc----------
Q 003038          211 RNEDVMYVIENLMS----KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM----------  276 (854)
Q Consensus       211 r~~ei~~v~~~L~r----~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~----------  276 (854)
                      |++++.++...|.+    ...++++|+||||+|||++++.++..+.... +..-.+..++.++.......          
T Consensus        24 r~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~-~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~  102 (387)
T 2v1u_A           24 REAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARA-SSLGVLVKPIYVNARHRETPYRVASAIAEA  102 (387)
T ss_dssp             CHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHH-HHHTCCEEEEEEETTTSCSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHH-hccCCCeEEEEEECCcCCCHHHHHHHHHHH
Confidence            99999999998844    4667899999999999999999998874410 00001467777776543211          


Q ss_pred             ------chHH-HHHHHHHHHHHHHhhhCCCeEEEeCccccc-ccc-ccccccccccchhhhHHHHHHHhhcccCCCCceE
Q 003038          277 ------NRVE-VEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFR-ASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARF  347 (854)
Q Consensus       277 ------~rge-~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~-~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l  347 (854)
                            ..|. ..+-+..+...+... ++++||||||+|++ ... ..             .....+-+.+........+
T Consensus       103 l~~~~~~~~~~~~~~~~~l~~~l~~~-~~~~vlilDEi~~l~~~~~~~-------------~~l~~l~~~~~~~~~~~~~  168 (387)
T 2v1u_A          103 VGVRVPFTGLSVGEVYERLVKRLSRL-RGIYIIVLDEIDFLPKRPGGQ-------------DLLYRITRINQELGDRVWV  168 (387)
T ss_dssp             HSCCCCSSCCCHHHHHHHHHHHHTTS-CSEEEEEEETTTHHHHSTTHH-------------HHHHHHHHGGGCC-----C
T ss_pred             hCCCCCCCCCCHHHHHHHHHHHHhcc-CCeEEEEEccHhhhcccCCCC-------------hHHHhHhhchhhcCCCceE
Confidence                  0111 223344455555544 56899999999999 542 10             1222222222211102369


Q ss_pred             EEEEecCHHHHHHhhccCCchhhhhcc--CCCCCCCchHHH
Q 003038          348 WLMGIATFQSYMRCKSGHPSLETLWSL--HPLTIPAGSLSL  386 (854)
Q Consensus       348 ~lIgatT~~ey~k~~~~~pale~~~~~--~~v~i~~~sl~~  386 (854)
                      .+|++|+...+..  ..++.+.+  +|  +.+.++..+...
T Consensus       169 ~~I~~t~~~~~~~--~l~~~l~~--r~~~~~i~l~~l~~~~  205 (387)
T 2v1u_A          169 SLVGITNSLGFVE--NLEPRVKS--SLGEVELVFPPYTAPQ  205 (387)
T ss_dssp             EEEEECSCSTTSS--SSCHHHHT--TTTSEECCBCCCCHHH
T ss_pred             EEEEEECCCchHh--hhCHHHHh--cCCCeEEeeCCCCHHH
Confidence            9999998765433  24777777  66  567887766443

>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=98.69  E-value=3.1e-08  Score=108.92  Aligned_cols=136  Identities=13%  Similarity=0.196  Sum_probs=76.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++||++++..+...+..      .          .+... ++|+||+|+|||+++++||+.+++....-+.++...+.
T Consensus        14 ~~~vg~~~~~~~l~~~~~~------~----------~~~~~-~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~~~~   76 (354)
T 1sxj_E           14 NALSHNEELTNFLKSLSDQ------P----------RDLPH-LLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFV   76 (354)
T ss_dssp             GGCCSCHHHHHHHHTTTTC------T----------TCCCC-EEEECSTTSSHHHHHHTHHHHHSCTTCCC---------
T ss_pred             HHhcCCHHHHHHHHHHHhh------C----------CCCCe-EEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecceeec
Confidence            3478999888776665411      1          02223 89999999999999999999887654433333322111


Q ss_pred             CcC-------CCccccccccccCC-CCCC-c--hHHHHHHHH-H-------------cCCCEEEEEecCCCCCHHHHHHH
Q 003038          698 STR-------ADSTEDSRNKRSRD-EQSC-S--YIERFAEAV-S-------------NNPHRVFLIEDVEQADYCSQKGF  752 (854)
Q Consensus       698 ~~~-------~~s~e~~~~~rl~~-~~g~-g--~~e~L~eav-~-------------~~p~~ViliDEieka~~~v~~~L  752 (854)
                      ...       ......+ + .+.. ..+. .  ....+.+.+ .             ..++.||+|||++.+++..++.|
T Consensus        77 ~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ls~l~~~~~vlilDE~~~L~~~~~~~L  154 (354)
T 1sxj_E           77 TASNRKLELNVVSSPYH-L-EITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAAL  154 (354)
T ss_dssp             ---------CCEECSSE-E-EECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSCHHHHHHH
T ss_pred             ccccccceeeeecccce-E-EecHhhcCCcchHHHHHHHHHHHHhccccccccccccCCCCeEEEEeCccccCHHHHHHH
Confidence            000       0000000 0 0000 0010 1  011222222 1             22567999999999999999999


Q ss_pred             HHhhhcCeEecCCCceeecCCeEEEEecCCC
Q 003038          753 KRAIESGRIVTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       753 l~~le~G~l~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                      ++.|++.           -.+++||++|+..
T Consensus       155 ~~~le~~-----------~~~~~~Il~t~~~  174 (354)
T 1sxj_E          155 RRTMEKY-----------SKNIRLIMVCDSM  174 (354)
T ss_dssp             HHHHHHS-----------TTTEEEEEEESCS
T ss_pred             HHHHHhh-----------cCCCEEEEEeCCH
Confidence            9999962           1457889988753

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=98.66  E-value=5.5e-08  Score=112.37  Aligned_cols=140  Identities=14%  Similarity=0.109  Sum_probs=92.2

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGD  306 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfide  306 (854)
                      .++++|+||||+|||++++++|..+          +..++.++...+...+.|+.+.++..+++.++..  .++|+||||
T Consensus        64 p~GvLL~GppGtGKTtLaraIa~~~----------~~~~i~i~g~~~~~~~~g~~~~~v~~lfq~a~~~--~p~il~IDE  131 (499)
T 2dhr_A           64 PKGVLLVGPPGVGKTHLARAVAGEA----------RVPFITASGSDFVEMFVGVGAARVRDLFETAKRH--APCIVFIDE  131 (499)
T ss_dssp             CSEEEEECSSSSSHHHHHHHHHHHT----------TCCEEEEEGGGGTSSCTTHHHHHHHHHTTTSSSS--SSCEEEEEC
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHh----------CCCEEEEehhHHHHhhhhhHHHHHHHHHHHHHhc--CCCEEEEeh
Confidence            3568999999999999999999764          3568899998888888999999999998887653  578999999


Q ss_pred             cccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCchH
Q 003038          307 LEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGSL  384 (854)
Q Consensus       307 l~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~sl  384 (854)
                      |+.+ ........+ .  ..-.++....+-..+.....+..+.+|++|+..+.     .||+|-|..|| ..|.|+.|++
T Consensus       132 Id~l~~~r~~~~~~-~--~~e~~~~l~~LL~~Ldg~~~~~~viviAatn~p~~-----LD~aLlr~gRfdr~i~i~~Pd~  203 (499)
T 2dhr_A          132 IDAVGRKRGSGVGG-G--NDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDI-----LDPALLRPGRFDRQIAIDAPDV  203 (499)
T ss_dssp             GGGTCCCSSSSTTT-S--SHHHHHHHHHHHHHGGGCCSSCCCEEEECCSCGGG-----SCTTTSSTTSSCCEEECCCCCH
T ss_pred             HHHHHHhhccCcCC-C--cHHHHHHHHHHHHHhcccccCccEEEEEecCChhh-----cCcccccccccceEEecCCCCH
Confidence            9999 433211000 0  00111233333333321111124778888876542     78999874445 2456666665


Q ss_pred             HH
Q 003038          385 SL  386 (854)
Q Consensus       385 ~~  386 (854)
                      ..
T Consensus       204 ~~  205 (499)
T 2dhr_A          204 KG  205 (499)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.65  E-value=5.3e-08  Score=106.19  Aligned_cols=102  Identities=11%  Similarity=0.056  Sum_probs=72.4

Q ss_pred             CcHHHHHHHHHHhhc----cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc---------
Q 003038          210 IRNEDVMYVIENLMS----KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM---------  276 (854)
Q Consensus       210 vr~~ei~~v~~~L~r----~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~---------  276 (854)
                      .||+|+.++...|..    .+.+|++|+||||||||++|+.++..+....--..+.+..++.++...+...         
T Consensus        24 ~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I~~  103 (318)
T 3te6_A           24 SQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWF  103 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHHHH
Confidence            399999999877655    3777899999999999999999999986532112233567888886544321         


Q ss_pred             -------chHHHHHHHHHHHHHHHhhhCCCeEEEeCcccccc
Q 003038          277 -------NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWAE  311 (854)
Q Consensus       277 -------~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l~  311 (854)
                             ..|+..+.|..+++.+....+.++|+||||+|.+.
T Consensus       104 ~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~  145 (318)
T 3te6_A          104 AISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLL  145 (318)
T ss_dssp             HHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSC
T ss_pred             HhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhh
Confidence                   12445566777777652111468999999999993

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=98.64  E-value=3.7e-08  Score=116.86  Aligned_cols=52  Identities=12%  Similarity=0.188  Sum_probs=39.8

Q ss_pred             CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCC----------ceeecCCeEEEEecCC
Q 003038          731 NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSG----------DEVSLGDAIVILSCES  782 (854)
Q Consensus       731 ~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G----------~~v~~~~aIiIlTsn~  782 (854)
                      ....|+|||||+++++.+|+.|+++|++|.++-..+          ..---.+.+||+++|.
T Consensus       200 a~~gvL~LDEi~~l~~~~q~~Ll~~Le~~~~~~~g~~~~~~~~~l~~~~~p~~~~vI~atn~  261 (604)
T 3k1j_A          200 AHKGVLFIDEIATLSLKMQQSLLTAMQEKKFPITGQSEMSSGAMVRTEPVPCDFVLVAAGNL  261 (604)
T ss_dssp             TTTSEEEETTGGGSCHHHHHHHHHHHHHSEECCBCSCTTSGGGGCBCSCEECCCEEEEEECH
T ss_pred             cCCCEEEEechhhCCHHHHHHHHHHHHcCcEEecccccccccccCCCCccceeEEEEEecCH
Confidence            345699999999999999999999999999875321          0111236789999883

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=98.64  E-value=4.8e-08  Score=111.67  Aligned_cols=127  Identities=9%  Similarity=0.050  Sum_probs=81.2

Q ss_pred             HHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhh
Q 003038          216 MYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSC  295 (854)
Q Consensus       216 ~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~  295 (854)
                      ..+...+...+-++++|+||||||||++++.++..+          +..++.++....   ..+++.+.+......... 
T Consensus        39 ~~L~~~i~~~~~~~vLL~GppGtGKTtlAr~ia~~~----------~~~f~~l~a~~~---~~~~ir~~~~~a~~~~~~-  104 (447)
T 3pvs_A           39 KPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIARYA----------NADVERISAVTS---GVKEIREAIERARQNRNA-  104 (447)
T ss_dssp             SHHHHHHHHTCCCEEEEECSTTSSHHHHHHHHHHHT----------TCEEEEEETTTC---CHHHHHHHHHHHHHHHHT-
T ss_pred             HHHHHHHHcCCCcEEEEECCCCCcHHHHHHHHHHHh----------CCCeEEEEeccC---CHHHHHHHHHHHHHhhhc-
Confidence            455555665666789999999999999999999874          456777764322   222333333322222221 


Q ss_pred             hCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-CCCCceEEEEEecCHHHHHHhhccCCchhhhhc
Q 003038          296 LGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGENARFWLMGIATFQSYMRCKSGHPSLETLWS  373 (854)
Q Consensus       296 ~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~  373 (854)
                       +.+.||||||||.+ .....                    .||.. ..+  .+++||+||...+   +..+++|-+  |
T Consensus       105 -~~~~iLfIDEI~~l~~~~q~--------------------~LL~~le~~--~v~lI~att~n~~---~~l~~aL~s--R  156 (447)
T 3pvs_A          105 -GRRTILFVDEVHRFNKSQQD--------------------AFLPHIEDG--TITFIGATTENPS---FELNSALLS--R  156 (447)
T ss_dssp             -TCCEEEEEETTTCC--------------------------CCHHHHHTT--SCEEEEEESSCGG---GSSCHHHHT--T
T ss_pred             -CCCcEEEEeChhhhCHHHHH--------------------HHHHHHhcC--ceEEEecCCCCcc---cccCHHHhC--c
Confidence             46899999999999 54221                    23322 223  5999999998765   356788888  6


Q ss_pred             cCCCCCCCchH
Q 003038          374 LHPLTIPAGSL  384 (854)
Q Consensus       374 ~~~v~i~~~sl  384 (854)
                      ++.+.++.++.
T Consensus       157 ~~v~~l~~l~~  167 (447)
T 3pvs_A          157 ARVYLLKSLST  167 (447)
T ss_dssp             EEEEECCCCCH
T ss_pred             eeEEeeCCcCH
Confidence            76666666553

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=98.64  E-value=1.6e-07  Score=103.92  Aligned_cols=144  Identities=12%  Similarity=0.032  Sum_probs=93.0

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC-CCceEEEccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS-HNNFVSIALSSF  696 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-~~~~i~id~s~~  696 (854)
                      ..++|+++.+..|...+.....|-.            .....++|+||+|+|||++++++++.+... ...++.++++..
T Consensus        17 ~~l~gr~~~~~~l~~~l~~~~~~~~------------~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~~~~   84 (389)
T 1fnn_A           17 KRLPHREQQLQQLDILLGNWLRNPG------------HHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIY   84 (389)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTT------------SSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTC
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCC------------CCCCeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeCccC
Confidence            5689999999999999887654310            011278999999999999999999998765 467888887654


Q ss_pred             cCcCCCccccccccccC----CCCCCchH---HHHHHHHHc-CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCce
Q 003038          697 SSTRADSTEDSRNKRSR----DEQSCSYI---ERFAEAVSN-NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDE  768 (854)
Q Consensus       697 ~~~~~~s~e~~~~~rl~----~~~g~g~~---e~L~eav~~-~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~  768 (854)
                      .+...   --..+...+    +..+....   +.+.+.+.. ....||+|||++.+++.+++.|++.+++..-       
T Consensus        85 ~~~~~---~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~-------  154 (389)
T 1fnn_A           85 RNFTA---IIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADK-------  154 (389)
T ss_dssp             CSHHH---HHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHH-------
T ss_pred             CCHHH---HHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCC-------
Confidence            41000   000000001    11121222   244555544 3468999999999999999999999975210       


Q ss_pred             eecCCeEEEEecCCC
Q 003038          769 VSLGDAIVILSCESF  783 (854)
Q Consensus       769 v~~~~aIiIlTsn~f  783 (854)
                      ..-.+..||++||..
T Consensus       155 ~~~~~~~iI~~~~~~  169 (389)
T 1fnn_A          155 LGAFRIALVIVGHND  169 (389)
T ss_dssp             HSSCCEEEEEEESST
T ss_pred             CCcCCEEEEEEECCc
Confidence            001356788888743

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=98.63  E-value=1.6e-08  Score=97.34  Aligned_cols=108  Identities=14%  Similarity=0.047  Sum_probs=69.3

Q ss_pred             cHHHHHHHHHHhhc--cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMS--KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEI  288 (854)
Q Consensus       211 r~~ei~~v~~~L~r--~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l  288 (854)
                      +.+.++++.+.+.+  +...|++|+||||||||.+|+.++.....       .+..++ ++.+.+...      ..+..+
T Consensus         6 ~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~~~~-------~~~~~v-~~~~~~~~~------~~~~~~   71 (145)
T 3n70_A            6 RSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFGRN-------AQGEFV-YRELTPDNA------PQLNDF   71 (145)
T ss_dssp             SSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHSSTT-------TTSCCE-EEECCTTTS------SCHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHhCCc-------cCCCEE-EECCCCCcc------hhhhcH
Confidence            45666666666543  47789999999999999999999876433       244567 777766543      112223


Q ss_pred             HHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHH
Q 003038          289 KNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQ  356 (854)
Q Consensus       289 ~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~  356 (854)
                      +..+     .+.+||||||+.+ ....                 ..+..++.....  ++++|++|+..
T Consensus        72 ~~~a-----~~g~l~ldei~~l~~~~q-----------------~~Ll~~l~~~~~--~~~~I~~t~~~  116 (145)
T 3n70_A           72 IALA-----QGGTLVLSHPEHLTREQQ-----------------YHLVQLQSQEHR--PFRLIGIGDTS  116 (145)
T ss_dssp             HHHH-----TTSCEEEECGGGSCHHHH-----------------HHHHHHHHSSSC--SSCEEEEESSC
T ss_pred             HHHc-----CCcEEEEcChHHCCHHHH-----------------HHHHHHHhhcCC--CEEEEEECCcC
Confidence            3332     2347999999999 4321                 234444432222  58999999853

>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=98.63  E-value=3.9e-08  Score=114.50  Aligned_cols=131  Identities=15%  Similarity=0.092  Sum_probs=79.0

Q ss_pred             CcccccHHHHHHHHHHHHHhh----cCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcc
Q 003038          618 KKVPWQKDTVYDIANTVLKCR----SGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIAL  693 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~r----sgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~  693 (854)
                      ..|+||++++..|...+....    .|+.++....     ..+...+||+||+|+|||.+|++||+.+   ...++.+++
T Consensus        39 ~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~-----~~~~~~lLL~GppGtGKTtla~~la~~l---~~~~i~in~  110 (516)
T 1sxj_A           39 QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDG-----SGVFRAAMLYGPPGIGKTTAAHLVAQEL---GYDILEQNA  110 (516)
T ss_dssp             GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTS-----TTSCSEEEEECSTTSSHHHHHHHHHHHT---TCEEEEECT
T ss_pred             HHhcCCHHHHHHHHHHHHHhHhhchhhccccCccC-----CCCCcEEEEECCCCCCHHHHHHHHHHHc---CCCEEEEeC
Confidence            358999999999999887643    3333322100     0133589999999999999999999998   357889988


Q ss_pred             ccccCcCCCccccccccccCCCC-CCchHHHHHHH-HHcCCCEEEEEecCCCCCHHHH---HHHHHhhhcC
Q 003038          694 SSFSSTRADSTEDSRNKRSRDEQ-SCSYIERFAEA-VSNNPHRVFLIEDVEQADYCSQ---KGFKRAIESG  759 (854)
Q Consensus       694 s~~~~~~~~s~e~~~~~rl~~~~-g~g~~e~L~ea-v~~~p~~ViliDEieka~~~v~---~~Ll~~le~G  759 (854)
                      +.+.....   ....+....... -.++.+...+. .......||||||||.+....+   +.|++.++++
T Consensus       111 s~~~~~~~---~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~l~~~  178 (516)
T 1sxj_A          111 SDVRSKTL---LNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKT  178 (516)
T ss_dssp             TSCCCHHH---HHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHHC
T ss_pred             CCcchHHH---HHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCCccchhhHHHHHHHHHHHHhc
Confidence            86552000   000000000000 00111000000 1234578999999999977544   8888888863

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=98.60  E-value=1.4e-07  Score=100.76  Aligned_cols=134  Identities=9%  Similarity=0.093  Sum_probs=87.2

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      -.++++|+||||+|||++++.+|..+          +..++.++...+...+.|+.+.++..++..++..  .|+|+|+|
T Consensus        43 ~~~GvlL~Gp~GtGKTtLakala~~~----------~~~~i~i~g~~l~~~~~~~~~~~i~~vf~~a~~~--~p~i~~~D  110 (274)
T 2x8a_A           43 TPAGVLLAGPPGCGKTLLAKAVANES----------GLNFISVKGPELLNMYVGESERAVRQVFQRAKNS--APCVIFFD  110 (274)
T ss_dssp             CCSEEEEESSTTSCHHHHHHHHHHHT----------TCEEEEEETTTTCSSTTHHHHHHHHHHHHHHHHT--CSEEEEEE
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHc----------CCCEEEEEcHHHHhhhhhHHHHHHHHHHHHHHhc--CCCeEeee
Confidence            34569999999999999999999763          3468888888888888999999999999998764  68999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhc-ccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc---CCCCCC
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL---HPLTIP  380 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~---~~v~i~  380 (854)
                      |++.+ ..+.....+      ...+.....-.-| +.... ..+.++++|+..+.     .||++-|--||   -.|..|
T Consensus       111 eid~~~~~r~~~~~~------~~~~~~~~~l~~Lsgg~~~-~~~i~ia~tn~p~~-----LD~al~r~gRfd~~i~~~~P  178 (274)
T 2x8a_A          111 EVDALCPRRSDRETG------ASVRVVNQLLTEMDGLEAR-QQVFIMAATNRPDI-----IDPAILRPGRLDKTLFVGLP  178 (274)
T ss_dssp             TCTTTCC---------------CTTHHHHHHHHHHTCCST-TCEEEEEEESCGGG-----SCHHHHSTTSSCEEEECCSC
T ss_pred             hhhhhhcccCCCcch------HHHHHHHHHHHhhhccccc-CCEEEEeecCChhh-----CCHhhcCcccCCeEEEeCCc
Confidence            99998 543211000      0111222222223 11111 24778888876553     49999763233   234555


Q ss_pred             Cch
Q 003038          381 AGS  383 (854)
Q Consensus       381 ~~s  383 (854)
                      +..
T Consensus       179 ~~~  181 (274)
T 2x8a_A          179 PPA  181 (274)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            443

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=98.59  E-value=1.3e-07  Score=95.35  Aligned_cols=143  Identities=6%  Similarity=-0.037  Sum_probs=89.0

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKN  290 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~  290 (854)
                      |++.+.++.+.+.+.+..+++|+||||+|||++++.++..+...     .....++.++.+....  ...+...+..+..
T Consensus        22 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~~~~~~-----~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~   94 (226)
T 2chg_A           22 QDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGE-----NWRDNFIEMNASDERG--IDVVRHKIKEFAR   94 (226)
T ss_dssp             CHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHHHGG-----GGGGGEEEEETTCTTC--HHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHhcc-----ccccceEEeccccccC--hHHHHHHHHHHhc
Confidence            88999999999988777789999999999999999999887432     1234566666543322  1222222222221


Q ss_pred             HHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchh
Q 003038          291 LVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLE  369 (854)
Q Consensus       291 ~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale  369 (854)
                      ......+++.||||||++++ ...                 ...+..++.....  .+.+|++|+...     ..+++|.
T Consensus        95 ~~~~~~~~~~vliiDe~~~l~~~~-----------------~~~l~~~l~~~~~--~~~~i~~~~~~~-----~~~~~l~  150 (226)
T 2chg_A           95 TAPIGGAPFKIIFLDEADALTADA-----------------QAALRRTMEMYSK--SCRFILSCNYVS-----RIIEPIQ  150 (226)
T ss_dssp             SCCSTTCSCEEEEEETGGGSCHHH-----------------HHHHHHHHHHTTT--TEEEEEEESCGG-----GSCHHHH
T ss_pred             ccCCCccCceEEEEeChhhcCHHH-----------------HHHHHHHHHhcCC--CCeEEEEeCChh-----hcCHHHH
Confidence            10000145899999999999 431                 1234444522122  477888876542     3467777


Q ss_pred             hhhccCCCCCCCchHHH
Q 003038          370 TLWSLHPLTIPAGSLSL  386 (854)
Q Consensus       370 ~~~~~~~v~i~~~sl~~  386 (854)
                      +  +|+.+.++..+...
T Consensus       151 ~--r~~~i~~~~~~~~~  165 (226)
T 2chg_A          151 S--RCAVFRFKPVPKEA  165 (226)
T ss_dssp             T--TSEEEECCCCCHHH
T ss_pred             H--hCceeecCCCCHHH
Confidence            7  66677777655433

>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=98.56  E-value=1.7e-07  Score=103.36  Aligned_cols=153  Identities=14%  Similarity=0.232  Sum_probs=95.3

Q ss_pred             cHHHHHHHHHHhhc----cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc----------
Q 003038          211 RNEDVMYVIENLMS----KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM----------  276 (854)
Q Consensus       211 r~~ei~~v~~~L~r----~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~----------  276 (854)
                      |++++.++.+.|.+    +..++++|+||||+|||++++.++..+.... +.   +..++.++.......          
T Consensus        25 r~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~-~~---~~~~~~i~~~~~~~~~~~~~~i~~~  100 (386)
T 2qby_A           25 REDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKF-LG---KFKHVYINTRQIDTPYRVLADLLES  100 (386)
T ss_dssp             CHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHT-CS---SCEEEEEEHHHHCSHHHHHHHHTTT
T ss_pred             hHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHh-cC---CceEEEEECCCCCCHHHHHHHHHHH
Confidence            99999999998874    3567899999999999999999998875421 00   456777664322110          


Q ss_pred             ------chHH-HHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEE
Q 003038          277 ------NRVE-VEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFW  348 (854)
Q Consensus       277 ------~rge-~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~  348 (854)
                            ..|. ..+.+..+.+.+... +.++||||||++++ ......             ....+..++... ....+.
T Consensus       101 l~~~~~~~~~~~~~~~~~l~~~l~~~-~~~~vlilDE~~~l~~~~~~~-------------~l~~l~~~~~~~-~~~~~~  165 (386)
T 2qby_A          101 LDVKVPFTGLSIAELYRRLVKAVRDY-GSQVVIVLDEIDAFVKKYNDD-------------ILYKLSRINSEV-NKSKIS  165 (386)
T ss_dssp             TSCCCCSSSCCHHHHHHHHHHHHHTC-CSCEEEEEETHHHHHHSSCST-------------HHHHHHHHHHSC-CC--EE
T ss_pred             hCCCCCCCCCCHHHHHHHHHHHHhcc-CCeEEEEEcChhhhhccCcCH-------------HHHHHhhchhhc-CCCeEE
Confidence                  0111 333345555555554 55899999999999 543211             233333444210 112599


Q ss_pred             EEEecCHHHHHHhhccCCchhhhhcc--CCCCCCCchHHH
Q 003038          349 LMGIATFQSYMRCKSGHPSLETLWSL--HPLTIPAGSLSL  386 (854)
Q Consensus       349 lIgatT~~ey~k~~~~~pale~~~~~--~~v~i~~~sl~~  386 (854)
                      +|++|+...+...  .++.+.+  +|  +.+.++..+...
T Consensus       166 ~I~~~~~~~~~~~--~~~~~~~--r~~~~~i~l~~l~~~~  201 (386)
T 2qby_A          166 FIGITNDVKFVDL--LDPRVKS--SLSEEEIIFPPYNAEE  201 (386)
T ss_dssp             EEEEESCGGGGGG--CTTHHHH--TTTTEEEEECCCCHHH
T ss_pred             EEEEECCCChHhh--hCHHHhc--cCCCeeEEeCCCCHHH
Confidence            9999987665432  4677766  55  456676655443

>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=98.53  E-value=1.6e-07  Score=103.97  Aligned_cols=137  Identities=13%  Similarity=0.175  Sum_probs=87.6

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC--------CCceE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS--------HNNFV  689 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~--------~~~~i  689 (854)
                      ..++|+++.+..+...+.....+              ++...++|+||+|+|||.+|+++++.+...        ...++
T Consensus        20 ~~l~gr~~~~~~l~~~l~~~~~~--------------~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~   85 (384)
T 2qby_B           20 KEIPFREDILRDAAIAIRYFVKN--------------EVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQA   85 (384)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHTT--------------CCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEE
T ss_pred             CCCCChHHHHHHHHHHHHHHHcC--------------CCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEE
Confidence            67999999999999998876542              123489999999999999999999987432        56788


Q ss_pred             EEcccccc-CcCCCcccccccccc----CCCCCC---chHHHHHHHHHcCCCEEEEEecCCCCCHH-HHHH-HHHhhhcC
Q 003038          690 SIALSSFS-STRADSTEDSRNKRS----RDEQSC---SYIERFAEAVSNNPHRVFLIEDVEQADYC-SQKG-FKRAIESG  759 (854)
Q Consensus       690 ~id~s~~~-~~~~~s~e~~~~~rl----~~~~g~---g~~e~L~eav~~~p~~ViliDEieka~~~-v~~~-Ll~~le~G  759 (854)
                      .+++.... +....-  ..-...+    .+..+.   ...+.+.+.+...+. ||+|||+|.+... .++. +...++..
T Consensus        86 ~i~~~~~~~~~~~~~--~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~-vlilDEi~~l~~~~~~~~~l~~l~~~~  162 (384)
T 2qby_B           86 YVNCREVGGTPQAVL--SSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRA-IIYLDEVDTLVKRRGGDIVLYQLLRSD  162 (384)
T ss_dssp             EEEHHHHCSCHHHHH--HHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCE-EEEEETTHHHHHSTTSHHHHHHHHTSS
T ss_pred             EEECccCCCCHHHHH--HHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCC-EEEEECHHHhccCCCCceeHHHHhcCC
Confidence            88876543 100000  0000111    001111   112355555655544 9999999998754 2555 55555431


Q ss_pred             eEecCCCceeecCCeEEEEecCCC
Q 003038          760 RIVTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       760 ~l~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                                  .+.+||+|||..
T Consensus       163 ------------~~~~iI~~t~~~  174 (384)
T 2qby_B          163 ------------ANISVIMISNDI  174 (384)
T ss_dssp             ------------SCEEEEEECSST
T ss_pred             ------------cceEEEEEECCC
Confidence                        678899999853

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=98.52  E-value=4.6e-07  Score=100.28  Aligned_cols=147  Identities=11%  Similarity=0.016  Sum_probs=92.2

Q ss_pred             cHHHHHHHHHHhhc----cCcC--CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc---c----
Q 003038          211 RNEDVMYVIENLMS----KRKR--NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM---N----  277 (854)
Q Consensus       211 r~~ei~~v~~~L~r----~~k~--n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~---~----  277 (854)
                      |++++.++...|.+    ...+  +++|+||||+|||++++.++..+....      +..++.++.......   +    
T Consensus        22 r~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~------~~~~~~i~~~~~~~~~~~~~~l~   95 (389)
T 1fnn_A           22 REQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKT------TARFVYINGFIYRNFTAIIGEIA   95 (389)
T ss_dssp             CHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSC------CCEEEEEETTTCCSHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhc------CeeEEEEeCccCCCHHHHHHHHH
Confidence            99999999998876    2334  799999999999999999998865421      456777764432210   0    


Q ss_pred             ---------hH-HHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-CC-CC
Q 003038          278 ---------RV-EVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IG-EN  344 (854)
Q Consensus       278 ---------rg-e~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~-g~  344 (854)
                               .| ....-+..+...+... ++++||||||+|++ ..                 ....+..++.. .. ++
T Consensus        96 ~~l~~~~~~~~~~~~~~~~~l~~~l~~~-~~~~vlilDE~~~l~~~-----------------~~~~L~~~~~~~~~~~~  157 (389)
T 1fnn_A           96 RSLNIPFPRRGLSRDEFLALLVEHLRER-DLYMFLVLDDAFNLAPD-----------------ILSTFIRLGQEADKLGA  157 (389)
T ss_dssp             HHTTCCCCSSCCCHHHHHHHHHHHHHHT-TCCEEEEEETGGGSCHH-----------------HHHHHHHHTTCHHHHSS
T ss_pred             HHhCccCCCCCCCHHHHHHHHHHHHhhc-CCeEEEEEECccccchH-----------------HHHHHHHHHHhCCCCCc
Confidence                     11 1222333344444443 56899999999999 22                 22344455522 11 00


Q ss_pred             ceEEEEEecCHHHHHHhhccCCchhhhhccC--CCCCCCchHH
Q 003038          345 ARFWLMGIATFQSYMRCKSGHPSLETLWSLH--PLTIPAGSLS  385 (854)
Q Consensus       345 g~l~lIgatT~~ey~k~~~~~pale~~~~~~--~v~i~~~sl~  385 (854)
                      ..+.+|++|+..++...  .++.+.+  +|.  .+.+++.+..
T Consensus       158 ~~~~iI~~~~~~~~~~~--l~~~~~~--r~~~~~i~~~pl~~~  196 (389)
T 1fnn_A          158 FRIALVIVGHNDAVLNN--LDPSTRG--IMGKYVIRFSPYTKD  196 (389)
T ss_dssp             CCEEEEEEESSTHHHHT--SCHHHHH--HHTTCEEECCCCBHH
T ss_pred             CCEEEEEEECCchHHHH--hCHHhhh--cCCCceEEeCCCCHH
Confidence            15999999876655543  4667766  454  4777765543

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=98.49  E-value=7.6e-08  Score=106.37  Aligned_cols=146  Identities=14%  Similarity=0.045  Sum_probs=81.9

Q ss_pred             cHHHHHH---HHHHhhccCc--CCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccc--------------
Q 003038          211 RNEDVMY---VIENLMSKRK--RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSIS--------------  271 (854)
Q Consensus       211 r~~ei~~---v~~~L~r~~k--~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~--------------  271 (854)
                      ++..++.   +.+.+.....  ++++|+||||+|||++++.+|..+.. ++       .++.++..              
T Consensus        49 ~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~~-~~-------~~~~~~~~~~~~~~~~~~~~~~  120 (368)
T 3uk6_A           49 QLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGP-DT-------PFTAIAGSEIFSLEMSKTEALT  120 (368)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHCS-SC-------CEEEEEGGGGSCSSSCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhcc-cC-------CcccccchhhhhcccchhHHHH
Confidence            5554433   4555554433  48999999999999999999998742 22       23333221              


Q ss_pred             -----------------------------------cccccchHHHHHHHHHHHHHHHhhh---CC----CeEEEeCcccc
Q 003038          272 -----------------------------------SFRHMNRVEVEQRVEEIKNLVRSCL---GR----GIVLNLGDLEW  309 (854)
Q Consensus       272 -----------------------------------~l~~~~rge~E~rl~~l~~~~~~~~---~~----~~ILfidel~~  309 (854)
                                                         .+..++.|++...+++++..+....   +.    |.||||||+|+
T Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~g~~~~~~~vl~IDEi~~  200 (368)
T 3uk6_A          121 QAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHM  200 (368)
T ss_dssp             HHHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHHTC---CBCEEEEESGGG
T ss_pred             HHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhhccccccCceEEEhhccc
Confidence                                               1233455666667777666654321   22    56999999999


Q ss_pred             c-cccccccccccccchhhhHHHHHHHhhcccCCC-------CceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCC
Q 003038          310 A-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGE-------NARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPA  381 (854)
Q Consensus       310 l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g-------~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~  381 (854)
                      + ...                 ...+.+++.....       +..+.+|++||...+   ...+|+|.+  ||+.+.++.
T Consensus       201 l~~~~-----------------~~~L~~~le~~~~~~~ii~t~~~~~~i~~t~~~~~---~~l~~~l~s--R~~~i~~~~  258 (368)
T 3uk6_A          201 LDIES-----------------FSFLNRALESDMAPVLIMATNRGITRIRGTSYQSP---HGIPIDLLD--RLLIVSTTP  258 (368)
T ss_dssp             SBHHH-----------------HHHHHHHTTCTTCCEEEEEESCSEEECBTSSCEEE---TTCCHHHHT--TEEEEEECC
T ss_pred             cChHH-----------------HHHHHHHhhCcCCCeeeeecccceeeeeccCCCCc---ccCCHHHHh--hccEEEecC
Confidence            9 431                 1223344421111       012555555654432   346788888  777788887


Q ss_pred             chHHH
Q 003038          382 GSLSL  386 (854)
Q Consensus       382 ~sl~~  386 (854)
                      ++...
T Consensus       259 ~~~~e  263 (368)
T 3uk6_A          259 YSEKD  263 (368)
T ss_dssp             CCHHH
T ss_pred             CCHHH
Confidence            76444

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=98.49  E-value=2e-07  Score=107.19  Aligned_cols=114  Identities=11%  Similarity=0.167  Sum_probs=69.9

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC-------CCceEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS-------HNNFVS  690 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-------~~~~i~  690 (854)
                      ..|+||++.+..+...+.+.                  ....+||+||+|||||.+|+.||+.+...       ...|+.
T Consensus       180 d~iiGr~~~i~~l~~~l~r~------------------~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~  241 (468)
T 3pxg_A          180 DPVIGRSKEIQRVIEVLSRR------------------TKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMT  241 (468)
T ss_dssp             CCCCCCHHHHHHHHHHHHCS------------------SSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEEC
T ss_pred             CCccCcHHHHHHHHHHHhcc------------------CCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEE
Confidence            35899999999888776531                  12367999999999999999999998542       345666


Q ss_pred             EccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceee
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVS  770 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~  770 (854)
                      +|++...     . +.+          ......+.+.+......|+|||    ...+.++.|+++|++|.+         
T Consensus       242 l~~~~~~-----~-g~~----------e~~~~~~~~~~~~~~~~iLfiD----~~~~a~~~L~~~L~~g~v---------  292 (468)
T 3pxg_A          242 LDMGTKY-----R-GEF----------EDRLKKVMDEIRQAGNIILFID----AAIDASNILKPSLARGEL---------  292 (468)
T ss_dssp             C--------------------------CTTHHHHHHHHHTCCCCEEEEC----C--------CCCTTSSSC---------
T ss_pred             eeCCccc-----c-chH----------HHHHHHHHHHHHhcCCeEEEEe----CchhHHHHHHHhhcCCCE---------
Confidence            6655100     0 000          0111245566667777899999    677899999999997744         


Q ss_pred             cCCeEEEEecCC
Q 003038          771 LGDAIVILSCES  782 (854)
Q Consensus       771 ~~~aIiIlTsn~  782 (854)
                          +||.++|.
T Consensus       293 ----~vI~at~~  300 (468)
T 3pxg_A          293 ----QCIGATTL  300 (468)
T ss_dssp             ----EEEEECCT
T ss_pred             ----EEEecCCH
Confidence                48887764

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=98.47  E-value=2.8e-07  Score=100.75  Aligned_cols=132  Identities=7%  Similarity=-0.014  Sum_probs=84.1

Q ss_pred             cHHHHHHHHHHhhc-----cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHH
Q 003038          211 RNEDVMYVIENLMS-----KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRV  285 (854)
Q Consensus       211 r~~ei~~v~~~L~r-----~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl  285 (854)
                      +++.++.+...+..     +..++++|+||||||||++++.++.+.          +..++.++...+.  ..|++...+
T Consensus        34 ~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~----------~~~~~~~~~~~~~--~~~~~~~~~  101 (338)
T 3pfi_A           34 QESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEM----------SANIKTTAAPMIE--KSGDLAAIL  101 (338)
T ss_dssp             CHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHT----------TCCEEEEEGGGCC--SHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHh----------CCCeEEecchhcc--chhHHHHHH
Confidence            67777777766654     234689999999999999999999873          4567777766543  233333222


Q ss_pred             HHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccC-----CC-----C------ceEE
Q 003038          286 EEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGI-----GE-----N------ARFW  348 (854)
Q Consensus       286 ~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~-----~g-----~------g~l~  348 (854)
                             ... ..+.|||||||+.+ ....                 ..+-..+...     ++     +      ..++
T Consensus       102 -------~~~-~~~~vl~lDEi~~l~~~~~-----------------~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (338)
T 3pfi_A          102 -------TNL-SEGDILFIDEIHRLSPAIE-----------------EVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFT  156 (338)
T ss_dssp             -------HTC-CTTCEEEEETGGGCCHHHH-----------------HHHHHHHHTSCC---------CCCCCCCCCCCE
T ss_pred             -------Hhc-cCCCEEEEechhhcCHHHH-----------------HHHHHHHHhccchhhcccCccccceecCCCCeE
Confidence                   222 45789999999998 4321                 1122222100     00     0      1389


Q ss_pred             EEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCchHHH
Q 003038          349 LMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGSLSL  386 (854)
Q Consensus       349 lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~sl~~  386 (854)
                      +|++|+....     .+|+|.+  || ..+.++.++...
T Consensus       157 ~i~atn~~~~-----l~~~L~~--R~~~~i~l~~~~~~e  188 (338)
T 3pfi_A          157 LIGATTRAGM-----LSNPLRD--RFGMQFRLEFYKDSE  188 (338)
T ss_dssp             EEEEESCGGG-----SCHHHHT--TCSEEEECCCCCHHH
T ss_pred             EEEeCCCccc-----cCHHHHh--hcCEEeeCCCcCHHH
Confidence            9999997442     5788887  67 667777766544

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.44  E-value=2e-07  Score=102.85  Aligned_cols=140  Identities=10%  Similarity=0.062  Sum_probs=86.7

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhC------CCCceEEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFG------SHNNFVSI  691 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg------~~~~~i~i  691 (854)
                      ..++|++..+..|...+.....+              .....++|+||+|+|||.+|+.+++.+..      ....++.+
T Consensus        19 ~~~~gr~~~~~~l~~~l~~~~~~--------------~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i   84 (387)
T 2v1u_A           19 DVLPHREAELRRLAEVLAPALRG--------------EKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYV   84 (387)
T ss_dssp             SCCTTCHHHHHHHHHTTGGGTSS--------------CCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEE
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcC--------------CCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEE
Confidence            67899999998888877654221              22347899999999999999999998743      25678889


Q ss_pred             ccccccCcCCCccccccccc----c---CCCCCCch---HHHHHHHHHcC-CCEEEEEecCCCCCHH--HHHHHHHhhhc
Q 003038          692 ALSSFSSTRADSTEDSRNKR----S---RDEQSCSY---IERFAEAVSNN-PHRVFLIEDVEQADYC--SQKGFKRAIES  758 (854)
Q Consensus       692 d~s~~~~~~~~s~e~~~~~r----l---~~~~g~g~---~e~L~eav~~~-p~~ViliDEieka~~~--v~~~Ll~~le~  758 (854)
                      ++....+      .......    +   .+..+...   .+.+.+.+... ...||+|||++.+...  .++.|...++.
T Consensus        85 ~~~~~~~------~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~  158 (387)
T 2v1u_A           85 NARHRET------PYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRI  158 (387)
T ss_dssp             ETTTSCS------HHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHG
T ss_pred             ECCcCCC------HHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhc
Confidence            8875541      0000000    0   01111112   22455555443 3569999999999876  77777777653


Q ss_pred             CeEecCCCceeecCCeEEEEecCCC
Q 003038          759 GRIVTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       759 G~l~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                      ..-..     + -.+.+||+++|..
T Consensus       159 ~~~~~-----~-~~~~~~I~~t~~~  177 (387)
T 2v1u_A          159 NQELG-----D-RVWVSLVGITNSL  177 (387)
T ss_dssp             GGCC-----------CEEEEECSCS
T ss_pred             hhhcC-----C-CceEEEEEEECCC
Confidence            11000     0 2356788888754

>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=98.44  E-value=6.9e-07  Score=93.68  Aligned_cols=138  Identities=14%  Similarity=0.108  Sum_probs=85.3

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGD  306 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfide  306 (854)
                      .++++|+||||+|||++++.++..+.          ..++.++...+...+.|+.+.++..+++.+...  .+.++|+||
T Consensus        49 ~~g~ll~G~~G~GKTtl~~~i~~~~~----------~~~i~~~~~~~~~~~~~~~~~~i~~~~~~~~~~--~~~i~~~De  116 (254)
T 1ixz_A           49 PKGVLLVGPPGVGKTHLARAVAGEAR----------VPFITASGSDFVEMFVGVGAARVRDLFETAKRH--APCIVFIDE  116 (254)
T ss_dssp             CSEEEEECCTTSSHHHHHHHHHHHTT----------CCEEEEEHHHHHHSCTTHHHHHHHHHHHHHTTS--SSEEEEEET
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhC----------CCEEEeeHHHHHHHHhhHHHHHHHHHHHHHHhc--CCeEEEehh
Confidence            45689999999999999999997642          456777777776667888888999999988753  579999999


Q ss_pred             cccc-cccccccccccccchhhhHHHHHHHhhccc-CCCCceEEEEEecCHHHHHHhhccCCchhhhhccC-CCCCCCch
Q 003038          307 LEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGENARFWLMGIATFQSYMRCKSGHPSLETLWSLH-PLTIPAGS  383 (854)
Q Consensus       307 l~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~-~v~i~~~s  383 (854)
                      ++.+ ........+ .  .....+.+..+-..+.. ...+ .+.++++|+..+     ..||++-|.-||. .+.|+.|+
T Consensus       117 id~l~~~~~~~~~~-~--~~~~~~~~~~ll~~l~g~~~~~-~~i~~a~t~~p~-----~ld~~l~r~~rf~~~i~i~~p~  187 (254)
T 1ixz_A          117 IDAVGRKRGSGVGG-G--NDEREQTLNQLLVEMDGFEKDT-AIVVMAATNRPD-----ILDPALLRPGRFDRQIAIDAPD  187 (254)
T ss_dssp             HHHHHC------------CHHHHHHHHHHHHHHHTCCTTC-CEEEEEEESCGG-----GSCGGGGSTTSSCEEEECCSCC
T ss_pred             hhhhhcccCccccc-c--chHHHHHHHHHHHHHhCCCCCC-CEEEEEccCCch-----hCCHHHcCCCcCCeEEeeCCcC
Confidence            9988 432210000 0  00111222333333321 1221 356666665543     2689998744442 45566665


Q ss_pred             HH
Q 003038          384 LS  385 (854)
Q Consensus       384 l~  385 (854)
                      ..
T Consensus       188 ~~  189 (254)
T 1ixz_A          188 VK  189 (254)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>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=98.42  E-value=4.9e-07  Score=100.10  Aligned_cols=151  Identities=15%  Similarity=0.094  Sum_probs=90.3

Q ss_pred             cHHHHHHHHHHhhc----cCcCCceeecCCCCCHHHHHHHHHHHHHcCCC-CcccCCceEEEccccccc-cc--c----h
Q 003038          211 RNEDVMYVIENLMS----KRKRNFVVVGECLASIEGVVRGVIDKIEKGDV-PEALRDVKCLPLSISSFR-HM--N----R  278 (854)
Q Consensus       211 r~~ei~~v~~~L~r----~~k~n~vLvGe~GvGKta~v~~la~~i~~~~v-p~~L~~~~~~~l~~~~l~-~~--~----r  278 (854)
                      |++++.++...|.+    +..++++|+||||+|||++++.++..+..... .....+..++.++..... ..  .    .
T Consensus        25 r~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~  104 (384)
T 2qby_B           25 REDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAVLSSLA  104 (384)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHHHHHHHH
Confidence            99999999887764    23567999999999999999999988754200 000115678888765433 10  0    1


Q ss_pred             HHH------------HHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCc
Q 003038          279 VEV------------EQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENA  345 (854)
Q Consensus       279 ge~------------E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g  345 (854)
                      .++            ...+..+...+...   +.||||||+|++ ......             .  -+..|+... .  
T Consensus       105 ~~l~~~~~~~~~~~~~~~~~~l~~~l~~~---~~vlilDEi~~l~~~~~~~-------------~--~l~~l~~~~-~--  163 (384)
T 2qby_B          105 GKLTGFSVPKHGINLGEYIDKIKNGTRNI---RAIIYLDEVDTLVKRRGGD-------------I--VLYQLLRSD-A--  163 (384)
T ss_dssp             HHHHCSCCCSSSSCTHHHHHHHHHHHSSS---CEEEEEETTHHHHHSTTSH-------------H--HHHHHHTSS-S--
T ss_pred             HHhcCCCCCCCCCCHHHHHHHHHHHhccC---CCEEEEECHHHhccCCCCc-------------e--eHHHHhcCC-c--
Confidence            111            22234444444432   349999999999 542110             1  022344321 2  


Q ss_pred             eEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCchHHH
Q 003038          346 RFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGSLSL  386 (854)
Q Consensus       346 ~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~sl~~  386 (854)
                      .+.+|++|+...+..  ..+|.+.+  +| +.+.++..+...
T Consensus       164 ~~~iI~~t~~~~~~~--~l~~~l~s--r~~~~i~l~~l~~~~  201 (384)
T 2qby_B          164 NISVIMISNDINVRD--YMEPRVLS--SLGPSVIFKPYDAEQ  201 (384)
T ss_dssp             CEEEEEECSSTTTTT--TSCHHHHH--TCCCEEEECCCCHHH
T ss_pred             ceEEEEEECCCchHh--hhCHHHHh--cCCCeEEECCCCHHH
Confidence            599999998765432  24677766  54 356666655433

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=98.41  E-value=7.6e-08  Score=92.43  Aligned_cols=105  Identities=15%  Similarity=0.143  Sum_probs=67.0

Q ss_pred             cHHHHHHHHHHhhc--cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMS--KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEI  288 (854)
Q Consensus       211 r~~ei~~v~~~L~r--~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l  288 (854)
                      +++.++++.+.+.+  +...|++|+||||+|||.+|++++...          + .++.++.+.+...+       ...+
T Consensus         9 ~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~~----------~-~~~~~~~~~~~~~~-------~~~~   70 (143)
T 3co5_A            9 NSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKNG----------T-PWVSPARVEYLIDM-------PMEL   70 (143)
T ss_dssp             CCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCTT----------S-CEECCSSTTHHHHC-------HHHH
T ss_pred             CCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhC----------C-CeEEechhhCChHh-------hhhH
Confidence            55666666665543  467899999999999999999887541          1 78888877654432       2333


Q ss_pred             HHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHH
Q 003038          289 KNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQ  356 (854)
Q Consensus       289 ~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~  356 (854)
                      ++.+     .+-+|||||++.+ ....                 ..+..++.. +.+..+++|++|+..
T Consensus        71 ~~~a-----~~~~l~lDei~~l~~~~q-----------------~~Ll~~l~~-~~~~~~~iI~~tn~~  116 (143)
T 3co5_A           71 LQKA-----EGGVLYVGDIAQYSRNIQ-----------------TGITFIIGK-AERCRVRVIASCSYA  116 (143)
T ss_dssp             HHHT-----TTSEEEEEECTTCCHHHH-----------------HHHHHHHHH-HTTTTCEEEEEEEEC
T ss_pred             HHhC-----CCCeEEEeChHHCCHHHH-----------------HHHHHHHHh-CCCCCEEEEEecCCC
Confidence            3332     2448999999999 4321                 123344421 111248999999854

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.41  E-value=8e-07  Score=96.87  Aligned_cols=139  Identities=10%  Similarity=0.065  Sum_probs=88.3

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC-------CCceEEE
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS-------HNNFVSI  691 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-------~~~~i~i  691 (854)
                      .++|.++-+..|...|..+..+              .+...++++||||+|||.+++.+++.+...       .-.++++
T Consensus        21 ~L~~Re~E~~~i~~~L~~~i~~--------------~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~I   86 (318)
T 3te6_A           21 LLKSQVEDFTRIFLPIYDSLMS--------------SQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHI   86 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHT--------------TCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEE
T ss_pred             ccCCHHHHHHHHHHHHHHHhcC--------------CCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEE
Confidence            3688888888888888876542              234588999999999999999999998532       1257888


Q ss_pred             ccccccCcCCCccccccc-c----ccCC---CCCCch--HHHHHHHH--HcCCCEEEEEecCCCCCHHHHHHHHHhhhcC
Q 003038          692 ALSSFSSTRADSTEDSRN-K----RSRD---EQSCSY--IERFAEAV--SNNPHRVFLIEDVEQADYCSQKGFKRAIESG  759 (854)
Q Consensus       692 d~s~~~~~~~~s~e~~~~-~----rl~~---~~g~g~--~e~L~eav--~~~p~~ViliDEieka~~~v~~~Ll~~le~G  759 (854)
                      ++..+.+       ...+ .    .+.+   ..+...  .+.+.+.+  ......||+|||||++.  -|+.|+..++-.
T Consensus        87 Nc~~~~t-------~~~~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~--~q~~L~~l~~~~  157 (318)
T 3te6_A           87 DALELAG-------MDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLL--SEKILQYFEKWI  157 (318)
T ss_dssp             ETTCCC---------HHHHHHHHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSC--CTHHHHHHHHHH
T ss_pred             eccccCC-------HHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhh--cchHHHHHHhcc
Confidence            8876652       1110 0    0101   111111  12233332  23456799999999998  577777777511


Q ss_pred             eEecCCCceeecCCeEEEEecCCCCCCCC
Q 003038          760 RIVTSSGDEVSLGDAIVILSCESFSSRSR  788 (854)
Q Consensus       760 ~l~d~~G~~v~~~~aIiIlTsn~f~~~s~  788 (854)
                        .      ..-++.+||+++|..+-+.+
T Consensus       158 --~------~~~s~~~vI~i~n~~d~~~~  178 (318)
T 3te6_A          158 --S------SKNSKLSIICVGGHNVTIRE  178 (318)
T ss_dssp             --H------CSSCCEEEEEECCSSCCCHH
T ss_pred             --c------ccCCcEEEEEEecCcccchh
Confidence              0      12346679999987765443

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=98.39  E-value=8.5e-07  Score=102.44  Aligned_cols=129  Identities=11%  Similarity=0.093  Sum_probs=81.3

Q ss_pred             CcccccHHHHHHHHHHHHHhhcC--CCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSG--TMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsg--l~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      ..|+|+++++..|.+.+...+.-  +.+-.       -.-|.+ ++|+||+|+|||.+|++||..+   ...|+.++++.
T Consensus        31 ~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg-------~~ip~G-vLL~GppGtGKTtLaraIa~~~---~~~~i~i~g~~   99 (499)
T 2dhr_A           31 KDVAGAEEAKEELKEIVEFLKNPSRFHEMG-------ARIPKG-VLLVGPPGVGKTHLARAVAGEA---RVPFITASGSD   99 (499)
T ss_dssp             TSSCSCHHHHHHHHHHHHHHHCGGGTTTTS-------CCCCSE-EEEECSSSSSHHHHHHHHHHHT---TCCEEEEEGGG
T ss_pred             HHcCCcHHHHHHHHHHHHHhhchhhhhhcc-------CCCCce-EEEECCCCCCHHHHHHHHHHHh---CCCEEEEehhH
Confidence            46899999999888887654320  00000       001233 8999999999999999999987   36789999887


Q ss_pred             ccCcCCCccccccccccCCCCCCchHH-HHHHHH---HcCCCEEEEEecCCCCCH--------------HHHHHHHHhhh
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIE-RFAEAV---SNNPHRVFLIEDVEQADY--------------CSQKGFKRAIE  757 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e-~L~eav---~~~p~~ViliDEieka~~--------------~v~~~Ll~~le  757 (854)
                      +.       +.+.          |... .+...+   +....+|+||||||.+..              ...+.|+..|+
T Consensus       100 ~~-------~~~~----------g~~~~~v~~lfq~a~~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ld  162 (499)
T 2dhr_A          100 FV-------EMFV----------GVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMD  162 (499)
T ss_dssp             GT-------SSCT----------THHHHHHHHHTTTSSSSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGG
T ss_pred             HH-------Hhhh----------hhHHHHHHHHHHHHHhcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhc
Confidence            65       1110          2221 222222   223458999999987632              34566777666


Q ss_pred             cCeEecCCCceeecCCeEEEEecCCC
Q 003038          758 SGRIVTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       758 ~G~l~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                      .|.-         -+..|+|.++|.-
T Consensus       163 g~~~---------~~~viviAatn~p  179 (499)
T 2dhr_A          163 GFEK---------DTAIVVMAATNRP  179 (499)
T ss_dssp             GCCS---------SCCCEEEECCSCG
T ss_pred             cccc---------CccEEEEEecCCh
Confidence            4421         2356788888753

>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=98.38  E-value=6.4e-07  Score=110.47  Aligned_cols=111  Identities=14%  Similarity=0.217  Sum_probs=65.3

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhC-------CCCceEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFG-------SHNNFVS  690 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg-------~~~~~i~  690 (854)
                      ..|+|+++.+..+...+.+.                  ....++|+||+|+|||.+|+.||+.+..       ....++.
T Consensus       170 d~viGr~~~i~~l~~~l~~~------------------~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~  231 (854)
T 1qvr_A          170 DPVIGRDEEIRRVIQILLRR------------------TKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVS  231 (854)
T ss_dssp             CCCCSCHHHHHHHHHHHHCS------------------SCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEE
T ss_pred             cccCCcHHHHHHHHHHHhcC------------------CCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEE
Confidence            45799998888887766431                  1235689999999999999999998843       2457788


Q ss_pred             EccccccCcCCCccccccccccCCCCCC--chHH---HHHHHHHcC-CCEEEEEecCCCCC--------HHHHHHHHHhh
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSC--SYIE---RFAEAVSNN-PHRVFLIEDVEQAD--------YCSQKGFKRAI  756 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~--g~~e---~L~eav~~~-p~~ViliDEieka~--------~~v~~~Ll~~l  756 (854)
                      ++++.+..                +..|  .+.+   .+.+.+... ...||||||++.+.        .++++.|++++
T Consensus       232 l~~~~l~~----------------g~~~~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l  295 (854)
T 1qvr_A          232 LQMGSLLA----------------GAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPAL  295 (854)
T ss_dssp             ECC---------------------------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHH
T ss_pred             eehHHhhc----------------cCccchHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCccchHHHHHHHHHHH
Confidence            88765531                0111  2222   334444443 56899999999987        67888999999


Q ss_pred             hcCeEe
Q 003038          757 ESGRIV  762 (854)
Q Consensus       757 e~G~l~  762 (854)
                      +.|.+.
T Consensus       296 ~~~~i~  301 (854)
T 1qvr_A          296 ARGELR  301 (854)
T ss_dssp             HTTCCC
T ss_pred             hCCCeE
Confidence            876543

>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=98.38  E-value=6.2e-07  Score=109.11  Aligned_cols=61  Identities=21%  Similarity=0.420  Sum_probs=51.5

Q ss_pred             cChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCChHHHHHHHhCCCHHHHHHHHHHHh
Q 003038           94 QFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVEQAV  167 (854)
Q Consensus        94 ~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~~~~~iL~~~Gi~~~~l~~~v~~~l  167 (854)
                      +++.+.++|..|...|...++    .         +|+++|||+|||+++.+.++|+.+|++.+.++..+...+
T Consensus         2 ~t~~a~~~l~~A~~~A~~~~h----~---------~i~~eHLLlaLl~~~~~~~iL~~~gvd~~~l~~~l~~~l   62 (758)
T 1r6b_X            2 LNQELELSLNMAFARAREHRH----E---------FMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFI   62 (758)
T ss_dssp             BCHHHHHHHHHHHHHHHHTTB----S---------EECHHHHHHHHTTSHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHcCC----C---------CccHHHHHHHHHcCcHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            467788888888888887632    2         599999999999988889999999999999998888654

>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=98.36  E-value=3.2e-07  Score=99.94  Aligned_cols=127  Identities=11%  Similarity=0.093  Sum_probs=78.3

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHH-HHHHHHHHhhhCCCeEEEe
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRV-EEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl-~~l~~~~~~~~~~~~ILfi  304 (854)
                      ..++++|+||||+|||++++.++..+...       +..++.++...+...+.+.+.... ..+.....    .+.||||
T Consensus        36 ~~~~lll~G~~GtGKT~la~~i~~~~~~~-------~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~vL~i  104 (324)
T 1l8q_A           36 LYNPIFIYGSVGTGKTHLLQAAGNEAKKR-------GYRVIYSSADDFAQAMVEHLKKGTINEFRNMYK----SVDLLLL  104 (324)
T ss_dssp             SCSSEEEECSSSSSHHHHHHHHHHHHHHT-------TCCEEEEEHHHHHHHHHHHHHHTCHHHHHHHHH----TCSEEEE
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHHHC-------CCEEEEEEHHHHHHHHHHHHHcCcHHHHHHHhc----CCCEEEE
Confidence            34789999999999999999999987653       567888887777655555544322 22222222    3679999


Q ss_pred             Cccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecC-HHHHHHhhccCCchhhhhcc---CCC
Q 003038          305 GDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIAT-FQSYMRCKSGHPSLETLWSL---HPL  377 (854)
Q Consensus       305 del~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT-~~ey~k~~~~~pale~~~~~---~~v  377 (854)
                      ||+|.+ +...               ...++-.++..  ..+  ...+|+++. +.++   ...++.|.+  ||   ..+
T Consensus       105 DEi~~l~~~~~---------------~~~~l~~~l~~~~~~~--~~iii~~~~~~~~l---~~l~~~L~s--R~~~~~~i  162 (324)
T 1l8q_A          105 DDVQFLSGKER---------------TQIEFFHIFNTLYLLE--KQIILASDRHPQKL---DGVSDRLVS--RFEGGILV  162 (324)
T ss_dssp             ECGGGGTTCHH---------------HHHHHHHHHHHHHHTT--CEEEEEESSCGGGC---TTSCHHHHH--HHHTSEEE
T ss_pred             cCcccccCChH---------------HHHHHHHHHHHHHHCC--CeEEEEecCChHHH---HHhhhHhhh--cccCceEE
Confidence            999999 5321               12233344321  223  244554443 2222   246788887  55   457


Q ss_pred             CCCCchHHH
Q 003038          378 TIPAGSLSL  386 (854)
Q Consensus       378 ~i~~~sl~~  386 (854)
                      .+++ +...
T Consensus       163 ~l~~-~~~e  170 (324)
T 1l8q_A          163 EIEL-DNKT  170 (324)
T ss_dssp             ECCC-CHHH
T ss_pred             EeCC-CHHH
Confidence            7777 6544

>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=98.35  E-value=1.1e-06  Score=94.97  Aligned_cols=133  Identities=10%  Similarity=0.033  Sum_probs=82.6

Q ss_pred             cHHHHHHHHHHhhc-----cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHH
Q 003038          211 RNEDVMYVIENLMS-----KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRV  285 (854)
Q Consensus       211 r~~ei~~v~~~L~r-----~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl  285 (854)
                      +++.++++...+.+     +..++++|+||||+|||++++.++..+          +..++.++...+..  .+      
T Consensus        17 ~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~----------~~~~~~~~~~~~~~--~~------   78 (324)
T 1hqc_A           17 QERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL----------GVNLRVTSGPAIEK--PG------   78 (324)
T ss_dssp             CHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHH----------TCCEEEECTTTCCS--HH------
T ss_pred             HHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHh----------CCCEEEEeccccCC--hH------
Confidence            77777777666653     244789999999999999999999875          24566666554432  22      


Q ss_pred             HHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccC-----CCC-----------ceEE
Q 003038          286 EEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGI-----GEN-----------ARFW  348 (854)
Q Consensus       286 ~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~-----~g~-----------g~l~  348 (854)
                       ++...+......+.+|||||++.+ ....                 ..+.+++...     .+.           ..++
T Consensus        79 -~l~~~l~~~~~~~~~l~lDEi~~l~~~~~-----------------~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~  140 (324)
T 1hqc_A           79 -DLAAILANSLEEGDILFIDEIHRLSRQAE-----------------EHLYPAMEDFVMDIVIGQGPAARTIRLELPRFT  140 (324)
T ss_dssp             -HHHHHHTTTCCTTCEEEETTTTSCCHHHH-----------------HHHHHHHHHSEEEECCSSSSSCCCEEEECCCCE
T ss_pred             -HHHHHHHHhccCCCEEEEECCcccccchH-----------------HHHHHHHHhhhhHHhccccccccccccCCCCEE
Confidence             233333331135779999999999 4321                 1122222100     000           1378


Q ss_pred             EEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCchHHH
Q 003038          349 LMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGSLSL  386 (854)
Q Consensus       349 lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~sl~~  386 (854)
                      +|++|+...     ..+++|.+  || +.+.++.++...
T Consensus       141 ~i~~t~~~~-----~~~~~l~~--R~~~~i~l~~~~~~e  172 (324)
T 1hqc_A          141 LIGATTRPG-----LITAPLLS--RFGIVEHLEYYTPEE  172 (324)
T ss_dssp             EEEEESCCS-----SCSCSTTT--TCSCEEECCCCCHHH
T ss_pred             EEEeCCCcc-----cCCHHHHh--cccEEEecCCCCHHH
Confidence            999998652     34677777  77 467777766544

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=98.34  E-value=1.8e-06  Score=87.84  Aligned_cols=144  Identities=11%  Similarity=0.033  Sum_probs=84.6

Q ss_pred             cHHHHHHHHHHhhccCc-CCceeecCCCCCHHHHHHHHHHHHHcCCCCccc--------------CCceEEEcccccccc
Q 003038          211 RNEDVMYVIENLMSKRK-RNFVVVGECLASIEGVVRGVIDKIEKGDVPEAL--------------RDVKCLPLSISSFRH  275 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k-~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L--------------~~~~~~~l~~~~l~~  275 (854)
                      |+++++++...+...+. ++++|+||||+|||++++.++..+.........              ....++.++...   
T Consensus        28 ~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---  104 (250)
T 1njg_A           28 QEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAAS---  104 (250)
T ss_dssp             CHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHTTCCSSEEEEETTC---
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhccCCcceEEecCcc---
Confidence            89999999998876543 458999999999999999999887643211000              001222222111   


Q ss_pred             cchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEe
Q 003038          276 MNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGI  352 (854)
Q Consensus       276 ~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIga  352 (854)
                         ......+.++++.+....  +++.||||||+|++ ..                 ....+..++.....  .+.+|.+
T Consensus       105 ---~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~-----------------~~~~l~~~l~~~~~--~~~~i~~  162 (250)
T 1njg_A          105 ---RTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRH-----------------SFNALLKTLEEPPE--HVKFLLA  162 (250)
T ss_dssp             ---GGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHH-----------------HHHHHHHHHHSCCT--TEEEEEE
T ss_pred             ---cccHHHHHHHHHHhhhchhcCCceEEEEECcccccHH-----------------HHHHHHHHHhcCCC--ceEEEEE
Confidence               111233455555543211  35799999999998 33                 12234445522122  4888888


Q ss_pred             cCHHHHHHhhccCCchhhhhccCCCCCCCchHHH
Q 003038          353 ATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSL  386 (854)
Q Consensus       353 tT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~  386 (854)
                      |+...     ...+++.+  ++..+.++..+...
T Consensus       163 t~~~~-----~~~~~l~~--r~~~i~l~~l~~~e  189 (250)
T 1njg_A          163 TTDPQ-----KLPVTILS--RCLQFHLKALDVEQ  189 (250)
T ss_dssp             ESCGG-----GSCHHHHT--TSEEEECCCCCHHH
T ss_pred             eCChH-----hCCHHHHH--HhhhccCCCCCHHH
Confidence            76432     23556666  56666676655433

>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=98.32  E-value=4.3e-07  Score=95.84  Aligned_cols=91  Identities=12%  Similarity=0.104  Sum_probs=55.3

Q ss_pred             cHHHHHHHHHHhhc--cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc---------chH
Q 003038          211 RNEDVMYVIENLMS--KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM---------NRV  279 (854)
Q Consensus       211 r~~ei~~v~~~L~r--~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~---------~rg  279 (854)
                      ++..++++++.+.+  +...+++|+||||||||.+++.++.....       .+..++.++++.+...         .+|
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~~~~-------~~~~~~~v~~~~~~~~~~~~~l~g~~~~   83 (265)
T 2bjv_A           11 EANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSSR-------WQGPFISLNCAALNENLLDSELFGHEAG   83 (265)
T ss_dssp             CCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHTSTT-------TTSCEEEEEGGGSCHHHHHHHHHCCC--
T ss_pred             CCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhcCc-------cCCCeEEEecCCCChhHHHHHhcCCccc
Confidence            55666666665543  46789999999999999999999976432       2457888887765321         111


Q ss_pred             HHHHHHHHHHHHHHhhhCCCeEEEeCccccc
Q 003038          280 EVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       280 e~E~rl~~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                      .+..........+...  .+.+|||||++.+
T Consensus        84 ~~~g~~~~~~~~l~~a--~~~~l~lDEi~~l  112 (265)
T 2bjv_A           84 AFTGAQKRHPGRFERA--DGGTLFLDELATA  112 (265)
T ss_dssp             -------CCCCHHHHT--TTSEEEEESGGGS
T ss_pred             ccccccccccchhhhc--CCcEEEEechHhc
Confidence            1111111001112222  2458999999999

>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=98.32  E-value=3.2e-06  Score=92.73  Aligned_cols=104  Identities=13%  Similarity=0.113  Sum_probs=71.5

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .++||+.++..|...|...+.    +         .++...++|+||+|+|||++|++||..+ +  ..+.....+.+. 
T Consensus        26 ~~~g~~~~~~~l~~~i~~~~~----~---------~~~~~~~ll~Gp~G~GKTTLa~~ia~~l-~--~~~~~~sg~~~~-   88 (334)
T 1in4_A           26 EFIGQENVKKKLSLALEAAKM----R---------GEVLDHVLLAGPPGLGKTTLAHIIASEL-Q--TNIHVTSGPVLV-   88 (334)
T ss_dssp             GCCSCHHHHHHHHHHHHHHHH----H---------TCCCCCEEEESSTTSSHHHHHHHHHHHH-T--CCEEEEETTTCC-
T ss_pred             HccCcHHHHHHHHHHHHHHHh----c---------CCCCCeEEEECCCCCcHHHHHHHHHHHh-C--CCEEEEechHhc-
Confidence            468999999999888876432    1         1234578999999999999999999988 2  122222211110 


Q ss_pred             cCCCccccccccccCCCCCCchHHHHHHHHH-cCCCEEEEEecCCCCCHHHHHHHHHhhhcCe
Q 003038          699 TRADSTEDSRNKRSRDEQSCSYIERFAEAVS-NNPHRVFLIEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~-~~p~~ViliDEieka~~~v~~~Ll~~le~G~  760 (854)
                                         .+  ..+...+. .....|++|||++.+.+.+++.|+..++++.
T Consensus        89 -------------------~~--~~l~~~~~~~~~~~v~~iDE~~~l~~~~~e~L~~~~~~~~  130 (334)
T 1in4_A           89 -------------------KQ--GDMAAILTSLERGDVLFIDEIHRLNKAVEELLYSAIEDFQ  130 (334)
T ss_dssp             -------------------SH--HHHHHHHHHCCTTCEEEEETGGGCCHHHHHHHHHHHHTSC
T ss_pred             -------------------CH--HHHHHHHHHccCCCEEEEcchhhcCHHHHHHHHHHHHhcc
Confidence                               01  11222222 2356899999999999999999999998764

>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=98.32  E-value=8e-07  Score=96.58  Aligned_cols=137  Identities=9%  Similarity=0.007  Sum_probs=89.3

Q ss_pred             CCCCC--cHHHHHHHHHHhhccCcCCceee-cCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHH
Q 003038          206 SLDPI--RNEDVMYVIENLMSKRKRNFVVV-GECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVE  282 (854)
Q Consensus       206 ~ldpv--r~~ei~~v~~~L~r~~k~n~vLv-Ge~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E  282 (854)
                      .++.+  +++.++.+...+.+.+..+++|+ ||||+|||++++.++..+          +..++.++.+...       .
T Consensus        24 ~~~~ivg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l----------~~~~~~i~~~~~~-------~   86 (324)
T 3u61_B           24 TIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDV----------NADMMFVNGSDCK-------I   86 (324)
T ss_dssp             STTTSCCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHT----------TEEEEEEETTTCC-------H
T ss_pred             CHHHHhCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHh----------CCCEEEEcccccC-------H
Confidence            34444  77778888888776666676555 569999999999999875          4678888765432       2


Q ss_pred             HHHHHHHHHHHhhh---CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHH
Q 003038          283 QRVEEIKNLVRSCL---GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSY  358 (854)
Q Consensus       283 ~rl~~l~~~~~~~~---~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey  358 (854)
                      ..+++++.......   +.+.||||||+|.+ +..                ....+..++....+  .+.+|++|+... 
T Consensus        87 ~~i~~~~~~~~~~~~~~~~~~vliiDEi~~l~~~~----------------~~~~L~~~le~~~~--~~~iI~~~n~~~-  147 (324)
T 3u61_B           87 DFVRGPLTNFASAASFDGRQKVIVIDEFDRSGLAE----------------SQRHLRSFMEAYSS--NCSIIITANNID-  147 (324)
T ss_dssp             HHHHTHHHHHHHBCCCSSCEEEEEEESCCCGGGHH----------------HHHHHHHHHHHHGG--GCEEEEEESSGG-
T ss_pred             HHHHHHHHHHHhhcccCCCCeEEEEECCcccCcHH----------------HHHHHHHHHHhCCC--CcEEEEEeCCcc-
Confidence            23334333332211   35789999999999 432                12234444421112  478888887643 


Q ss_pred             HHhhccCCchhhhhccCCCCCCCchH
Q 003038          359 MRCKSGHPSLETLWSLHPLTIPAGSL  384 (854)
Q Consensus       359 ~k~~~~~pale~~~~~~~v~i~~~sl  384 (854)
                          ..+|+|.+  ||+.+.++.++.
T Consensus       148 ----~l~~~l~s--R~~~i~~~~~~~  167 (324)
T 3u61_B          148 ----GIIKPLQS--RCRVITFGQPTD  167 (324)
T ss_dssp             ----GSCTTHHH--HSEEEECCCCCH
T ss_pred             ----ccCHHHHh--hCcEEEeCCCCH
Confidence                46788988  777888877763

>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=98.32  E-value=9.1e-07  Score=90.78  Aligned_cols=78  Identities=10%  Similarity=0.087  Sum_probs=57.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      ..++|+||+|+|||++|+++++.+......++.++++++.       ...  ...+            +.+  ....||+
T Consensus        53 ~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~-------~~~--~~~~------------~~~--~~~~vli  109 (242)
T 3bos_A           53 QAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGIHA-------SIS--TALL------------EGL--EQFDLIC  109 (242)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEGGGGG-------GSC--GGGG------------TTG--GGSSEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHH-------HHH--HHHH------------Hhc--cCCCEEE
Confidence            4789999999999999999999987666778888877654       111  0000            001  2357999


Q ss_pred             EecCCCCCHHH--HHHHHHhhhc
Q 003038          738 IEDVEQADYCS--QKGFKRAIES  758 (854)
Q Consensus       738 iDEieka~~~v--~~~Ll~~le~  758 (854)
                      |||++.++...  ++.|+..++.
T Consensus       110 iDe~~~~~~~~~~~~~l~~~l~~  132 (242)
T 3bos_A          110 IDDVDAVAGHPLWEEAIFDLYNR  132 (242)
T ss_dssp             EETGGGGTTCHHHHHHHHHHHHH
T ss_pred             EeccccccCCHHHHHHHHHHHHH
Confidence            99999998766  8888888764

>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=98.31  E-value=5.9e-07  Score=96.32  Aligned_cols=155  Identities=12%  Similarity=0.110  Sum_probs=91.9

Q ss_pred             cHHHHHHHHHHhhc--------------cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc-
Q 003038          211 RNEDVMYVIENLMS--------------KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH-  275 (854)
Q Consensus       211 r~~ei~~v~~~L~r--------------~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~-  275 (854)
                      .++.++.+...+.+              +..++++|+||||||||++++.++..+          +..++.++.+.+.. 
T Consensus        20 ~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l----------~~~~~~i~~~~~~~~   89 (310)
T 1ofh_A           20 QADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA----------NAPFIKVEATKFTEV   89 (310)
T ss_dssp             CHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHH----------TCCEEEEEGGGGSSC
T ss_pred             hHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHh----------CCCEEEEcchhcccC
Confidence            55666666666554              356789999999999999999999876          34788888887765 


Q ss_pred             cchHH-HHHHHHHHHHHH----HhhhCCCeEEEeCccccc-cccccccccccccchhhhHH-HHHHHhhcccCC------
Q 003038          276 MNRVE-VEQRVEEIKNLV----RSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHI-IMEIGKLVCGIG------  342 (854)
Q Consensus       276 ~~rge-~E~rl~~l~~~~----~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~-~~~~~~ll~~~~------  342 (854)
                      +|.|. .+..+++++...    ... ..+.||||||++.+ ......  +    +.....+ ...+-.++....      
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~vl~iDEi~~l~~~~~~~--~----~~~~~~~~~~~Ll~~le~~~~~~~~~  162 (310)
T 1ofh_A           90 GYVGKEVDSIIRDLTDSAGGAIDAV-EQNGIVFIDEIDKICKKGEYS--G----ADVSREGVQRDLLPLVEGSTVSTKHG  162 (310)
T ss_dssp             CSGGGSTTHHHHHHHHTTTTCHHHH-HHHCEEEEECGGGGSCCSSCC--S----SHHHHHHHHHHHHHHHHCCEEEETTE
T ss_pred             CccCccHHHHHHHHHHHhhHHHhhc-cCCCEEEEEChhhcCcccccc--c----cchhHHHHHHHHHHHhcCCeEecccc
Confidence            45543 344566665522    211 13579999999999 443211  0    1111111 122333332100      


Q ss_pred             --CCceEEEEEecCHHHHHHhhccCCchhhhhccC-CCCCCCchHH
Q 003038          343 --ENARFWLMGIATFQSYMRCKSGHPSLETLWSLH-PLTIPAGSLS  385 (854)
Q Consensus       343 --g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~-~v~i~~~sl~  385 (854)
                        ..+.+.+|+++++.... -...+|+|.+  ||. .|.++.++..
T Consensus       163 ~~~~~~~~~i~~~~~~~~~-~~~l~~~l~~--R~~~~i~~~~~~~~  205 (310)
T 1ofh_A          163 MVKTDHILFIASGAFQVAR-PSDLIPELQG--RLPIRVELTALSAA  205 (310)
T ss_dssp             EEECTTCEEEEEECCSSSC-GGGSCHHHHH--TCCEEEECCCCCHH
T ss_pred             cccCCcEEEEEcCCcccCC-cccCCHHHHh--hCCceEEcCCcCHH
Confidence              01248899987432111 1246788888  775 4777766643

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=98.31  E-value=1.9e-06  Score=91.76  Aligned_cols=139  Identities=14%  Similarity=0.090  Sum_probs=85.9

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGD  306 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfide  306 (854)
                      .++++|+||||+|||++++.++..+.          ..++.++...+...+.|+.+.++..+++.+...  .+.|+|+||
T Consensus        73 ~~gvll~Gp~GtGKTtl~~~i~~~~~----------~~~i~~~~~~~~~~~~~~~~~~i~~~~~~~~~~--~~~i~~iDe  140 (278)
T 1iy2_A           73 PKGVLLVGPPGVGKTHLARAVAGEAR----------VPFITASGSDFVEMFVGVGAARVRDLFETAKRH--APCIVFIDE  140 (278)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHTT----------CCEEEEEHHHHHHSTTTHHHHHHHHHHHHHHTS--CSEEEEEET
T ss_pred             CCeEEEECCCcChHHHHHHHHHHHcC----------CCEEEecHHHHHHHHhhHHHHHHHHHHHHHHhc--CCcEEehhh
Confidence            34589999999999999999997642          457777777776667788888999999988754  588999999


Q ss_pred             cccc-cccccccccccccchhhhHHHHHHHhhccc-CCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCch
Q 003038          307 LEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGS  383 (854)
Q Consensus       307 l~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~s  383 (854)
                      ++.+ ........+   ......+.+..+-..+.. ...+ .+.++++|+..+     ..||++-|.-+| ..|.|+.|+
T Consensus       141 id~l~~~~~~~~~~---~~~~~~~~~~~ll~~lsgg~~~~-~~i~~a~t~~p~-----~ld~~l~r~~rf~~~i~i~~p~  211 (278)
T 1iy2_A          141 IDAVGRKRGSGVGG---GNDEREQTLNQLLVEMDGFEKDT-AIVVMAATNRPD-----ILDPALLRPGRFDRQIAIDAPD  211 (278)
T ss_dssp             HHHHHCC-----------CHHHHHHHHHHHHHHTTCCTTC-CEEEEEEESCTT-----SSCHHHHSTTSSCCEEECCCCC
T ss_pred             hHhhhcccccccCC---cchHHHHHHHHHHHHHhCCCCCC-CEEEEEecCCch-----hCCHhHcCCCcCCeEEEeCCcC
Confidence            9988 432210000   000011222222222321 1111 366666666543     368888774344 245666666


Q ss_pred             HHH
Q 003038          384 LSL  386 (854)
Q Consensus       384 l~~  386 (854)
                      ...
T Consensus       212 ~~~  214 (278)
T 1iy2_A          212 VKG  214 (278)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>3fh2_A Probable ATP-dependent protease (heat shock prote; struct genomics, PSI2, MCSG, protein structure initiative; 1.60A {Corynebacterium glutamicum}

Probab=98.30  E-value=1.3e-06  Score=84.29  Aligned_cols=65  Identities=11%  Similarity=0.099  Sum_probs=59.9

Q ss_pred             HhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHh
Q 003038           10 QGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVAL   77 (854)
Q Consensus        10 ~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L   77 (854)
                      ..||+.+.++|+.|..+|+++||.+|+++|||+||+.++++.+.++|.++|+++   +.|+..+...+
T Consensus        80 ~~~s~~~~~vL~~A~~~a~~~~~~~i~~eHlLlall~~~~~~a~~iL~~~gv~~---~~l~~~l~~~~  144 (146)
T 3fh2_A           80 IPFTPRAKKVLELSLREGLQMGHKYIGTEFLLLGLIREGEGVAAQVLVKLGADL---PRVRQQVIQLL  144 (146)
T ss_dssp             CCBCHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHCSSHHHHHHHHHTCCH---HHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHhCCCcHHHHHHHHcCCCH---HHHHHHHHHHh
Confidence            369999999999999999999999999999999999998889999999999987   78888887655

>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=98.29  E-value=2e-07  Score=109.17  Aligned_cols=127  Identities=9%  Similarity=0.023  Sum_probs=74.8

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc---------cchHHHHHHHHHHHHHHHhhhC
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH---------MNRVEVEQRVEEIKNLVRSCLG  297 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~---------~~rge~E~rl~~l~~~~~~~~~  297 (854)
                      ..+++|+||||||||++++.++..+          +..++.++++.+..         .|.|....++..++..+...  
T Consensus       108 g~~vll~Gp~GtGKTtlar~ia~~l----------~~~~~~i~~~~~~~~~~~~g~~~~~ig~~~~~~~~~~~~a~~~--  175 (543)
T 3m6a_A          108 GPILCLAGPPGVGKTSLAKSIAKSL----------GRKFVRISLGGVRDESEIRGHRRTYVGAMPGRIIQGMKKAGKL--  175 (543)
T ss_dssp             SCEEEEESSSSSSHHHHHHHHHHHH----------TCEEEEECCCC--------------------CHHHHHHTTCSS--
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhc----------CCCeEEEEecccchhhhhhhHHHHHhccCchHHHHHHHHhhcc--
Confidence            5579999999999999999999876          33566666554322         36677777777777665543  


Q ss_pred             CCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccC---------CCC----ceEEEEEecCHHHHHHhhc
Q 003038          298 RGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGI---------GEN----ARFWLMGIATFQSYMRCKS  363 (854)
Q Consensus       298 ~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~---------~g~----g~l~lIgatT~~ey~k~~~  363 (854)
                       +.||||||++.+ ......             ....+-.+|.+.         .+.    +.+.+|+||+...     .
T Consensus       176 -~~vl~lDEid~l~~~~~~~-------------~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI~ttN~~~-----~  236 (543)
T 3m6a_A          176 -NPVFLLDEIDKMSSDFRGD-------------PSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFIATANNLA-----T  236 (543)
T ss_dssp             -SEEEEEEESSSCC----------------------CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEEEECSSTT-----T
T ss_pred             -CCEEEEhhhhhhhhhhccC-------------HHHHHHHHHhhhhcceeecccCCeeecccceEEEeccCccc-----c
Confidence             349999999999 432210             111122222110         000    3588998887643     5


Q ss_pred             cCCchhhhhccCCCCCCCchHHH
Q 003038          364 GHPSLETLWSLHPLTIPAGSLSL  386 (854)
Q Consensus       364 ~~pale~~~~~~~v~i~~~sl~~  386 (854)
                      .+|+|.+  ||+.|.++.++...
T Consensus       237 l~~aL~~--R~~vi~~~~~~~~e  257 (543)
T 3m6a_A          237 IPGPLRD--RMEIINIAGYTEIE  257 (543)
T ss_dssp             SCHHHHH--HEEEEECCCCCHHH
T ss_pred             CCHHHHh--hcceeeeCCCCHHH
Confidence            6799999  77778888776543

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=98.29  E-value=1.1e-06  Score=107.09  Aligned_cols=114  Identities=12%  Similarity=0.208  Sum_probs=69.3

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC-------CCceEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS-------HNNFVS  690 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-------~~~~i~  690 (854)
                      ..|+||++.+..+...+.+.                  ....+||+||+|||||.+|++||+.+...       ...++.
T Consensus       180 d~iiG~~~~i~~l~~~l~~~------------------~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~~  241 (758)
T 3pxi_A          180 DPVIGRSKEIQRVIEVLSRR------------------TKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMT  241 (758)
T ss_dssp             CCCCCCHHHHHHHHHHHHCS------------------SSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEEC
T ss_pred             CCccCchHHHHHHHHHHhCC------------------CCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEEE
Confidence            35899999999888876531                  12368999999999999999999998542       234444


Q ss_pred             EccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceee
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVS  770 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~  770 (854)
                      +|+.  .        ++     .+... .....+.+.+......|||||    ...+.++.|+++++.|.+         
T Consensus       242 ~~~g--~--------~~-----~G~~e-~~l~~~~~~~~~~~~~iLfiD----~~~~~~~~L~~~l~~~~v---------  292 (758)
T 3pxi_A          242 LDMG--T--------KY-----RGEFE-DRLKKVMDEIRQAGNIILFID----AAIDASNILKPSLARGEL---------  292 (758)
T ss_dssp             C-------------------------C-TTHHHHHHHHHTCCCCEEEEC----C--------CCCTTSSSC---------
T ss_pred             eccc--c--------cc-----cchHH-HHHHHHHHHHHhcCCEEEEEc----CchhHHHHHHHHHhcCCE---------
Confidence            4440  0        00     00000 111245555666777899999    677899999999997644         


Q ss_pred             cCCeEEEEecCC
Q 003038          771 LGDAIVILSCES  782 (854)
Q Consensus       771 ~~~aIiIlTsn~  782 (854)
                          ++|.++|.
T Consensus       293 ----~~I~at~~  300 (758)
T 3pxi_A          293 ----QCIGATTL  300 (758)
T ss_dssp             ----EEEEECCT
T ss_pred             ----EEEeCCCh
Confidence                48888874

>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=98.28  E-value=2.4e-06  Score=84.69  Aligned_cols=101  Identities=13%  Similarity=0.081  Sum_probs=61.8

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHh-CCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVF-GSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVF  736 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lf-g~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vi  736 (854)
                      ..++|+||+|+|||+++++|+..+. .....++.+++.++.       +...  ......  .. +.+.+.+.  ...|+
T Consensus        39 ~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~~~~~~~-------~~~~--~~~~~~--~~-~~~~~~~~--~~~ll  104 (180)
T 3ec2_A           39 KGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFDTKDLI-------FRLK--HLMDEG--KD-TKFLKTVL--NSPVL  104 (180)
T ss_dssp             CEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEEEHHHHH-------HHHH--HHHHHT--CC-SHHHHHHH--TCSEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEEEHHHHH-------HHHH--HHhcCc--hH-HHHHHHhc--CCCEE
Confidence            4789999999999999999999885 223344555554433       1100  000000  00 02333333  34699


Q ss_pred             EEecCC--CCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCC
Q 003038          737 LIEDVE--QADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       737 liDEie--ka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      +|||++  ..++..+..|.+.++.-.          -.+..+|+|||.
T Consensus       105 ilDE~~~~~~~~~~~~~l~~ll~~~~----------~~~~~ii~tsn~  142 (180)
T 3ec2_A          105 VLDDLGSERLSDWQRELISYIITYRY----------NNLKSTIITTNY  142 (180)
T ss_dssp             EEETCSSSCCCHHHHHHHHHHHHHHH----------HTTCEEEEECCC
T ss_pred             EEeCCCCCcCCHHHHHHHHHHHHHHH----------HcCCCEEEEcCC
Confidence            999998  678888888888886411          123457778873

>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=98.27  E-value=6.5e-07  Score=98.61  Aligned_cols=138  Identities=14%  Similarity=0.117  Sum_probs=85.8

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC---CCceEEEccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS---HNNFVSIALS  694 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~---~~~~i~id~s  694 (854)
                      ..++|+++.+..|...+.....+              ++...++|+||+|+|||++++.+++.+...   ...++.+++.
T Consensus        20 ~~~~gr~~e~~~l~~~l~~~~~~--------------~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~   85 (386)
T 2qby_A           20 DELPHREDQIRKIASILAPLYRE--------------EKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTR   85 (386)
T ss_dssp             SCCTTCHHHHHHHHHSSGGGGGT--------------CCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcC--------------CCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECC
Confidence            56799998888887776654321              223478999999999999999999987432   4577888876


Q ss_pred             cccCcCCCccccccccccCC----CCCCchH---HHHHHHHHcCC-CEEEEEecCCCCC----HHHHHHHHHhhhcCeEe
Q 003038          695 SFSSTRADSTEDSRNKRSRD----EQSCSYI---ERFAEAVSNNP-HRVFLIEDVEQAD----YCSQKGFKRAIESGRIV  762 (854)
Q Consensus       695 ~~~~~~~~s~e~~~~~rl~~----~~g~g~~---e~L~eav~~~p-~~ViliDEieka~----~~v~~~Ll~~le~G~l~  762 (854)
                      .......   --..+...++    ..+....   +.+.+.+.... ..||+|||++.+.    .+++..|++.++..   
T Consensus        86 ~~~~~~~---~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~---  159 (386)
T 2qby_A           86 QIDTPYR---VLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEV---  159 (386)
T ss_dssp             HHCSHHH---HHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSC---
T ss_pred             CCCCHHH---HHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhc---
Confidence            4431000   0000000010    1111122   24566666543 6899999999875    66778888888643   


Q ss_pred             cCCCceeecCCeEEEEecCC
Q 003038          763 TSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       763 d~~G~~v~~~~aIiIlTsn~  782 (854)
                             .-.+.+||++++.
T Consensus       160 -------~~~~~~~I~~~~~  172 (386)
T 2qby_A          160 -------NKSKISFIGITND  172 (386)
T ss_dssp             -------CC--EEEEEEESC
T ss_pred             -------CCCeEEEEEEECC
Confidence                   1135668888864

>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=98.27  E-value=8.1e-07  Score=103.37  Aligned_cols=139  Identities=9%  Similarity=0.005  Sum_probs=85.6

Q ss_pred             cHHHHHHHHHHhhcc-----------------CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccc
Q 003038          211 RNEDVMYVIENLMSK-----------------RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSF  273 (854)
Q Consensus       211 r~~ei~~v~~~L~r~-----------------~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l  273 (854)
                      +++.++.+.+.|..-                 ..++++|+||||+|||++|+.+|..+          +..++.++.+.+
T Consensus        44 ~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l----------~~~~i~in~s~~  113 (516)
T 1sxj_A           44 NKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL----------GYDILEQNASDV  113 (516)
T ss_dssp             CHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT----------TCEEEEECTTSC
T ss_pred             CHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHc----------CCCEEEEeCCCc
Confidence            788888888887651                 34789999999999999999999875          568888888766


Q ss_pred             cccchHHHHHHH---------HHHHHHH----HhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcc
Q 003038          274 RHMNRVEVEQRV---------EEIKNLV----RSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVC  339 (854)
Q Consensus       274 ~~~~rge~E~rl---------~~l~~~~----~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~  339 (854)
                      ......  +..+         ..++..+    ... +.+.||||||++.+ .....              +...+.+++.
T Consensus       114 ~~~~~~--~~~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~vliIDEid~l~~~~~~--------------~l~~L~~~l~  176 (516)
T 1sxj_A          114 RSKTLL--NAGVKNALDNMSVVGYFKHNEEAQNLN-GKHFVIIMDEVDGMSGGDRG--------------GVGQLAQFCR  176 (516)
T ss_dssp             CCHHHH--HHTGGGGTTBCCSTTTTTC----CCSS-TTSEEEEECSGGGCCTTSTT--------------HHHHHHHHHH
T ss_pred             chHHHH--HHHHHHHhccccHHHHHhhhhhhhhcc-CCCeEEEEECCCccchhhHH--------------HHHHHHHHHH
Confidence            543211  1111         1112211    111 45899999999999 53221              3344556664


Q ss_pred             cCCCCceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHH
Q 003038          340 GIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSL  386 (854)
Q Consensus       340 ~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~  386 (854)
                      ....  .+.+|++++...      .-+.|.+  +.+.+.++.++...
T Consensus       177 ~~~~--~iIli~~~~~~~------~l~~l~~--r~~~i~f~~~~~~~  213 (516)
T 1sxj_A          177 KTST--PLILICNERNLP------KMRPFDR--VCLDIQFRRPDANS  213 (516)
T ss_dssp             HCSS--CEEEEESCTTSS------TTGGGTT--TSEEEECCCCCHHH
T ss_pred             hcCC--CEEEEEcCCCCc------cchhhHh--ceEEEEeCCCCHHH
Confidence            3222  477777765321      1234545  44566666665443

>3fes_A ATP-dependent CLP endopeptidase; alpha-helical bundles, structural genomics, PSI-2, protein S initiative; HET: PG4 EPE; 1.82A {Clostridium difficile}

Probab=98.26  E-value=1e-06  Score=84.93  Aligned_cols=64  Identities=8%  Similarity=0.064  Sum_probs=58.3

Q ss_pred             HhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHH
Q 003038           10 QGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVA   76 (854)
Q Consensus        10 ~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~   76 (854)
                      ..||+.+.++|+.|..+|+++||.+|+++|||+||+.++++.+.++|.++|+++   +.|+..+...
T Consensus        80 ~~~s~~~~~vl~~A~~~A~~~~~~~v~~eHlLlAll~~~~~~a~~iL~~~gv~~---~~l~~~i~~~  143 (145)
T 3fes_A           80 IVLSPRSKQILELSGMFANKLKTNYIGTEHILLAIIQEGEGIANKILNYAGVND---RTLAQLTIDM  143 (145)
T ss_dssp             CEECHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHCCHHHHHHHHHHTCHH---HHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCCCcHHHHHHHHcCCCH---HHHHHHHHHH
Confidence            359999999999999999999999999999999999999888999999999976   7888777654

>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=98.24  E-value=2.6e-06  Score=92.63  Aligned_cols=87  Identities=13%  Similarity=0.171  Sum_probs=59.9

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      ..++|+||+|+|||++|++++..+......++.+++..+.       .... ..+..    +..+.+.+..+.  ..|+|
T Consensus        38 ~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~~~~~-------~~~~-~~~~~----~~~~~~~~~~~~--~~vL~  103 (324)
T 1l8q_A           38 NPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFA-------QAMV-EHLKK----GTINEFRNMYKS--VDLLL  103 (324)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHHH-------HHHH-HHHHH----TCHHHHHHHHHT--CSEEE
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEHHHHH-------HHHH-HHHHc----CcHHHHHHHhcC--CCEEE
Confidence            4789999999999999999999887656788888877554       1110 00000    111233444432  57999


Q ss_pred             EecCCCCCH--HHHHHHHHhhhc
Q 003038          738 IEDVEQADY--CSQKGFKRAIES  758 (854)
Q Consensus       738 iDEieka~~--~v~~~Ll~~le~  758 (854)
                      ||||+.+..  ..|..|+..++.
T Consensus       104 iDEi~~l~~~~~~~~~l~~~l~~  126 (324)
T 1l8q_A          104 LDDVQFLSGKERTQIEFFHIFNT  126 (324)
T ss_dssp             EECGGGGTTCHHHHHHHHHHHHH
T ss_pred             EcCcccccCChHHHHHHHHHHHH
Confidence            999999876  778888888763

>3f8t_A Predicted ATPase involved in replication control, CDC46/MCM family; helicase, MCM homolog, DNA replication, ATP-binding, DNA-binding; 1.90A {Methanopyrus kandleri AV19}

Probab=98.23  E-value=8.1e-07  Score=100.66  Aligned_cols=146  Identities=14%  Similarity=0.202  Sum_probs=93.1

Q ss_pred             HHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHH-HHHHhCCC
Q 003038          607 ENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKEL-ARLVFGSH  685 (854)
Q Consensus       607 e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~L-A~~lfg~~  685 (854)
                      ..+..|.+.+.. |+||+++...|.-++..   |-.+          .+...++|+.|++|+ ||.+|+.+ ++.+ . .
T Consensus       203 ~~~~~l~~sIap-I~G~e~vK~aLll~L~G---G~~k----------~rgdihVLL~G~PGt-KS~Lar~i~~~i~-p-R  265 (506)
T 3f8t_A          203 DPLTTFARAIAP-LPGAEEVGKMLALQLFS---CVGK----------NSERLHVLLAGYPVV-CSEILHHVLDHLA-P-R  265 (506)
T ss_dssp             CHHHHHHHHHCC-STTCHHHHHHHHHHHTT---CCSS----------GGGCCCEEEESCHHH-HHHHHHHHHHHTC-S-S
T ss_pred             HHHHHHHHHhcc-cCCCHHHHHHHHHHHcC---Cccc----------cCCceeEEEECCCCh-HHHHHHHHHHHhC-C-C
Confidence            456788889999 99999887666555433   2111          133458999999999 99999999 7765 1 1


Q ss_pred             CceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCC
Q 003038          686 NNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSS  765 (854)
Q Consensus       686 ~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~  765 (854)
                      ..|+...++...        ..... ...+.|+.+.   .+++-.....|+|+|||+++++..|..|+++|++|.++-. 
T Consensus       266 ~~ft~g~~ss~~--------gLt~s-~r~~tG~~~~---~G~l~LAdgGvl~lDEIn~~~~~~qsaLlEaMEe~~VtI~-  332 (506)
T 3f8t_A          266 GVYVDLRRTELT--------DLTAV-LKEDRGWALR---AGAAVLADGGILAVDHLEGAPEPHRWALMEAMDKGTVTVD-  332 (506)
T ss_dssp             EEEEEGGGCCHH--------HHSEE-EEESSSEEEE---ECHHHHTTTSEEEEECCTTCCHHHHHHHHHHHHHSEEEET-
T ss_pred             eEEecCCCCCcc--------CceEE-EEcCCCcccC---CCeeEEcCCCeeehHhhhhCCHHHHHHHHHHHhCCcEEEC-
Confidence            122222221100        00000 0011111000   1112223468999999999999999999999999999977 


Q ss_pred             Cceeec-CCeEEEEecCCCC
Q 003038          766 GDEVSL-GDAIVILSCESFS  784 (854)
Q Consensus       766 G~~v~~-~~aIiIlTsn~f~  784 (854)
                      |.  .+ .++.||.|+|.-.
T Consensus       333 G~--~lparf~VIAA~NP~~  350 (506)
T 3f8t_A          333 GI--ALNARCAVLAAINPGE  350 (506)
T ss_dssp             TE--EEECCCEEEEEECCCC
T ss_pred             CE--EcCCCeEEEEEeCccc
Confidence            66  43 5788999999643

>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=98.22  E-value=9.7e-07  Score=97.80  Aligned_cols=75  Identities=9%  Similarity=0.092  Sum_probs=59.8

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc-cchHHH-HHHHHHHHHHH----HhhhCCC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH-MNRVEV-EQRVEEIKNLV----RSCLGRG  299 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~-~~rge~-E~rl~~l~~~~----~~~~~~~  299 (854)
                      ...+++|+||||||||++++.+|...          +..++.++.+.+.. +|.|+. +..+.+++...    ...  .+
T Consensus        50 ~~~~vll~GppGtGKT~la~~ia~~~----------~~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~--~~  117 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLAETLARLL----------DVPFTMADATTLTEAGYVGEDVENIIQKLLQKCDYDVQKA--QR  117 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHT----------TCCEEEEEHHHHTTCHHHHHHHTHHHHHHHHHTTTCHHHH--HH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHc----------CCCEEEechHHhcccccccccHHHHHHHHHHHhhhhHHhc--CC
Confidence            46789999999999999999999874          56899999988874 488875 66677777664    322  36


Q ss_pred             eEEEeCccccc-cc
Q 003038          300 IVLNLGDLEWA-EF  312 (854)
Q Consensus       300 ~ILfidel~~l-~~  312 (854)
                      .||||||++.+ ..
T Consensus       118 ~vl~lDEid~l~~~  131 (363)
T 3hws_A          118 GIVYIDQIDKISRK  131 (363)
T ss_dssp             CEEEEECHHHHCCC
T ss_pred             cEEEEeChhhhccc
Confidence            79999999999 44

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=98.21  E-value=9.7e-06  Score=86.52  Aligned_cols=95  Identities=13%  Similarity=0.150  Sum_probs=62.9

Q ss_pred             EEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchH----HHHHHHHHcCCCEE
Q 003038          660 LFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYI----ERFAEAVSNNPHRV  735 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~----e~L~eav~~~p~~V  735 (854)
                      ++|+||+|+|||+++++||..+ +  ..++.++.+++.       ...          .|..    ..+.+..+....+|
T Consensus        47 vlL~Gp~GtGKTtLakala~~~-~--~~~i~i~g~~l~-------~~~----------~~~~~~~i~~vf~~a~~~~p~i  106 (274)
T 2x8a_A           47 VLLAGPPGCGKTLLAKAVANES-G--LNFISVKGPELL-------NMY----------VGESERAVRQVFQRAKNSAPCV  106 (274)
T ss_dssp             EEEESSTTSCHHHHHHHHHHHT-T--CEEEEEETTTTC-------SST----------THHHHHHHHHHHHHHHHTCSEE
T ss_pred             EEEECCCCCcHHHHHHHHHHHc-C--CCEEEEEcHHHH-------hhh----------hhHHHHHHHHHHHHHHhcCCCe
Confidence            8999999999999999999976 3  368888876543       110          0111    13444444556689


Q ss_pred             EEEecCCCCC-----------HHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCC
Q 003038          736 FLIEDVEQAD-----------YCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       736 iliDEieka~-----------~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                      +++|||+..-           ..+.+.++..|+.|.         .-+.+|++.++|.-
T Consensus       107 ~~~Deid~~~~~r~~~~~~~~~~~~~~~l~~Lsgg~---------~~~~~i~ia~tn~p  156 (274)
T 2x8a_A          107 IFFDEVDALCPRRSDRETGASVRVVNQLLTEMDGLE---------ARQQVFIMAATNRP  156 (274)
T ss_dssp             EEEETCTTTCC---------CTTHHHHHHHHHHTCC---------STTCEEEEEEESCG
T ss_pred             EeeehhhhhhcccCCCcchHHHHHHHHHHHhhhccc---------ccCCEEEEeecCCh
Confidence            9999999752           235566666676542         12456788888753

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=98.17  E-value=4.3e-07  Score=98.50  Aligned_cols=141  Identities=11%  Similarity=0.066  Sum_probs=80.0

Q ss_pred             cHHHHHHHHHHhhc--cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc------------
Q 003038          211 RNEDVMYVIENLMS--KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM------------  276 (854)
Q Consensus       211 r~~ei~~v~~~L~r--~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~------------  276 (854)
                      +...++++++.+.+  +...+++|+||||||||.+++.++....+       .+..|+.++++.+...            
T Consensus         7 ~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~-------~~~~~v~v~~~~~~~~l~~~~lfg~~~g   79 (304)
T 1ojl_A            7 SSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSAR-------SDRPLVTLNCAALNESLLESELFGHEKG   79 (304)
T ss_dssp             CSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHHSSC-------SSSCCCEEECSSCCHHHHHHHHTCCCSS
T ss_pred             CCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHhCcc-------cCCCeEEEeCCCCChHHHHHHhcCcccc
Confidence            55667777766655  57789999999999999999999986433       2446777776655321            


Q ss_pred             -chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-----CCC----Cc
Q 003038          277 -NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-----IGE----NA  345 (854)
Q Consensus       277 -~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-----~~g----~g  345 (854)
                       +.|.... ...++..+     .+.+||||||+.+ ...                 ...+-.+|..     .++    ..
T Consensus        80 ~~tg~~~~-~~g~~~~a-----~~g~L~LDEi~~l~~~~-----------------q~~Ll~~l~~~~~~~~g~~~~~~~  136 (304)
T 1ojl_A           80 AFTGADKR-REGRFVEA-----DGGTLFLDEIGDISPLM-----------------QVRLLRAIQEREVQRVGSNQTISV  136 (304)
T ss_dssp             CCC---CC-CCCHHHHH-----TTSEEEEESCTTCCHHH-----------------HHHHHHHHHSSBCCBTTBCCCCBC
T ss_pred             ccCchhhh-hcCHHHhc-----CCCEEEEeccccCCHHH-----------------HHHHHHHHhcCEeeecCCcccccC
Confidence             1111111 11222222     2447999999998 431                 1123333321     000    12


Q ss_pred             eEEEEEecCHHHHHHhh--ccCCchhhhhccCCCCCCCch
Q 003038          346 RFWLMGIATFQSYMRCK--SGHPSLETLWSLHPLTIPAGS  383 (854)
Q Consensus       346 ~l~lIgatT~~ey~k~~--~~~pale~~~~~~~v~i~~~s  383 (854)
                      .+++|+||+..-.....  ..++.|-.  ||..+.|.-|.
T Consensus       137 ~~riI~atn~~l~~~v~~g~fr~~L~~--Rl~~~~i~lPp  174 (304)
T 1ojl_A          137 DVRLIAATHRDLAEEVSAGRFRQDLYY--RLNVVAIEMPS  174 (304)
T ss_dssp             CCEEEEEESSCHHHHHHHTSSCHHHHH--HHSSEEEECCC
T ss_pred             CeEEEEecCccHHHHHHhCCcHHHHHh--hcCeeEEeccC
Confidence            58999999875222111  12445555  77666544333

>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=98.17  E-value=3.4e-06  Score=88.40  Aligned_cols=96  Identities=11%  Similarity=0.168  Sum_probs=60.0

Q ss_pred             EEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCc--hHHHHHHHHHcCCCEEEE
Q 003038          660 LFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCS--YIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g--~~e~L~eav~~~p~~Vil  737 (854)
                      ++|+||+|+|||+++++|+..+   ...++.++...+.       ...        .+.+  ....+.+.......++++
T Consensus        52 ~ll~G~~G~GKTtl~~~i~~~~---~~~~i~~~~~~~~-------~~~--------~~~~~~~i~~~~~~~~~~~~~i~~  113 (254)
T 1ixz_A           52 VLLVGPPGVGKTHLARAVAGEA---RVPFITASGSDFV-------EMF--------VGVGAARVRDLFETAKRHAPCIVF  113 (254)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHT---TCCEEEEEHHHHH-------HSC--------TTHHHHHHHHHHHHHTTSSSEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHh---CCCEEEeeHHHHH-------HHH--------hhHHHHHHHHHHHHHHhcCCeEEE
Confidence            8999999999999999999987   2567888766443       110        0100  011344444444568999


Q ss_pred             EecCCCCC--------------HHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCC
Q 003038          738 IEDVEQAD--------------YCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       738 iDEieka~--------------~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      +||||.+.              ....+.++..|+.|.-         -+..|++.++|.
T Consensus       114 ~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~~---------~~~~i~~a~t~~  163 (254)
T 1ixz_A          114 IDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEK---------DTAIVVMAATNR  163 (254)
T ss_dssp             EETHHHHHC---------CHHHHHHHHHHHHHHHTCCT---------TCCEEEEEEESC
T ss_pred             ehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCCC---------CCCEEEEEccCC
Confidence            99997542              1245566666664321         134567777764

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.15  E-value=4.3e-06  Score=90.00  Aligned_cols=139  Identities=9%  Similarity=-0.054  Sum_probs=87.6

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKN  290 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~  290 (854)
                      +++.++.+...+...+..+++|+||||+|||++++.+++.+....     .+..++.++.+....  .    ..++++++
T Consensus        26 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~-----~~~~~~~~~~~~~~~--~----~~i~~~~~   94 (323)
T 1sxj_B           26 NKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRS-----YADGVLELNASDDRG--I----DVVRNQIK   94 (323)
T ss_dssp             CTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGG-----HHHHEEEECTTSCCS--H----HHHHTHHH
T ss_pred             CHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCc-----ccCCEEEecCccccC--h----HHHHHHHH
Confidence            888899998888876666799999999999999999999875421     123466665543221  2    23444555


Q ss_pred             HHHh----h-hCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhcc
Q 003038          291 LVRS----C-LGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSG  364 (854)
Q Consensus       291 ~~~~----~-~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~  364 (854)
                      .+..    . .+++.||+|||+|.+ ...                 ...+..++....+  ...+|.+|+...     ..
T Consensus        95 ~~~~~~~~~~~~~~~viiiDe~~~l~~~~-----------------~~~L~~~le~~~~--~~~~il~~~~~~-----~l  150 (323)
T 1sxj_B           95 HFAQKKLHLPPGKHKIVILDEADSMTAGA-----------------QQALRRTMELYSN--STRFAFACNQSN-----KI  150 (323)
T ss_dssp             HHHHBCCCCCTTCCEEEEEESGGGSCHHH-----------------HHTTHHHHHHTTT--TEEEEEEESCGG-----GS
T ss_pred             HHHhccccCCCCCceEEEEECcccCCHHH-----------------HHHHHHHHhccCC--CceEEEEeCChh-----hc
Confidence            4441    0 134789999999999 431                 1123334421112  377888776521     34


Q ss_pred             CCchhhhhccCCCCCCCchHHH
Q 003038          365 HPSLETLWSLHPLTIPAGSLSL  386 (854)
Q Consensus       365 ~pale~~~~~~~v~i~~~sl~~  386 (854)
                      .|++.+  |++.+.++.++...
T Consensus       151 ~~~l~s--r~~~i~~~~~~~~~  170 (323)
T 1sxj_B          151 IEPLQS--QCAILRYSKLSDED  170 (323)
T ss_dssp             CHHHHT--TSEEEECCCCCHHH
T ss_pred             hhHHHh--hceEEeecCCCHHH
Confidence            677777  66677777665443

>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=98.11  E-value=5.2e-06  Score=94.62  Aligned_cols=88  Identities=19%  Similarity=0.201  Sum_probs=58.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCC--CCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGS--HNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRV  735 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~--~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~V  735 (854)
                      ..++|+||+|+|||++|++|+..+...  ...++.+++..+.       .... . .+..   +..+.+.+..+ ....|
T Consensus       131 ~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~~~~-------~~~~-~-~~~~---~~~~~~~~~~~-~~~~v  197 (440)
T 2z4s_A          131 NPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFL-------NDLV-D-SMKE---GKLNEFREKYR-KKVDI  197 (440)
T ss_dssp             CCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHHHHH-------HHHH-H-HHHT---TCHHHHHHHHT-TTCSE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHH-------HHHH-H-HHHc---ccHHHHHHHhc-CCCCE
Confidence            479999999999999999999988543  4567888776553       1110 0 0000   01112233222 14579


Q ss_pred             EEEecCCCCCH--HHHHHHHHhhhc
Q 003038          736 FLIEDVEQADY--CSQKGFKRAIES  758 (854)
Q Consensus       736 iliDEieka~~--~v~~~Ll~~le~  758 (854)
                      +|||||+.+..  ..|+.|+..|+.
T Consensus       198 L~IDEi~~l~~~~~~q~~l~~~l~~  222 (440)
T 2z4s_A          198 LLIDDVQFLIGKTGVQTELFHTFNE  222 (440)
T ss_dssp             EEEECGGGGSSCHHHHHHHHHHHHH
T ss_pred             EEEeCcccccCChHHHHHHHHHHHH
Confidence            99999999876  788889888864

>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=98.10  E-value=1.8e-06  Score=92.76  Aligned_cols=142  Identities=6%  Similarity=-0.022  Sum_probs=85.5

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKN  290 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~  290 (854)
                      +++.++.+...+...+..+++|+||||+|||++++.++..+....     .+..++.++.+....  ...+...+.++..
T Consensus        22 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~-----~~~~~~~~~~~~~~~--~~~~~~~~~~~~~   94 (319)
T 2chq_A           22 QDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGEN-----WRDNFIEMNASDERG--IDVVRHKIKEFAR   94 (319)
T ss_dssp             CHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHHHHTTC-----HHHHCEEEETTSTTC--TTTSSHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHHhcCCc-----ccCCeEEEeCccccC--hHHHHHHHHHHHh
Confidence            778888888888776666899999999999999999999875321     123466666554322  1111122222211


Q ss_pred             HHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchh
Q 003038          291 LVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLE  369 (854)
Q Consensus       291 ~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale  369 (854)
                      ...-..+++.||+|||+|.+ ...                 ...+..++.....  .+.+|++|+...     ...|++.
T Consensus        95 ~~~~~~~~~~vliiDe~~~l~~~~-----------------~~~L~~~le~~~~--~~~~i~~~~~~~-----~l~~~l~  150 (319)
T 2chq_A           95 TAPIGGAPFKIIFLDEADALTADA-----------------QAALRRTMEMYSK--SCRFILSCNYVS-----RIIEPIQ  150 (319)
T ss_dssp             SCCSSSCCCEEEEEETGGGSCHHH-----------------HHTTGGGTSSSSS--SEEEEEEESCGG-----GSCHHHH
T ss_pred             cCCCCCCCceEEEEeCCCcCCHHH-----------------HHHHHHHHHhcCC--CCeEEEEeCChh-----hcchHHH
Confidence            10000034789999999999 421                 1123334421112  488888887532     3467777


Q ss_pred             hhhccCCCCCCCchHH
Q 003038          370 TLWSLHPLTIPAGSLS  385 (854)
Q Consensus       370 ~~~~~~~v~i~~~sl~  385 (854)
                      +  |++.+.++.++..
T Consensus       151 s--r~~~i~~~~~~~~  164 (319)
T 2chq_A          151 S--RCAVFRFKPVPKE  164 (319)
T ss_dssp             T--TCEEEECCCCCHH
T ss_pred             h--hCeEEEecCCCHH
Confidence            7  6667777665543

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.10  E-value=2.4e-06  Score=86.16  Aligned_cols=86  Identities=9%  Similarity=0.146  Sum_probs=52.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      ..++|+||+|+|||.+|++|+..+......++.++++++.       ....  ......  .+ ..+.+.+...  .||+
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~~~-------~~~~--~~~~~~--~~-~~~~~~~~~~--~~li  120 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPELF-------RELK--HSLQDQ--TM-NEKLDYIKKV--PVLM  120 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEEHHHHH-------HHHH--HC---C--CC-HHHHHHHHHS--SEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEhHHHH-------HHHH--HHhccc--hH-HHHHHHhcCC--CEEE
Confidence            4789999999999999999999987666677777776543       1110  001001  11 2233444433  4999


Q ss_pred             EecCCC--CCHHHHHHHH-Hhhh
Q 003038          738 IEDVEQ--ADYCSQKGFK-RAIE  757 (854)
Q Consensus       738 iDEiek--a~~~v~~~Ll-~~le  757 (854)
                      ||||+.  .+...+..|+ .+++
T Consensus       121 lDei~~~~~~~~~~~~ll~~~l~  143 (202)
T 2w58_A          121 LDDLGAEAMSSWVRDDVFGPILQ  143 (202)
T ss_dssp             EEEECCC---CCGGGTTHHHHHH
T ss_pred             EcCCCCCcCCHHHHHHHHHHHHH
Confidence            999965  4444455333 4554

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=98.10  E-value=2.4e-06  Score=97.38  Aligned_cols=141  Identities=8%  Similarity=0.038  Sum_probs=81.6

Q ss_pred             HHHHHHhhccC-cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHH-HHHHHHHHH
Q 003038          216 MYVIENLMSKR-KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQR-VEEIKNLVR  293 (854)
Q Consensus       216 ~~v~~~L~r~~-k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~r-l~~l~~~~~  293 (854)
                      ..+..+..... .++++|+||||+|||+++++++..+...     ..+.+++.++...+...+.+.+... +..+.....
T Consensus       118 ~~~~~~a~~~~~~~~lll~Gp~G~GKTtLa~aia~~l~~~-----~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~~~  192 (440)
T 2z4s_A          118 HAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQN-----EPDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYR  192 (440)
T ss_dssp             HHHHHHHHSTTSSCCEEEECSSSSSHHHHHHHHHHHHHHH-----CCSSCEEEEEHHHHHHHHHHHHHTTCHHHHHHHHT
T ss_pred             HHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHh-----CCCCeEEEeeHHHHHHHHHHHHHcccHHHHHHHhc
Confidence            33444433323 5789999999999999999999887542     1256778887776654333333322 111222111


Q ss_pred             hhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecC-HHHHHHhhccCCchh
Q 003038          294 SCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIAT-FQSYMRCKSGHPSLE  369 (854)
Q Consensus       294 ~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT-~~ey~k~~~~~pale  369 (854)
                         ..+.||||||+|.+ +...               ...++-.++..  ..|  ...+|++.. +.++   ...++.|.
T Consensus       193 ---~~~~vL~IDEi~~l~~~~~---------------~q~~l~~~l~~l~~~~--~~iIitt~~~~~~l---~~l~~~L~  249 (440)
T 2z4s_A          193 ---KKVDILLIDDVQFLIGKTG---------------VQTELFHTFNELHDSG--KQIVICSDREPQKL---SEFQDRLV  249 (440)
T ss_dssp             ---TTCSEEEEECGGGGSSCHH---------------HHHHHHHHHHHHHTTT--CEEEEEESSCGGGC---SSCCHHHH
T ss_pred             ---CCCCEEEEeCcccccCChH---------------HHHHHHHHHHHHHHCC--CeEEEEECCCHHHH---HHHHHHHH
Confidence               15789999999999 6321               11233333311  223  355665543 3332   23567777


Q ss_pred             hhhcc---CCCCCCCchHHH
Q 003038          370 TLWSL---HPLTIPAGSLSL  386 (854)
Q Consensus       370 ~~~~~---~~v~i~~~sl~~  386 (854)
                      +  ||   ..+.++.++...
T Consensus       250 s--R~~~g~~i~l~~p~~e~  267 (440)
T 2z4s_A          250 S--RFQMGLVAKLEPPDEET  267 (440)
T ss_dssp             H--HHHSSBCCBCCCCCHHH
T ss_pred             h--hccCCeEEEeCCCCHHH
Confidence            7  66   577888777654

>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=98.10  E-value=7.4e-06  Score=91.36  Aligned_cols=137  Identities=7%  Similarity=0.011  Sum_probs=77.6

Q ss_pred             cHHHHHHHHHHh-hc------cCcCCcee--ecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc------c
Q 003038          211 RNEDVMYVIENL-MS------KRKRNFVV--VGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR------H  275 (854)
Q Consensus       211 r~~ei~~v~~~L-~r------~~k~n~vL--vGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~------~  275 (854)
                      |++|+.++.+.| .+      ...++++|  +||||+|||++++.++..+.... +..-.+..++.++.....      .
T Consensus        27 R~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  105 (412)
T 1w5s_A           27 RRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAA-AKEGLTVKQAYVNAFNAPNLYTILS  105 (412)
T ss_dssp             SCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHH-HHTTCCEEEEEEEGGGCCSHHHHHH
T ss_pred             hHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHH-hccCCceeEEEEECCCCCCHHHHHH
Confidence            999999999988 42      24557888  89999999999999998865410 000013455665542111      0


Q ss_pred             c----------chHH-HHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-CC
Q 003038          276 M----------NRVE-VEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-IG  342 (854)
Q Consensus       276 ~----------~rge-~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-~~  342 (854)
                      .          ..|. .+.-+..+.+.+... ++++||+|||+|++ ...... .          .....+..++.. ..
T Consensus       106 ~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~-~~~~llvlDe~~~l~~~~~~~-~----------~~l~~l~~~~~~~~~  173 (412)
T 1w5s_A          106 LIVRQTGYPIQVRGAPALDILKALVDNLYVE-NHYLLVILDEFQSMLSSPRIA-A----------EDLYTLLRVHEEIPS  173 (412)
T ss_dssp             HHHHHHTCCCCCTTCCHHHHHHHHHHHHHHH-TCEEEEEEESTHHHHSCTTSC-H----------HHHHHHHTHHHHSCC
T ss_pred             HHHHHhCCCCCCCCCCHHHHHHHHHHHHHhc-CCeEEEEEeCHHHHhhccCcc-h----------HHHHHHHHHHHhccc
Confidence            0          0111 222334444444433 56899999999999 541100 0          122233344421 10


Q ss_pred             -C-CceEEEEEecCHHHHHH
Q 003038          343 -E-NARFWLMGIATFQSYMR  360 (854)
Q Consensus       343 -g-~g~l~lIgatT~~ey~k  360 (854)
                       + +..+.+|++|+..++..
T Consensus       174 ~~~~~~v~lI~~~~~~~~~~  193 (412)
T 1w5s_A          174 RDGVNRIGFLLVASDVRALS  193 (412)
T ss_dssp             TTSCCBEEEEEEEEETHHHH
T ss_pred             CCCCceEEEEEEeccccHHH
Confidence             1 13699999986555443

>2y1q_A CLPC N-domain, negative regulator of genetic competence CLPC/MEC; transcription, proteolysis; 1.50A {Bacillus subtilis} PDB: 2y1r_A* 2k77_A

Probab=98.09  E-value=7.4e-06  Score=79.04  Aligned_cols=66  Identities=18%  Similarity=0.149  Sum_probs=59.0

Q ss_pred             HhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhc
Q 003038           10 QGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALN   78 (854)
Q Consensus        10 ~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~   78 (854)
                      ..||+.+.++|+.|..+|+.+||.+|+++|||+||+.++++.+.++|..+|+++   +.++..+.....
T Consensus        78 ~~~s~~~~~vL~~A~~~A~~~~~~~i~~ehlLlall~~~~~~a~~~L~~~gi~~---~~l~~~i~~~~g  143 (150)
T 2y1q_A           78 IHYTPRAKKVIELSMDEARKLGHSYVGTEHILLGLIREGEGVAARVLNNLGVSL---NKARQQVLQLLG  143 (150)
T ss_dssp             CEECHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHCCSHHHHHHHHTTCCH---HHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHhCCCcHHHHHHHHcCCCH---HHHHHHHHHHHC
Confidence            369999999999999999999999999999999999988888889999999987   678877766554

>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=98.09  E-value=4.3e-06  Score=90.10  Aligned_cols=139  Identities=7%  Similarity=-0.009  Sum_probs=82.8

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKN  290 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~  290 (854)
                      +++.++.+...+...+..+++|+||||+|||++++.++..+....     ....++.++.+....  ...+...+.+...
T Consensus        30 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~l~~~~-----~~~~~~~~~~~~~~~--~~~~~~~~~~~~~  102 (327)
T 1iqp_A           30 QEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGEN-----WRHNFLELNASDERG--INVIREKVKEFAR  102 (327)
T ss_dssp             CHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGG-----HHHHEEEEETTCHHH--HHTTHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCc-----ccCceEEeeccccCc--hHHHHHHHHHHHh
Confidence            788888888888877666899999999999999999999875321     123456665443221  1111222222211


Q ss_pred             HHHhhh-CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCch
Q 003038          291 LVRSCL-GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSL  368 (854)
Q Consensus       291 ~~~~~~-~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pal  368 (854)
                      .. ... +++.||+|||+|.+ ...                 ...+..++.....  .+++|.+|+...     ...|++
T Consensus       103 ~~-~~~~~~~~vliiDe~~~l~~~~-----------------~~~L~~~le~~~~--~~~~i~~~~~~~-----~l~~~l  157 (327)
T 1iqp_A          103 TK-PIGGASFKIIFLDEADALTQDA-----------------QQALRRTMEMFSS--NVRFILSCNYSS-----KIIEPI  157 (327)
T ss_dssp             SC-CGGGCSCEEEEEETGGGSCHHH-----------------HHHHHHHHHHTTT--TEEEEEEESCGG-----GSCHHH
T ss_pred             hC-CcCCCCCeEEEEeCCCcCCHHH-----------------HHHHHHHHHhcCC--CCeEEEEeCCcc-----ccCHHH
Confidence            00 000 35789999999999 431                 1233444421112  377888876532     245667


Q ss_pred             hhhhccCCCCCCCch
Q 003038          369 ETLWSLHPLTIPAGS  383 (854)
Q Consensus       369 e~~~~~~~v~i~~~s  383 (854)
                      .+  |++.+.++..+
T Consensus       158 ~s--r~~~~~~~~l~  170 (327)
T 1iqp_A          158 QS--RCAIFRFRPLR  170 (327)
T ss_dssp             HH--TEEEEECCCCC
T ss_pred             Hh--hCcEEEecCCC
Confidence            66  55566665544

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=98.07  E-value=7.3e-06  Score=87.20  Aligned_cols=67  Identities=15%  Similarity=0.250  Sum_probs=45.2

Q ss_pred             EEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCc--hHHHHHHHHHcCCCEEEE
Q 003038          660 LFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCS--YIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g--~~e~L~eav~~~p~~Vil  737 (854)
                      ++|+||+|+|||+++++|+..+-   ..++.+++..+.       ...        .+..  ....+.+.......++++
T Consensus        76 vll~Gp~GtGKTtl~~~i~~~~~---~~~i~~~~~~~~-------~~~--------~~~~~~~i~~~~~~~~~~~~~i~~  137 (278)
T 1iy2_A           76 VLLVGPPGVGKTHLARAVAGEAR---VPFITASGSDFV-------EMF--------VGVGAARVRDLFETAKRHAPCIVF  137 (278)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHTT---CCEEEEEHHHHH-------HST--------TTHHHHHHHHHHHHHHTSCSEEEE
T ss_pred             EEEECCCcChHHHHHHHHHHHcC---CCEEEecHHHHH-------HHH--------hhHHHHHHHHHHHHHHhcCCcEEe
Confidence            89999999999999999999872   567888766443       110        0000  111344444445568999


Q ss_pred             EecCCCC
Q 003038          738 IEDVEQA  744 (854)
Q Consensus       738 iDEieka  744 (854)
                      +|||+.+
T Consensus       138 iDeid~l  144 (278)
T 1iy2_A          138 IDEIDAV  144 (278)
T ss_dssp             EETHHHH
T ss_pred             hhhhHhh
Confidence            9999753

>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=98.05  E-value=7e-06  Score=89.64  Aligned_cols=140  Identities=13%  Similarity=0.092  Sum_probs=82.6

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKN  290 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~  290 (854)
                      +++.++.+...+...+..+++|+||||+|||++++.++..+...+    .....++.++.+....  .+.+.+.+.....
T Consensus        42 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~----~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~  115 (353)
T 1sxj_D           42 QDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPD----LMKSRILELNASDERG--ISIVREKVKNFAR  115 (353)
T ss_dssp             CCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHH----HHTTSEEEECSSSCCC--HHHHTTHHHHHHH
T ss_pred             CHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHhCCCc----ccccceEEEccccccc--hHHHHHHHHHHhh
Confidence            777788888888776667899999999999999999999875310    1124566666554321  1222222222211


Q ss_pred             H-----------HHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHH
Q 003038          291 L-----------VRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSY  358 (854)
Q Consensus       291 ~-----------~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey  358 (854)
                      .           .... +.+.||||||++.+ ...                 ...+..++.....  ..++|.+|+... 
T Consensus       116 ~~~~~~~~~~~~~~~~-~~~~vliiDE~~~l~~~~-----------------~~~Ll~~le~~~~--~~~~il~~~~~~-  174 (353)
T 1sxj_D          116 LTVSKPSKHDLENYPC-PPYKIIILDEADSMTADA-----------------QSALRRTMETYSG--VTRFCLICNYVT-  174 (353)
T ss_dssp             SCCCCCCTTHHHHSCC-CSCEEEEETTGGGSCHHH-----------------HHHHHHHHHHTTT--TEEEEEEESCGG-
T ss_pred             hcccccchhhcccCCC-CCceEEEEECCCccCHHH-----------------HHHHHHHHHhcCC--CceEEEEeCchh-
Confidence            1           1111 34679999999999 431                 1233444421112  255565665322 


Q ss_pred             HHhhccCCchhhhhccCCCCCCCch
Q 003038          359 MRCKSGHPSLETLWSLHPLTIPAGS  383 (854)
Q Consensus       359 ~k~~~~~pale~~~~~~~v~i~~~s  383 (854)
                          ...|++.+  |++.+.++..+
T Consensus       175 ----~l~~~l~s--R~~~i~~~~~~  193 (353)
T 1sxj_D          175 ----RIIDPLAS--QCSKFRFKALD  193 (353)
T ss_dssp             ----GSCHHHHH--HSEEEECCCCC
T ss_pred             ----hCcchhhc--cCceEEeCCCC
Confidence                35677777  66666665544

>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=98.04  E-value=8.3e-06  Score=90.65  Aligned_cols=75  Identities=9%  Similarity=0.112  Sum_probs=51.0

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc-ccchHHH-HHHHHHHHHHH----HhhhCCC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR-HMNRVEV-EQRVEEIKNLV----RSCLGRG  299 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~-~~~rge~-E~rl~~l~~~~----~~~~~~~  299 (854)
                      ...+++|+||||||||++++.+|..+          +..++.++...+. +++.|+- +..+..++...    ...  .+
T Consensus        71 ~~~~ill~Gp~GtGKT~la~~la~~l----------~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~--~~  138 (376)
T 1um8_A           71 SKSNILLIGPTGSGKTLMAQTLAKHL----------DIPIAISDATSLTEAGYVGEDVENILTRLLQASDWNVQKA--QK  138 (376)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHT----------TCCEEEEEGGGCC--------CTHHHHHHHHHTTTCHHHH--TT
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHHh----------CCCEEEecchhhhhcCcCCccHHHHHHHHHhhccchhhhc--CC
Confidence            45789999999999999999999874          4578888888775 3565653 44555555432    222  46


Q ss_pred             eEEEeCccccc-cc
Q 003038          300 IVLNLGDLEWA-EF  312 (854)
Q Consensus       300 ~ILfidel~~l-~~  312 (854)
                      .||||||++.+ ..
T Consensus       139 ~vl~iDEi~~l~~~  152 (376)
T 1um8_A          139 GIVFIDEIDKISRL  152 (376)
T ss_dssp             SEEEEETGGGC---
T ss_pred             eEEEEcCHHHHhhh
Confidence            79999999999 54

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=98.03  E-value=1.1e-05  Score=88.68  Aligned_cols=141  Identities=11%  Similarity=0.031  Sum_probs=82.7

Q ss_pred             cHHHHHHHHHHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCCCcc--------------cCCceEEEcccccccc
Q 003038          211 RNEDVMYVIENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDVPEA--------------LRDVKCLPLSISSFRH  275 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~vp~~--------------L~~~~~~~l~~~~l~~  275 (854)
                      |++.++.+...+...+..+ ++|+||||+|||++++.++..+.....+..              -....++.++...-. 
T Consensus        21 ~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-   99 (373)
T 1jr3_A           21 QEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRT-   99 (373)
T ss_dssp             CHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCSSSHHHHHHHTSCCSSCEEEETTCSC-
T ss_pred             cHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhccCCCceEEecccccC-
Confidence            8888998888887655444 689999999999999999998754221100              000123333322100 


Q ss_pred             cchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEe
Q 003038          276 MNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGI  352 (854)
Q Consensus       276 ~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIga  352 (854)
                       ..    ..++++++.+....  +++.||+|||+|++ ..                 ....+..++....+  .+.+|++
T Consensus       100 -~~----~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~-----------------~~~~Ll~~le~~~~--~~~~Il~  155 (373)
T 1jr3_A          100 -KV----EDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRH-----------------SFNALLKTLEEPPE--HVKFLLA  155 (373)
T ss_dssp             -CS----SCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHH-----------------HHHHHHHHHHSCCS--SEEEEEE
T ss_pred             -CH----HHHHHHHHHHhhccccCCeEEEEEECcchhcHH-----------------HHHHHHHHHhcCCC--ceEEEEE
Confidence             11    12445666555321  45789999999999 43                 12234455522122  4888888


Q ss_pred             cCHHHHHHhhccCCchhhhhccCCCCCCCch
Q 003038          353 ATFQSYMRCKSGHPSLETLWSLHPLTIPAGS  383 (854)
Q Consensus       353 tT~~ey~k~~~~~pale~~~~~~~v~i~~~s  383 (854)
                      |+...     ...+++.+  +++.+.++..+
T Consensus       156 ~~~~~-----~l~~~l~s--r~~~i~~~~l~  179 (373)
T 1jr3_A          156 TTDPQ-----KLPVTILS--RCLQFHLKALD  179 (373)
T ss_dssp             ESCGG-----GSCHHHHT--TSEEEECCCCC
T ss_pred             eCChH-----hCcHHHHh--heeEeeCCCCC
Confidence            87432     23456655  55556665554

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=98.01  E-value=7.9e-06  Score=79.13  Aligned_cols=72  Identities=11%  Similarity=0.152  Sum_probs=54.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLI  738 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vili  738 (854)
                      .++|+||+|+|||+++++|+..+.......+.++..++.       ..            .        +.. ...|++|
T Consensus        38 ~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~~~~~~-------~~------------~--------~~~-~~~lLil   89 (149)
T 2kjq_A           38 FIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYIDAASMP-------LT------------D--------AAF-EAEYLAV   89 (149)
T ss_dssp             EEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEETTTSC-------CC------------G--------GGG-GCSEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEcHHHhh-------HH------------H--------HHh-CCCEEEE
Confidence            688999999999999999999886544456777766544       11            0        011 2479999


Q ss_pred             ecCCCCCHHHHHHHHHhhhc
Q 003038          739 EDVEQADYCSQKGFKRAIES  758 (854)
Q Consensus       739 DEieka~~~v~~~Ll~~le~  758 (854)
                      ||++..+...+..|++.|+.
T Consensus        90 DE~~~~~~~~~~~l~~li~~  109 (149)
T 2kjq_A           90 DQVEKLGNEEQALLFSIFNR  109 (149)
T ss_dssp             ESTTCCCSHHHHHHHHHHHH
T ss_pred             eCccccChHHHHHHHHHHHH
Confidence            99999988778888888863

>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=97.93  E-value=1e-05  Score=82.78  Aligned_cols=82  Identities=4%  Similarity=0.048  Sum_probs=57.1

Q ss_pred             HHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHH
Q 003038          212 NEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNL  291 (854)
Q Consensus       212 ~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~  291 (854)
                      ++-+..+...+.....++++|+||||+|||++++.++..+...       +..++.++...+......        ++..
T Consensus        37 ~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~la~~l~~~~~~~-------~~~~~~~~~~~~~~~~~~--------~~~~  101 (242)
T 3bos_A           37 DELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANEL-------ERRSFYIPLGIHASISTA--------LLEG  101 (242)
T ss_dssp             HHHHHHHHHHHHTCSCSEEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEEEGGGGGGSCGG--------GGTT
T ss_pred             HHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHHc-------CCeEEEEEHHHHHHHHHH--------HHHh
Confidence            3555666555555578899999999999999999999987653       456677776665543211        1111


Q ss_pred             HHhhhCCCeEEEeCccccc-cc
Q 003038          292 VRSCLGRGIVLNLGDLEWA-EF  312 (854)
Q Consensus       292 ~~~~~~~~~ILfidel~~l-~~  312 (854)
                      +    ..+.||||||++.+ ..
T Consensus       102 ~----~~~~vliiDe~~~~~~~  119 (242)
T 3bos_A          102 L----EQFDLICIDDVDAVAGH  119 (242)
T ss_dssp             G----GGSSEEEEETGGGGTTC
T ss_pred             c----cCCCEEEEeccccccCC
Confidence            1    24679999999999 53

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=97.87  E-value=3.4e-06  Score=91.90  Aligned_cols=134  Identities=5%  Similarity=-0.031  Sum_probs=79.4

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccc------ccccc-----chH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSIS------SFRHM-----NRV  279 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~------~l~~~-----~rg  279 (854)
                      +++.++.+...+..  .+|++|+||||+|||++++.++..+          +..++.++..      .+...     ..|
T Consensus        32 ~~~~~~~l~~~l~~--~~~vll~G~pGtGKT~la~~la~~~----------~~~~~~i~~~~~~~~~~l~g~~~~~~~~~   99 (331)
T 2r44_A           32 QKYMINRLLIGICT--GGHILLEGVPGLAKTLSVNTLAKTM----------DLDFHRIQFTPDLLPSDLIGTMIYNQHKG   99 (331)
T ss_dssp             CHHHHHHHHHHHHH--TCCEEEESCCCHHHHHHHHHHHHHT----------TCCEEEEECCTTCCHHHHHEEEEEETTTT
T ss_pred             cHHHHHHHHHHHHc--CCeEEEECCCCCcHHHHHHHHHHHh----------CCCeEEEecCCCCChhhcCCceeecCCCC
Confidence            66777777777764  5799999999999999999999875          2344444432      11111     011


Q ss_pred             HHHHHHHHHHHHHHhhhC--CCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc-----CC----CCceE
Q 003038          280 EVEQRVEEIKNLVRSCLG--RGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG-----IG----ENARF  347 (854)
Q Consensus       280 e~E~rl~~l~~~~~~~~~--~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-----~~----g~g~l  347 (854)
                      .+.         . .. +  .+.||||||++.+ ....                 ..+..++..     .+    -...+
T Consensus       100 ~~~---------~-~~-g~l~~~vl~iDEi~~~~~~~~-----------------~~Ll~~l~~~~~~~~g~~~~~~~~~  151 (331)
T 2r44_A          100 NFE---------V-KK-GPVFSNFILADEVNRSPAKVQ-----------------SALLECMQEKQVTIGDTTYPLDNPF  151 (331)
T ss_dssp             EEE---------E-EE-CTTCSSEEEEETGGGSCHHHH-----------------HHHHHHHHHSEEEETTEEEECCSSC
T ss_pred             ceE---------e-cc-CcccccEEEEEccccCCHHHH-----------------HHHHHHHhcCceeeCCEEEECCCCE
Confidence            110         0 00 1  1259999999998 4321                 111122210     00    01258


Q ss_pred             EEEEecCHHHHHHhhccCCchhhhhccC-CCCCCCchHHH
Q 003038          348 WLMGIATFQSYMRCKSGHPSLETLWSLH-PLTIPAGSLSL  386 (854)
Q Consensus       348 ~lIgatT~~ey~k~~~~~pale~~~~~~-~v~i~~~sl~~  386 (854)
                      ++|+++++.+|......+|+|.+  ||. .+.|+.++...
T Consensus       152 ~viat~np~~~~~~~~l~~~l~~--Rf~~~i~i~~p~~~~  189 (331)
T 2r44_A          152 LVLATQNPVEQEGTYPLPEAQVD--RFMMKIHLTYLDKES  189 (331)
T ss_dssp             EEEEEECTTCCSCCCCCCHHHHT--TSSEEEECCCCCHHH
T ss_pred             EEEEecCCCcccCcccCCHHHHh--heeEEEEcCCCCHHH
Confidence            89988887665433346789988  775 37777766544

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=97.87  E-value=5.8e-06  Score=89.76  Aligned_cols=40  Identities=15%  Similarity=0.124  Sum_probs=32.8

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHh-CCCCceEEEcccccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVF-GSHNNFVSIALSSFS  697 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lf-g~~~~~i~id~s~~~  697 (854)
                      ..++|+||+|+|||.||++||..+. .....++.+.++++.
T Consensus       153 ~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~~~~l~  193 (308)
T 2qgz_A          153 KGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSFA  193 (308)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEEHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEHHHHH
Confidence            4789999999999999999999887 555667777766543

>1k6k_A ATP-dependent CLP protease ATP-binding subunit CLPA; chaperone, ATPase, adaptor binding, X-RAY, structure, N-domain, hydrolase; 1.80A {Escherichia coli} SCOP: a.174.1.1 PDB: 1r6c_X 1r6o_A* 1r6q_A* 1mg9_B* 1lzw_B* 1mbx_A* 1mbv_A 1mbu_A*

Probab=97.85  E-value=2.4e-05  Score=74.70  Aligned_cols=61  Identities=11%  Similarity=0.049  Sum_probs=55.1

Q ss_pred             HhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHH
Q 003038           10 QGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCF   73 (854)
Q Consensus        10 ~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l   73 (854)
                      ..||+.+.++|+.|..+|+.+|+.||+++|||+||+.++++.+.++|..+|+++   +.++..+
T Consensus        78 ~~~s~~~~~~l~~A~~~A~~~~~~~i~~ehLLlall~~~~~~~~~iL~~~gi~~---~~l~~~i  138 (143)
T 1k6k_A           78 TQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSR---LDVVNFI  138 (143)
T ss_dssp             CEECHHHHHHHHHHHHHHHSSSCSCBCHHHHHHHHTTCTTSHHHHHHHHTTCCH---HHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhCcCcHHHHHHHHcCCCH---HHHHHHH
Confidence            369999999999999999999999999999999999988887899999999987   5666554

>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=97.81  E-value=4.4e-05  Score=82.91  Aligned_cols=37  Identities=14%  Similarity=0.201  Sum_probs=34.1

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      |++|+.++.+ |.+   +.++|+||+|+|||++++.++.+.
T Consensus        18 R~~el~~L~~-l~~---~~v~i~G~~G~GKT~L~~~~~~~~   54 (357)
T 2fna_A           18 REKEIEKLKG-LRA---PITLVLGLRRTGKSSIIKIGINEL   54 (357)
T ss_dssp             CHHHHHHHHH-TCS---SEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             hHHHHHHHHH-hcC---CcEEEECCCCCCHHHHHHHHHHhc
Confidence            9999999999 775   689999999999999999999875

>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=97.80  E-value=3e-05  Score=86.42  Aligned_cols=140  Identities=9%  Similarity=0.002  Sum_probs=84.7

Q ss_pred             CcccccHHHHHHHHHHH-HHhhcCCCcccCCCcCCcccCcceeEEE--ecCCCchHHHHHHHHHHHHhCC------CCce
Q 003038          618 KKVPWQKDTVYDIANTV-LKCRSGTMRRKGKFKDHSEVKEETWLFF--QGVDADAKEKIAKELARLVFGS------HNNF  688 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v-~~~rsgl~~~~~~~~~~~~~kp~~~lLf--~Gp~GvGKt~lAr~LA~~lfg~------~~~~  688 (854)
                      ..++|.+..+..|...+ .....|...            ....+++  +||+|+|||++++.+++.+...      ...+
T Consensus        22 ~~l~gR~~el~~l~~~l~~~~~~~~~~------------~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~   89 (412)
T 1w5s_A           22 PELRVRRGEAEALARIYLNRLLSGAGL------------SDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQ   89 (412)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCB------------CCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             CCCCChHHHHHHHHHHHhHHHhcCCCC------------CCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeE
Confidence            56899999999999888 766554211            1247788  9999999999999999877431      3456


Q ss_pred             EEEccccccCcCCCcccccccccc---CC---C-CCCchH---HHHHHHHHc-CCCEEEEEecCCCCC------HHHHHH
Q 003038          689 VSIALSSFSSTRADSTEDSRNKRS---RD---E-QSCSYI---ERFAEAVSN-NPHRVFLIEDVEQAD------YCSQKG  751 (854)
Q Consensus       689 i~id~s~~~~~~~~s~e~~~~~rl---~~---~-~g~g~~---e~L~eav~~-~p~~ViliDEieka~------~~v~~~  751 (854)
                      +.+++.....      .......+   ++   + .+....   +.+.+.+.. ....||+|||++.++      .+++..
T Consensus        90 ~~~~~~~~~~------~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~  163 (412)
T 1w5s_A           90 AYVNAFNAPN------LYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYT  163 (412)
T ss_dssp             EEEEGGGCCS------HHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHH
T ss_pred             EEEECCCCCC------HHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHH
Confidence            7787654331      00001110   11   1 121122   245555543 445799999999874      477777


Q ss_pred             HHHhhhcCeEecCCCceeecCCeEEEEecC
Q 003038          752 FKRAIESGRIVTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       752 Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn  781 (854)
                      |++.+++....   +  . -.+..||+|++
T Consensus       164 l~~~~~~~~~~---~--~-~~~v~lI~~~~  187 (412)
T 1w5s_A          164 LLRVHEEIPSR---D--G-VNRIGFLLVAS  187 (412)
T ss_dssp             HHTHHHHSCCT---T--S-CCBEEEEEEEE
T ss_pred             HHHHHHhcccC---C--C-CceEEEEEEec
Confidence            77777653110   0  0 13566777775

>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=97.72  E-value=2.1e-05  Score=85.75  Aligned_cols=31  Identities=13%  Similarity=0.134  Sum_probs=25.8

Q ss_pred             hhccCcCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          222 LMSKRKRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       222 L~r~~k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      +......+++|+||||+|||.+++.++..+.
T Consensus        40 ~~~~~~~~vLl~G~~GtGKT~la~~la~~~~   70 (350)
T 1g8p_A           40 AVDPGIGGVLVFGDRGTGKSTAVRALAALLP   70 (350)
T ss_dssp             HHCGGGCCEEEECCGGGCTTHHHHHHHHHSC
T ss_pred             hhCCCCceEEEECCCCccHHHHHHHHHHhCc
Confidence            3334567899999999999999999998764

>1khy_A CLPB protein; alpha helix, chaperone; 1.95A {Escherichia coli} SCOP: a.174.1.1

Probab=97.71  E-value=7e-05  Score=71.86  Aligned_cols=61  Identities=15%  Similarity=0.167  Sum_probs=53.2

Q ss_pred             HhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHH
Q 003038           10 QGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFN   74 (854)
Q Consensus        10 ~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~   74 (854)
                      ..||+.+.++|+.|..+|+.+||.+|+++|||+||+ ++++.+.++|..+|+++   +.|+..+.
T Consensus        81 ~~~s~~~~~vl~~A~~~a~~~~~~~i~~ehlLlall-~~~~~~~~~L~~~gi~~---~~l~~~l~  141 (148)
T 1khy_A           81 VQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAAL-ESRGTLADILKAAGATT---ANITQAIE  141 (148)
T ss_dssp             -CBCHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHH-TSCHHHHHHHHHTTCCH---HHHHHHHH
T ss_pred             cCcCHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHH-cCCcHHHHHHHHcCCCH---HHHHHHHH
Confidence            369999999999999999999999999999999999 45667889999999987   56666553

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.68  E-value=6.7e-05  Score=80.45  Aligned_cols=89  Identities=12%  Similarity=0.149  Sum_probs=56.7

Q ss_pred             cHHHHHHHHHHhhccC---------cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc-----
Q 003038          211 RNEDVMYVIENLMSKR---------KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM-----  276 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~---------k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~-----  276 (854)
                      .++.++.+...+.+..         ..+++|+||||+|||++++.++..+...       +..++.++++.+...     
T Consensus        22 ~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~-------~~~~~~~~~~~~~~~~~~~~   94 (311)
T 4fcw_A           22 QDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT-------EEAMIRIDMTEYMEKHAVSR   94 (311)
T ss_dssp             CHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSC-------GGGEEEEEGGGCCSTTHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcCC-------CcceEEeecccccccccHHH
Confidence            4455666666555431         2478999999999999999999987543       345777777655321     


Q ss_pred             -------chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc
Q 003038          277 -------NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       277 -------~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                             +.|.-+  ...+...+...  .+.||||||++.+
T Consensus        95 l~g~~~~~~~~~~--~~~~~~~~~~~--~~~vl~lDEi~~l  131 (311)
T 4fcw_A           95 LIGAPPGYVGYEE--GGQLTEAVRRR--PYSVILFDAIEKA  131 (311)
T ss_dssp             HHCCCTTSTTTTT--CCHHHHHHHHC--SSEEEEEETGGGS
T ss_pred             hcCCCCccccccc--cchHHHHHHhC--CCeEEEEeChhhc
Confidence                   111000  01233344443  5689999999988

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=97.65  E-value=8e-05  Score=80.67  Aligned_cols=38  Identities=16%  Similarity=0.216  Sum_probs=34.8

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      |++|+.++.+.+...  +.++|+|++|+|||++++.++.+
T Consensus        17 R~~el~~L~~~l~~~--~~v~i~G~~G~GKT~Ll~~~~~~   54 (350)
T 2qen_A           17 REEESRKLEESLENY--PLTLLLGIRRVGKSSLLRAFLNE   54 (350)
T ss_dssp             CHHHHHHHHHHHHHC--SEEEEECCTTSSHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcC--CeEEEECCCcCCHHHHHHHHHHH
Confidence            999999999988753  78999999999999999999876

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.65  E-value=3.6e-05  Score=77.43  Aligned_cols=86  Identities=13%  Similarity=0.184  Sum_probs=52.2

Q ss_pred             HHHHHHHHhhccC----cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHH-HHHHHHH
Q 003038          214 DVMYVIENLMSKR----KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEV-EQRVEEI  288 (854)
Q Consensus       214 ei~~v~~~L~r~~----k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~-E~rl~~l  288 (854)
                      -+..+...+....    .++++|+||||+|||+++++++..+...       +..++.++...+.......+ +..+..+
T Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~  109 (202)
T 2w58_A           37 AIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKR-------NVSSLIVYVPELFRELKHSLQDQTMNEK  109 (202)
T ss_dssp             HHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHHHTT-------TCCEEEEEHHHHHHHHHHC---CCCHHH
T ss_pred             HHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHc-------CCeEEEEEhHHHHHHHHHHhccchHHHH
Confidence            3444444444331    1789999999999999999999987643       34555555554433211111 0112334


Q ss_pred             HHHHHhhhCCCeEEEeCccccc
Q 003038          289 KNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       289 ~~~~~~~~~~~~ILfidel~~l  310 (854)
                      ++.+...    .+|||||++..
T Consensus       110 ~~~~~~~----~~lilDei~~~  127 (202)
T 2w58_A          110 LDYIKKV----PVLMLDDLGAE  127 (202)
T ss_dssp             HHHHHHS----SEEEEEEECCC
T ss_pred             HHHhcCC----CEEEEcCCCCC
Confidence            4555542    38999999776

>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=97.64  E-value=1.8e-05  Score=78.31  Aligned_cols=76  Identities=12%  Similarity=0.102  Sum_probs=45.9

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHH-HHHHHHHHHhhhCCCeEEE
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQR-VEEIKNLVRSCLGRGIVLN  303 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~r-l~~l~~~~~~~~~~~~ILf  303 (854)
                      ...++++|+||||+|||++++.++..+...      .|..++.++...+....+..+... ...+++.+.    .+-||+
T Consensus        36 ~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~------~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~lli  105 (180)
T 3ec2_A           36 EEGKGLTFVGSPGVGKTHLAVATLKAIYEK------KGIRGYFFDTKDLIFRLKHLMDEGKDTKFLKTVL----NSPVLV  105 (180)
T ss_dssp             GGCCEEEECCSSSSSHHHHHHHHHHHHHHH------SCCCCCEEEHHHHHHHHHHHHHHTCCSHHHHHHH----TCSEEE
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHHHHHHH------cCCeEEEEEHHHHHHHHHHHhcCchHHHHHHHhc----CCCEEE
Confidence            456889999999999999999999987511      122333344444433222221111 112333333    356899


Q ss_pred             eCccccc
Q 003038          304 LGDLEWA  310 (854)
Q Consensus       304 idel~~l  310 (854)
                      |||++..
T Consensus       106 lDE~~~~  112 (180)
T 3ec2_A          106 LDDLGSE  112 (180)
T ss_dssp             EETCSSS
T ss_pred             EeCCCCC
Confidence            9999754

>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=97.63  E-value=0.00027  Score=77.31  Aligned_cols=147  Identities=7%  Similarity=-0.020  Sum_probs=85.5

Q ss_pred             cHHHHHHHHHHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCCCcc--------------cCCceEEEcccccccc
Q 003038          211 RNEDVMYVIENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDVPEA--------------LRDVKCLPLSISSFRH  275 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~vp~~--------------L~~~~~~~l~~~~l~~  275 (854)
                      .++.++++...+..++-.+ .+|+||||+|||++++.+|+.+........              .....++.++...- .
T Consensus         7 ~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~-~   85 (334)
T 1a5t_A            7 LRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKG-K   85 (334)
T ss_dssp             GHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTT-C
T ss_pred             hHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEecccc-C
Confidence            4566777777777655444 899999999999999999998865432110              00123444443210 0


Q ss_pred             cchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEe
Q 003038          276 MNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGI  352 (854)
Q Consensus       276 ~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIga  352 (854)
                      ...+  -..++++++.+....  ++.-|++|||+|.+ ..                 +...+-+.|.....  ...+|.+
T Consensus        86 ~~~~--i~~ir~l~~~~~~~~~~~~~kvviIdead~l~~~-----------------a~naLLk~lEep~~--~~~~Il~  144 (334)
T 1a5t_A           86 NTLG--VDAVREVTEKLNEHARLGGAKVVWVTDAALLTDA-----------------AANALLKTLEEPPA--ETWFFLA  144 (334)
T ss_dssp             SSBC--HHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCHH-----------------HHHHHHHHHTSCCT--TEEEEEE
T ss_pred             CCCC--HHHHHHHHHHHhhccccCCcEEEEECchhhcCHH-----------------HHHHHHHHhcCCCC--CeEEEEE
Confidence            0111  123456666665321  45789999999999 43                 12234445521112  3777777


Q ss_pred             cCHHHHHHhhccCCchhhhhccCCCCCCCchHHH
Q 003038          353 ATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSL  386 (854)
Q Consensus       353 tT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~  386 (854)
                      |+..+     ...|++.+  |.+.+.++.++...
T Consensus       145 t~~~~-----~l~~ti~S--Rc~~~~~~~~~~~~  171 (334)
T 1a5t_A          145 TREPE-----RLLATLRS--RCRLHYLAPPPEQY  171 (334)
T ss_dssp             ESCGG-----GSCHHHHT--TSEEEECCCCCHHH
T ss_pred             eCChH-----hCcHHHhh--cceeeeCCCCCHHH
Confidence            66421     35677877  66667776655433

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.60  E-value=0.00011  Score=80.38  Aligned_cols=133  Identities=11%  Similarity=0.028  Sum_probs=75.7

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKN  290 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~  290 (854)
                      .++-+..+...+...+-.+.+|+||||+|||++++.+|..+....     ....++.++.+....  ..    .+++++.
T Consensus        30 ~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~~l~~~~-----~~~~~~~~~~~~~~~--~~----~ir~~i~   98 (340)
T 1sxj_C           30 QNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKN-----YSNMVLELNASDDRG--ID----VVRNQIK   98 (340)
T ss_dssp             CHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTS-----HHHHEEEECTTSCCS--HH----HHHTHHH
T ss_pred             cHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-----ccceEEEEcCccccc--HH----HHHHHHH
Confidence            344455555555554556689999999999999999999875321     123566666543211  12    2333333


Q ss_pred             HHHhh----hCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccC
Q 003038          291 LVRSC----LGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGH  365 (854)
Q Consensus       291 ~~~~~----~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~  365 (854)
                      .+.+.    .++.-|++|||+|.+ ...                 ...+..++.....  ...+|.+|+...     ...
T Consensus        99 ~~~~~~~~~~~~~~viiiDe~~~l~~~~-----------------~~~L~~~le~~~~--~~~~il~~n~~~-----~i~  154 (340)
T 1sxj_C           99 DFASTRQIFSKGFKLIILDEADAMTNAA-----------------QNALRRVIERYTK--NTRFCVLANYAH-----KLT  154 (340)
T ss_dssp             HHHHBCCSSSCSCEEEEETTGGGSCHHH-----------------HHHHHHHHHHTTT--TEEEEEEESCGG-----GSC
T ss_pred             HHHhhcccCCCCceEEEEeCCCCCCHHH-----------------HHHHHHHHhcCCC--CeEEEEEecCcc-----ccc
Confidence            33321    024689999999999 431                 2234455521112  366777776431     345


Q ss_pred             CchhhhhccCCCCCC
Q 003038          366 PSLETLWSLHPLTIP  380 (854)
Q Consensus       366 pale~~~~~~~v~i~  380 (854)
                      |++.+  |++.+.+.
T Consensus       155 ~~i~s--R~~~~~~~  167 (340)
T 1sxj_C          155 PALLS--QCTRFRFQ  167 (340)
T ss_dssp             HHHHT--TSEEEECC
T ss_pred             hhHHh--hceeEecc
Confidence            66766  44444443

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.56  E-value=0.0001  Score=80.65  Aligned_cols=43  Identities=7%  Similarity=0.042  Sum_probs=33.0

Q ss_pred             cHHHHHHHHHHh-hccCcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          211 RNEDVMYVIENL-MSKRKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       211 r~~ei~~v~~~L-~r~~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      .++.+..+...+ ...+..+.+|+||+|+|||++++.++..+..
T Consensus        19 ~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~~~la~~l~~   62 (354)
T 1sxj_E           19 NEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFG   62 (354)
T ss_dssp             CHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSC
T ss_pred             CHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHHHHHHHHHcC
Confidence            556666666666 4445556999999999999999999997643

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=97.48  E-value=0.00012  Score=74.41  Aligned_cols=25  Identities=20%  Similarity=0.333  Sum_probs=23.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhC
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFG  683 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg  683 (854)
                      .++|+||+|+|||++|.+||+.+.|
T Consensus        60 ~ili~GPPGtGKTt~a~ala~~l~g   84 (212)
T 1tue_A           60 CLVFCGPANTGKSYFGMSFIHFIQG   84 (212)
T ss_dssp             EEEEESCGGGCHHHHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCC
Confidence            6899999999999999999999855

>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=97.41  E-value=8.7e-05  Score=84.24  Aligned_cols=69  Identities=7%  Similarity=0.160  Sum_probs=56.5

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc-cchHH-HHHHHHHHHHHHHhhhCCCeEEE
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH-MNRVE-VEQRVEEIKNLVRSCLGRGIVLN  303 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~-~~rge-~E~rl~~l~~~~~~~~~~~~ILf  303 (854)
                      .++|++|+||||||||++++.||..+          +..++.++.+.+.. +|.|+ .+..++.++..+...      ++
T Consensus        49 ~~~~iLl~GppGtGKT~lar~lA~~l----------~~~~~~v~~~~~~~~g~vG~d~e~~lr~lf~~a~~~------~~  112 (444)
T 1g41_A           49 TPKNILMIGPTGVGKTEIARRLAKLA----------NAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAMKL------VR  112 (444)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHT----------TCCEEEEEGGGGC----CCCCTHHHHHHHHHHHHHH------HH
T ss_pred             CCceEEEEcCCCCCHHHHHHHHHHHc----------CCCceeecchhhcccceeeccHHHHHHHHHHHHHhc------ch
Confidence            35789999999999999999999874          67899999988887 68884 899999999988764      46


Q ss_pred             eCccccc
Q 003038          304 LGDLEWA  310 (854)
Q Consensus       304 idel~~l  310 (854)
                      +||+..+
T Consensus       113 ~De~d~~  119 (444)
T 1g41_A          113 QQEIAKN  119 (444)
T ss_dssp             HHHHHSC
T ss_pred             hhhhhhh
Confidence            8998777

>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=97.34  E-value=0.00053  Score=92.64  Aligned_cols=99  Identities=11%  Similarity=0.104  Sum_probs=72.6

Q ss_pred             EEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEe
Q 003038          660 LFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIE  739 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliD  739 (854)
                      .++.||+|+|||++++.||+.+   ...+++++|++-.       +...           ....+.++++..  .+++||
T Consensus       648 ~~l~GpaGtGKTe~vk~LA~~l---g~~~v~~nc~e~l-------d~~~-----------lg~~~~g~~~~G--aw~~~D  704 (2695)
T 4akg_A          648 GCFFGPAGTGKTETVKAFGQNL---GRVVVVFNCDDSF-------DYQV-----------LSRLLVGITQIG--AWGCFD  704 (2695)
T ss_dssp             EEEECCTTSCHHHHHHHHHHTT---TCCCEEEETTSSC-------CHHH-----------HHHHHHHHHHHT--CEEEEE
T ss_pred             CcccCCCCCCcHHHHHHHHHHh---CCcEEEEECCCCC-------ChhH-----------hhHHHHHHHhcC--CEeeeh
Confidence            4688999999999999999988   4678999998655       1111           112345555443  699999


Q ss_pred             cCCCCCHHHHHHH-------HHhhhcCe--EecCCCceeecC-CeEEEEecCC
Q 003038          740 DVEQADYCSQKGF-------KRAIESGR--IVTSSGDEVSLG-DAIVILSCES  782 (854)
Q Consensus       740 Eieka~~~v~~~L-------l~~le~G~--l~d~~G~~v~~~-~aIiIlTsn~  782 (854)
                      ||++++++++..|       +.++.++.  +. -.|+.+.+. ++.|++|.|.
T Consensus       705 E~nr~~~evLs~l~~~l~~i~~al~~~~~~i~-~~g~~i~l~~~~~vfiT~NP  756 (2695)
T 4akg_A          705 EFNRLDEKVLSAVSANIQQIQNGLQVGKSHIT-LLEEETPLSPHTAVFITLNP  756 (2695)
T ss_dssp             TTTSSCHHHHHHHHHHHHHHHHHHHHTCSEEE-CSSSEEECCTTCEEEEEECC
T ss_pred             hhhhcChHHHHHHHHHHHHHHHHHHcCCcEEe-eCCcEEecCCCceEEEEeCC
Confidence            9999999999988       56665554  33 347788775 5667778885

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=97.28  E-value=0.00011  Score=79.58  Aligned_cols=73  Identities=18%  Similarity=0.191  Sum_probs=44.8

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHH-cCCCCcccCCceEEEcccccccccchHHH-HHHHHHHHHHHHhhhCCCeEEEe
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIE-KGDVPEALRDVKCLPLSISSFRHMNRVEV-EQRVEEIKNLVRSCLGRGIVLNL  304 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~-~~~vp~~L~~~~~~~l~~~~l~~~~rge~-E~rl~~l~~~~~~~~~~~~ILfi  304 (854)
                      .+|++|+||||||||.++.+++..+. ..       +..++.++...|....++.+ +..+.++++.+..    .-||||
T Consensus       152 ~~~lll~G~~GtGKT~La~aia~~~~~~~-------g~~v~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~----~~lLii  220 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAAMAHELSEKK-------GVSTTLLHFPSFAIDVKNAISNGSVKEEIDAVKN----VPVLIL  220 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHHHHS-------CCCEEEEEHHHHHHHHHCCCC----CCTTHHHHT----SSEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHhc-------CCcEEEEEHHHHHHHHHHHhccchHHHHHHHhcC----CCEEEE
Confidence            68999999999999999999999876 42       34555555544433111100 0112233444443    348999


Q ss_pred             Cccccc
Q 003038          305 GDLEWA  310 (854)
Q Consensus       305 del~~l  310 (854)
                      |||...
T Consensus       221 Ddig~~  226 (308)
T 2qgz_A          221 DDIGAE  226 (308)
T ss_dssp             ETCCC-
T ss_pred             cCCCCC
Confidence            999665

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=97.14  E-value=8.3e-05  Score=85.93  Aligned_cols=39  Identities=10%  Similarity=0.087  Sum_probs=32.7

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +++.++.++..+..  +.|++|+||||||||.+|+++|..+
T Consensus        27 q~~~i~~l~~al~~--~~~VLL~GpPGtGKT~LAraLa~~l   65 (500)
T 3nbx_X           27 RSHAIRLCLLAALS--GESVFLLGPPGIAKSLIARRLKFAF   65 (500)
T ss_dssp             CHHHHHHHHHHHHH--TCEEEEECCSSSSHHHHHHHGGGGB
T ss_pred             HHHHHHHHHHHHhc--CCeeEeecCchHHHHHHHHHHHHHH
Confidence            56677777777664  5799999999999999999999875

>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=97.13  E-value=0.00031  Score=76.28  Aligned_cols=73  Identities=12%  Similarity=0.105  Sum_probs=51.9

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..+.++|+||||+|||+++..+|..  .|.      .+.+++++....+..+..+.++.+..+.+.+.+.   + +||||
T Consensus       122 ~gsviLI~GpPGsGKTtLAlqlA~~--~G~------~VlyIs~~~eE~v~~~~~~le~~l~~i~~~l~~~---~-LLVID  189 (331)
T 2vhj_A          122 ASGMVIVTGKGNSGKTPLVHALGEA--LGG------KDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQH---R-VIVID  189 (331)
T ss_dssp             ESEEEEEECSCSSSHHHHHHHHHHH--HHT------TSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHC---S-EEEEE
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHh--CCC------CEEEEEecchhhhhhhhcCHHHHHHHHHHHHhhC---C-EEEEe
Confidence            4455799999999999999999976  221      2345565322222233366778888888888765   4 99999


Q ss_pred             ccccc
Q 003038          306 DLEWA  310 (854)
Q Consensus       306 el~~l  310 (854)
                      +|..+
T Consensus       190 sI~aL  194 (331)
T 2vhj_A          190 SLKNV  194 (331)
T ss_dssp             CCTTT
T ss_pred             ccccc
Confidence            99999

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=97.06  E-value=2.2e-05  Score=92.85  Aligned_cols=23  Identities=4%  Similarity=0.132  Sum_probs=21.1

Q ss_pred             CceeecCCCCCHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      |++|+||||||||.+++.+|...
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~~  351 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRVA  351 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTTC
T ss_pred             ceEEECCCchHHHHHHHHHHHhC
Confidence            89999999999999999998654

>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=97.05  E-value=0.0026  Score=68.77  Aligned_cols=87  Identities=15%  Similarity=0.118  Sum_probs=53.5

Q ss_pred             HHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHh
Q 003038          215 VMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRS  294 (854)
Q Consensus       215 i~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~  294 (854)
                      +..+...+..++..+.+|+||||+|||++++.+|.....  ...  ....++.++.+.   ...|  -..++++++.+..
T Consensus         6 ~~~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~la~~~~~--~~~--~~~d~~~l~~~~---~~~~--id~ir~li~~~~~   76 (305)
T 2gno_A            6 LETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEK--FPP--KASDVLEIDPEG---ENIG--IDDIRTIKDFLNY   76 (305)
T ss_dssp             HHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHT--SCC--CTTTEEEECCSS---SCBC--HHHHHHHHHHHTS
T ss_pred             HHHHHHHHHCCCCcEEEEECCCCCCHHHHHHHHHHhCch--hhc--cCCCEEEEcCCc---CCCC--HHHHHHHHHHHhh
Confidence            344444455445557899999999999999999975321  111  233455565431   0111  1235567777654


Q ss_pred             hh--CCCeEEEeCccccc
Q 003038          295 CL--GRGIVLNLGDLEWA  310 (854)
Q Consensus       295 ~~--~~~~ILfidel~~l  310 (854)
                      ..  ++.-|++|||+|.+
T Consensus        77 ~p~~~~~kvviIdead~l   94 (305)
T 2gno_A           77 SPELYTRKYVIVHDCERM   94 (305)
T ss_dssp             CCSSSSSEEEEETTGGGB
T ss_pred             ccccCCceEEEeccHHHh
Confidence            31  34579999999999

>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=97.04  E-value=0.0012  Score=72.22  Aligned_cols=64  Identities=13%  Similarity=0.116  Sum_probs=40.3

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCcc
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDL  307 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfidel  307 (854)
                      .+++|+||||+|||++++.+|..+.          +.+...+...+..  .++    +..++.   .. ..+.|+||||+
T Consensus        52 ~~~ll~Gp~G~GKTTLa~~ia~~l~----------~~~~~~sg~~~~~--~~~----l~~~~~---~~-~~~~v~~iDE~  111 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLAHIIASELQ----------TNIHVTSGPVLVK--QGD----MAAILT---SL-ERGDVLFIDEI  111 (334)
T ss_dssp             CCEEEESSTTSSHHHHHHHHHHHHT----------CCEEEEETTTCCS--HHH----HHHHHH---HC-CTTCEEEEETG
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHhC----------CCEEEEechHhcC--HHH----HHHHHH---Hc-cCCCEEEEcch
Confidence            6899999999999999999998762          2233222221111  111    222222   21 24569999999


Q ss_pred             ccc-c
Q 003038          308 EWA-E  311 (854)
Q Consensus       308 ~~l-~  311 (854)
                      |.+ .
T Consensus       112 ~~l~~  116 (334)
T 1in4_A          112 HRLNK  116 (334)
T ss_dssp             GGCCH
T ss_pred             hhcCH
Confidence            999 5

>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=97.01  E-value=0.00086  Score=70.96  Aligned_cols=90  Identities=14%  Similarity=0.243  Sum_probs=54.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH--hCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCC-E
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV--FGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPH-R  734 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l--fg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~-~  734 (854)
                      ..++|+||+|+|||.+|++||..+  +|      .++   +..      ..+...                   ..+. .
T Consensus       105 n~~~l~GppgtGKt~~a~ala~~~~l~G------~vn---~~~------~~f~l~-------------------~~~~k~  150 (267)
T 1u0j_A          105 NTIWLFGPATTGKTNIAEAIAHTVPFYG------CVN---WTN------ENFPFN-------------------DCVDKM  150 (267)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHSSCEE------ECC---TTC------SSCTTG-------------------GGSSCS
T ss_pred             cEEEEECCCCCCHHHHHHHHHhhhcccc------eee---ccc------cccccc-------------------cccccE
Confidence            369999999999999999999963  33      111   110      001100                   1122 3


Q ss_pred             EEEEecCCCCCHHHHHHHHHhhhcCeEe-cCC-CceeecCCeEEEEecCC
Q 003038          735 VFLIEDVEQADYCSQKGFKRAIESGRIV-TSS-GDEVSLGDAIVILSCES  782 (854)
Q Consensus       735 ViliDEieka~~~v~~~Ll~~le~G~l~-d~~-G~~v~~~~aIiIlTsn~  782 (854)
                      |++.||. .+..+.++.++.+++-+.+. |.+ ...+....+-||+|||.
T Consensus       151 i~l~Ee~-~~~~d~~~~lr~i~~G~~~~id~K~k~~~~v~~tPvIitsN~  199 (267)
T 1u0j_A          151 VIWWEEG-KMTAKVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNT  199 (267)
T ss_dssp             EEEECSC-CEETTTHHHHHHHHTTCCEEC------CCEECCCCEEEEESS
T ss_pred             EEEeccc-cchhHHHHHHHHHhCCCcEEEecCcCCcccccCCCEEEEecC
Confidence            5555555 45567888899988744444 322 23456778889999985

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=97.00  E-value=0.0015  Score=70.48  Aligned_cols=52  Identities=6%  Similarity=0.041  Sum_probs=40.7

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      .++|.+..+..|...+..   |                 ..++++||.|+|||++++.+++.+ +    .+.+++..
T Consensus        13 ~~~gR~~el~~L~~~l~~---~-----------------~~v~i~G~~G~GKT~Ll~~~~~~~-~----~~~~~~~~   64 (350)
T 2qen_A           13 DIFDREEESRKLEESLEN---Y-----------------PLTLLLGIRRVGKSSLLRAFLNER-P----GILIDCRE   64 (350)
T ss_dssp             GSCSCHHHHHHHHHHHHH---C-----------------SEEEEECCTTSSHHHHHHHHHHHS-S----EEEEEHHH
T ss_pred             hcCChHHHHHHHHHHHhc---C-----------------CeEEEECCCcCCHHHHHHHHHHHc-C----cEEEEeec
Confidence            468888888888777653   1                 278999999999999999999875 2    67777654

>3zri_A CLPB protein, CLPV; chaperone, HSP100 proteins, AAA+ proteins, T6SS, secretion,; 1.80A {Vibrio cholerae} PDB: 3zrj_A

Probab=96.99  E-value=0.0014  Score=64.75  Aligned_cols=61  Identities=26%  Similarity=0.336  Sum_probs=52.0

Q ss_pred             cChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC--hHHHHHHHhCCCHHHHHHHHHHHhh
Q 003038           94 QFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP--SVSRVMREAGFSSTQVKSNVEQAVS  168 (854)
Q Consensus        94 ~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~--~~~~iL~~~Gi~~~~l~~~v~~~l~  168 (854)
                      +++.+.++|+.|.+.|...++    .         +|+++|||+||++++  .+.++|.++|++.+.++..+. .+.
T Consensus        25 fT~~a~~aL~~A~~~A~~~~h----~---------~I~~EHLLlaLL~~~~~~a~~iL~~~gvd~~~l~~~l~-~l~   87 (171)
T 3zri_A           25 LNAQSKLALEQAASLCIERQH----P---------EVTLEHYLDVLLDNPLSDVRLVLKQAGLEVDQVKQAIA-STY   87 (171)
T ss_dssp             BCHHHHHHHHHHHHHHHHHTC----S---------EECHHHHHHHHTTCTTSHHHHHHHHTTCCHHHHHHHHH-HHS
T ss_pred             cCHHHHHHHHHHHHHHHHcCC----C---------cccHHHHHHHHHHccCcHHHHHHHHcCCCHHHHHHHHH-HHh
Confidence            578888888888888887642    2         599999999999974  689999999999999999888 663

>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=96.97  E-value=0.0017  Score=71.71  Aligned_cols=99  Identities=12%  Similarity=0.234  Sum_probs=64.7

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCC-CCceEEEc-cccccCcCCCccccccccc-cCCCCCCchHHHHHHHHHcCC
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGS-HNNFVSIA-LSSFSSTRADSTEDSRNKR-SRDEQSCSYIERFAEAVSNNP  732 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-~~~~i~id-~s~~~~~~~~s~e~~~~~r-l~~~~g~g~~e~L~eav~~~p  732 (854)
                      +.+.+++.||+|+|||++.++|+..+-.. ...++.+. --+|.....    ...+.. ........|.+.|..+++.+|
T Consensus       122 ~~g~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed~~e~~~~~~----~~~v~q~~~~~~~~~~~~~La~aL~~~P  197 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESK----KCLVNQREVHRDTLGFSEALRSALREDP  197 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCCCS----SSEEEEEEBTTTBSCHHHHHHHHTTSCC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccCcHHhhhhcc----ccceeeeeeccccCCHHHHHHHHhhhCc
Confidence            45689999999999999999999988533 33444432 222321000    000100 111222366667888888888


Q ss_pred             CEEEEEecCCCCCHHHHHHHHHhhhcCeE
Q 003038          733 HRVFLIEDVEQADYCSQKGFKRAIESGRI  761 (854)
Q Consensus       733 ~~ViliDEieka~~~v~~~Ll~~le~G~l  761 (854)
                       .||++||+-  +++....++++.+.|..
T Consensus       198 -dvillDEp~--d~e~~~~~~~~~~~G~~  223 (356)
T 3jvv_A          198 -DIILVGEMR--DLETIRLALTAAETGHL  223 (356)
T ss_dssp             -SEEEESCCC--SHHHHHHHHHHHHTTCE
T ss_pred             -CEEecCCCC--CHHHHHHHHHHHhcCCE
Confidence             799999997  78888888898887643

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.93  E-value=0.00071  Score=65.23  Aligned_cols=61  Identities=11%  Similarity=-0.002  Sum_probs=44.5

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..++++|+||+|+|||++++.++..+..       .|.+++.++...+...              .+.   .++-||+||
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~~~~-------~g~~~~~~~~~~~~~~--------------~~~---~~~~lLilD   90 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQALE-------AGKNAAYIDAASMPLT--------------DAA---FEAEYLAVD   90 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHHHHT-------TTCCEEEEETTTSCCC--------------GGG---GGCSEEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHh-------cCCcEEEEcHHHhhHH--------------HHH---hCCCEEEEe
Confidence            5678999999999999999999988753       2455666665555432              011   135689999


Q ss_pred             ccccc
Q 003038          306 DLEWA  310 (854)
Q Consensus       306 el~~l  310 (854)
                      |++.+
T Consensus        91 E~~~~   95 (149)
T 2kjq_A           91 QVEKL   95 (149)
T ss_dssp             STTCC
T ss_pred             Ccccc
Confidence            99887

>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=96.93  E-value=0.0036  Score=68.30  Aligned_cols=94  Identities=7%  Similarity=0.082  Sum_probs=64.6

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCC-CceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHH----cCC
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSH-NNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVS----NNP  732 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~-~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~----~~p  732 (854)
                      ..+||+||+|.||++.++.|++.++... ..+..+.   +.       ..           ... ..+.+.+.    ..+
T Consensus        19 ~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~---~~-------~~-----------~~~-~~l~~~~~~~plf~~   76 (343)
T 1jr3_D           19 AAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFS---ID-------PN-----------TDW-NAIFSLCQAMSLFAS   76 (343)
T ss_dssp             SEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEE---CC-------TT-----------CCH-HHHHHHHHHHHHCCS
T ss_pred             cEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEE---ec-------CC-----------CCH-HHHHHHhcCcCCccC
Confidence            4899999999999999999999886421 1211111   11       00           011 12333333    356


Q ss_pred             CEEEEEecCCC-CCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCCC
Q 003038          733 HRVFLIEDVEQ-ADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESFS  784 (854)
Q Consensus       733 ~~ViliDEiek-a~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f~  784 (854)
                      ++||+|||+++ ++...++.|++++++-           -.+++|||+++..+
T Consensus        77 ~kvvii~~~~~kl~~~~~~aLl~~le~p-----------~~~~~~il~~~~~~  118 (343)
T 1jr3_D           77 RQTLLLLLPENGPNAAINEQLLTLTGLL-----------HDDLLLIVRGNKLS  118 (343)
T ss_dssp             CEEEEEECCSSCCCTTHHHHHHHHHTTC-----------BTTEEEEEEESCCC
T ss_pred             CeEEEEECCCCCCChHHHHHHHHHHhcC-----------CCCeEEEEEcCCCC
Confidence            89999999999 9999999999999851           24788888876544

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=96.87  E-value=0.0012  Score=89.75  Aligned_cols=117  Identities=11%  Similarity=0.087  Sum_probs=73.0

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCc--cccccccccCCCCCCchHHHHHHHHHcCCCEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADS--TEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVF  736 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s--~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vi  736 (854)
                      .+||+||+|+|||.+++.....+.  ...++.+++|..+++...-  .+..-.++.....|.     ++.+.+....-||
T Consensus      1306 pvLL~GptGtGKT~li~~~L~~l~--~~~~~~infS~~Tta~~l~~~~e~~~e~~~~~~~G~-----~~~p~~~Gk~~Vl 1378 (3245)
T 3vkg_A         1306 PLILCGPPGSGKTMTLTSTLRAFP--DFEVVSLNFSSATTPELLLKTFDHHCEYKRTPSGET-----VLRPTQLGKWLVV 1378 (3245)
T ss_dssp             CCEEESSTTSSHHHHHHHHGGGCT--TEEEEEECCCTTCCHHHHHHHHHHHEEEEECTTSCE-----EEEESSTTCEEEE
T ss_pred             cEEEECCCCCCHHHHHHHHHHhCC--CCceEEEEeeCCCCHHHHHHHHhhcceEEeccCCCc-----ccCCCcCCceEEE
Confidence            689999999999977654433333  2467889988776310000  000000000000000     0000001224599


Q ss_pred             EEecCCCCCHH------HHHHHHHhhhcCeEecC-CCceeecCCeEEEEecCC
Q 003038          737 LIEDVEQADYC------SQKGFKRAIESGRIVTS-SGDEVSLGDAIVILSCES  782 (854)
Q Consensus       737 liDEieka~~~------v~~~Ll~~le~G~l~d~-~G~~v~~~~aIiIlTsn~  782 (854)
                      ||||++...++      +...|.|.||.|.+.|. .+..+...+..||.|+|.
T Consensus      1379 FiDDiNmp~~D~yGtQ~~ielLrqlld~~g~yd~~~~~~~~i~d~~~vaamnP 1431 (3245)
T 3vkg_A         1379 FCDEINLPSTDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNP 1431 (3245)
T ss_dssp             EETTTTCCCCCTTSCCHHHHHHHHHHHHSEEEETTTTEEEEESSEEEEEEECC
T ss_pred             EecccCCCCccccccccHHHHHHHHHHcCCeEECCCCeEEEecCeEEEEEcCC
Confidence            99999998876      89999999999988885 456678899999999984

>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=96.86  E-value=0.0046  Score=70.50  Aligned_cols=116  Identities=10%  Similarity=0.092  Sum_probs=66.3

Q ss_pred             cccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC-ceEEEccccccC-
Q 003038          621 PWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN-NFVSIALSSFSS-  698 (854)
Q Consensus       621 ~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~-~~i~id~s~~~~-  698 (854)
                      .+|.+|+..+...|..                   +.+.+++.|++|+|||+++..++..+..... .++.+..+.-.. 
T Consensus        28 ~~Q~~av~~~~~~i~~-------------------~~~~~li~G~aGTGKT~ll~~~~~~l~~~~~~~il~~a~T~~Aa~   88 (459)
T 3upu_A           28 EGQKNAFNIVMKAIKE-------------------KKHHVTINGPAGTGATTLTKFIIEALISTGETGIILAAPTHAAKK   88 (459)
T ss_dssp             HHHHHHHHHHHHHHHS-------------------SSCEEEEECCTTSCHHHHHHHHHHHHHHTTCCCEEEEESSHHHHH
T ss_pred             HHHHHHHHHHHHHHhc-------------------CCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCceEEEecCcHHHHH
Confidence            5799999888877653                   1238999999999999999999998865443 333332110000 


Q ss_pred             -----cCCCccccccccccCC--CCCC-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhh
Q 003038          699 -----TRADSTEDSRNKRSRD--EQSC-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIE  757 (854)
Q Consensus       699 -----~~~~s~e~~~~~rl~~--~~g~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le  757 (854)
                           .......-|+..++..  .... .+..  ...-....+.+|++||+..+++..+..|++.+.
T Consensus        89 ~l~~~~~~~~~T~h~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~iiiDE~~~~~~~~~~~l~~~~~  153 (459)
T 3upu_A           89 ILSKLSGKEASTIHSILKINPVTYEENVLFEQ--KEVPDLAKCRVLICDEVSMYDRKLFKILLSTIP  153 (459)
T ss_dssp             HHHHHHSSCEEEHHHHHTEEEEECSSCEEEEE--CSCCCCSSCSEEEESCGGGCCHHHHHHHHHHSC
T ss_pred             HHHhhhccchhhHHHHhccCcccccccchhcc--cccccccCCCEEEEECchhCCHHHHHHHHHhcc
Confidence                 0000000011000000  0000 0000  000011247899999999999999999999886

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=96.84  E-value=0.0036  Score=67.61  Aligned_cols=35  Identities=17%  Similarity=0.220  Sum_probs=28.9

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      .++++||.|+|||++++.+++.+ +  ...+.+++..+
T Consensus        32 ~v~i~G~~G~GKT~L~~~~~~~~-~--~~~~~~~~~~~   66 (357)
T 2fna_A           32 ITLVLGLRRTGKSSIIKIGINEL-N--LPYIYLDLRKF   66 (357)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH-T--CCEEEEEGGGG
T ss_pred             cEEEECCCCCCHHHHHHHHHHhc-C--CCEEEEEchhh
Confidence            78999999999999999999887 2  24677887654

>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=96.83  E-value=0.0033  Score=68.26  Aligned_cols=72  Identities=11%  Similarity=0.270  Sum_probs=44.8

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLI  738 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vili  738 (854)
                      .++|+||+|+|||.+|..+|.. -|..-.|+.+...+..          ...   ........+.+.+.+.+.+  +|+|
T Consensus       125 viLI~GpPGsGKTtLAlqlA~~-~G~~VlyIs~~~eE~v----------~~~---~~~le~~l~~i~~~l~~~~--LLVI  188 (331)
T 2vhj_A          125 MVIVTGKGNSGKTPLVHALGEA-LGGKDKYATVRFGEPL----------SGY---NTDFNVFVDDIARAMLQHR--VIVI  188 (331)
T ss_dssp             EEEEECSCSSSHHHHHHHHHHH-HHTTSCCEEEEBSCSS----------TTC---BCCHHHHHHHHHHHHHHCS--EEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHh-CCCCEEEEEecchhhh----------hhh---hcCHHHHHHHHHHHHhhCC--EEEE
Confidence            5689999999999999999987 3433445655323211          000   0000022234666776666  9999


Q ss_pred             ecCCCCCH
Q 003038          739 EDVEQADY  746 (854)
Q Consensus       739 DEieka~~  746 (854)
                      |+|.-+.+
T Consensus       189 DsI~aL~~  196 (331)
T 2vhj_A          189 DSLKNVIG  196 (331)
T ss_dssp             ECCTTTC-
T ss_pred             eccccccc
Confidence            99998754

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=96.82  E-value=0.0014  Score=77.48  Aligned_cols=41  Identities=17%  Similarity=0.251  Sum_probs=30.2

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      ..+.+.+.+..... ...+++|+||||+|||++++.++..+.
T Consensus        45 G~~~~l~~l~~~i~-~g~~vll~Gp~GtGKTtlar~ia~~l~   85 (604)
T 3k1j_A           45 GQEHAVEVIKTAAN-QKRHVLLIGEPGTGKSMLGQAMAELLP   85 (604)
T ss_dssp             SCHHHHHHHHHHHH-TTCCEEEECCTTSSHHHHHHHHHHTSC
T ss_pred             CchhhHhhcccccc-CCCEEEEEeCCCCCHHHHHHHHhccCC
Confidence            34444444444443 457999999999999999999998653

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=96.81  E-value=0.00053  Score=68.54  Aligned_cols=93  Identities=10%  Similarity=0.062  Sum_probs=51.5

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc---cccCcCCCccccccccccC-CCCCC--chHHHHHHHHHcCC
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS---SFSSTRADSTEDSRNKRSR-DEQSC--SYIERFAEAVSNNP  732 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s---~~~~~~~~s~e~~~~~rl~-~~~g~--g~~e~L~eav~~~p  732 (854)
                      ..+++||+|+|||+++..++..+.+...+.+.+...   .|.       +..-.+++- .....  .-.+.+.+.+. .+
T Consensus         5 i~vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~~~~~~d~r~~-------~~~i~s~~g~~~~~~~~~~~~~~~~~~~-~~   76 (184)
T 2orw_A            5 LTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKIDSRYH-------STMIVSHSGNGVEAHVIERPEEMRKYIE-ED   76 (184)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCEEEEEEEC-----C-------CCEECC----CEECEEESSGGGGGGGCC-TT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeeccccccC-------cccEEecCCCceeeEEECCHHHHHHHhc-CC
Confidence            578999999999999977766554433333332211   111       000011100 00000  00012222222 35


Q ss_pred             CEEEEEecCCCCCHHHHHHHHHhhhcC
Q 003038          733 HRVFLIEDVEQADYCSQKGFKRAIESG  759 (854)
Q Consensus       733 ~~ViliDEieka~~~v~~~Ll~~le~G  759 (854)
                      +.+|+|||+...++++.+.|....++|
T Consensus        77 ~dvviIDE~Q~~~~~~~~~l~~l~~~~  103 (184)
T 2orw_A           77 TRGVFIDEVQFFNPSLFEVVKDLLDRG  103 (184)
T ss_dssp             EEEEEECCGGGSCTTHHHHHHHHHHTT
T ss_pred             CCEEEEECcccCCHHHHHHHHHHHHCC
Confidence            789999999999999888888888764

>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=96.72  E-value=0.0038  Score=64.37  Aligned_cols=98  Identities=13%  Similarity=0.014  Sum_probs=57.8

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccC-CCCCC--chHHHHHHHHHc---
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSR-DEQSC--SYIERFAEAVSN---  730 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~-~~~g~--g~~e~L~eav~~---  730 (854)
                      ....+++||+|+|||+++..++..+-+.....+.+....-.  +  + +..-.+++- ..+..  ...+.+.+.+++   
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~d~--r--~-~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~   86 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDT--R--S-IRNIQSRTGTSLPSVEVESAPEILNYIMSNSF   86 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCG--G--G-CSSCCCCCCCSSCCEEESSTHHHHHHHHSTTS
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEeccCc--h--H-HHHHHHhcCCCccccccCCHHHHHHHHHHHhh
Confidence            35778889999999999998887665555555555322111  0  0 111112210 00110  112356666665   


Q ss_pred             -CCCEEEEEecCCCCCHHHHHHHHHhhhcC
Q 003038          731 -NPHRVFLIEDVEQADYCSQKGFKRAIESG  759 (854)
Q Consensus       731 -~p~~ViliDEieka~~~v~~~Ll~~le~G  759 (854)
                       .++.||+|||+.-++.+....+..+.+.|
T Consensus        87 ~~~~dvViIDEaQ~l~~~~ve~l~~L~~~g  116 (223)
T 2b8t_A           87 NDETKVIGIDEVQFFDDRICEVANILAENG  116 (223)
T ss_dssp             CTTCCEEEECSGGGSCTHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEecCccCcHHHHHHHHHHHhCC
Confidence             45899999999999888767666555543

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=96.68  E-value=0.0011  Score=77.73  Aligned_cols=40  Identities=10%  Similarity=0.033  Sum_probs=34.8

Q ss_pred             cHHHHHHHHHHhhc--cCcCCceeecCCCCCHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMS--KRKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       211 r~~ei~~v~~~L~r--~~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      |++++.++.+.|..  ...+-++|+|++|+|||++|..++.+
T Consensus       129 R~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~  170 (591)
T 1z6t_A          129 RKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRD  170 (591)
T ss_dssp             CHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             cHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhc
Confidence            99999999999974  34456899999999999999999865

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=96.66  E-value=0.0036  Score=69.46  Aligned_cols=53  Identities=19%  Similarity=0.215  Sum_probs=37.2

Q ss_pred             HHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc
Q 003038          213 EDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR  274 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~  274 (854)
                      .++.+.+.-++ ....++++.||+|+||+.+++.+...-.+       ++ .|+.++++.+-
T Consensus       139 ~~~~~~~~~~a-~~~~~vli~GesGtGKe~lAr~ih~~s~r-------~~-~fv~vnc~~~~  191 (368)
T 3dzd_A          139 LEIKRLIPKIA-KSKAPVLITGESGTGKEIVARLIHRYSGR-------KG-AFVDLNCASIP  191 (368)
T ss_dssp             HHHHHHHHHHH-TSCSCEEEECCTTSSHHHHHHHHHHHHCC-------CS-CEEEEESSSSC
T ss_pred             HHHHhhhhhhh-ccchhheEEeCCCchHHHHHHHHHHhccc-------cC-CcEEEEcccCC
Confidence            34444555444 46778999999999999999988765321       12 39999988653

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=96.63  E-value=0.002  Score=70.44  Aligned_cols=78  Identities=10%  Similarity=0.076  Sum_probs=55.7

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHc----CC-C--------------CcccCCceEEEcccccc-ccc-chHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEK----GD-V--------------PEALRDVKCLPLSISSF-RHM-NRVEVEQR  284 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~----~~-v--------------p~~L~~~~~~~l~~~~l-~~~-~rge~E~r  284 (854)
                      +++.++|+||+|+|||+++..||+++..    .| .              ++...++.-+-++...+ ... ..++|.+.
T Consensus        39 ~~~lIvI~GPTgsGKTtLa~~LA~~l~~eiIs~Ds~qvYr~mdIgTakp~~eE~~gvphhlidi~~~~~e~~s~~~F~~~  118 (339)
T 3a8t_A           39 KEKLLVLMGATGTGKSRLSIDLAAHFPLEVINSDKMQVYKGLDITTNKISVPDRGGVPHHLLGEVDPARGELTPADFRSL  118 (339)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHTTSCEEEEECCSSTTBSSCTTTTTCCCSGGGTTCCEESSSCBCGGGCCCCHHHHHHH
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHCCCcEEcccccccccceeeecCCCCHHHHcCCCEeeccccCcccCccCHHHHHHH
Confidence            4457899999999999999999988631    00 0              45666666666666555 333 57889898


Q ss_pred             HHHHHHHHHhhhCCCeEEEeC
Q 003038          285 VEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       285 l~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..++++++...  ++++|+++
T Consensus       119 a~~~i~~i~~~--g~~pIlvG  137 (339)
T 3a8t_A          119 AGKAVSEITGR--RKLPVLVG  137 (339)
T ss_dssp             HHHHHHHHHHT--TCEEEEEC
T ss_pred             HHHHHHHHHhc--CCeEEEEc
Confidence            89899888765  45666655

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=96.58  E-value=0.0055  Score=83.61  Aligned_cols=99  Identities=12%  Similarity=0.077  Sum_probs=69.2

Q ss_pred             EEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEec
Q 003038          661 FFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIED  740 (854)
Q Consensus       661 Lf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDE  740 (854)
                      ...||.|+|||++++.||+.+ |  ..++.++|++-.       +...+           ...+.+++..  ..-.+|||
T Consensus       608 ~~~GPaGtGKTet~k~La~~l-g--r~~~vfnC~~~~-------d~~~~-----------g~i~~G~~~~--GaW~cfDE  664 (3245)
T 3vkg_A          608 NPFGPAGTGKTETVKALGSQL-G--RFVLVFCCDEGF-------DLQAM-----------SRIFVGLCQC--GAWGCFDE  664 (3245)
T ss_dssp             EEECSTTSSHHHHHHHHHHHT-T--CCEEEEECSSCC-------CHHHH-----------HHHHHHHHHH--TCEEEEET
T ss_pred             CCCCCCCCCHHHHHHHHHHHh-C--CeEEEEeCCCCC-------CHHHH-----------HHHHhhHhhc--CcEEEehh
Confidence            467999999999999999998 4  678899988654       11111           1123444443  45778999


Q ss_pred             CCCCCHHHHHHHHHhhh---------cCeEecCCCceeecC-CeEEEEecCC
Q 003038          741 VEQADYCSQKGFKRAIE---------SGRIVTSSGDEVSLG-DAIVILSCES  782 (854)
Q Consensus       741 ieka~~~v~~~Ll~~le---------~G~l~d~~G~~v~~~-~aIiIlTsn~  782 (854)
                      |++++++++..+.+.|.         ..++.-..|++|.+. ++.|++|.|.
T Consensus       665 fNrl~~~vLSvv~~qi~~I~~a~~~~~~~~~~~~G~~i~l~~~~~vfiTmNp  716 (3245)
T 3vkg_A          665 FNRLEERILSAVSQQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNP  716 (3245)
T ss_dssp             TTSSCHHHHHHHHHHHHHHHHHHHHTCSEECCC---CEECCTTCEEEECBCC
T ss_pred             hhcCCHHHHHHHHHHHHHHHHHHHcCCCeEEecCCCEEeecCCeEEEEEeCC
Confidence            99999999999888665         345544347788875 5677888885

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=96.57  E-value=0.0067  Score=64.01  Aligned_cols=98  Identities=16%  Similarity=0.286  Sum_probs=56.0

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCC-CCceEEEccc-cccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCC
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGS-HNNFVSIALS-SFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPH  733 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-~~~~i~id~s-~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~  733 (854)
                      +...+++.||+|+|||++.+.|+..+-.. ...++..+-. +|.......   .-..+.++-....|...|..+++.+| 
T Consensus        24 ~g~~v~i~Gp~GsGKSTll~~l~g~~~~~~~G~I~~~g~~i~~~~~~~~~---~v~q~~~gl~~~~l~~~la~aL~~~p-   99 (261)
T 2eyu_A           24 KMGLILVTGPTGSGKSTTIASMIDYINQTKSYHIITIEDPIEYVFKHKKS---IVNQREVGEDTKSFADALRAALREDP-   99 (261)
T ss_dssp             SSEEEEEECSTTCSHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCCCSSS---EEEEEEBTTTBSCHHHHHHHHHHHCC-
T ss_pred             CCCEEEEECCCCccHHHHHHHHHHhCCCCCCCEEEEcCCcceeecCCcce---eeeHHHhCCCHHHHHHHHHHHHhhCC-
Confidence            34689999999999999999999987432 2233222211 111000000   00000111011245447888888877 


Q ss_pred             EEEEEecCCCCCHHHHHHHHHhhhcC
Q 003038          734 RVFLIEDVEQADYCSQKGFKRAIESG  759 (854)
Q Consensus       734 ~ViliDEieka~~~v~~~Ll~~le~G  759 (854)
                      .||++||.-  |++....+++....|
T Consensus       100 ~illlDEp~--D~~~~~~~l~~~~~g  123 (261)
T 2eyu_A          100 DVIFVGEMR--DLETVETALRAAETG  123 (261)
T ss_dssp             SEEEESCCC--SHHHHHHHHHHHHTT
T ss_pred             CEEEeCCCC--CHHHHHHHHHHHccC
Confidence            699999997  776655555555444

>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=96.54  E-value=0.0024  Score=63.42  Aligned_cols=23  Identities=13%  Similarity=0.245  Sum_probs=21.1

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+.|.||+|+|||++.+.|+..+
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l   24 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            36789999999999999999987

>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=96.41  E-value=0.0043  Score=60.54  Aligned_cols=25  Identities=24%  Similarity=0.379  Sum_probs=22.4

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ...++|+|+||+|||++++.|++++
T Consensus         3 ~~~i~l~G~~GsGKST~a~~La~~l   27 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhc
Confidence            3568999999999999999999875

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=96.33  E-value=0.01  Score=66.26  Aligned_cols=52  Identities=15%  Similarity=0.197  Sum_probs=36.8

Q ss_pred             HHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc
Q 003038          215 VMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR  274 (854)
Q Consensus       215 i~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~  274 (854)
                      +.+.+.-++ ....+++|.||+|+|||.+++.+...-..       .+..|+.++++.+.
T Consensus       149 l~~~i~~~a-~~~~~vli~Ge~GtGK~~lAr~ih~~s~r-------~~~~fv~v~~~~~~  200 (387)
T 1ny5_A          149 ILEKIKKIS-CAECPVLITGESGVGKEVVARLIHKLSDR-------SKEPFVALNVASIP  200 (387)
T ss_dssp             HHHHHHHHT-TCCSCEEEECSTTSSHHHHHHHHHHHSTT-------TTSCEEEEETTTSC
T ss_pred             HHHHHHHhc-CCCCCeEEecCCCcCHHHHHHHHHHhcCC-------CCCCeEEEecCCCC
Confidence            333444444 46778899999999999999988765221       34578999987653

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=96.29  E-value=0.0084  Score=66.55  Aligned_cols=98  Identities=14%  Similarity=0.260  Sum_probs=57.7

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCC-CCceEEEccc-cccCcCCCccccccccc-cCCCCCCchHHHHHHHHHcCC
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGS-HNNFVSIALS-SFSSTRADSTEDSRNKR-SRDEQSCSYIERFAEAVSNNP  732 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-~~~~i~id~s-~~~~~~~~s~e~~~~~r-l~~~~g~g~~e~L~eav~~~p  732 (854)
                      +.+.+++.||+|+|||++.++|+..+-.. ...++.++-. ++.-....+    -+.. .++.....|...|..+++.+|
T Consensus       135 ~g~~i~ivG~~GsGKTTll~~l~~~~~~~~~g~I~~~e~~~e~~~~~~~~----~v~Q~~~g~~~~~~~~~l~~~L~~~p  210 (372)
T 2ewv_A          135 KMGLILVTGPTGSGKSTTIASMIDYINQTKSYHIITIEDPIEYVFKHKKS----IVNQREVGEDTKSFADALRAALREDP  210 (372)
T ss_dssp             SSEEEEEECSSSSSHHHHHHHHHHHHHHHSCCEEEEEESSCCSCCCCSSS----EEEEEEBTTTBSCSHHHHHHHTTSCC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhcCcCCCcEEEEecccHhhhhccCce----EEEeeecCCCHHHHHHHHHHHhhhCc
Confidence            34689999999999999999999987533 3344444321 111000000    0000 011011244456888888876


Q ss_pred             CEEEEEecCCCCCHHHHHHHHHhhhcCe
Q 003038          733 HRVFLIEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       733 ~~ViliDEieka~~~v~~~Ll~~le~G~  760 (854)
                       .+|++||+-  +++....++++...|.
T Consensus       211 -d~illdE~~--d~e~~~~~l~~~~~g~  235 (372)
T 2ewv_A          211 -DVIFVGEMR--DLETVETALRAAETGH  235 (372)
T ss_dssp             -SEEEESCCC--SHHHHHHHHHHHTTTC
T ss_pred             -CEEEECCCC--CHHHHHHHHHHHhcCC
Confidence             689999997  6665555556555553

>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=96.19  E-value=0.012  Score=66.97  Aligned_cols=36  Identities=14%  Similarity=0.222  Sum_probs=27.9

Q ss_pred             HHHHhhcc-CcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          218 VIENLMSK-RKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       218 v~~~L~r~-~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      +|+.|.-- +....+|+|+||||||+++..++..+..
T Consensus       141 ~ID~L~pi~kGq~~~i~G~sGvGKTtL~~~l~~~~~~  177 (473)
T 1sky_E          141 VVDLLAPYIKGGKIGLFGGAGVGKTVLIQELIHNIAQ  177 (473)
T ss_dssp             HHHHHSCEETTCEEEEECCSSSCHHHHHHHHHHHHHH
T ss_pred             HHHHHhhhccCCEEEEECCCCCCccHHHHHHHhhhhh
Confidence            56665432 3456899999999999999999988764

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=95.90  E-value=0.0047  Score=60.68  Aligned_cols=34  Identities=12%  Similarity=-0.033  Sum_probs=28.2

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcc
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLS  269 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~  269 (854)
                      ..++++|+|+||+|||++++.||+++          +..++..|
T Consensus         4 ~~~~i~l~G~~GsGKst~a~~La~~l----------~~~~i~~d   37 (185)
T 3trf_A            4 NLTNIYLIGLMGAGKTSVGSQLAKLT----------KRILYDSD   37 (185)
T ss_dssp             -CCEEEEECSTTSSHHHHHHHHHHHH----------CCCEEEHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHh----------CCCEEECh
Confidence            46789999999999999999999885          45677665

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=95.86  E-value=0.011  Score=64.55  Aligned_cols=92  Identities=9%  Similarity=0.092  Sum_probs=56.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc-cccCcCCCcccccc-ccccCCCCCCchHHHHHHHHHcCCCEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS-SFSSTRADSTEDSR-NKRSRDEQSCSYIERFAEAVSNNPHRV  735 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s-~~~~~~~~s~e~~~-~~rl~~~~g~g~~e~L~eav~~~p~~V  735 (854)
                      ..+++.||+|+|||++.++|+..+- .....|.++.. ++..      ..+. .-.+..+.|......|..+++.+| .+
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~~~-~~~g~i~i~~~~e~~~------~~~~~~i~~~~ggg~~~r~~la~aL~~~p-~i  243 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEFIP-KEERIISIEDTEEIVF------KHHKNYTQLFFGGNITSADCLKSCLRMRP-DR  243 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGGSC-TTSCEEEEESSCCCCC------SSCSSEEEEECBTTBCHHHHHHHHTTSCC-SE
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCc-CCCcEEEECCeecccc------ccchhEEEEEeCCChhHHHHHHHHhhhCC-CE
Confidence            3789999999999999999998774 34566777643 2210      0010 000111112233336778888777 68


Q ss_pred             EEEecCCCCCHHHHHHHHHhhhcCe
Q 003038          736 FLIEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       736 iliDEieka~~~v~~~Ll~~le~G~  760 (854)
                      +++||+--  .+++.. ++.+..|.
T Consensus       244 lildE~~~--~e~~~~-l~~~~~g~  265 (330)
T 2pt7_A          244 IILGELRS--SEAYDF-YNVLCSGH  265 (330)
T ss_dssp             EEECCCCS--THHHHH-HHHHHTTC
T ss_pred             EEEcCCCh--HHHHHH-HHHHhcCC
Confidence            88999875  456654 45555553

>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=95.76  E-value=0.012  Score=63.60  Aligned_cols=77  Identities=9%  Similarity=0.138  Sum_probs=52.1

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHc------------C------C-CCcccCCceEEEccccccccc-chHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEK------------G------D-VPEALRDVKCLPLSISSFRHM-NRVEVEQRVE  286 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~------------~------~-vp~~L~~~~~~~l~~~~l~~~-~rge~E~rl~  286 (854)
                      ++-++|+||+|||||+++..||+++..            +      . -|+.+.++.-+-+|.-.+... ..|+|.+...
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~~~~~~iis~Ds~QvYr~~~igTakp~~~E~~gvphhlid~~~~~e~~s~~~F~~~a~   82 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAKRLNGEVISGDSMQVYRGMDIGTAKITAEEMDGVPHHLIDIKDPSESFSVADFQDLAT   82 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHTTTEEEEECCGGGGBTTCCTTTTCCCHHHHTTCCEESSSCBCTTSCCCHHHHHHHHH
T ss_pred             CcEEEEECCCcCCHHHHHHHHHHhCccceeecCcccceeeeeecCCCCCHHHHcCCCEEEeccCChhhhccHHHHHHHHH
Confidence            445788999999999999999987521            0      0 113444554444554444443 5789999999


Q ss_pred             HHHHHHHhhhCCCeEEEeC
Q 003038          287 EIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       287 ~l~~~~~~~~~~~~ILfid  305 (854)
                      .+++.+.+.  +.+.|+++
T Consensus        83 ~~i~~i~~~--gk~pIlVG   99 (322)
T 3exa_A           83 PLITEIHER--GRLPFLVG   99 (322)
T ss_dssp             HHHHHHHHT--TCEEEEES
T ss_pred             HHHHHHHhC--CCcEEEEc
Confidence            999998875  45555555

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=95.76  E-value=0.009  Score=60.07  Aligned_cols=94  Identities=12%  Similarity=0.016  Sum_probs=53.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc---cccCcCCCccccccccccC---CCCCCchHHHHHHHHHcC
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS---SFSSTRADSTEDSRNKRSR---DEQSCSYIERFAEAVSNN  731 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s---~~~~~~~~s~e~~~~~rl~---~~~g~g~~e~L~eav~~~  731 (854)
                      -..+++||.|+|||+.+..++...-+...+.+-+...   .|.       +..-.+++-   ......-.+.+.+.+. .
T Consensus         9 ~i~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~k~~~d~r~~-------~~~i~s~~g~~~~a~~~~~~~~i~~~~~-~   80 (191)
T 1xx6_A            9 WVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYS-------KEDVVSHMGEKEQAVAIKNSREILKYFE-E   80 (191)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC--------------CEEECTTSCEEECEEESSSTHHHHHCC-T
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccCccch-------HHHHHhhcCCceeeEeeCCHHHHHHHHh-c
Confidence            3678899999999988887777664444444444311   121       111111110   0000000123444433 3


Q ss_pred             CCEEEEEecCCCCCHHHHHHHHHhhhcC
Q 003038          732 PHRVFLIEDVEQADYCSQKGFKRAIESG  759 (854)
Q Consensus       732 p~~ViliDEieka~~~v~~~Ll~~le~G  759 (854)
                      ++.+|+|||+.-.+++....|....+.|
T Consensus        81 ~~dvViIDEaqfl~~~~v~~l~~l~~~~  108 (191)
T 1xx6_A           81 DTEVIAIDEVQFFDDEIVEIVNKIAESG  108 (191)
T ss_dssp             TCSEEEECSGGGSCTHHHHHHHHHHHTT
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            6899999999999888877666655554

>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=95.69  E-value=0.02  Score=64.02  Aligned_cols=76  Identities=8%  Similarity=0.055  Sum_probs=55.7

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHc----C--------------C-CCcccCCceEEEccccccccc-chHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEK----G--------------D-VPEALRDVKCLPLSISSFRHM-NRVEVEQRVEE  287 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~----~--------------~-vp~~L~~~~~~~l~~~~l~~~-~rge~E~rl~~  287 (854)
                      +-++|+||+|+|||+++..||.++..    .              . -++...++.-+-++.-.+... ..|+|.+....
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~~~~iis~Ds~QvYr~l~i~T~kp~~~E~~gv~hhlid~~~~~~~~s~~~F~~~a~~   82 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKFNGEVINSDSMQVYKDIPIITNKHPLQEREGIPHHVMNHVDWSEEYYSHRFETECMN   82 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHHTEEEEECCTTTTBSSCTTTTTCCCGGGTTTCCEESCSCBCTTSCCCHHHHHHHHHH
T ss_pred             cEEEEECcchhhHHHHHHHHHHHCCCeEeecCccceecccccccCCCCHHHHcCchhhcCCccChHhHhhHHHHHHHHHH
Confidence            45789999999999999999998632    0              1 125566666666666555554 58999999999


Q ss_pred             HHHHHHhhhCCCeEEEeC
Q 003038          288 IKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       288 l~~~~~~~~~~~~ILfid  305 (854)
                      +++.+.+.  +.+.|+++
T Consensus        83 ~i~~i~~~--g~~pilVG   98 (409)
T 3eph_A           83 AIEDIHRR--GKIPIVVG   98 (409)
T ss_dssp             HHHHHHTT--TCEEEEEC
T ss_pred             HHHHHHhc--CCCEEEEC
Confidence            99999876  45556665

>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=95.65  E-value=0.097  Score=59.12  Aligned_cols=42  Identities=17%  Similarity=0.140  Sum_probs=33.3

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +..+++|.||+|+|||+++..||..+-.....+.-+++..|.
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~~D~~r  137 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAADVYR  137 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEEECCSC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEecCccc
Confidence            346999999999999999999998886555666666665543

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=95.65  E-value=0.019  Score=62.35  Aligned_cols=67  Identities=10%  Similarity=0.105  Sum_probs=46.4

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccc-----------------------------ccccc-
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSIS-----------------------------SFRHM-  276 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~-----------------------------~l~~~-  276 (854)
                      ++.++|+||+|+|||+++..||.++          +..++++|--                             .+... 
T Consensus         5 ~~~i~i~GptGsGKTtla~~La~~l----------~~~iis~Ds~qvy~~~~igTakp~~~e~~gvph~lid~~~~~~~~   74 (323)
T 3crm_A            5 PPAIFLMGPTAAGKTDLAMALADAL----------PCELISVDSALIYRGMDIGTAKPSRELLARYPHRLIDIRDPAESY   74 (323)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHS----------CEEEEEECTTTTBTTCCTTTTCCCHHHHHHSCEETSSCBCTTSCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc----------CCcEEeccchhhhcCCCcccCCCCHHHHcCCCEEEeeccCccccc
Confidence            3478999999999999999999874          3456665421                             11111 


Q ss_pred             chHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          277 NRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       277 ~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..++|-+...++++++...  +.++|+++
T Consensus        75 ~~~~F~~~a~~~i~~i~~~--g~~~IlvG  101 (323)
T 3crm_A           75 SAAEFRADALAAMAKATAR--GRIPLLVG  101 (323)
T ss_dssp             CHHHHHHHHHHHHHHHHHT--TCEEEEEE
T ss_pred             CHHHHHHHHHHHHHHHHHc--CCeEEEEC
Confidence            3577888888888887764  35555554

>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=95.61  E-value=0.018  Score=67.21  Aligned_cols=39  Identities=15%  Similarity=0.099  Sum_probs=34.1

Q ss_pred             cHHHHHHHHHHhhcc---CcCCceeecCCCCCHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSK---RKRNFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       211 r~~ei~~v~~~L~r~---~k~n~vLvGe~GvGKta~v~~la~  249 (854)
                      |++++.++++.|...   .-+-+.|+|.+|+|||++|..++.
T Consensus       133 R~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~  174 (549)
T 2a5y_B          133 REYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALS  174 (549)
T ss_dssp             CHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             chHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHH
Confidence            999999999999765   235578999999999999999985

>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=95.57  E-value=0.1  Score=59.05  Aligned_cols=91  Identities=10%  Similarity=0.104  Sum_probs=53.6

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCC----ccccccccccCCCCCCchHH---HHHHHH
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRAD----STEDSRNKRSRDEQSCSYIE---RFAEAV  728 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~----s~e~~~~~rl~~~~g~g~~e---~L~eav  728 (854)
                      +..+++|.|++|+|||+++..||..+-.......-+++..|......    ..+...+.-...+.+....+   ...+..
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~~D~~R~aa~eqL~~~~~~~gvpv~~~~~~~dp~~i~~~al~~a  178 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDTWRPGAYHQLRQLLDRYHIEVFGNPQEKDAIKLAKEGVDYF  178 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECCCSSTHHHHHHHHHHGGGTCEEECCTTCCCHHHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCcchhHHHHHHHHHHhcCCcEEecCCCCCHHHHHHHHHHHH
Confidence            35799999999999999999999988766667777777655420000    00000000000011111111   223344


Q ss_pred             HcCCCEEEEEecCCCCCH
Q 003038          729 SNNPHRVFLIEDVEQADY  746 (854)
Q Consensus       729 ~~~p~~ViliDEieka~~  746 (854)
                      +.+.+.||+||..-..+.
T Consensus       179 ~~~~~DvVIIDTaGrl~~  196 (443)
T 3dm5_A          179 KSKGVDIIIVDTAGRHKE  196 (443)
T ss_dssp             HHTTCSEEEEECCCCSSC
T ss_pred             HhCCCCEEEEECCCcccc
Confidence            556789999999987763

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=95.33  E-value=0.02  Score=75.43  Aligned_cols=91  Identities=13%  Similarity=0.009  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHc-CCCCcccCCceEEEccc--ccccccchH---------
Q 003038          212 NEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEK-GDVPEALRDVKCLPLSI--SSFRHMNRV---------  279 (854)
Q Consensus       212 ~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~-~~vp~~L~~~~~~~l~~--~~l~~~~rg---------  279 (854)
                      -.++..++.+--=.+.+|++|+||||+|||.++.+++....+ |.      .+.|+...-  ..+.+...|         
T Consensus      1412 ~~~LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~ea~~~G~------~v~Fi~~e~~~~~l~a~~~G~dl~~l~v~ 1485 (2050)
T 3cmu_A         1412 SLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGK------TCAFIDAEHALDPIYARKLGVDIDNLLCS 1485 (2050)
T ss_dssp             CHHHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTC------CEEEECTTSCCCHHHHHHTTCCTTTCEEE
T ss_pred             CHHHHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCC------cEEEEEcccccCHHHHHHcCCCchhceee
Confidence            344555554222357899999999999999999998876543 21      233444331  111111112         


Q ss_pred             ---HHHHHHHHHHHHHHhhhCCCeEEEeCccccc
Q 003038          280 ---EVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       280 ---e~E~rl~~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                         ..|+-+..+...+++.  ++.+||||+|..+
T Consensus      1486 ~~~~~E~~l~~~~~lvr~~--~~~lVVIDsi~al 1517 (2050)
T 3cmu_A         1486 QPDTGEQALEICDALARSG--AVDVIVVDSVAAL 1517 (2050)
T ss_dssp             CCSSHHHHHHHHHHHHHHT--CCSEEEESCGGGC
T ss_pred             cCChHHHHHHHHHHHHhcC--CCCEEEEcChhHh
Confidence               3345555555666664  6899999999766

>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=95.24  E-value=0.062  Score=59.68  Aligned_cols=38  Identities=13%  Similarity=0.092  Sum_probs=30.7

Q ss_pred             HHHHHHhhcc-CcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          216 MYVIENLMSK-RKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       216 ~~v~~~L~r~-~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      -++|+++.-= +.....|+|++|+|||+++..++.-|..
T Consensus       162 iraID~~~pi~rGQr~~IvG~sG~GKTtLl~~Iar~i~~  200 (422)
T 3ice_A          162 ARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAY  200 (422)
T ss_dssp             HHHHHHHSCCBTTCEEEEECCSSSSHHHHHHHHHHHHHH
T ss_pred             ceeeeeeeeecCCcEEEEecCCCCChhHHHHHHHHHHhh
Confidence            3667776533 5678999999999999999999988765

>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=95.22  E-value=0.024  Score=57.28  Aligned_cols=26  Identities=8%  Similarity=0.263  Sum_probs=22.8

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +.+-++|+||+|+|||++++.|+...
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~~   43 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQN   43 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhhC
Confidence            45668999999999999999999764

>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=95.22  E-value=0.016  Score=55.45  Aligned_cols=91  Identities=21%  Similarity=0.290  Sum_probs=48.1

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccc--ccc----ccccCCCCCCc-hHHHHHHHHHcC
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTE--DSR----NKRSRDEQSCS-YIERFAEAVSNN  731 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e--~~~----~~rl~~~~g~g-~~e~L~eav~~~  731 (854)
                      .++|.||+|+|||++|+.| +.+ |    +..++++++.........  ...    ...+....+.. +.+.+.+.+...
T Consensus         3 ~I~l~G~~GsGKsT~a~~L-~~~-g----~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   76 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL-KER-G----AKVIVMSDVVRKRYSIEAKPGERLMDFAKRLREIYGDGVVARLCVEELGTS   76 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH-HHT-T----CEEEEHHHHHHHHHHHHC---CCHHHHHHHHHHHHCTTHHHHHHHHHHCSC
T ss_pred             EEEEECCCCCCHHHHHHHH-HHC-C----CcEEEHhHHHHHHHHhcCCChhHHHHHHHHHHhhCCHHHHHHHHHHHHHhc
Confidence            5789999999999999999 544 3    334444433210000000  000    00000000111 112345555456


Q ss_pred             CCEEEEEecCCCCCHHHHHHHHHhhh
Q 003038          732 PHRVFLIEDVEQADYCSQKGFKRAIE  757 (854)
Q Consensus       732 p~~ViliDEieka~~~v~~~Ll~~le  757 (854)
                      +..+|++|.+  .++.....|.+.+.
T Consensus        77 ~~~~vi~dg~--~~~~~~~~l~~~~~  100 (179)
T 3lw7_A           77 NHDLVVFDGV--RSLAEVEEFKRLLG  100 (179)
T ss_dssp             CCSCEEEECC--CCHHHHHHHHHHHC
T ss_pred             CCCeEEEeCC--CCHHHHHHHHHHhC
Confidence            6778999998  66766677777664

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=95.19  E-value=0.067  Score=60.25  Aligned_cols=96  Identities=11%  Similarity=0.193  Sum_probs=57.7

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc-cccCcCCCccccccccccC-CCCCCchHHHHHHHHHcCCC
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS-SFSSTRADSTEDSRNKRSR-DEQSCSYIERFAEAVSNNPH  733 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s-~~~~~~~~s~e~~~~~rl~-~~~g~g~~e~L~eav~~~p~  733 (854)
                      +.+.+++.||+|+|||++.++|+..+-.....++.+.-. +|.       -.+.....+ ...++.|.+.|..+++++| 
T Consensus       166 ~ggii~I~GpnGSGKTTlL~allg~l~~~~g~I~~~ed~ie~~-------~~~~~q~~v~~~~g~~f~~~lr~~Lrq~p-  237 (418)
T 1p9r_A          166 PHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEFD-------IDGIGQTQVNPRVDMTFARGLRAILRQDP-  237 (418)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCSC-------CSSSEEEECBGGGTBCHHHHHHHHGGGCC-
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHhhcCCCCCEEEEecccchhc-------cCCcceEEEccccCcCHHHHHHHHhccCC-
Confidence            346899999999999999999999885444455544321 111       000000001 1123456667788888888 


Q ss_pred             EEEEEecCCCCCHHHHHHHHHhhhcCeE
Q 003038          734 RVFLIEDVEQADYCSQKGFKRAIESGRI  761 (854)
Q Consensus       734 ~ViliDEieka~~~v~~~Ll~~le~G~l  761 (854)
                      .+|++.||.  +.......+++...|.+
T Consensus       238 d~i~vgEiR--d~et~~~~l~a~~tGhl  263 (418)
T 1p9r_A          238 DVVMVGEIR--DLETAQIAVQASLTGHL  263 (418)
T ss_dssp             SEEEESCCC--SHHHHHHHHHHHHTTCE
T ss_pred             CeEEEcCcC--CHHHHHHHHHHHHhCCC
Confidence            577889876  44433344455555643

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=95.15  E-value=0.013  Score=58.61  Aligned_cols=34  Identities=15%  Similarity=0.147  Sum_probs=28.3

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcc
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLS  269 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~  269 (854)
                      ..++++|+|+||+|||++++.||+++          +..++..|
T Consensus        24 ~~~~i~l~G~~GsGKsTl~~~La~~l----------~~~~i~~d   57 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLGKAFARKL----------NVPFIDLD   57 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHH----------TCCEEEHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHc----------CCCEEcch
Confidence            45689999999999999999999886          45666654

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=95.14  E-value=0.034  Score=56.06  Aligned_cols=35  Identities=6%  Similarity=0.107  Sum_probs=26.1

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      ..+++.||+|+|||++++.|+..+-.....++.++
T Consensus        24 ~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~   58 (235)
T 2w0m_A           24 FFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVT   58 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEE
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            37889999999999999999976643333444444

>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=95.07  E-value=0.011  Score=57.56  Aligned_cols=34  Identities=15%  Similarity=0.343  Sum_probs=27.6

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      .+++.|++|+|||++|++||+.+ +  ..++.++.+.
T Consensus         5 ~i~l~G~~GsGKST~a~~La~~l-~--~~~~~~~~D~   38 (178)
T 1qhx_A            5 MIILNGGSSAGKSGIVRCLQSVL-P--EPWLAFGVDS   38 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHS-S--SCEEEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc-C--CCeEEeccch
Confidence            68899999999999999999987 2  3567665543

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=95.00  E-value=0.058  Score=57.49  Aligned_cols=25  Identities=8%  Similarity=0.191  Sum_probs=22.0

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ...+||+|+||+|||++++.|+.++
T Consensus        33 ~~livl~G~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           33 PTAFLLGGQPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4568999999999999999999874

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=95.00  E-value=0.015  Score=59.13  Aligned_cols=26  Identities=19%  Similarity=0.121  Sum_probs=23.4

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +||+.+++||||+|||+++.++|..+
T Consensus        57 kkn~ili~GPPGtGKTt~a~ala~~l   82 (212)
T 1tue_A           57 KKNCLVFCGPANTGKSYFGMSFIHFI   82 (212)
T ss_dssp             TCSEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             cccEEEEECCCCCCHHHHHHHHHHHh
Confidence            56779999999999999999999875

>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=94.98  E-value=0.036  Score=64.50  Aligned_cols=44  Identities=16%  Similarity=0.184  Sum_probs=35.0

Q ss_pred             cccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHH
Q 003038          621 PWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELAR  679 (854)
Q Consensus       621 ~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~  679 (854)
                      +|-+..+..|...+.....               ....++.++|+.|+|||+||+.+++
T Consensus       131 ~GR~~~~~~l~~~L~~~~~---------------~~~~vv~I~G~gGvGKTtLA~~v~~  174 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCD---------------LDSFFLFLHGRAGSGKSVIASQALS  174 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTT---------------SSSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccC---------------CCceEEEEEcCCCCCHHHHHHHHHH
Confidence            5999888888888754210               2246889999999999999999996

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=94.92  E-value=0.036  Score=65.04  Aligned_cols=97  Identities=13%  Similarity=0.120  Sum_probs=54.1

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc---CCCccccccccccCC--CCCCchHHHHHHHHHcCC
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST---RADSTEDSRNKRSRD--EQSCSYIERFAEAVSNNP  732 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~---~~~s~e~~~~~rl~~--~~g~g~~e~L~eav~~~p  732 (854)
                      ..+++.||+|+|||++++.|+..+-.....++-...+.-...   .....+...+.+++.  +.++.+     ..-...+
T Consensus       205 ~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~ApT~~Aa~~L~e~~~~~a~Tih~ll~~~~~~~~~-----~~~~~~~  279 (574)
T 3e1s_A          205 RLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKAARRLGEVTGRTASTVHRLLGYGPQGFRH-----NHLEPAP  279 (574)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHHTSCEEEHHHHTTEETTEESC-----SSSSCCS
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEecCcHHHHHHhHhhhcccHHHHHHHHcCCcchhhh-----hhccccc
Confidence            378999999999999999999887654444433321100000   000000001111110  000000     0001125


Q ss_pred             CEEEEEecCCCCCHHHHHHHHHhhhcC
Q 003038          733 HRVFLIEDVEQADYCSQKGFKRAIESG  759 (854)
Q Consensus       733 ~~ViliDEieka~~~v~~~Ll~~le~G  759 (854)
                      +.+|++||+..++...+..|++++..|
T Consensus       280 ~dvlIIDEasml~~~~~~~Ll~~~~~~  306 (574)
T 3e1s_A          280 YDLLIVDEVSMMGDALMLSLLAAVPPG  306 (574)
T ss_dssp             CSEEEECCGGGCCHHHHHHHHTTSCTT
T ss_pred             CCEEEEcCccCCCHHHHHHHHHhCcCC
Confidence            789999999999999999998888644

>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=94.88  E-value=0.03  Score=72.83  Aligned_cols=80  Identities=14%  Similarity=0.008  Sum_probs=55.3

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccc--cccc--------ccchHH----HHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSI--SSFR--------HMNRVE----VEQRVEEIKNL  291 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~--~~l~--------~~~rge----~E~rl~~l~~~  291 (854)
                      +.+.++|+||||||||.++.+++..-....-|     .-|++++-  ..+.        ..+.++    -|+.+..++..
T Consensus      1081 ~g~~~l~~G~~g~GKT~la~~~~~~~~~~g~~-----~~fi~~~~~~~~~~~~~~G~d~~~~~~~~~~~~e~~l~~~~~~ 1155 (1706)
T 3cmw_A         1081 MGRIVEIYGPESSGKTTLTLQVIAAAQREGKT-----CAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDAL 1155 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTTCC-----EEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCChHHHHHHHHHHhhhcCCc-----eeEEEcccchHHHHHHHhCCCHHHHhhccccchHHHHHHHHHH
Confidence            34458889999999999999988654433111     23444332  1111        234566    78999888888


Q ss_pred             HHhhhCCCeEEEeCccccc-cc
Q 003038          292 VRSCLGRGIVLNLGDLEWA-EF  312 (854)
Q Consensus       292 ~~~~~~~~~ILfidel~~l-~~  312 (854)
                      +++.  .++++|+|+|..| ..
T Consensus      1156 ar~~--~~~~i~~d~~~al~~~ 1175 (1706)
T 3cmw_A         1156 ARSG--AVDVIVVDSVAALTPK 1175 (1706)
T ss_dssp             HHHT--CCSEEEESCGGGCCCH
T ss_pred             HHhc--CCeEEEeCchHhcCcc
Confidence            8875  7999999999999 44

>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=94.85  E-value=0.019  Score=56.71  Aligned_cols=36  Identities=8%  Similarity=0.158  Sum_probs=28.5

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcc
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLS  269 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~  269 (854)
                      .+..+++|+|+||+|||++++.|+.++         .|..++.+|
T Consensus         8 ~~~~~I~l~G~~GsGKSTv~~~La~~l---------~g~~~id~d   43 (184)
T 1y63_A            8 PKGINILITGTPGTGKTSMAEMIAAEL---------DGFQHLEVG   43 (184)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHHS---------TTEEEEEHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhc---------CCCEEeeHH
Confidence            356789999999999999999999862         255666654

>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=94.82  E-value=0.022  Score=55.71  Aligned_cols=26  Identities=12%  Similarity=0.037  Sum_probs=23.8

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +..+++|+|+||+|||++++.|++++
T Consensus        10 ~~~~i~i~G~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           10 LLPNILLTGTPGVGKTTLGKELASKS   35 (180)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHHHh
Confidence            56789999999999999999999875

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=94.79  E-value=0.056  Score=53.06  Aligned_cols=25  Identities=16%  Similarity=0.272  Sum_probs=21.8

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      .+-++|+||+|+|||++++.|+...
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~~~   29 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLITKH   29 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3467899999999999999999865

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=94.77  E-value=0.053  Score=53.29  Aligned_cols=27  Identities=11%  Similarity=0.020  Sum_probs=23.6

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ...++|+|.||+|||++++.|+..+..
T Consensus        13 ~~~i~l~G~~GsGKsT~~~~L~~~l~~   39 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTIATRLADLLQK   39 (186)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            446899999999999999999998753

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=94.77  E-value=0.019  Score=56.25  Aligned_cols=24  Identities=25%  Similarity=0.483  Sum_probs=22.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..++|.||+|+|||++|+.||+.+
T Consensus         6 ~~i~l~G~~GsGKst~a~~La~~l   29 (185)
T 3trf_A            6 TNIYLIGLMGAGKTSVGSQLAKLT   29 (185)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            368899999999999999999987

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=94.73  E-value=0.07  Score=66.17  Aligned_cols=40  Identities=15%  Similarity=0.119  Sum_probs=34.8

Q ss_pred             cHHHHHHHHHHhhc-cCcCCceeecCCCCCHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMS-KRKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       211 r~~ei~~v~~~L~r-~~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      |++++.++.+.|.. ...+-+.|+|++|+|||++|..++..
T Consensus       133 Re~eLeeL~elL~~~d~~RVV~IvGmGGIGKTTLAk~Vy~d  173 (1221)
T 1vt4_I          133 RLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLS  173 (1221)
T ss_dssp             CHHHHHHHHHHHHHCCSSCEEEECCSTTSSHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccCCCeEEEEEcCCCccHHHHHHHHHHh
Confidence            99999999999986 34466889999999999999999853

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=94.73  E-value=0.046  Score=55.04  Aligned_cols=27  Identities=15%  Similarity=-0.130  Sum_probs=23.3

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      ....++|+||||+|||+++..++..+.
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~l~~~~~   48 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFSLHFIAKGL   48 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            456789999999999999999997664

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=94.65  E-value=0.042  Score=72.41  Aligned_cols=84  Identities=8%  Similarity=0.038  Sum_probs=48.6

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc-CCCcccccccccc-CCCCCC--chHHHHHHHHHcCCC
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST-RADSTEDSRNKRS-RDEQSC--SYIERFAEAVSNNPH  733 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~-~~~s~e~~~~~rl-~~~~g~--g~~e~L~eav~~~p~  733 (854)
                      ..++|+||+|+|||.||.+++...-......+.++..+.... .... ....+..+ +..+..  -+.+.+...++....
T Consensus      1428 ~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~e~~~~~l~a~~-~G~dl~~l~v~~~~~~E~~l~~~~~lvr~~~~ 1506 (2050)
T 3cmu_A         1428 RIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARK-LGVDIDNLLCSQPDTGEQALEICDALARSGAV 1506 (2050)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHH-TTCCTTTCEEECCSSHHHHHHHHHHHHHHTCC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEcccccCHHHHHH-cCCCchhceeecCChHHHHHHHHHHHHhcCCC
Confidence            479999999999999999998876554455666665532200 0000 00000011 111111  122244556677788


Q ss_pred             EEEEEecCC
Q 003038          734 RVFLIEDVE  742 (854)
Q Consensus       734 ~ViliDEie  742 (854)
                      +||+||+++
T Consensus      1507 ~lVVIDsi~ 1515 (2050)
T 3cmu_A         1507 DVIVVDSVA 1515 (2050)
T ss_dssp             SEEEESCGG
T ss_pred             CEEEEcChh
Confidence            999999997

>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=94.64  E-value=0.069  Score=57.61  Aligned_cols=65  Identities=8%  Similarity=0.097  Sum_probs=45.4

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccc-----------------------------cccccc-ch
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSI-----------------------------SSFRHM-NR  278 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~-----------------------------~~l~~~-~r  278 (854)
                      -++|+||+|+|||+++..||+++          +..+++.|.                             -.+... ..
T Consensus        12 ~i~i~GptgsGKt~la~~La~~~----------~~~iis~Ds~qvY~~~~igTakp~~~E~~~v~hhlid~~~~~e~~s~   81 (316)
T 3foz_A           12 AIFLMGPTASGKTALAIELRKIL----------PVELISVDSALIYKGMDIGTAKPNAEELLAAPHRLLDIRDPSQAYSA   81 (316)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS----------CEEEEECCTTTTBTTCCTTTTCCCHHHHHHSCEETSSCBCTTSCCCH
T ss_pred             EEEEECCCccCHHHHHHHHHHhC----------CCcEEecccccccccccccCCCCCHHHHcCCCEEEeccCCccccccH
Confidence            36789999999999999999884          234555432                             222222 57


Q ss_pred             HHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          279 VEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       279 ge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      |+|.+....+++.+.+.  +.+.|+++
T Consensus        82 ~~f~~~a~~~i~~i~~~--g~~pilVG  106 (316)
T 3foz_A           82 ADFRRDALAEMADITAA--GRIPLLVG  106 (316)
T ss_dssp             HHHHHHHHHHHHHHHHT--TCEEEEEE
T ss_pred             HHHHHHHHHHHHHHHhC--CCcEEEEc
Confidence            88888888888888875  34555554

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=94.63  E-value=0.024  Score=55.24  Aligned_cols=24  Identities=17%  Similarity=0.306  Sum_probs=22.0

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ++++|+|+||+|||++++.||.++
T Consensus         5 ~~i~i~G~~GsGKsTla~~La~~l   28 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLARALAKDL   28 (175)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHc
Confidence            379999999999999999999875

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=94.62  E-value=0.12  Score=58.48  Aligned_cols=98  Identities=7%  Similarity=0.116  Sum_probs=56.2

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCC-CCceEEEccccccCcCCCc----cccccccccC-CCCCCchHHH---HH
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGS-HNNFVSIALSSFSSTRADS----TEDSRNKRSR-DEQSCSYIER---FA  725 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-~~~~i~id~s~~~~~~~~s----~e~~~~~rl~-~~~g~g~~e~---L~  725 (854)
                      ++...++|.|+.|+|||+++-.||..+-.. ..+..-+|+..|.......    .....+ .++ .+.+..-.+.   ..
T Consensus        98 ~~~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D~~r~~a~~ql~~~~~~~~l-~v~~~~~~~dp~~i~~~~l  176 (433)
T 2xxa_A           98 QPPAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADVYRPAAIKQLETLAEQVGV-DFFPSDVGQKPVDIVNAAL  176 (433)
T ss_dssp             SSSEEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECCCSSTTHHHHHHHHHHHHTC-EECCCCSSSCHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecCCCCccHHHHHHhhcccCCe-eEEeCCCCCCHHHHHHHHH
Confidence            345688999999999999999999888655 5677778877654210000    000000 011 1111111122   23


Q ss_pred             HHHHcCCCEEEEEecCCCCCH--HHHHHHH
Q 003038          726 EAVSNNPHRVFLIEDVEQADY--CSQKGFK  753 (854)
Q Consensus       726 eav~~~p~~ViliDEieka~~--~v~~~Ll  753 (854)
                      +.++...|.+||||=.-..+.  ...+.|.
T Consensus       177 ~~~~~~~~D~VIIDTpG~l~~~~~l~~~L~  206 (433)
T 2xxa_A          177 KEAKLKFYDVLLVDTAGRLHVDEAMMDEIK  206 (433)
T ss_dssp             HHHHHTTCSEEEEECCCCCTTCHHHHHHHH
T ss_pred             HHHHhCCCCEEEEECCCcccccHHHHHHHH
Confidence            334446789999998766543  3444443

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=94.61  E-value=0.016  Score=58.65  Aligned_cols=21  Identities=5%  Similarity=0.017  Sum_probs=17.3

Q ss_pred             ceeecCCCCCHHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~  250 (854)
                      .+++|+||+|||+++...+..
T Consensus         8 ~l~tG~pGsGKT~~a~~~~~~   28 (199)
T 2r2a_A            8 CLITGTPGSGKTLKMVSMMAN   28 (199)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHH
Confidence            478999999999998776544

>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=94.61  E-value=0.037  Score=55.80  Aligned_cols=27  Identities=19%  Similarity=0.103  Sum_probs=23.2

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +...-++|+||+|+|||++++.|+...
T Consensus         6 ~~g~~i~l~GpsGsGKsTl~~~L~~~~   32 (208)
T 3tau_A            6 ERGLLIVLSGPSGVGKGTVREAVFKDP   32 (208)
T ss_dssp             CCCCEEEEECCTTSCHHHHHHHHHHST
T ss_pred             CCCcEEEEECcCCCCHHHHHHHHHhhC
Confidence            345668999999999999999999875

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=94.56  E-value=0.063  Score=56.05  Aligned_cols=23  Identities=4%  Similarity=0.093  Sum_probs=21.0

Q ss_pred             CceeecCCCCCHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      .++|+|+||+|||++++.||.++
T Consensus         3 li~I~G~~GSGKSTla~~La~~~   25 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQET   25 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHhcC
Confidence            47899999999999999999875

>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=94.55  E-value=0.085  Score=53.67  Aligned_cols=26  Identities=8%  Similarity=-0.023  Sum_probs=22.8

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ...-++|+||||+|||+++..++..+
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~~~   48 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAVTC   48 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHH
Confidence            56678999999999999999999764

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=94.52  E-value=0.024  Score=56.68  Aligned_cols=24  Identities=25%  Similarity=0.444  Sum_probs=22.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..++|.||+|+|||++++.||+.+
T Consensus        26 ~~i~l~G~~GsGKsTl~~~La~~l   49 (199)
T 3vaa_A           26 VRIFLTGYMGAGKTTLGKAFARKL   49 (199)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHc
Confidence            478999999999999999999988

>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=94.51  E-value=0.044  Score=55.30  Aligned_cols=37  Identities=19%  Similarity=0.089  Sum_probs=27.6

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhC------CCCceEEEccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFG------SHNNFVSIALS  694 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg------~~~~~i~id~s  694 (854)
                      ..+.+.||+|+|||++++.|+..+.-      .....+.++..
T Consensus        26 ~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~   68 (231)
T 4a74_A           26 AITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTE   68 (231)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECC
Confidence            48899999999999999999986532      12345666543

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=94.48  E-value=0.053  Score=54.29  Aligned_cols=40  Identities=13%  Similarity=0.172  Sum_probs=29.6

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      ...+.+.|++|+|||++++.|+..+-.....++.+++..+
T Consensus        22 ~~~i~i~G~~GsGKstl~~~l~~~~~~~~~~v~~~~~d~~   61 (201)
T 1rz3_A           22 RLVLGIDGLSRSGKTTLANQLSQTLREQGISVCVFHMDDH   61 (201)
T ss_dssp             SEEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEGGGG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhcCCeEEEeccCcc
Confidence            3488999999999999999999987433334555555443

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=94.41  E-value=0.015  Score=58.31  Aligned_cols=24  Identities=13%  Similarity=0.277  Sum_probs=21.9

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHh
Q 003038          659 WLFFQGVDADAKEKIAKELARLVF  682 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lf  682 (854)
                      .+.|.||+|+|||++.+.|+..+-
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~~~   26 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhhcc
Confidence            578999999999999999999874

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=94.40  E-value=0.024  Score=55.55  Aligned_cols=37  Identities=11%  Similarity=0.077  Sum_probs=28.6

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      .++|.|++|+|||++|+.|++.+-.....+..+++++
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~~~~~~   39 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGD   39 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTTTCCEEEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCceEEEEECCh
Confidence            5789999999999999999998843333466666443

>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=94.35  E-value=0.037  Score=53.67  Aligned_cols=35  Identities=17%  Similarity=0.192  Sum_probs=27.9

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      ...+++.||+|+|||++++.|+..+ |    .+.+|...+
T Consensus         8 g~~i~l~G~~GsGKSTl~~~l~~~~-g----~~~i~~d~~   42 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVASEVAHQL-H----AAFLDGDFL   42 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHH-T----CEEEEGGGG
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHhh-C----cEEEeCccc
Confidence            3478999999999999999999986 3    456665544

>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=94.33  E-value=0.03  Score=54.87  Aligned_cols=32  Identities=19%  Similarity=0.125  Sum_probs=26.4

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcc
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLS  269 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~  269 (854)
                      ..++|+|+||+|||++++.|+.++          |..++..|
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~l----------g~~~id~D   34 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKAL----------GVGLLDTD   34 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHH----------TCCEEEHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHc----------CCCEEeCc
Confidence            468999999999999999999875          45566655

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=94.27  E-value=0.089  Score=54.72  Aligned_cols=24  Identities=13%  Similarity=0.037  Sum_probs=21.5

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ..++|+|+||+|||++++.|+.++
T Consensus        33 ~~i~l~G~~GsGKSTla~~L~~~l   56 (253)
T 2p5t_B           33 IAILLGGQSGAGKTTIHRIKQKEF   56 (253)
T ss_dssp             EEEEEESCGGGTTHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            357999999999999999999875

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=94.26  E-value=0.032  Score=57.03  Aligned_cols=97  Identities=10%  Similarity=-0.017  Sum_probs=51.5

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccC-CCC--CCchHHHHHHHHHcCCCEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSR-DEQ--SCSYIERFAEAVSNNPHRV  735 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~-~~~--g~g~~e~L~eav~~~p~~V  735 (854)
                      ..+++||.|.|||+.+..++...-+...+.+-+...--..+.    +..-.+++- .-.  .....+.+.+.+. .++.|
T Consensus        30 l~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~k~~~d~R~g----e~~i~s~~g~~~~a~~~~~~~~~~~~~~-~~~dv  104 (214)
T 2j9r_A           30 IEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCIDNRYS----EEDVVSHNGLKVKAVPVSASKDIFKHIT-EEMDV  104 (214)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEECC---------------------CCEEECSSGGGGGGGCC-SSCCE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccCCcch----HHHHHhhcCCeeEEeecCCHHHHHHHHh-cCCCE
Confidence            456899999999988888887665555555555322111000    111111110 000  0000112223222 36899


Q ss_pred             EEEecCCCCCHHHHHHHHHhhhcCe
Q 003038          736 FLIEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       736 iliDEieka~~~v~~~Ll~~le~G~  760 (854)
                      |+|||+.-.+++....|..+.+.|.
T Consensus       105 ViIDEaQF~~~~~V~~l~~l~~~~~  129 (214)
T 2j9r_A          105 IAIDEVQFFDGDIVEVVQVLANRGY  129 (214)
T ss_dssp             EEECCGGGSCTTHHHHHHHHHHTTC
T ss_pred             EEEECcccCCHHHHHHHHHHhhCCC
Confidence            9999999998887777766566553

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=94.22  E-value=0.038  Score=55.09  Aligned_cols=26  Identities=15%  Similarity=0.135  Sum_probs=23.2

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ....++|+|+||+|||++++.|+.++
T Consensus        17 ~~~~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           17 FPGSIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             CSSCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            35679999999999999999999885

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=94.19  E-value=0.03  Score=54.02  Aligned_cols=24  Identities=8%  Similarity=0.123  Sum_probs=22.3

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      .|++|.|.||+|||++++.||.++
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~l   31 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLAL   31 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            589999999999999999999875

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=94.15  E-value=0.031  Score=53.51  Aligned_cols=22  Identities=5%  Similarity=0.067  Sum_probs=19.5

Q ss_pred             CCceeecCCCCCHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      ..++|+|+||+|||++++.| .+
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L-~~   23 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL-KE   23 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH-HH
T ss_pred             cEEEEECCCCCCHHHHHHHH-HH
Confidence            46899999999999999999 54

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=94.12  E-value=0.16  Score=59.45  Aligned_cols=28  Identities=21%  Similarity=0.171  Sum_probs=24.6

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ..++.+|.|+||+|||+++..++..+..
T Consensus       203 ~~~~~~I~G~pGTGKTt~i~~l~~~l~~  230 (574)
T 3e1s_A          203 GHRLVVLTGGPGTGKSTTTKAVADLAES  230 (574)
T ss_dssp             TCSEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             hCCEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            3578999999999999999999987765

>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=94.11  E-value=0.035  Score=58.61  Aligned_cols=41  Identities=10%  Similarity=0.159  Sum_probs=29.8

Q ss_pred             CCCCcHHHHHH-HHHHhhcc-C-cCCceeecCCCCCHHHHHHHHHHH
Q 003038          207 LDPIRNEDVMY-VIENLMSK-R-KRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       207 ldpvr~~ei~~-v~~~L~r~-~-k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      +||+   .+.. +...|.++ . ||+++|+||||+|||.++.+||..
T Consensus        84 ~~~~---~~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~  127 (267)
T 1u0j_A           84 YDPQ---YAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHT  127 (267)
T ss_dssp             CCHH---HHHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCHH---HHHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhh
Confidence            5663   3333 44444544 3 667999999999999999999986

>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=94.09  E-value=0.041  Score=54.93  Aligned_cols=40  Identities=10%  Similarity=0.212  Sum_probs=29.4

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      ...+.|.||+|+|||++++.||..+.......+.+|...+
T Consensus        25 g~~i~l~G~sGsGKSTl~~~La~~l~~~G~~~~~~d~d~~   64 (200)
T 3uie_A           25 GCVIWVTGLSGSGKSTLACALNQMLYQKGKLCYILDGDNV   64 (200)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCceEEEecCchh
Confidence            3478899999999999999999998632233246665433

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=94.09  E-value=0.055  Score=56.31  Aligned_cols=37  Identities=22%  Similarity=0.227  Sum_probs=29.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..++|.|++|+|||++|+.|++.+.   ...+.+|...+.
T Consensus        33 ~~i~l~G~~GsGKSTla~~L~~~l~---~~~~~~~~D~~r   69 (253)
T 2p5t_B           33 IAILLGGQSGAGKTTIHRIKQKEFQ---GNIVIIDGDSFR   69 (253)
T ss_dssp             EEEEEESCGGGTTHHHHHHHHHHTT---TCCEEECGGGGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcC---CCcEEEecHHHH
Confidence            5789999999999999999999873   234666665553

>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=94.07  E-value=0.074  Score=53.53  Aligned_cols=28  Identities=7%  Similarity=0.071  Sum_probs=24.7

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      .....++|+|+||+|||++++.|+..+.
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            4566889999999999999999999875

>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=94.06  E-value=0.031  Score=54.90  Aligned_cols=24  Identities=21%  Similarity=0.318  Sum_probs=22.3

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..++|.|++|+|||++|+.|++.+
T Consensus         6 ~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            6 ALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc
Confidence            378999999999999999999987

>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=94.02  E-value=0.085  Score=66.68  Aligned_cols=41  Identities=10%  Similarity=0.024  Sum_probs=34.4

Q ss_pred             cHHHHHHHHHHhhcc--CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSK--RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       211 r~~ei~~v~~~L~r~--~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      |++++.++.+.|...  ..+-+.|+|++|+|||++|..++.+.
T Consensus       129 R~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~  171 (1249)
T 3sfz_A          129 RKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDH  171 (1249)
T ss_dssp             CHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCH
T ss_pred             HHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcCh
Confidence            999999999999643  33457799999999999999988763

>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=94.02  E-value=0.22  Score=53.38  Aligned_cols=88  Identities=9%  Similarity=0.080  Sum_probs=50.8

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCC----ccccccccccCC-CCCCchHH---HHHHHH
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRAD----STEDSRNKRSRD-EQSCSYIE---RFAEAV  728 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~----s~e~~~~~rl~~-~~g~g~~e---~L~eav  728 (854)
                      ..+++|.|++|+|||+++..||..+-........+|+.-+......    ..+...+. ++. +.+..-.+   ...+.+
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~~~D~~r~~a~~ql~~~~~~~~v~-v~~~~~~~~p~~~~~~~l~~~  176 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVGADVYRPAALEQLQQLGQQIGVP-VYGEPGEKDVVGIAKRGVEKF  176 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEEECCCSSSHHHHHHHHHHHHHTCC-EECCTTCCCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEecCCCCHHHHHHHHHHhccCCeE-EEecCCCCCHHHHHHHHHHHH
Confidence            4588889999999999999999888655556666776644310000    00000000 111 11111112   233444


Q ss_pred             HcCCCEEEEEecCCCCC
Q 003038          729 SNNPHRVFLIEDVEQAD  745 (854)
Q Consensus       729 ~~~p~~ViliDEieka~  745 (854)
                      +...|.+|+||=.-..+
T Consensus       177 ~~~~~D~ViIDTpg~~~  193 (297)
T 1j8m_F          177 LSEKMEIIIVDTAGRHG  193 (297)
T ss_dssp             HHTTCSEEEEECCCSCC
T ss_pred             HhCCCCEEEEeCCCCcc
Confidence            44778999999877666

>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=93.99  E-value=0.027  Score=54.16  Aligned_cols=23  Identities=9%  Similarity=0.052  Sum_probs=21.3

Q ss_pred             CceeecCCCCCHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      .++|+|+||+|||++++.|++++
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l   25 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKEL   25 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57999999999999999999875

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=93.99  E-value=0.1  Score=56.52  Aligned_cols=42  Identities=14%  Similarity=0.177  Sum_probs=33.3

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      ++..+++|.||+|+|||+++..||..+-.....+.-+|+.-+
T Consensus       103 ~~~~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVllid~D~~  144 (320)
T 1zu4_A          103 NRLNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAAADTF  144 (320)
T ss_dssp             TSCEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECCCS
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCc
Confidence            345689999999999999999999987655566666776644

>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=93.99  E-value=0.032  Score=54.61  Aligned_cols=24  Identities=8%  Similarity=-0.021  Sum_probs=22.2

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHh
Q 003038          659 WLFFQGVDADAKEKIAKELARLVF  682 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lf  682 (854)
                      .++|.|++|+|||++++.||+.+-
T Consensus         5 ~I~i~G~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A            5 VVVVTGVPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            689999999999999999999873

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=93.96  E-value=0.065  Score=57.11  Aligned_cols=36  Identities=17%  Similarity=0.251  Sum_probs=28.1

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      ..++|.||+|+|||++|+.|++.+-   ..++.|+...+
T Consensus        34 ~livl~G~sGsGKSTla~~L~~~~~---~~~~~Is~D~~   69 (287)
T 1gvn_B           34 TAFLLGGQPGSGKTSLRSAIFEETQ---GNVIVIDNDTF   69 (287)
T ss_dssp             EEEEEECCTTSCTHHHHHHHHHHTT---TCCEEECTHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC---CCeEEEechHh
Confidence            4789999999999999999998762   24566765433

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=93.95  E-value=0.091  Score=54.21  Aligned_cols=22  Identities=9%  Similarity=-0.077  Sum_probs=19.9

Q ss_pred             EEEecCCCchHHHHHHHHHHHH
Q 003038          660 LFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ++++||+|+|||.+|..++..+
T Consensus       111 ~ll~~~tG~GKT~~a~~~~~~~  132 (237)
T 2fz4_A          111 GCIVLPTGSGKTHVAMAAINEL  132 (237)
T ss_dssp             EEEEESSSTTHHHHHHHHHHHS
T ss_pred             EEEEeCCCCCHHHHHHHHHHHc
Confidence            7899999999999999888765

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=93.94  E-value=0.071  Score=53.79  Aligned_cols=23  Identities=9%  Similarity=-0.006  Sum_probs=19.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..||.|++|+|||.+|..++...
T Consensus         7 i~l~tG~pGsGKT~~a~~~~~~~   29 (199)
T 2r2a_A            7 ICLITGTPGSGKTLKMVSMMAND   29 (199)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHH
Confidence            67899999999999998875543

>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=93.82  E-value=0.18  Score=55.50  Aligned_cols=86  Identities=9%  Similarity=-0.041  Sum_probs=49.3

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccc--cccccC-CCCCCchHH---HHHHHHHcC
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDS--RNKRSR-DEQSCSYIE---RFAEAVSNN  731 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~--~~~rl~-~~~g~g~~e---~L~eav~~~  731 (854)
                      ..++++||+|+|||+|+..++..+-......+.++..+-....  -....  ...++. ..+. ...+   .+...++..
T Consensus        62 ~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~E~s~~~~--ra~rlgv~~~~l~i~~~~-~~e~~l~~~~~l~~~~  138 (356)
T 3hr8_A           62 RIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAEHALDPV--YAKNLGVDLKSLLISQPD-HGEQALEIVDELVRSG  138 (356)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHH--HHHHHTCCGGGCEEECCS-SHHHHHHHHHHHHHTS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEecccccchH--HHHHcCCchhhhhhhhcc-CHHHHHHHHHHHhhhc
Confidence            4789999999999999999998775444566777654322000  00000  001111 1111 1222   233344456


Q ss_pred             CCEEEEEecCCCCCH
Q 003038          732 PHRVFLIEDVEQADY  746 (854)
Q Consensus       732 p~~ViliDEieka~~  746 (854)
                      ...+|+||.+-.+.+
T Consensus       139 ~~dlvVIDSi~~l~~  153 (356)
T 3hr8_A          139 VVDLIVVDSVAALVP  153 (356)
T ss_dssp             CCSEEEEECTTTCCC
T ss_pred             CCCeEEehHhhhhcC
Confidence            678999999987764

>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=93.82  E-value=0.066  Score=54.51  Aligned_cols=38  Identities=16%  Similarity=0.017  Sum_probs=28.9

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhC------CCCceEEEcccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFG------SHNNFVSIALSS  695 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg------~~~~~i~id~s~  695 (854)
                      ..++|.||+|+|||++++.|+..+.-      .....+.++...
T Consensus        25 ~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~   68 (243)
T 1n0w_A           25 SITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEG   68 (243)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSS
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCC
Confidence            47899999999999999999985321      135667777554

>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=93.76  E-value=0.035  Score=53.26  Aligned_cols=23  Identities=22%  Similarity=0.405  Sum_probs=21.5

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.||+|+|||++|+.|++.+
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l   25 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKEL   25 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999999999987

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=93.75  E-value=0.23  Score=57.84  Aligned_cols=45  Identities=22%  Similarity=0.278  Sum_probs=35.0

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHH
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELA  678 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA  678 (854)
                      ..++|-+..+..|...+....                ....+++++||.|+|||+||+.++
T Consensus       124 ~~~vGR~~~l~~L~~~L~~~~----------------~~~~~v~I~G~~GiGKTtLa~~~~  168 (591)
T 1z6t_A          124 VVFVTRKKLVNAIQQKLSKLK----------------GEPGWVTIHGMAGCGKSVLAAEAV  168 (591)
T ss_dssp             SSCCCCHHHHHHHHHHHTTST----------------TSCEEEEEECCTTSSHHHHHHHHH
T ss_pred             CeecccHHHHHHHHHHHhccc----------------CCCceEEEEcCCCCCHHHHHHHHH
Confidence            457899988888887765321                123478999999999999999987

>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=93.69  E-value=0.23  Score=54.47  Aligned_cols=40  Identities=5%  Similarity=0.034  Sum_probs=29.8

Q ss_pred             HHHHHHHHhhcc--CcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          214 DVMYVIENLMSK--RKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       214 ei~~v~~~L~r~--~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ..+.++.-|...  +...++|+|.||||||+++..|+..+..
T Consensus        64 ~~~~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~~l~~  105 (355)
T 3p32_A           64 QAQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHLIE  105 (355)
T ss_dssp             HHHHHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            355556555533  3446899999999999999999988754

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=93.68  E-value=0.045  Score=57.15  Aligned_cols=31  Identities=19%  Similarity=0.283  Sum_probs=25.0

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      .+++.||+|+|||++|+.||+.+ +  ..++..|
T Consensus         3 li~I~G~~GSGKSTla~~La~~~-~--~~~i~~D   33 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQET-G--WPVVALD   33 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH-C--CCEEECC
T ss_pred             EEEEECCCCcCHHHHHHHHHhcC-C--CeEEecc
Confidence            57899999999999999999987 3  3455444

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=93.68  E-value=0.045  Score=53.84  Aligned_cols=26  Identities=15%  Similarity=0.148  Sum_probs=23.3

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +...++|+|+||+|||++++.|++++
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            45689999999999999999999874

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=93.64  E-value=0.051  Score=52.38  Aligned_cols=24  Identities=17%  Similarity=0.209  Sum_probs=21.9

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +.++|+|+||+|||++++.|+.++
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~l   26 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARAL   26 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999999875

>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=93.63  E-value=0.036  Score=55.42  Aligned_cols=24  Identities=13%  Similarity=0.256  Sum_probs=21.3

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      |.+||+||+|||||+|++.|..+.
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~   25 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhC
Confidence            468999999999999999998764

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=93.59  E-value=0.15  Score=55.68  Aligned_cols=76  Identities=17%  Similarity=0.197  Sum_probs=44.9

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHc----CC-------C--------CcccCCceEEEccccccccc-chHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEK----GD-------V--------PEALRDVKCLPLSISSFRHM-NRVEVEQRVEE  287 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~----~~-------v--------p~~L~~~~~~~l~~~~l~~~-~rge~E~rl~~  287 (854)
                      ..++|+||+|+|||+++..||.++..    .|       +        ++...++.-.-+++-..... ..++|.+....
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l~~~iis~Ds~qvYr~~~i~Takp~~eE~~~v~hhl~di~~~~~~~~~~dF~~~a~~   87 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKFNGEIISGDSMQVYQGMDIGTAKVTTEEMEGIPHYMIDILPPDASFSAYEFKKRAEK   87 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTEEEEECCSSTTBTTCCTTTTCCCTTTTTTCCEESSSCBCTTSCCCHHHHHHHHHH
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHcCCceeccccccccccccccccCCCHHHHHHHHHHHHHHhCCccccCHHHHHHHHHH
Confidence            46889999999999999999988531    00       0        12222222111111111112 56788777777


Q ss_pred             HHHHHHhhhCCCeEEEeC
Q 003038          288 IKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       288 l~~~~~~~~~~~~ILfid  305 (854)
                      .+..+...  +.++|+++
T Consensus        88 ~i~~i~~~--g~~~IlvG  103 (340)
T 3d3q_A           88 YIKDITRR--GKVPIIAG  103 (340)
T ss_dssp             HHHHHHHT--TCEEEEEC
T ss_pred             HHHHHHhC--CCcEEEEC
Confidence            77777653  45666666

>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=93.56  E-value=0.049  Score=55.09  Aligned_cols=26  Identities=12%  Similarity=0.132  Sum_probs=23.1

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +..+++|+|+||+|||++++.|+.++
T Consensus         3 ~~~~I~l~G~~GsGKsT~a~~La~~l   28 (220)
T 1aky_A            3 ESIRMVLIGPPGAGKGTQAPNLQERF   28 (220)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            45679999999999999999999875

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=93.56  E-value=0.13  Score=55.90  Aligned_cols=37  Identities=19%  Similarity=0.214  Sum_probs=28.0

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      +...+.|.||+|+|||++++.||..+-.....+.-.+
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~l~~~~g~V~l~g  164 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANWLKNHGFSVVIAA  164 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEe
Confidence            3458999999999999999999988754433433333

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=93.55  E-value=0.12  Score=56.78  Aligned_cols=41  Identities=10%  Similarity=-0.040  Sum_probs=29.8

Q ss_pred             HHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          213 EDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      .++.+++.+-.=...+.++|+|+||+|||+++..++..+.+
T Consensus        47 ~~LD~~Lg~GGl~~G~iv~I~G~pGsGKTtLal~la~~~~~   87 (349)
T 2zr9_A           47 ISLDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQA   87 (349)
T ss_dssp             HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            55665553111125677999999999999999999877764

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=93.54  E-value=0.046  Score=54.46  Aligned_cols=34  Identities=18%  Similarity=0.321  Sum_probs=27.0

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      ..++|.|++|+|||++|+.|++.+ |    +..++...+
T Consensus        19 ~~I~l~G~~GsGKSTla~~L~~~l-g----~~~i~~d~~   52 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEAIAEAC-G----YPFIEGDAL   52 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHHHHHHH-T----CCEEEGGGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh-C----CEEEeCCcC
Confidence            378999999999999999999987 3    345555544

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=93.54  E-value=0.17  Score=54.32  Aligned_cols=33  Identities=15%  Similarity=0.205  Sum_probs=26.4

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCce
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNF  688 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~  688 (854)
                      +...+.|.||+|+|||++++.||..+-.....+
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~l~~~~g~V  131 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHRLKNEGTKV  131 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHHHHHTTCCE
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHHcCCeE
Confidence            445899999999999999999999875433333

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=93.50  E-value=0.056  Score=53.94  Aligned_cols=34  Identities=24%  Similarity=0.325  Sum_probs=27.6

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      ..+.+.||+|+|||++++.|+..+ |    .+.++...+
T Consensus        30 ~~i~l~G~~GsGKSTl~~~L~~~~-g----~~~i~~d~~   63 (200)
T 4eun_A           30 RHVVVMGVSGSGKTTIAHGVADET-G----LEFAEADAF   63 (200)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH-C----CEEEEGGGG
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhh-C----CeEEccccc
Confidence            478899999999999999999987 3    456665544

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=93.49  E-value=0.039  Score=53.30  Aligned_cols=25  Identities=28%  Similarity=0.379  Sum_probs=22.4

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +.+++|+|+||+|||++++.|+..+
T Consensus         4 ~~~i~l~G~~GsGKSTl~~~La~~l   28 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTIGRQLAQQL   28 (173)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHh
Confidence            4679999999999999999999874

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=93.49  E-value=0.067  Score=53.75  Aligned_cols=25  Identities=16%  Similarity=0.266  Sum_probs=23.0

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHh
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVF  682 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lf  682 (854)
                      ..+.+.||+|+|||++++.|+..+-
T Consensus        23 ~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           23 QLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             EEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4788999999999999999999885

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=93.41  E-value=0.23  Score=57.15  Aligned_cols=41  Identities=17%  Similarity=0.243  Sum_probs=29.5

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      +...++|+|++|+|||+++..||..+-....+...+++..|
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd~D~~  140 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICADTF  140 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEECCS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEecccc
Confidence            44689999999999999999999877533345555555433

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=93.39  E-value=0.073  Score=52.25  Aligned_cols=38  Identities=18%  Similarity=0.216  Sum_probs=29.1

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      ...++|.|++|+|||++++.||+.+-.....++.+|..
T Consensus        13 ~~~i~l~G~~GsGKsT~~~~L~~~l~~~~~~~~~~~~d   50 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLDGD   50 (186)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEeeHH
Confidence            34788999999999999999999885444445555543

>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=93.36  E-value=0.056  Score=52.72  Aligned_cols=24  Identities=25%  Similarity=0.331  Sum_probs=22.1

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..++|.|++|+|||++++.||+.+
T Consensus        12 ~~i~i~G~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           12 PNILLTGTPGVGKTTLGKELASKS   35 (180)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHh
Confidence            368899999999999999999987

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=93.36  E-value=0.055  Score=53.85  Aligned_cols=26  Identities=12%  Similarity=0.093  Sum_probs=22.9

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      .+..++|+|+||+|||++++.|+.++
T Consensus        19 ~~~~I~l~G~~GsGKST~a~~La~~l   44 (201)
T 2cdn_A           19 SHMRVLLLGPPGAGKGTQAVKLAEKL   44 (201)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            44578999999999999999999875

>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=93.33  E-value=0.042  Score=54.83  Aligned_cols=29  Identities=7%  Similarity=-0.023  Sum_probs=25.3

Q ss_pred             ccCcCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          224 SKRKRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       224 r~~k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      ......++|+|++|+|||++++.|+..+.
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            35667889999999999999999998874

>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=93.29  E-value=0.048  Score=55.20  Aligned_cols=25  Identities=16%  Similarity=0.151  Sum_probs=22.8

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHH
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ...++|.|++|+|||++|+.||+.+
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~l   28 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQERF   28 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc
Confidence            3478999999999999999999987

>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=93.27  E-value=0.082  Score=52.90  Aligned_cols=73  Identities=11%  Similarity=-0.032  Sum_probs=0.0

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccc-------------------------cccc--c
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISS-------------------------FRHM--N  277 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~-------------------------l~~~--~  277 (854)
                      ....-++|+|+||+|||+++..++.          ..+..++-++...                         ....  .
T Consensus        18 ~~G~~~~i~G~~GsGKTtl~~~l~~----------~~~~~v~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (220)
T 2cvh_A           18 APGVLTQVYGPYASGKTTLALQTGL----------LSGKKVAYVDTEGGFSPERLVQMAETRGLNPEEALSRFILFTPSD   87 (220)
T ss_dssp             CTTSEEEEECSTTSSHHHHHHHHHH----------HHCSEEEEEESSCCCCHHHHHHHHHTTTCCHHHHHHHEEEECCTT
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHH----------HcCCcEEEEECCCCCCHHHHHHHHHhcCCChHHHhhcEEEEecCC


Q ss_pred             hHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc
Q 003038          278 RVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       278 rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                      -.+..+++..+...+.+.   +-+|+|||+..+
T Consensus        88 ~~~~~~~~~~~~~l~~~~---~~lliiD~~~~~  117 (220)
T 2cvh_A           88 FKEQRRVIGSLKKTVDSN---FALVVVDSITAH  117 (220)
T ss_dssp             TSHHHHHHHHHHHHCCTT---EEEEEEECCCCC
T ss_pred             HHHHHHHHHHHHHHhhcC---CCEEEEcCcHHH

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=93.26  E-value=0.12  Score=53.98  Aligned_cols=27  Identities=7%  Similarity=0.011  Sum_probs=23.7

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ...++|+|.||+|||++++.|+.++..
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~L~~   30 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKILSK   30 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            457899999999999999999998753

>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=93.23  E-value=0.04  Score=54.07  Aligned_cols=26  Identities=8%  Similarity=0.117  Sum_probs=23.0

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      .+..++|+|+||+|||++++.|++++
T Consensus         4 ~~~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            4 TPALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHc
Confidence            34578999999999999999999875

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=93.20  E-value=0.043  Score=54.56  Aligned_cols=25  Identities=8%  Similarity=0.069  Sum_probs=21.0

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHc
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      -.+++|++|+|||+++-.++.+...
T Consensus         5 i~vi~G~~gsGKTT~ll~~~~~~~~   29 (184)
T 2orw_A            5 LTVITGPMYSGKTTELLSFVEIYKL   29 (184)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4679999999999999888877643

>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=93.17  E-value=0.052  Score=53.04  Aligned_cols=25  Identities=8%  Similarity=0.061  Sum_probs=22.1

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ...++|+|+||+|||++++.|+++.
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~l   30 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            3568999999999999999999874

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=93.11  E-value=0.061  Score=51.83  Aligned_cols=25  Identities=24%  Similarity=0.312  Sum_probs=22.7

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHH
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..++++.|++|+|||++|+.||+.+
T Consensus         7 ~~~i~l~G~~GsGKSTva~~La~~l   31 (168)
T 1zuh_A            7 MQHLVLIGFMGSGKSSLAQELGLAL   31 (168)
T ss_dssp             -CEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHh
Confidence            4589999999999999999999987

>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=93.10  E-value=0.048  Score=53.27  Aligned_cols=26  Identities=15%  Similarity=0.121  Sum_probs=23.2

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      ...++|.|+||+|||++++.|+.++.
T Consensus         3 ~~~I~i~G~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            35689999999999999999999874

>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=93.10  E-value=0.054  Score=54.51  Aligned_cols=22  Identities=23%  Similarity=0.220  Sum_probs=20.4

Q ss_pred             CceeecCCCCCHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~  250 (854)
                      +++|+|+||+|||++++.|+++
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEK   23 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4889999999999999999977

>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=93.08  E-value=0.076  Score=51.76  Aligned_cols=37  Identities=8%  Similarity=0.148  Sum_probs=28.7

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      ..+.|.|++|+|||++++.|+..+....-+++.+|..
T Consensus         6 ~~i~l~G~~GsGKST~~~~L~~~l~~~g~~~i~~d~~   42 (179)
T 2pez_A            6 CTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGD   42 (179)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHhhCCCcEEEECCh
Confidence            3678999999999999999999875333456666643

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=93.06  E-value=0.05  Score=54.28  Aligned_cols=27  Identities=26%  Similarity=0.393  Sum_probs=23.5

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +....++|+|++|+|||++++.|+..+
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            456789999999999999999999875

>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=93.05  E-value=0.047  Score=53.61  Aligned_cols=36  Identities=28%  Similarity=0.324  Sum_probs=28.0

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      ..+.+.||+|+|||++++.|+.. ++  ...+.++...+
T Consensus        10 ~~i~l~G~~GsGKSTl~~~La~~-~~--~g~i~i~~d~~   45 (191)
T 1zp6_A           10 NILLLSGHPGSGKSTIAEALANL-PG--VPKVHFHSDDL   45 (191)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHTC-SS--SCEEEECTTHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHhc-cC--CCeEEEcccch
Confidence            47889999999999999999986 33  34567765543

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=93.04  E-value=0.23  Score=54.77  Aligned_cols=33  Identities=15%  Similarity=0.205  Sum_probs=26.5

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCce
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNF  688 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~  688 (854)
                      +..++.|.||+|+|||++++.||..+-.....+
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~l~~~~G~V  188 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHRLKNEGTKV  188 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHHHTTCCE
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhhccccCCEE
Confidence            445899999999999999999999875433333

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=93.03  E-value=0.051  Score=54.09  Aligned_cols=33  Identities=18%  Similarity=0.304  Sum_probs=26.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      ..++|.|++|+|||++|+.|++.+ |    +..++++.
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~~~~-g----~~~i~~d~   48 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLVKDY-S----FVHLSAGD   48 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHS-S----CEEEEHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc-C----ceEEeHHH
Confidence            478999999999999999999876 3    34555443

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=92.98  E-value=0.063  Score=52.52  Aligned_cols=25  Identities=16%  Similarity=0.080  Sum_probs=22.2

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ...++|+|+||+|||++++.|+.++
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            4568999999999999999999874

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=92.96  E-value=0.054  Score=53.00  Aligned_cols=23  Identities=13%  Similarity=0.135  Sum_probs=21.6

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.|++|+|||++|+.|++.+
T Consensus         5 ~I~l~G~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A            5 VVFVLGGPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            68899999999999999999986

>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=92.95  E-value=0.06  Score=52.62  Aligned_cols=23  Identities=22%  Similarity=0.377  Sum_probs=21.5

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.|++|+|||++|+.||+.+
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~l   26 (184)
T 2iyv_A            4 KAVLVGLPGSGKSTIGRRLAKAL   26 (184)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHc
Confidence            47899999999999999999987

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=92.94  E-value=0.28  Score=54.17  Aligned_cols=85  Identities=9%  Similarity=0.023  Sum_probs=47.2

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcC-CCccccccccccC-CCCCCchHH---HHHHHHHcCCC
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTR-ADSTEDSRNKRSR-DEQSCSYIE---RFAEAVSNNPH  733 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~-~~s~e~~~~~rl~-~~~g~g~~e---~L~eav~~~p~  733 (854)
                      .++++||+|+|||.+|..+|..+-......+.++...-.... ... -.....+++ ..+. ...+   .+...++....
T Consensus        76 li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~E~s~~~~~a~~-~g~d~~~l~i~~~~-~~e~~l~~l~~l~~~~~~  153 (366)
T 1xp8_A           76 ITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALDPVYARA-LGVNTDELLVSQPD-NGEQALEIMELLVRSGAI  153 (366)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHH-TTCCGGGCEEECCS-SHHHHHHHHHHHHTTTCC
T ss_pred             EEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEECCCChhHHHHHH-cCCCHHHceeecCC-cHHHHHHHHHHHHhcCCC
Confidence            678899999999999999987764334466666654321000 000 000011111 1111 1222   23333445678


Q ss_pred             EEEEEecCCCCC
Q 003038          734 RVFLIEDVEQAD  745 (854)
Q Consensus       734 ~ViliDEieka~  745 (854)
                      .+|+||.+.-+.
T Consensus       154 ~lVVIDsl~~l~  165 (366)
T 1xp8_A          154 DVVVVDSVAALT  165 (366)
T ss_dssp             SEEEEECTTTCC
T ss_pred             CEEEEeChHHhc
Confidence            899999998775

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=92.92  E-value=0.048  Score=52.62  Aligned_cols=23  Identities=26%  Similarity=0.432  Sum_probs=21.6

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+.+.||+|+|||++++.||..+
T Consensus         6 ~i~l~G~~GsGKSTl~~~La~~l   28 (173)
T 1kag_A            6 NIFLVGPMGAGKSTIGRQLAQQL   28 (173)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999999987

>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=92.92  E-value=0.11  Score=59.67  Aligned_cols=39  Identities=18%  Similarity=0.124  Sum_probs=28.5

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      +...++|+||+|+|||++++.||.++-.....+...+..
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll~~~~G~V~l~g~D  330 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGD  330 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEECCC
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHhhhcCCeEEEecCc
Confidence            345899999999999999999999875433333333333

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=92.91  E-value=0.2  Score=59.11  Aligned_cols=28  Identities=11%  Similarity=0.152  Sum_probs=23.8

Q ss_pred             CCEEEEEecCCCCCHHHHHHHHHhhhcC
Q 003038          732 PHRVFLIEDVEQADYCSQKGFKRAIESG  759 (854)
Q Consensus       732 p~~ViliDEieka~~~v~~~Ll~~le~G  759 (854)
                      +..+|+|||+..++......|++.+..|
T Consensus       262 ~~d~lIIDEAsml~~~~~~~Ll~~l~~~  289 (608)
T 1w36_D          262 HLDVLVVDEASMIDLPMMSRLIDALPDH  289 (608)
T ss_dssp             SCSEEEECSGGGCBHHHHHHHHHTCCTT
T ss_pred             CCCEEEEechhhCCHHHHHHHHHhCCCC
Confidence            5679999999999998888888887543

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=92.90  E-value=0.073  Score=54.50  Aligned_cols=26  Identities=12%  Similarity=0.165  Sum_probs=21.8

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +.+-++|+||||+||+|.++-|+++.
T Consensus        28 k~kiI~llGpPGsGKgTqa~~L~~~~   53 (217)
T 3umf_A           28 KAKVIFVLGGPGSGKGTQCEKLVQKF   53 (217)
T ss_dssp             SCEEEEEECCTTCCHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            34456788999999999999999874

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=92.87  E-value=0.05  Score=53.65  Aligned_cols=33  Identities=18%  Similarity=0.332  Sum_probs=26.7

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      ..++|.|++|+|||++|+.||+.+ |    +..++++.
T Consensus        13 ~~I~l~G~~GsGKsT~a~~L~~~l-~----~~~i~~d~   45 (199)
T 2bwj_A           13 KIIFIIGGPGSGKGTQCEKLVEKY-G----FTHLSTGE   45 (199)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH-T----CEEEEHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh-C----CeEEcHHH
Confidence            378999999999999999999987 3    45565543

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=92.84  E-value=0.045  Score=59.72  Aligned_cols=32  Identities=16%  Similarity=0.263  Sum_probs=25.8

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      ..+++.||+|+|||+||..||+.+ +  ..+|..|
T Consensus        41 ~lIvI~GPTgsGKTtLa~~LA~~l-~--~eiIs~D   72 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLSIDLAAHF-P--LEVINSD   72 (339)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTTS-C--EEEEECC
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHC-C--CcEEccc
Confidence            378999999999999999999987 2  2455544

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=92.84  E-value=0.071  Score=54.07  Aligned_cols=23  Identities=13%  Similarity=0.043  Sum_probs=20.8

Q ss_pred             CceeecCCCCCHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +++|+||||+||+|.++-||++.
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~   24 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEK   24 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999999999874

>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=92.83  E-value=0.065  Score=52.78  Aligned_cols=36  Identities=17%  Similarity=0.306  Sum_probs=28.4

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..+++.|++|+|||++++.||+.++|    +..+|++.+.
T Consensus        11 ~~I~l~G~~GsGKSTv~~~La~~l~g----~~~id~d~~~   46 (184)
T 1y63_A           11 INILITGTPGTGKTSMAEMIAAELDG----FQHLEVGKLV   46 (184)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHSTT----EEEEEHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhcCC----CEEeeHHHHH
Confidence            37899999999999999999998543    5556665443

>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=92.83  E-value=0.063  Score=56.14  Aligned_cols=37  Identities=14%  Similarity=0.319  Sum_probs=27.9

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      ..++|.|++|+|||++|+.|++.+-.....++.++..
T Consensus         5 ~lIvl~G~pGSGKSTla~~La~~L~~~g~~~i~~~~D   41 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSD   41 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEECTH
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEECch
Confidence            4789999999999999999999863223345545544

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=92.82  E-value=0.069  Score=52.63  Aligned_cols=25  Identities=8%  Similarity=0.110  Sum_probs=22.6

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ...++|+|+||+|||++++.|++++
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l   36 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKY   36 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            4579999999999999999999875

>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=92.81  E-value=0.064  Score=51.66  Aligned_cols=23  Identities=26%  Similarity=0.426  Sum_probs=21.5

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.|++|+|||++|+.||+.+
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~l   26 (173)
T 1e6c_A            4 PIFMVGARGCGMTTVGRELARAL   26 (173)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999999999987

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=92.80  E-value=0.047  Score=52.77  Aligned_cols=22  Identities=14%  Similarity=0.087  Sum_probs=20.1

Q ss_pred             CCceeecCCCCCHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~  249 (854)
                      ..++|+|+||+|||++++.|+.
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            4578999999999999999997

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=92.80  E-value=0.056  Score=52.51  Aligned_cols=23  Identities=26%  Similarity=0.406  Sum_probs=21.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+++.|++|+|||++|+.||+.+
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l   28 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDL   28 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHc
Confidence            47889999999999999999987

>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=92.80  E-value=0.08  Score=52.64  Aligned_cols=23  Identities=22%  Similarity=0.240  Sum_probs=21.8

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.|++|+|||++|+.||+.+
T Consensus        22 ~I~l~G~~GsGKST~a~~La~~l   44 (201)
T 2cdn_A           22 RVLLLGPPGAGKGTQAVKLAEKL   44 (201)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            78899999999999999999987

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=92.77  E-value=0.047  Score=53.35  Aligned_cols=24  Identities=17%  Similarity=0.048  Sum_probs=22.1

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      .++|.|+||+|||++++.|++++.
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~   26 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILD   26 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            579999999999999999999875

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=92.76  E-value=0.064  Score=52.74  Aligned_cols=24  Identities=13%  Similarity=0.223  Sum_probs=22.3

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..++|.|++|+|||++|+.||+.+
T Consensus        10 ~~I~l~G~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A           10 NIIFVVGGPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            378999999999999999999987

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=92.74  E-value=0.16  Score=58.62  Aligned_cols=92  Identities=15%  Similarity=0.210  Sum_probs=57.0

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc-cccCcCCCcccccc---ccc-cCCCCCCchHHHHHHHHHcCCC
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS-SFSSTRADSTEDSR---NKR-SRDEQSCSYIERFAEAVSNNPH  733 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s-~~~~~~~~s~e~~~---~~r-l~~~~g~g~~e~L~eav~~~p~  733 (854)
                      .+++.||+|+|||++.++|+..+ ......+.++-. ++...     ..+.   ..+ .+...+.++.+.+..++|.+|.
T Consensus       262 ~i~I~GptGSGKTTlL~aL~~~i-~~~~giitied~~E~~~~-----~~~~v~~~~r~~~~~~~~~~~~~l~~~LR~~PD  335 (511)
T 2oap_1          262 SAIVVGETASGKTTTLNAIMMFI-PPDAKVVSIEDTREIKLY-----HENWIAEVTRTGMGEGEIDMYDLLRAALRQRPD  335 (511)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGGS-CTTCCEEEEESSCCCCCC-----CSSEEEEECBCCSSSCCBCHHHHHHTTGGGCCS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC-CCCCCEEEEcCcccccCC-----CCCeEEEEeecccccCCcCHHHHHHHhhccCCC
Confidence            58999999999999999999877 445567777533 23210     0110   011 0111122555567777888885


Q ss_pred             EEEEEecCCCCCHHHHHHHHHhhhcCe
Q 003038          734 RVFLIEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       734 ~ViliDEieka~~~v~~~Ll~~le~G~  760 (854)
                       +|++.|+--  .++. .+++++..|.
T Consensus       336 -~iivgEir~--~E~~-~~l~a~~tGh  358 (511)
T 2oap_1          336 -YIIVGEVRG--REAQ-TLFQAMSTGH  358 (511)
T ss_dssp             -EEEESCCCS--THHH-HHHHHHHTTC
T ss_pred             -eEEeCCcCH--HHHH-HHHHhhcCCC
Confidence             557899863  4554 4567777774

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=92.72  E-value=0.067  Score=53.74  Aligned_cols=23  Identities=26%  Similarity=0.248  Sum_probs=20.9

Q ss_pred             CceeecCCCCCHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +++|+|+||+|||++++.|+++.
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            47899999999999999999874

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=92.72  E-value=0.062  Score=54.50  Aligned_cols=31  Identities=35%  Similarity=0.415  Sum_probs=25.8

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      .++|.||||+||++.|+.||+.+     .+.+|...
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~-----g~~~istG   32 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEK-----GFVHISTG   32 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH-----CCEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH-----CCeEEcHH
Confidence            47889999999999999999987     46666654

>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=92.69  E-value=0.12  Score=53.48  Aligned_cols=26  Identities=4%  Similarity=-0.005  Sum_probs=22.8

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +..+++|.|+||+|||++++.|+++.
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            44578999999999999999999874

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=92.66  E-value=0.078  Score=54.27  Aligned_cols=32  Identities=16%  Similarity=0.262  Sum_probs=26.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      ..++|.||||+||++.|+.||+.+     .+..|...
T Consensus        30 kiI~llGpPGsGKgTqa~~L~~~~-----g~~hIstG   61 (217)
T 3umf_A           30 KVIFVLGGPGSGKGTQCEKLVQKF-----HFNHLSSG   61 (217)
T ss_dssp             EEEEEECCTTCCHHHHHHHHHHHH-----CCEEECHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHH-----CCceEcHH
Confidence            477888999999999999999987     46666544

>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=92.66  E-value=0.14  Score=56.26  Aligned_cols=84  Identities=10%  Similarity=0.044  Sum_probs=47.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccc--cccccC-CCCCCchHH--HHHH-HHHcCC
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDS--RNKRSR-DEQSCSYIE--RFAE-AVSNNP  732 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~--~~~rl~-~~~g~g~~e--~L~e-av~~~p  732 (854)
                      .++++||+|+|||++|..++..+-......+.++...-....  -....  ...++. ..+. ...+  .+.+ .++...
T Consensus        63 iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~E~~~~~~--~a~~lG~~~~~l~i~~~~-~~e~~l~~~~~l~~~~~  139 (349)
T 2zr9_A           63 VIEIYGPESSGKTTVALHAVANAQAAGGIAAFIDAEHALDPE--YAKKLGVDTDSLLVSQPD-TGEQALEIADMLVRSGA  139 (349)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHH--HHHHTTCCGGGCEEECCS-SHHHHHHHHHHHHTTTC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCCCcCHH--HHHHcCCCHHHeEEecCC-CHHHHHHHHHHHHhcCC
Confidence            788999999999999999987665444556666654321000  00000  011111 1111 1222  2233 344556


Q ss_pred             CEEEEEecCCCCC
Q 003038          733 HRVFLIEDVEQAD  745 (854)
Q Consensus       733 ~~ViliDEieka~  745 (854)
                      ..+|+||++.-+-
T Consensus       140 ~~lIVIDsl~~l~  152 (349)
T 2zr9_A          140 LDIIVIDSVAALV  152 (349)
T ss_dssp             CSEEEEECGGGCC
T ss_pred             CCEEEEcChHhhc
Confidence            7899999998875

>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=92.65  E-value=0.071  Score=54.84  Aligned_cols=27  Identities=11%  Similarity=0.086  Sum_probs=22.6

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ..=.+++|++|+|||+.+-+++.+...
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~   38 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEY   38 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHH
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHh
Confidence            345677899999999999999988764

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=92.63  E-value=0.37  Score=51.47  Aligned_cols=40  Identities=15%  Similarity=0.305  Sum_probs=31.3

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhC-CCCceEEEccccc
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFG-SHNNFVSIALSSF  696 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg-~~~~~i~id~s~~  696 (854)
                      ...++|.||+|+|||+++..||..+-. ....+..+++..|
T Consensus       105 g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~D~~  145 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITTDTY  145 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEECCCS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEecCcc
Confidence            358999999999999999999988753 4446666666544

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=92.62  E-value=0.06  Score=52.04  Aligned_cols=34  Identities=18%  Similarity=0.265  Sum_probs=25.8

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      .++|.|++|+|||++|+.|++..    ..+..++...+
T Consensus         4 ~I~i~G~~GsGKST~a~~L~~~~----~~~~~i~~d~~   37 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWAREFIAKN----PGFYNINRDDY   37 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHS----TTEEEECHHHH
T ss_pred             EEEEecCCCCCHHHHHHHHHhhc----CCcEEecHHHH
Confidence            68899999999999999999841    23556655433

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=92.62  E-value=0.18  Score=51.92  Aligned_cols=38  Identities=13%  Similarity=0.060  Sum_probs=26.5

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      |+.....+-.++.   .++.+|+||+|+|||.++-.++...
T Consensus        95 ~~~Q~~ai~~~~~---~~~~ll~~~tG~GKT~~a~~~~~~~  132 (237)
T 2fz4_A           95 RDYQEKALERWLV---DKRGCIVLPTGSGKTHVAMAAINEL  132 (237)
T ss_dssp             CHHHHHHHHHHTT---TSEEEEEESSSTTHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHh---CCCEEEEeCCCCCHHHHHHHHHHHc
Confidence            4444444444443   2459999999999999998887663

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=92.62  E-value=0.066  Score=53.61  Aligned_cols=26  Identities=19%  Similarity=0.300  Sum_probs=23.0

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +...++|+|+||+|||++++.|+...
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            45678999999999999999999875

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=92.61  E-value=0.075  Score=50.97  Aligned_cols=23  Identities=9%  Similarity=0.031  Sum_probs=21.1

Q ss_pred             CceeecCCCCCHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +++|+|+||+|||++++.|+.++
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l   24 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSL   24 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999999999875

>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=92.52  E-value=0.095  Score=50.74  Aligned_cols=25  Identities=16%  Similarity=0.276  Sum_probs=22.0

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ...++|+|+||+|||++++.|+..+
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            3468999999999999999999874

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=92.51  E-value=0.49  Score=50.53  Aligned_cols=27  Identities=11%  Similarity=0.059  Sum_probs=24.3

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      ..+.++|+|++|+|||+++..||..+.
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~  130 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISM  130 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            456789999999999999999998886

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=92.47  E-value=0.23  Score=50.45  Aligned_cols=28  Identities=7%  Similarity=-0.110  Sum_probs=23.6

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ....++|+|+||+|||+++..++..+..
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~~   49 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGLK   49 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            5667899999999999999988776653

>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=92.46  E-value=0.09  Score=53.82  Aligned_cols=26  Identities=12%  Similarity=0.027  Sum_probs=23.1

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +..+++|+|+||+|||++++.|+.++
T Consensus        15 ~~~~I~l~G~~GsGKsT~a~~La~~l   40 (233)
T 1ak2_A           15 KGVRAVLLGPPGAGKGTQAPKLAKNF   40 (233)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            34579999999999999999999885

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=92.45  E-value=0.079  Score=52.66  Aligned_cols=25  Identities=12%  Similarity=0.062  Sum_probs=22.1

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      +...++|+|+||+|||++++.|+.+
T Consensus        14 ~~~~I~l~G~~GsGKsT~~~~L~~~   38 (203)
T 1ukz_A           14 QVSVIFVLGGPGAGKGTQCEKLVKD   38 (203)
T ss_dssp             TCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3457899999999999999999976

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=92.44  E-value=0.079  Score=53.90  Aligned_cols=25  Identities=12%  Similarity=0.052  Sum_probs=22.3

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ...++|+|+||+|||++++.|+.++
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            4679999999999999999999873

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=92.43  E-value=1.4  Score=49.62  Aligned_cols=28  Identities=11%  Similarity=-0.057  Sum_probs=24.4

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ..+.++++|.+|||||+++..||..+..
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l~~  126 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFLRE  126 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3457888999999999999999998875

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=92.41  E-value=0.072  Score=52.01  Aligned_cols=23  Identities=26%  Similarity=0.289  Sum_probs=21.6

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.|++|+|||++|+.||+.+
T Consensus         6 ~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            6 AVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            68899999999999999999976

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=92.39  E-value=0.061  Score=52.56  Aligned_cols=25  Identities=8%  Similarity=0.081  Sum_probs=22.3

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ...++|+|+||+|||++++.|+++.
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4578999999999999999999874

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=92.39  E-value=0.11  Score=52.28  Aligned_cols=35  Identities=14%  Similarity=0.058  Sum_probs=28.1

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEE
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSI  691 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~i  691 (854)
                      .+.+++++++|.|||+.|-.+|--..|...++.-+
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~v   62 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVV   62 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            46889999999999999999997666766555544

>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=92.38  E-value=0.079  Score=57.13  Aligned_cols=32  Identities=25%  Similarity=0.447  Sum_probs=25.8

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      ..+++.||+|+|||+||..||+.+ +  ..+|+.|
T Consensus        11 ~~i~i~GptgsGKt~la~~La~~~-~--~~iis~D   42 (316)
T 3foz_A           11 KAIFLMGPTASGKTALAIELRKIL-P--VELISVD   42 (316)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHS-C--EEEEECC
T ss_pred             cEEEEECCCccCHHHHHHHHHHhC-C--CcEEecc
Confidence            468899999999999999999986 2  3455554

>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=92.37  E-value=0.26  Score=53.20  Aligned_cols=96  Identities=7%  Similarity=-0.004  Sum_probs=53.4

Q ss_pred             HHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCccc-CCceEEEcccc----cccc-----c------
Q 003038          213 EDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEAL-RDVKCLPLSIS----SFRH-----M------  276 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L-~~~~~~~l~~~----~l~~-----~------  276 (854)
                      .++..++.= .=.....++|+|+||+|||+++..+|..+....--..+ ..+-+++....    .+..     +      
T Consensus        94 ~~LD~~L~G-Gl~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~~~~~~g~~~~~~  172 (324)
T 2z43_A           94 QALDGLLAG-GIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKALGLDIDNV  172 (324)
T ss_dssp             HHHHHHTTT-SEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHHHHHHTTCCHHHH
T ss_pred             hhHHHhcCC-CCCCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHHhCCCHHHH
Confidence            555555420 01256789999999999999999999775432000000 12333333322    0100     0      


Q ss_pred             ----------chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc
Q 003038          277 ----------NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       277 ----------~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                                ...+..+.+..+...+++. .++-+|+||.+..+
T Consensus       173 ~~~l~~~~~~~~~~~~~~l~~l~~~~~~~-~~~~lvVIDsl~~l  215 (324)
T 2z43_A          173 MNNIYYIRAINTDHQIAIVDDLQELVSKD-PSIKLIVVDSVTSH  215 (324)
T ss_dssp             HHTEEEEECCSHHHHHHHHHHHHHHHHHC-TTEEEEEETTTTHH
T ss_pred             hccEEEEeCCCHHHHHHHHHHHHHHHHhc-cCCCEEEEeCcHHH
Confidence                      1122333455566666652 35789999999888

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=92.29  E-value=0.075  Score=53.81  Aligned_cols=26  Identities=8%  Similarity=-0.006  Sum_probs=23.0

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +..+++|+|+||+|||++++.||.++
T Consensus         4 ~~~~I~l~G~~GsGKsT~~~~La~~l   29 (222)
T 1zak_A            4 DPLKVMISGAPASGKGTQCELIKTKY   29 (222)
T ss_dssp             CSCCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            34579999999999999999999875

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=92.29  E-value=0.066  Score=53.56  Aligned_cols=24  Identities=17%  Similarity=0.098  Sum_probs=22.0

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..++|.||+|+|||++++.|++.+
T Consensus        13 ~~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           13 PPLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhC
Confidence            378999999999999999999976

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=92.29  E-value=0.09  Score=50.40  Aligned_cols=23  Identities=17%  Similarity=0.371  Sum_probs=21.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.|++|+|||++|+.|++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l   24 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSL   24 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999987

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=92.28  E-value=0.082  Score=51.50  Aligned_cols=34  Identities=12%  Similarity=0.147  Sum_probs=27.7

Q ss_pred             HHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHH
Q 003038          215 VMYVIENLMSKRKRNFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       215 i~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~  249 (854)
                      +.++.+ |-++++-+++++|++|||||+++..+..
T Consensus         5 ~~~~~~-~~~~~~~~i~v~G~~~~GKssl~~~l~~   38 (187)
T 1zj6_A            5 FTRIWR-LFNHQEHKVIIVGLDNAGKTTILYQFSM   38 (187)
T ss_dssp             HHHHHH-HHTTSCEEEEEEESTTSSHHHHHHHHHT
T ss_pred             HHHHHH-hcCCCccEEEEECCCCCCHHHHHHHHhc
Confidence            456666 5566788999999999999999988763

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=92.22  E-value=0.17  Score=55.84  Aligned_cols=91  Identities=14%  Similarity=0.033  Sum_probs=51.7

Q ss_pred             HHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccc--ccc---c--------c-h
Q 003038          213 EDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISS--FRH---M--------N-R  278 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~--l~~---~--------~-r  278 (854)
                      .++..++.+=-=.....++|.|+||+|||+++..+|..+....     ..+-+++++.+.  +.+   +        + -
T Consensus        60 ~~LD~~Lg~GGl~~G~li~I~G~pGsGKTtlal~la~~~~~~g-----~~vlyi~~E~s~~~~~a~~~g~d~~~l~i~~~  134 (366)
T 1xp8_A           60 LSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKAG-----GTCAFIDAEHALDPVYARALGVNTDELLVSQP  134 (366)
T ss_dssp             HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT-----CCEEEEESSCCCCHHHHHHTTCCGGGCEEECC
T ss_pred             HHHHHHhCCCCccCCcEEEEEcCCCCChHHHHHHHHHHHHHCC-----CeEEEEECCCChhHHHHHHcCCCHHHceeecC
Confidence            5565555310012566789999999999999999998876421     134445544321  000   0        0 0


Q ss_pred             HHHHHHHHHHHHHHHhhhCCCeEEEeCccccc
Q 003038          279 VEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       279 ge~E~rl~~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                      ..+|+-+..+...+++  .+.-+|+||.+..+
T Consensus       135 ~~~e~~l~~l~~l~~~--~~~~lVVIDsl~~l  164 (366)
T 1xp8_A          135 DNGEQALEIMELLVRS--GAIDVVVVDSVAAL  164 (366)
T ss_dssp             SSHHHHHHHHHHHHTT--TCCSEEEEECTTTC
T ss_pred             CcHHHHHHHHHHHHhc--CCCCEEEEeChHHh
Confidence            1233333333333333  35678999999988

>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=92.20  E-value=0.28  Score=53.98  Aligned_cols=42  Identities=10%  Similarity=-0.035  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          212 NEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       212 ~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      -.++..++.+=-=...+.++|.|+||+|||+++..+|..+..
T Consensus        48 ~~~LD~~Lg~GGl~~G~ii~I~G~pGsGKTtLal~la~~~~~   89 (356)
T 1u94_A           48 SLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQR   89 (356)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            355666543100135678999999999999999999987765

>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=92.19  E-value=0.25  Score=54.29  Aligned_cols=86  Identities=7%  Similarity=0.010  Sum_probs=48.7

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccc--cccccC--CCCCC-chHHHHHHHHHcCCC
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDS--RNKRSR--DEQSC-SYIERFAEAVSNNPH  733 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~--~~~rl~--~~~g~-g~~e~L~eav~~~p~  733 (854)
                      .+++.|++|+|||.+|..+|..+-......+.++...-..... . ...  ...++.  .+... ...+.+...++....
T Consensus        65 ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~E~s~~~~~-a-~~~g~~~~~l~i~~~~~~e~~~~~~~~l~~~~~~  142 (356)
T 1u94_A           65 IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIY-A-RKLGVDIDNLLCSQPDTGEQALEICDALARSGAV  142 (356)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHH-H-HHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCCccHHH-H-HHcCCChhheeeeCCCCHHHHHHHHHHHHhccCC
Confidence            7889999999999999999987654445677777643210000 0 000  011111  11110 111123334456778


Q ss_pred             EEEEEecCCCCCH
Q 003038          734 RVFLIEDVEQADY  746 (854)
Q Consensus       734 ~ViliDEieka~~  746 (854)
                      .+|+||.+-.+.+
T Consensus       143 ~lVVIDsl~~l~~  155 (356)
T 1u94_A          143 DVIVVDSVAALTP  155 (356)
T ss_dssp             SEEEEECGGGCCC
T ss_pred             CEEEEcCHHHhcc
Confidence            9999999987763

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=92.18  E-value=0.094  Score=53.05  Aligned_cols=25  Identities=12%  Similarity=0.134  Sum_probs=22.4

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ..+++|+|+||+|||++++.|+.++
T Consensus         5 ~~~I~l~G~~GsGKsT~a~~La~~l   29 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQCEFIKKEY   29 (217)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHh
Confidence            3568999999999999999999875

>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=92.17  E-value=0.066  Score=53.94  Aligned_cols=24  Identities=8%  Similarity=0.128  Sum_probs=21.8

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..+.|.||+|+|||++++.|+..+
T Consensus         9 ~~i~l~GpsGsGKsTl~~~L~~~~   32 (208)
T 3tau_A            9 LLIVLSGPSGVGKGTVREAVFKDP   32 (208)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHST
T ss_pred             cEEEEECcCCCCHHHHHHHHHhhC
Confidence            378899999999999999999875

>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=92.14  E-value=0.059  Score=52.88  Aligned_cols=25  Identities=4%  Similarity=0.045  Sum_probs=21.8

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      ....++|+|+||+|||++++.|+..
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            4557899999999999999999865

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=92.11  E-value=0.23  Score=53.50  Aligned_cols=27  Identities=11%  Similarity=-0.044  Sum_probs=23.3

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      .+-++++|++|+|||+++.-||..+..
T Consensus       104 ~~vi~ivG~~GsGKTTl~~~LA~~l~~  130 (306)
T 1vma_A          104 PFVIMVVGVNGTGKTTSCGKLAKMFVD  130 (306)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCChHHHHHHHHHHHHHh
Confidence            445789999999999999999988764

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=92.10  E-value=0.082  Score=52.17  Aligned_cols=23  Identities=17%  Similarity=0.261  Sum_probs=21.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+.|.|++|+|||++++.||+.+
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l   24 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKL   24 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHHhc
Confidence            47899999999999999999987

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=92.08  E-value=0.2  Score=54.27  Aligned_cols=62  Identities=19%  Similarity=0.128  Sum_probs=40.7

Q ss_pred             cccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhC--CCCceEEEccccc
Q 003038          621 PWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFG--SHNNFVSIALSSF  696 (854)
Q Consensus       621 ~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg--~~~~~i~id~s~~  696 (854)
                      +|...+...+...+.....              .+....+.+.||+|+|||++++.|+..+-.  .......+.+..|
T Consensus        70 ~~~~~~l~~~~~~~l~~~~--------------~~~p~iigI~GpsGSGKSTl~~~L~~ll~~~~~~~~v~~i~~D~f  133 (321)
T 3tqc_A           70 VTARQTLQQATYQFLGKPE--------------PKVPYIIGIAGSVAVGKSTTSRVLKALLSRWPDHPNVEVITTDGF  133 (321)
T ss_dssp             HHHHHHHHHHHHHHHTCCC--------------CCCCEEEEEECCTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGG
T ss_pred             hcchHHHHHHHHHHhccCC--------------CCCCEEEEEECCCCCCHHHHHHHHHHHhcccCCCCeEEEEeeccc
Confidence            5666666776666665321              123358899999999999999999998731  1223444444443

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=92.08  E-value=0.057  Score=52.56  Aligned_cols=24  Identities=17%  Similarity=0.196  Sum_probs=18.0

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..++|.|++|+|||++|+.||+.+
T Consensus         6 ~~I~l~G~~GsGKST~a~~La~~l   29 (183)
T 2vli_A            6 PIIWINGPFGVGKTHTAHTLHERL   29 (183)
T ss_dssp             CEEEEECCC----CHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            378899999999999999999876

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=92.08  E-value=0.091  Score=52.17  Aligned_cols=23  Identities=26%  Similarity=0.456  Sum_probs=21.8

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.|++|+|||++|+.|++.+
T Consensus         6 ~I~i~G~~GsGKsT~~~~L~~~l   28 (213)
T 2plr_A            6 LIAFEGIDGSGKSSQATLLKDWI   28 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH
Confidence            68999999999999999999987

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=92.08  E-value=0.68  Score=54.53  Aligned_cols=28  Identities=14%  Similarity=0.125  Sum_probs=24.1

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      +++.+++.|+||+|||+++..+...+.+
T Consensus       163 ~~~~~vi~G~pGTGKTt~l~~ll~~l~~  190 (608)
T 1w36_D          163 TRRISVISGGPGTGKTTTVAKLLAALIQ  190 (608)
T ss_dssp             TBSEEEEECCTTSTHHHHHHHHHHHHHH
T ss_pred             cCCCEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            4678999999999999999988877654

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=92.04  E-value=0.086  Score=57.22  Aligned_cols=31  Identities=26%  Similarity=0.391  Sum_probs=25.2

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      .+++.||+|+|||++|+.||+.+ +  ..++..|
T Consensus         7 ~i~i~GptGsGKTtla~~La~~l-~--~~iis~D   37 (323)
T 3crm_A            7 AIFLMGPTAAGKTDLAMALADAL-P--CELISVD   37 (323)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS-C--EEEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc-C--CcEEecc
Confidence            68899999999999999999987 2  2445444

>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=92.03  E-value=0.089  Score=52.50  Aligned_cols=24  Identities=21%  Similarity=0.452  Sum_probs=22.3

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..++|.|++|+|||++|+.|++.+
T Consensus        10 ~~I~l~G~~GsGKsT~~~~L~~~l   33 (215)
T 1nn5_A           10 ALIVLEGVDRAGKSTQSRKLVEAL   33 (215)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHH
Confidence            478999999999999999999987

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=92.02  E-value=0.48  Score=50.92  Aligned_cols=42  Identities=19%  Similarity=0.296  Sum_probs=31.8

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      ++..+++|.||+|+|||+++..||..+-.....+.-+++..|
T Consensus       102 ~~~~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~~D~~  143 (306)
T 1vma_A          102 EPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADTF  143 (306)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEECTT
T ss_pred             CCCeEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEccccc
Confidence            344689999999999999999999887544445555665544

>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=91.99  E-value=0.11  Score=53.85  Aligned_cols=32  Identities=13%  Similarity=0.210  Sum_probs=25.9

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      ..++|.||+|+|||++|+.|++.+     .+..++.+
T Consensus        30 ~~I~l~G~~GsGKsT~a~~L~~~~-----g~~~is~~   61 (243)
T 3tlx_A           30 GRYIFLGAPGSGKGTQSLNLKKSH-----CYCHLSTG   61 (243)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH-----CCEEEEHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh-----CCeEEecH
Confidence            478999999999999999999877     24555544

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=91.97  E-value=0.11  Score=50.83  Aligned_cols=34  Identities=21%  Similarity=0.218  Sum_probs=25.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      .+.|.|++|+|||++|+.|++.+-...-.++..|
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~~~g~~~i~~d   35 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYR   35 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            4689999999999999999998732123444443

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=91.95  E-value=0.1  Score=52.07  Aligned_cols=24  Identities=25%  Similarity=0.531  Sum_probs=22.3

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..++|.|++|+|||++|+.|++.+
T Consensus        11 ~~I~l~G~~GsGKST~~~~L~~~l   34 (212)
T 2wwf_A           11 KFIVFEGLDRSGKSTQSKLLVEYL   34 (212)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHH
Confidence            478999999999999999999976

>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=91.91  E-value=0.11  Score=52.25  Aligned_cols=37  Identities=16%  Similarity=0.235  Sum_probs=28.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHh-CCCCceEEEccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVF-GSHNNFVSIALS  694 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lf-g~~~~~i~id~s  694 (854)
                      ..++|.|++|+|||++++.|++.+. .....++.+|..
T Consensus        26 ~~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~~~d   63 (211)
T 1m7g_A           26 LTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGD   63 (211)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhccccCCcEEEECCh
Confidence            4788999999999999999999885 222346677643

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=91.90  E-value=0.077  Score=52.06  Aligned_cols=23  Identities=17%  Similarity=0.192  Sum_probs=21.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+.|.||+|+|||++++.|+..+
T Consensus         7 ~i~i~GpsGsGKSTL~~~L~~~~   29 (180)
T 1kgd_A            7 TLVLLGAHGVGRRHIKNTLITKH   29 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            78999999999999999999875

>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=91.87  E-value=0.27  Score=54.08  Aligned_cols=43  Identities=12%  Similarity=-0.013  Sum_probs=31.2

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      .-.++.+++.+=-=....-++|+||||+|||+++..++..+..
T Consensus        45 G~~~LD~~Lg~GGi~~G~i~~I~GppGsGKSTLal~la~~~~~   87 (356)
T 3hr8_A           45 GSLAIDIATGVGGYPRGRIVEIFGQESSGKTTLALHAIAEAQK   87 (356)
T ss_dssp             SCHHHHHHTSSSSEETTEEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHhccCCccCCcEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            4467777664100124667899999999999999999987654

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=91.85  E-value=0.12  Score=52.90  Aligned_cols=25  Identities=16%  Similarity=0.260  Sum_probs=21.5

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      ...+++|+|++|||||+++..+...
T Consensus        28 ~~~~i~lvG~~g~GKStlin~l~g~   52 (239)
T 3lxx_A           28 SQLRIVLVGKTGAGKSATGNSILGR   52 (239)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CceEEEEECCCCCCHHHHHHHHcCC
Confidence            4568999999999999999987753

>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=91.83  E-value=0.084  Score=52.67  Aligned_cols=28  Identities=18%  Similarity=0.134  Sum_probs=24.3

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      +...++|+|+||+|||++++.|++++..
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~L~~~l~~   35 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQSRKLVEALCA   35 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4567899999999999999999998743

>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=91.81  E-value=0.22  Score=53.20  Aligned_cols=26  Identities=15%  Similarity=0.368  Sum_probs=23.2

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHh
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVF  682 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lf  682 (854)
                      ...+.+.||+|+|||++|+.|++.+-
T Consensus        31 ~~ii~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           31 PLFIFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhh
Confidence            35788999999999999999999884

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=91.77  E-value=0.083  Score=53.47  Aligned_cols=23  Identities=13%  Similarity=0.133  Sum_probs=21.8

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.||+|+|||++|+.||+.+
T Consensus         7 ~I~l~G~~GsGKsT~~~~La~~l   29 (222)
T 1zak_A            7 KVMISGAPASGKGTQCELIKTKY   29 (222)
T ss_dssp             CEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            68899999999999999999987

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=91.75  E-value=0.084  Score=52.10  Aligned_cols=23  Identities=13%  Similarity=0.226  Sum_probs=21.3

Q ss_pred             CceeecCCCCCHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      .++|+|+||+|||++++.|++++
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l   24 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKL   24 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHHhc
Confidence            47899999999999999999876

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=91.74  E-value=0.12  Score=50.40  Aligned_cols=34  Identities=3%  Similarity=-0.076  Sum_probs=26.8

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcc
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLS  269 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~  269 (854)
                      .++|.|.||+|||++++.|+.++..       .|..++..+
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~~-------~g~~~i~~d   35 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLKQ-------KGYFVSLYR   35 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHH-------TTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH-------CCCeEEEEe
Confidence            4789999999999999999988643       245566654

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=91.72  E-value=0.89  Score=52.94  Aligned_cols=42  Identities=12%  Similarity=0.128  Sum_probs=34.0

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSIS  271 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~  271 (854)
                      -.+.++.|.+|+|||.+++.++..+....-|+   .++|+-+|..
T Consensus       214 ~pHlLIaG~TGSGKS~~L~tlI~sLl~~~sP~---ev~lilIDpK  255 (574)
T 2iut_A          214 MPHLLVAGTTGSGKSVGVNAMLLSILFKSTPS---EARLIMIDPK  255 (574)
T ss_dssp             SCCEEEECCTTSSHHHHHHHHHHHHHTTCCTT---TEEEEEECSS
T ss_pred             CCeeEEECCCCCCHHHHHHHHHHHHHHhCCCc---ceEEEEeCCC
Confidence            47999999999999999999988887665563   4577777754

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=91.67  E-value=0.088  Score=52.30  Aligned_cols=26  Identities=15%  Similarity=-0.100  Sum_probs=23.0

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      ...++|.|+||+|||++++.|++++.
T Consensus         4 ~~~I~i~G~~GsGKsT~~~~L~~~l~   29 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQATLLKDWIE   29 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            35689999999999999999999863

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=91.62  E-value=0.13  Score=51.70  Aligned_cols=38  Identities=13%  Similarity=0.059  Sum_probs=29.0

Q ss_pred             HHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          214 DVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       214 ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      .+.++-..+.+.+..+++++|.+|||||+++..|+...
T Consensus        17 ~~~~~~~~~~~~~~~~i~i~G~~g~GKTTl~~~l~~~~   54 (221)
T 2wsm_A           17 LAEKNREALRESGTVAVNIMGAIGSGKTLLIERTIERI   54 (221)
T ss_dssp             HHHHHHHHHHHHTCEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcccCceEEEEEcCCCCCHHHHHHHHHHHh
Confidence            34444444445567789999999999999999998775

>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=91.58  E-value=0.29  Score=63.75  Aligned_cols=78  Identities=12%  Similarity=0.089  Sum_probs=51.2

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc---------------chHHHHHHHHHHH
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM---------------NRVEVEQRVEEIK  289 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~---------------~rge~E~rl~~l~  289 (854)
                      ....+++|+|+||+|||.++..++.....       .|..++-++.......               ++.+..+.+.+++
T Consensus        32 ~~G~i~lI~G~pGsGKT~LAlqla~~~~~-------~G~~vlYI~te~~~~~l~~~~lg~dl~~i~i~~p~t~e~l~~ll  104 (1706)
T 3cmw_A           32 PMGRIVEIYGPESSGKTTLTLQVIAAAQR-------EGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEIC  104 (1706)
T ss_dssp             ETTSEEEEECSTTSSHHHHHHHHHHHHHH-------TTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhh-------CCCceEEEEecCccHHHHHHhhccCccceeeeccCcHHHHHHHH
Confidence            46789999999999999999998876443       1334444443322111               0112244566777


Q ss_pred             HHHHhhhCCCeEEEeCccccc
Q 003038          290 NLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       290 ~~~~~~~~~~~ILfidel~~l  310 (854)
                      +.+.+. +.+.+|+||+|-.+
T Consensus       105 ~~L~~~-~~~~LVVIDSLt~L  124 (1706)
T 3cmw_A          105 DALARS-GAVDVIVVDSVAAL  124 (1706)
T ss_dssp             HHHHHH-TCCSEEEESCSTTC
T ss_pred             HHHHhc-cCCCEEEEcchhhh
Confidence            776554 45789999999888

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=91.56  E-value=0.22  Score=54.70  Aligned_cols=24  Identities=25%  Similarity=0.491  Sum_probs=22.0

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..++|.|++|+|||+++++||+.+
T Consensus        25 ~~i~l~G~~G~GKTTl~~~la~~l   48 (359)
T 2ga8_A           25 VCVILVGSPGSGKSTIAEELCQII   48 (359)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHh
Confidence            468899999999999999999877

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=91.55  E-value=0.098  Score=51.84  Aligned_cols=24  Identities=8%  Similarity=0.281  Sum_probs=21.8

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..+.|.||+|+|||++++.|+..+
T Consensus         8 ~ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            8 NLFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             cEEEEECcCCCCHHHHHHHHHhhC
Confidence            378899999999999999999974

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=91.50  E-value=0.098  Score=52.50  Aligned_cols=23  Identities=13%  Similarity=0.202  Sum_probs=21.0

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.||+|+|||++|+.||+.+
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            36789999999999999999877

>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=91.50  E-value=0.33  Score=48.79  Aligned_cols=29  Identities=7%  Similarity=-0.019  Sum_probs=25.5

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ..+-++++++.+|.|||+++-|+|.|...
T Consensus        26 ~~~g~i~v~tG~GkGKTTaA~GlalRA~g   54 (196)
T 1g5t_A           26 EERGIIIVFTGNGKGKTTAAFGTAARAVG   54 (196)
T ss_dssp             -CCCCEEEEESSSSCHHHHHHHHHHHHHH
T ss_pred             ccCceEEEECCCCCCHHHHHHHHHHHHHH
Confidence            36789999999999999999999998764

>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=91.49  E-value=0.11  Score=53.04  Aligned_cols=24  Identities=21%  Similarity=0.173  Sum_probs=22.3

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..++|.|++|+|||++|+.||+.+
T Consensus        17 ~~I~l~G~~GsGKsT~a~~La~~l   40 (233)
T 1ak2_A           17 VRAVLLGPPGAGKGTQAPKLAKNF   40 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            378999999999999999999987

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=91.47  E-value=0.19  Score=48.97  Aligned_cols=26  Identities=8%  Similarity=0.213  Sum_probs=22.3

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHH
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      ....+++|+|++|||||+++..+...
T Consensus        21 ~~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           21 GGLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            35678999999999999999988754

>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=91.45  E-value=0.13  Score=50.13  Aligned_cols=24  Identities=17%  Similarity=0.205  Sum_probs=22.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..++|.|++|+|||++|+.|++.+
T Consensus         7 ~~I~l~G~~GsGKsT~~~~L~~~l   30 (194)
T 1qf9_A            7 NVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            378999999999999999999987

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=91.38  E-value=0.29  Score=53.85  Aligned_cols=93  Identities=12%  Similarity=0.138  Sum_probs=54.9

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc-cccCcCCCccccccccccCC--C------CCCchHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS-SFSSTRADSTEDSRNKRSRD--E------QSCSYIERFAEAV  728 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s-~~~~~~~~s~e~~~~~rl~~--~------~g~g~~e~L~eav  728 (854)
                      ..+++.||+|+|||++.++|+..+ ......|.++.. ++...   . ....+ .+..  .      .+....+.|..++
T Consensus       176 ~~i~ivG~sGsGKSTll~~l~~~~-~~~~g~I~ie~~~e~~~~---~-~~~~v-~~v~~q~~~~~~~~~~t~~~~i~~~l  249 (361)
T 2gza_A          176 RVIVVAGETGSGKTTLMKALMQEI-PFDQRLITIEDVPELFLP---D-HPNHV-HLFYPSEAKEEENAPVTAATLLRSCL  249 (361)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHTTS-CTTSCEEEEESSSCCCCT---T-CSSEE-EEECC----------CCHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcC-CCCceEEEECCccccCcc---c-cCCEE-EEeecCccccccccccCHHHHHHHHH
Confidence            478999999999999999999876 334566777632 22200   0 00111 0111  0      1112334566666


Q ss_pred             HcCCCEEEEEecCCCCCHHHHHHHHHhhhcCe
Q 003038          729 SNNPHRVFLIEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       729 ~~~p~~ViliDEieka~~~v~~~Ll~~le~G~  760 (854)
                      +..| .+++++|+..  .++.. +++.+..|.
T Consensus       250 ~~~p-d~~l~~e~r~--~~~~~-~l~~l~~g~  277 (361)
T 2gza_A          250 RMKP-TRILLAELRG--GEAYD-FINVAASGH  277 (361)
T ss_dssp             TSCC-SEEEESCCCS--THHHH-HHHHHHTTC
T ss_pred             hcCC-CEEEEcCchH--HHHHH-HHHHHhcCC
Confidence            6666 4778899874  34555 567777774

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=91.36  E-value=1.3  Score=43.40  Aligned_cols=26  Identities=0%  Similarity=0.020  Sum_probs=19.4

Q ss_pred             cCCceeecCCCCCHHHHH-HHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVV-RGVIDKIE  252 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v-~~la~~i~  252 (854)
                      .+|+++.+|+|+|||.+. -.+...+.
T Consensus        38 ~~~~li~~~TGsGKT~~~~~~~~~~l~   64 (207)
T 2gxq_A           38 GKDLIGQARTGTGKTLAFALPIAERLA   64 (207)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHCC
T ss_pred             CCCEEEECCCCChHHHHHHHHHHHHHh
Confidence            478999999999999764 34445543

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=91.35  E-value=0.11  Score=51.89  Aligned_cols=26  Identities=15%  Similarity=0.207  Sum_probs=21.7

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ..+-++|+||+|+|||++++.|+...
T Consensus         3 ~g~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             --CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            34678999999999999999998765

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=91.32  E-value=0.094  Score=53.33  Aligned_cols=24  Identities=8%  Similarity=0.170  Sum_probs=22.0

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..++|.|++|+|||++|+.||+.+
T Consensus         8 ~~I~l~G~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A            8 LRAVIMGAPGSGKGTVSSRITTHF   31 (227)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            368999999999999999999976

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=91.29  E-value=0.11  Score=51.91  Aligned_cols=28  Identities=7%  Similarity=0.083  Sum_probs=24.0

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      +...++|.|+||+|||++++.|++++..
T Consensus         9 ~~~~I~l~G~~GsGKST~~~~L~~~l~~   36 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQSKLLVEYLKN   36 (212)
T ss_dssp             CSCEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             cCCEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            3456899999999999999999988643

>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=91.28  E-value=0.13  Score=51.24  Aligned_cols=38  Identities=24%  Similarity=0.277  Sum_probs=28.6

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +...+.+.|++|+|||++++.|++.+-    .+..+++..+.
T Consensus        20 ~~~~i~i~G~~GsGKSTl~~~L~~~~~----~~~~i~~D~~~   57 (207)
T 2qt1_A           20 KTFIIGISGVTNSGKTTLAKNLQKHLP----NCSVISQDDFF   57 (207)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTTST----TEEEEEGGGGB
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhcC----CcEEEeCCccc
Confidence            334788999999999999999998651    35566665543

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=91.27  E-value=0.25  Score=49.69  Aligned_cols=89  Identities=10%  Similarity=0.074  Sum_probs=49.8

Q ss_pred             eEEEecCCCchHH-HHHHHHHHHHhCCCCceEEEccc---cccCcCCCcccccccccc---CCCCCCchHHHHHHHHHcC
Q 003038          659 WLFFQGVDADAKE-KIAKELARLVFGSHNNFVSIALS---SFSSTRADSTEDSRNKRS---RDEQSCSYIERFAEAVSNN  731 (854)
Q Consensus       659 ~lLf~Gp~GvGKt-~lAr~LA~~lfg~~~~~i~id~s---~~~~~~~~s~e~~~~~rl---~~~~g~g~~e~L~eav~~~  731 (854)
                      -++++||.|.||| +|.+++.+..... .+.+.+...   .|.       .. -+++.   +......-.+.+.+..  .
T Consensus        22 l~fiyG~MgsGKTt~Ll~~i~n~~~~~-~kvl~~kp~~D~R~~-------~~-i~S~~g~~~~A~~~~~~~d~~~~~--~   90 (195)
T 1w4r_A           22 IQVILGPMFSGKSTELMRRVRRFQIAQ-YKCLVIKYAKDTRYS-------SS-FCTHDRNTMEALPACLLRDVAQEA--L   90 (195)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTT-CCEEEEEETTCCCGG-------GS-CCHHHHHHSEEEEESSGGGGHHHH--H
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHcC-CeEEEEccccCccch-------hh-hhhccCCcccceecCCHHHHHHhc--c
Confidence            5677999999999 9999999888754 445555422   121       00 01111   0000000111233333  3


Q ss_pred             CCEEEEEecCCCCCHHHHHHHHHhhhcC
Q 003038          732 PHRVFLIEDVEQADYCSQKGFKRAIESG  759 (854)
Q Consensus       732 p~~ViliDEieka~~~v~~~Ll~~le~G  759 (854)
                      +..||+|||+.-. ++....+..+.+.|
T Consensus        91 ~~DvIlIDEaQFf-k~~ve~~~~L~~~g  117 (195)
T 1w4r_A           91 GVAVIGIDEGQFF-PDIVEFCEAMANAG  117 (195)
T ss_dssp             TCSEEEESSGGGC-TTHHHHHHHHHHTT
T ss_pred             CCCEEEEEchhhh-HHHHHHHHHHHHCC
Confidence            4789999999999 77555554444544

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=91.27  E-value=0.11  Score=52.42  Aligned_cols=24  Identities=13%  Similarity=0.117  Sum_probs=22.1

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..++|.|++|+|||++|+.||+.+
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            368899999999999999999987

>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=91.21  E-value=0.19  Score=47.30  Aligned_cols=74  Identities=11%  Similarity=0.069  Sum_probs=0.0

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc-chHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM-NRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~-~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      +++++|++|||||+++..+...-.....|..-.....+..+--.+.-- .-|.  ++...+....-.. ...+|+++|
T Consensus         2 ki~~~G~~~~GKssl~~~l~~~~~~~~~~t~~~~~~~~~~~~~~~~i~Dt~G~--~~~~~~~~~~~~~-~d~~i~v~d   76 (164)
T 1r8s_A            2 RILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQ--DKIRPLWRHYFQN-TQGLIFVVD   76 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHCSSCCCCCSSCCEEEEECSSCEEEEEECCCC--GGGHHHHHHHTTT-CSEEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHcCCcCcccCcCceeEEEEEECCEEEEEEEcCCC--hhhHHHHHHHhcc-CCEEEEEEE

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=91.15  E-value=0.15  Score=52.41  Aligned_cols=30  Identities=0%  Similarity=-0.154  Sum_probs=26.2

Q ss_pred             ccCcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          224 SKRKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       224 r~~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      +|.+-|+++.|+||||||+++-.+|..+..
T Consensus         3 ~~g~l~I~~~~kgGvGKTt~a~~la~~l~~   32 (228)
T 2r8r_A            3 ARGRLKVFLGAAPGVGKTYAMLQAAHAQLR   32 (228)
T ss_dssp             CCCCEEEEEESSTTSSHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCCCcHHHHHHHHHHHHHH
Confidence            467789999999999999999999888765

>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=91.13  E-value=0.098  Score=52.58  Aligned_cols=22  Identities=14%  Similarity=0.249  Sum_probs=20.4

Q ss_pred             EEEecCCCchHHHHHHHHHHHH
Q 003038          660 LFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ++|.||+|+|||++|+.||+.+
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3dl0_A            3 LVLMGLPGAGKGTQGERIVEKY   24 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6789999999999999999876

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=91.13  E-value=0.49  Score=52.48  Aligned_cols=38  Identities=11%  Similarity=0.175  Sum_probs=30.9

Q ss_pred             HHHHHHhhc-cCcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          216 MYVIENLMS-KRKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       216 ~~v~~~L~r-~~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      -++|+.|.- .+.....|+|++|+|||+++..++..+..
T Consensus       163 iraID~l~PigrGQR~lIfg~~g~GKT~Ll~~Ia~~i~~  201 (427)
T 3l0o_A          163 TRLIDLFAPIGKGQRGMIVAPPKAGKTTILKEIANGIAE  201 (427)
T ss_dssp             HHHHHHHSCCBTTCEEEEEECTTCCHHHHHHHHHHHHHH
T ss_pred             chhhhhcccccCCceEEEecCCCCChhHHHHHHHHHHhh
Confidence            477888764 36678899999999999999999987754

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=91.08  E-value=0.15  Score=55.97  Aligned_cols=28  Identities=11%  Similarity=0.137  Sum_probs=23.9

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      ....|++|+|+||+|||++++.||..+.
T Consensus        22 g~~~~i~l~G~~G~GKTTl~~~la~~l~   49 (359)
T 2ga8_A           22 NYRVCVILVGSPGSGKSTIAEELCQIIN   49 (359)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCeeEEEEECCCCCcHHHHHHHHHHHhC
Confidence            3456799999999999999999998753

>2fh5_B SR-beta, signal recognition particle receptor beta subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Mus musculus} SCOP: c.37.1.8 PDB: 2go5_2

Probab=91.08  E-value=0.16  Score=50.57  Aligned_cols=26  Identities=15%  Similarity=0.230  Sum_probs=21.1

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +.-+++|+|++|||||+++..+...-
T Consensus         6 ~~~ki~vvG~~~~GKTsli~~l~~~~   31 (214)
T 2fh5_B            6 SQRAVLFVGLCDSGKTLLFVRLLTGQ   31 (214)
T ss_dssp             --CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            55689999999999999999887643

>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=91.07  E-value=0.11  Score=51.52  Aligned_cols=26  Identities=15%  Similarity=0.116  Sum_probs=22.8

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +...++|.|++|+|||++++.|++++
T Consensus         3 ~~~~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHTS
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            34578999999999999999999874

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=91.06  E-value=0.25  Score=58.24  Aligned_cols=38  Identities=16%  Similarity=0.125  Sum_probs=29.5

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccc
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSI  270 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~  270 (854)
                      +...++|+|.||+|||++++.|++++..       +|..++.+|.
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~L~~-------~G~~~v~lDg   88 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEYLVC-------HGIPCYTLDG   88 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHH-------TTCCEEEESH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHHh-------cCCeEEEech
Confidence            3456899999999999999999998754       2455666653

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=91.01  E-value=0.099  Score=51.82  Aligned_cols=25  Identities=12%  Similarity=0.101  Sum_probs=22.4

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHh
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVF  682 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lf  682 (854)
                      ..+.|.||+|+|||++++.|+..+.
T Consensus         7 ~~i~l~G~~GsGKSTl~~~L~~~~~   31 (207)
T 2j41_A            7 LLIVLSGPSGVGKGTVRKRIFEDPS   31 (207)
T ss_dssp             CEEEEECSTTSCHHHHHHHHHHCTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhhC
Confidence            3788999999999999999999763

>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=91.00  E-value=0.12  Score=50.85  Aligned_cols=34  Identities=21%  Similarity=0.109  Sum_probs=25.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      .+.|.||+|+|||++++.|+...-    ..+.++...+
T Consensus         4 ii~l~G~~GaGKSTl~~~L~~~~~----g~~~i~~d~~   37 (189)
T 2bdt_A            4 LYIITGPAGVGKSTTCKRLAAQLD----NSAYIEGDII   37 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSS----SEEEEEHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHhcccC----CeEEEcccch
Confidence            678999999999999999998431    2255554443

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=90.91  E-value=0.16  Score=55.40  Aligned_cols=33  Identities=21%  Similarity=0.214  Sum_probs=26.6

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      .+++.||+|+|||++|+.||+.+ +    ...|++..|
T Consensus         9 lI~I~GptgSGKTtla~~La~~l-~----~~iis~Ds~   41 (340)
T 3d3q_A            9 LIVIVGPTASGKTELSIEVAKKF-N----GEIISGDSM   41 (340)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHT-T----EEEEECCSS
T ss_pred             eEEEECCCcCcHHHHHHHHHHHc-C----Cceeccccc
Confidence            68899999999999999999987 2    344555555

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=90.90  E-value=0.13  Score=50.08  Aligned_cols=25  Identities=4%  Similarity=0.110  Sum_probs=21.2

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      ...+++++|++|||||+++..+...
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            4457899999999999999988753

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=90.85  E-value=0.12  Score=51.57  Aligned_cols=23  Identities=17%  Similarity=0.190  Sum_probs=21.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+.|+||+|+|||++.+.|+..+
T Consensus         6 ~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            6 PVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            67899999999999999999876

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=90.83  E-value=0.075  Score=51.68  Aligned_cols=25  Identities=4%  Similarity=0.015  Sum_probs=18.1

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ...++|+|.||+|||++++.|+.++
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~l   29 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHERL   29 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhc
Confidence            3568999999999999999999874

>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=90.81  E-value=0.14  Score=57.06  Aligned_cols=31  Identities=13%  Similarity=0.220  Sum_probs=25.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      .+++.||+|+|||+||..||+.+-   ..+|+.|
T Consensus         4 ~i~i~GptgsGKttla~~La~~~~---~~iis~D   34 (409)
T 3eph_A            4 VIVIAGTTGVGKSQLSIQLAQKFN---GEVINSD   34 (409)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHT---EEEEECC
T ss_pred             EEEEECcchhhHHHHHHHHHHHCC---CeEeecC
Confidence            688999999999999999999873   2455554

>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=90.81  E-value=0.14  Score=52.78  Aligned_cols=24  Identities=13%  Similarity=0.180  Sum_probs=22.1

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..+.+.||+|+|||++++.|++.+
T Consensus        28 ~~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           28 LRAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999999999876

>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=90.73  E-value=0.11  Score=56.00  Aligned_cols=31  Identities=23%  Similarity=0.187  Sum_probs=24.8

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      .+++.||+|+|||++|..||+.+ +  ..+|+.|
T Consensus         5 ~i~i~GptgsGKt~la~~La~~~-~--~~iis~D   35 (322)
T 3exa_A            5 LVAIVGPTAVGKTKTSVMLAKRL-N--GEVISGD   35 (322)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHTT-T--EEEEECC
T ss_pred             EEEEECCCcCCHHHHHHHHHHhC-c--cceeecC
Confidence            67899999999999999999976 2  2445444

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=90.72  E-value=0.13  Score=52.41  Aligned_cols=23  Identities=9%  Similarity=0.076  Sum_probs=21.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.|++|+|||++|+.||+.+
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            47899999999999999999987

>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=90.69  E-value=0.13  Score=51.70  Aligned_cols=23  Identities=13%  Similarity=0.130  Sum_probs=21.2

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.|++|+|||++|+.||+.+
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            36899999999999999999977

>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=90.69  E-value=0.13  Score=50.72  Aligned_cols=23  Identities=13%  Similarity=0.423  Sum_probs=20.8

Q ss_pred             CceeecCCCCCHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ++.|+||+|+|||++++.++..+
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l   24 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999999999775

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=90.67  E-value=0.14  Score=53.47  Aligned_cols=25  Identities=16%  Similarity=0.127  Sum_probs=23.3

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ..+++|+|++|+|||++++.||.++
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~~l   72 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMARSL   72 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhc
Confidence            6789999999999999999999875

>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=90.65  E-value=0.11  Score=52.18  Aligned_cols=23  Identities=13%  Similarity=0.260  Sum_probs=21.1

Q ss_pred             CceeecCCCCCHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +++|.|+||+|||++++.|+.++
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            47999999999999999999875

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=90.65  E-value=0.088  Score=50.77  Aligned_cols=33  Identities=9%  Similarity=0.147  Sum_probs=24.4

Q ss_pred             HHHHHHhhc-cCcCCceeecCCCCCHHHHHHHHH
Q 003038          216 MYVIENLMS-KRKRNFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       216 ~~v~~~L~r-~~k~n~vLvGe~GvGKta~v~~la  248 (854)
                      .++++-+.. +++-+++++|++|||||+++..+.
T Consensus         6 ~~~~~~~~~~~~~~~i~v~G~~~~GKssli~~l~   39 (183)
T 1moz_A            6 SSMFDKLWGSNKELRILILGLDGAGKTTILYRLQ   39 (183)
T ss_dssp             HHHHGGGTTCSSCEEEEEEEETTSSHHHHHHHTC
T ss_pred             HHHHHHhcCCCCccEEEEECCCCCCHHHHHHHHh
Confidence            344443333 567789999999999999997654

>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=90.62  E-value=0.49  Score=53.47  Aligned_cols=27  Identities=15%  Similarity=0.085  Sum_probs=23.7

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      .+-++++|++|||||+++..||..+.+
T Consensus       100 p~vIlivG~~G~GKTTt~~kLA~~l~~  126 (443)
T 3dm5_A          100 PTILLMVGIQGSGKTTTVAKLARYFQK  126 (443)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             CeEEEEECcCCCCHHHHHHHHHHHHHH
Confidence            445789999999999999999988865

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=90.53  E-value=0.22  Score=49.61  Aligned_cols=42  Identities=2%  Similarity=0.115  Sum_probs=31.2

Q ss_pred             cHHHHHHHHHHhhcc---CcCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSK---RKRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       211 r~~ei~~v~~~L~r~---~k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      |++-+..+++-+..+   ...-+.|+|++|+|||++++.|+..+.
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~~~~   47 (201)
T 1rz3_A            3 LRDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTLR   47 (201)
T ss_dssp             HHHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            556677777665543   223478899999999999999998764

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=90.53  E-value=0.18  Score=50.64  Aligned_cols=28  Identities=14%  Similarity=0.190  Sum_probs=23.9

Q ss_pred             ccCcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          224 SKRKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       224 r~~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      .++...++|+|.+|||||+++..++...
T Consensus        35 ~~~~~~i~ivG~~gvGKTtl~~~l~~~~   62 (226)
T 2hf9_A           35 KHGVVAFDFMGAIGSGKTLLIEKLIDNL   62 (226)
T ss_dssp             HTTCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             hCCCeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3456789999999999999999998764

>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=90.47  E-value=0.1  Score=52.80  Aligned_cols=30  Identities=17%  Similarity=0.151  Sum_probs=24.6

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      .++|.||+|+|||++|.+|++..+    .+|.-|
T Consensus        36 ~ilI~GpsGsGKStLA~~La~~g~----~iIsdD   65 (205)
T 2qmh_A           36 GVLITGDSGVGKSETALELVQRGH----RLIADD   65 (205)
T ss_dssp             EEEEECCCTTTTHHHHHHHHTTTC----EEEESS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhCC----eEEecc
Confidence            589999999999999999998752    455544

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=90.40  E-value=0.71  Score=51.92  Aligned_cols=42  Identities=19%  Similarity=0.251  Sum_probs=33.5

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +..+++|.|+.|+|||+++..||..+-.....+.-+++.-+.
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllvd~D~~r  138 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQR  138 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECCSSC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEeeccccC
Confidence            345888899999999999999999887666677777765443

>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=90.38  E-value=0.15  Score=51.37  Aligned_cols=23  Identities=17%  Similarity=0.307  Sum_probs=21.6

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+.+.||+|+|||++++.|++.+
T Consensus         7 ~i~i~G~~GsGKSTl~~~L~~~~   29 (227)
T 1cke_A            7 VITIDGPSGAGKGTLCKAMAEAL   29 (227)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            68899999999999999999976

>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=90.34  E-value=0.15  Score=52.56  Aligned_cols=25  Identities=12%  Similarity=0.095  Sum_probs=22.6

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ...++|+|+||+|||++++.|++++
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            4679999999999999999999875

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=90.33  E-value=0.36  Score=57.30  Aligned_cols=69  Identities=12%  Similarity=0.082  Sum_probs=38.8

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLI  738 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vili  738 (854)
                      ..|++||||+|||.++-.+...+......++....+                       .--.+.+.+.+......++-+
T Consensus       207 ~~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~a~T-----------------------N~AvD~i~erL~~~~~~ilRl  263 (646)
T 4b3f_X          207 LAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPS-----------------------NIAVDNLVERLALCKQRILRL  263 (646)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESS-----------------------HHHHHHHHHHHHHTTCCEEEC
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEcCc-----------------------hHHHHHHHHHHHhcCCceEEe
Confidence            578999999999977665555554433333322211                       012234555555555566666


Q ss_pred             ecCCCCCHHHHH
Q 003038          739 EDVEQADYCSQK  750 (854)
Q Consensus       739 DEieka~~~v~~  750 (854)
                      -.-.+.++.++.
T Consensus       264 G~~~r~~~~~~~  275 (646)
T 4b3f_X          264 GHPARLLESIQQ  275 (646)
T ss_dssp             SCCSSCCHHHHT
T ss_pred             cchhhhhhhhhh
Confidence            555555555443

>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=90.31  E-value=0.81  Score=52.01  Aligned_cols=38  Identities=13%  Similarity=0.191  Sum_probs=30.9

Q ss_pred             HHHHHhhcc-CcCCceeecCCCCCHHHHHHHHHHHHHcC
Q 003038          217 YVIENLMSK-RKRNFVVVGECLASIEGVVRGVIDKIEKG  254 (854)
Q Consensus       217 ~v~~~L~r~-~k~n~vLvGe~GvGKta~v~~la~~i~~~  254 (854)
                      ++|+.|.-= +.....|+|++|||||+++..++..+.+.
T Consensus       142 r~ID~l~pigkGQr~~Ifgg~G~GKT~L~~~i~~~~~~~  180 (482)
T 2ck3_D          142 KVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKA  180 (482)
T ss_dssp             HHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHTTTT
T ss_pred             EEEecccccccCCeeeeecCCCCChHHHHHHHHHhhHhh
Confidence            677777532 66778899999999999999999888654

>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=90.31  E-value=0.5  Score=51.66  Aligned_cols=38  Identities=13%  Similarity=0.140  Sum_probs=31.1

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      ...+.|.|++|+|||+++..|+..+......+..++..
T Consensus        79 ~~~I~i~G~~G~GKSTl~~~L~~~l~~~g~kV~vi~~D  116 (355)
T 3p32_A           79 AHRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLAVD  116 (355)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEEEC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHhCCCceEEEecC
Confidence            35789999999999999999999887666666666554

>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=90.27  E-value=0.13  Score=50.85  Aligned_cols=23  Identities=17%  Similarity=0.427  Sum_probs=21.7

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+.|.|++|+|||++++.|++.+
T Consensus         6 ~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            6 LIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHTS
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH
Confidence            68999999999999999999976

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=90.25  E-value=0.58  Score=52.98  Aligned_cols=55  Identities=9%  Similarity=0.080  Sum_probs=37.4

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccc
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSIS  271 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~  271 (854)
                      .=.++..++.  .=....-++|.|+||+|||+++..+|..+....    =..+-+++++++
T Consensus       189 G~~~LD~~~g--Gl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~----g~~Vl~~s~E~s  243 (454)
T 2r6a_A          189 GFTELDRMTS--GFQRSDLIIVAARPSVGKTAFALNIAQNVATKT----NENVAIFSLEMS  243 (454)
T ss_dssp             SCHHHHHHHS--SBCTTCEEEEECCTTSCHHHHHHHHHHHHHHHS----SCCEEEEESSSC
T ss_pred             CcHHHHhhcC--CCCCCCEEEEECCCCCCHHHHHHHHHHHHHHhC----CCcEEEEECCCC
Confidence            3456777662  223566789999999999999999999876420    023556666653

>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=90.24  E-value=0.27  Score=53.07  Aligned_cols=38  Identities=21%  Similarity=0.114  Sum_probs=28.7

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCC------CCceEEEcccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGS------HNNFVSIALSS  695 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~------~~~~i~id~s~  695 (854)
                      ..++++||+|+|||.+|..+|..+--.      ....+.++...
T Consensus       108 ~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~  151 (324)
T 2z43_A          108 TMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEG  151 (324)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSS
T ss_pred             cEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            378999999999999999999865221      34667776553

>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=90.22  E-value=0.31  Score=52.41  Aligned_cols=35  Identities=14%  Similarity=0.131  Sum_probs=27.3

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEE
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSI  691 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~i  691 (854)
                      ...+.|.||+|+|||++++.||..+-.....+.-.
T Consensus       102 g~vi~lvG~nGsGKTTll~~Lagll~~~~g~V~l~  136 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFC  136 (304)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEE
Confidence            35889999999999999999999886544443333

>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=90.18  E-value=0.16  Score=51.14  Aligned_cols=25  Identities=8%  Similarity=0.125  Sum_probs=21.9

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +..+.|+|++|+|||++++.|+..+
T Consensus         5 ~~~i~i~G~~GsGKSTl~~~L~~~~   29 (227)
T 1cke_A            5 APVITIDGPSGAGKGTLCKAMAEAL   29 (227)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3568999999999999999999764

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=90.18  E-value=0.17  Score=50.47  Aligned_cols=25  Identities=28%  Similarity=0.286  Sum_probs=22.8

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHH
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ...+.+.||+|+|||++++.|+..+
T Consensus         6 ~~~i~i~G~~GsGKSTl~~~l~~~~   30 (211)
T 3asz_A            6 PFVIGIAGGTASGKTTLAQALARTL   30 (211)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHh
Confidence            3478899999999999999999987

>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=90.17  E-value=0.43  Score=53.28  Aligned_cols=38  Identities=13%  Similarity=0.027  Sum_probs=27.7

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhC------CCCceEEEcccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFG------SHNNFVSIALSS  695 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg------~~~~~i~id~s~  695 (854)
                      ..+.++||+|+|||+|++.|+-...-      .....+.++..+
T Consensus       179 ei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~  222 (400)
T 3lda_A          179 SITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEG  222 (400)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSS
T ss_pred             cEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCC
Confidence            37899999999999999987744321      234577777553

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=90.11  E-value=0.23  Score=51.72  Aligned_cols=38  Identities=18%  Similarity=0.271  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhhcc--CcCCceeecCCCCCHHHHHHHHHHH
Q 003038          213 EDVMYVIENLMSK--RKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       213 ~ei~~v~~~L~r~--~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      +.+..++.-+...  +.-+++|+|.+|||||+++..+...
T Consensus        20 ~~l~~~~~~~~~~~~~~~~I~lvG~~g~GKSSLin~l~~~   59 (262)
T 3def_A           20 EKLIEFFGKLKQKDMNSMTVLVLGKGGVGKSSTVNSLIGE   59 (262)
T ss_dssp             HHHHHHHHHHHHTTCCEEEEEEEECTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHHHHhhccCCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3344444444443  4458999999999999999988753

>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=90.08  E-value=0.16  Score=50.32  Aligned_cols=31  Identities=10%  Similarity=0.086  Sum_probs=0.0

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcc
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLS  269 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~  269 (854)
                      ..+.|+|++|+|||++++.|+. +          |..++..|
T Consensus         2 ~~i~i~G~~GsGKSTl~~~L~~-~----------g~~~i~~d   32 (204)
T 2if2_A            2 KRIGLTGNIGCGKSTVAQMFRE-L----------GAYVLDAD   32 (204)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH-T----------TCEEEEHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHH-C----------CCEEEEcc

>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=90.07  E-value=0.58  Score=50.99  Aligned_cols=39  Identities=5%  Similarity=-0.043  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          213 EDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      .++..++.= .=.....++|+||||+|||+++..+|....
T Consensus       109 ~~LD~~LgG-Gl~~G~i~~I~G~~GsGKTtla~~la~~~~  147 (343)
T 1v5w_A          109 QEFDKLLGG-GIESMAITEAFGEFRTGKTQLSHTLCVTAQ  147 (343)
T ss_dssp             HHHHHHTTS-SBCSSEEEEEECCTTCTHHHHHHHHHHHTT
T ss_pred             hhHHHHhcC-CCCCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            456555420 012566789999999999999999987643

>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=90.04  E-value=0.25  Score=55.74  Aligned_cols=42  Identities=19%  Similarity=0.295  Sum_probs=31.9

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +...++|.|++|+|||+++..||..+-.......-+++..|.
T Consensus        98 ~~~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~~D~~r  139 (432)
T 2v3c_C           98 KQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYR  139 (432)
T ss_dssp             SCCCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEECCSCCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeccccC
Confidence            345899999999999999999998775333456666666543

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=90.02  E-value=0.2  Score=50.22  Aligned_cols=39  Identities=10%  Similarity=0.060  Sum_probs=28.1

Q ss_pred             HHHHHHHHhhcc--CcCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          214 DVMYVIENLMSK--RKRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       214 ei~~v~~~L~r~--~k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      -+.++.+-+..+  ...-+.|+|++|+|||++++.|+..+.
T Consensus         7 ~~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A            7 LCQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             HHHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            344555544432  344578999999999999999998765

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=89.97  E-value=0.36  Score=46.69  Aligned_cols=25  Identities=12%  Similarity=0.266  Sum_probs=21.4

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      .+.+++|+|++|||||+++..+...
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 3pqc_A           22 LKGEVAFVGRSNVGKSSLLNALFNR   46 (195)
T ss_dssp             TTCEEEEEEBTTSSHHHHHHHHHTS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHcC
Confidence            4568999999999999999987654

>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=89.95  E-value=0.23  Score=48.01  Aligned_cols=27  Identities=11%  Similarity=0.326  Sum_probs=24.0

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCC
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSH  685 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~  685 (854)
                      ..+.|.||.|+|||++.|.|+..+ +..
T Consensus        34 e~v~L~G~nGaGKTTLlr~l~g~l-~~~   60 (158)
T 1htw_A           34 IMVYLNGDLGAGKTTLTRGMLQGI-GHQ   60 (158)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT-TCC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhC-CCC
Confidence            478899999999999999999998 543

>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=89.93  E-value=0.15  Score=50.03  Aligned_cols=21  Identities=5%  Similarity=0.167  Sum_probs=19.3

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .++|+|++|+|||++++.|+.
T Consensus         4 ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            4 LYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHhc
Confidence            578999999999999999986

>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=89.87  E-value=0.75  Score=58.01  Aligned_cols=47  Identities=23%  Similarity=0.235  Sum_probs=36.4

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHH
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARL  680 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~  680 (854)
                      ..++|-++.+..|...+....                .....+.++|+.|+|||+||+.++..
T Consensus       124 ~~~vgR~~~~~~l~~~l~~~~----------------~~~~~v~i~G~gG~GKTtLa~~~~~~  170 (1249)
T 3sfz_A          124 VIFVTRKKLVHAIQQKLWKLN----------------GEPGWVTIYGMAGCGKSVLAAEAVRD  170 (1249)
T ss_dssp             SSCCCCHHHHHHHHHHHHTTT----------------TSCEEEEEECSTTSSHHHHHHHHTCC
T ss_pred             ceeccHHHHHHHHHHHHhhcc----------------CCCCEEEEEeCCCCCHHHHHHHHhcC
Confidence            457899988888888876421                12357889999999999999988754

>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=89.78  E-value=0.17  Score=53.56  Aligned_cols=23  Identities=17%  Similarity=0.130  Sum_probs=20.7

Q ss_pred             CCceeecCCCCCHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      ..++|+|+||+|||++++.|+++
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            45899999999999999999975

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=89.76  E-value=0.14  Score=50.22  Aligned_cols=24  Identities=8%  Similarity=0.120  Sum_probs=19.9

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~  249 (854)
                      +.-+++++|++|||||+++..+..
T Consensus        22 ~~~ki~~vG~~~vGKSsli~~l~~   45 (190)
T 1m2o_B           22 KHGKLLFLGLDNAGKTTLLHMLKN   45 (190)
T ss_dssp             --CEEEEEESTTSSHHHHHHHHHH
T ss_pred             CccEEEEECCCCCCHHHHHHHHhc
Confidence            455899999999999999998774

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=89.68  E-value=0.15  Score=47.75  Aligned_cols=23  Identities=17%  Similarity=0.303  Sum_probs=20.0

Q ss_pred             CCceeecCCCCCHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      .+++++|++|||||+++..+...
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            36899999999999999988753

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=89.67  E-value=0.17  Score=51.53  Aligned_cols=23  Identities=22%  Similarity=0.101  Sum_probs=21.0

Q ss_pred             CceeecCCCCCHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +++|.|+||+|||++++.|+.++
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            47899999999999999999875

>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=89.66  E-value=0.19  Score=50.64  Aligned_cols=24  Identities=17%  Similarity=0.180  Sum_probs=21.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..+.|.||+|+|||+|++.|++.+
T Consensus        20 ~~ivl~GPSGaGKsTL~~~L~~~~   43 (197)
T 3ney_A           20 KTLVLIGASGVGRSHIKNALLSQN   43 (197)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CEEEEECcCCCCHHHHHHHHHhhC
Confidence            378899999999999999999864

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=89.62  E-value=0.17  Score=50.02  Aligned_cols=25  Identities=16%  Similarity=0.321  Sum_probs=21.6

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ..-+.|+||+|+|||++++.|+..+
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            4567899999999999999998763

>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=89.62  E-value=0.3  Score=52.83  Aligned_cols=85  Identities=9%  Similarity=0.072  Sum_probs=47.3

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhC--CCCceEEEccccccCc-CCCccccccccccC-CCCCCchHHHH----HHH--
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFG--SHNNFVSIALSSFSST-RADSTEDSRNKRSR-DEQSCSYIERF----AEA--  727 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg--~~~~~i~id~s~~~~~-~~~s~e~~~~~rl~-~~~g~g~~e~L----~ea--  727 (854)
                      +..++.||+|+|||.|+..++...-.  .....+.||.-+-... +.... .....+++ ..+.  ..+++    .+.  
T Consensus        29 GiteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~ra~~l-Gvd~d~llv~~~~--~~E~~~l~i~~~l~  105 (333)
T 3io5_A           29 GLLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPAYLRSM-GVDPERVIHTPVQ--SLEQLRIDMVNQLD  105 (333)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHHHHHHT-TCCGGGEEEEECS--BHHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHHHHHHh-CCCHHHeEEEcCC--CHHHHHHHHHHHHH
Confidence            46899999999999999877765532  2456777875432210 00000 00011111 1111  12222    223  


Q ss_pred             -HHcCCCEEEEEecCCCCC
Q 003038          728 -VSNNPHRVFLIEDVEQAD  745 (854)
Q Consensus       728 -v~~~p~~ViliDEieka~  745 (854)
                       ++.....+|++|-|--+.
T Consensus       106 ~i~~~~~~lvVIDSI~aL~  124 (333)
T 3io5_A          106 AIERGEKVVVFIDSLGNLA  124 (333)
T ss_dssp             TCCTTCCEEEEEECSTTCB
T ss_pred             HhhccCceEEEEecccccc
Confidence             466678999999998774

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=89.57  E-value=0.71  Score=52.09  Aligned_cols=53  Identities=8%  Similarity=0.011  Sum_probs=36.3

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcC-CCCcccCCceEEEccc
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKG-DVPEALRDVKCLPLSI  270 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~-~vp~~L~~~~~~~l~~  270 (854)
                      .=.++..++.=|  ....-++|.|+||+|||+++..+|..+..+ .     ..+-++++.+
T Consensus       186 G~~~LD~~lgGl--~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g-----~~vl~~slE~  239 (444)
T 2q6t_A          186 GFKELDQLIGTL--GPGSLNIIAARPAMGKTAFALTIAQNAALKEG-----VGVGIYSLEM  239 (444)
T ss_dssp             SCHHHHHHHCCC--CTTCEEEEEECTTSCHHHHHHHHHHHHHHTTC-----CCEEEEESSS
T ss_pred             CCHhhhhhcCCc--CCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCC-----CeEEEEECCC
Confidence            345666665212  245568999999999999999999988753 2     1345566654

>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=89.57  E-value=0.25  Score=51.16  Aligned_cols=39  Identities=21%  Similarity=0.353  Sum_probs=30.0

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCC------CCceEEEcccccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGS------HNNFVSIALSSFS  697 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~------~~~~i~id~s~~~  697 (854)
                      ..+.+.|++|+|||++|+.|++.+ |-      ....+.+++..|.
T Consensus        23 ~iI~I~G~~GSGKST~a~~L~~~l-g~~~~d~~~~~~~~i~~D~~~   67 (252)
T 1uj2_A           23 FLIGVSGGTASGKSSVCAKIVQLL-GQNEVDYRQKQVVILSQDSFY   67 (252)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT-TGGGSCGGGCSEEEEEGGGGB
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHh-hhhcccccCCceEEEecCccc
Confidence            478999999999999999999976 31      1234567777665

>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=89.54  E-value=0.34  Score=51.96  Aligned_cols=40  Identities=23%  Similarity=0.189  Sum_probs=29.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHh--CCCCceEEEcccccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVF--GSHNNFVSIALSSFS  697 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lf--g~~~~~i~id~s~~~  697 (854)
                      ..+.+.||+|+|||++++.|+..+-  .....+..+++..+.
T Consensus        81 ~iigI~G~~GsGKSTl~~~L~~~l~~~~~~G~i~vi~~d~~~  122 (308)
T 1sq5_A           81 YIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFL  122 (308)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGGB
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHhhCCCCCeEEEEecCCcc
Confidence            4788999999999999999999874  233344455555443

>2xtp_A GTPase IMAP family member 2; immune system, G protein; HET: MSE; 1.50A {Homo sapiens} PDB: 2xto_A* 2xtm_A* 2xtn_A* 3p1j_A

Probab=89.53  E-value=0.42  Score=49.37  Aligned_cols=24  Identities=8%  Similarity=0.196  Sum_probs=21.0

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~  249 (854)
                      ..-+++|+|.+|||||+++..+..
T Consensus        21 ~~~~I~lvG~~g~GKStl~n~l~~   44 (260)
T 2xtp_A           21 SELRIILVGKTGTGKSAAGNSILR   44 (260)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHT
T ss_pred             CceEEEEECCCCCCHHHHHHHHhC
Confidence            456899999999999999998864

>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=89.52  E-value=0.12  Score=51.48  Aligned_cols=23  Identities=22%  Similarity=0.434  Sum_probs=21.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+.|.|++|+|||++++.|++.+
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l   24 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAF   24 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH
Confidence            47899999999999999999987

>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=89.52  E-value=0.22  Score=48.46  Aligned_cols=37  Identities=16%  Similarity=0.169  Sum_probs=28.4

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcc
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLS  269 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~  269 (854)
                      +...++|+|++|+|||++++.|+..+..       .|..++.++
T Consensus         4 ~g~~i~l~G~~GsGKST~~~~L~~~l~~-------~g~~~i~~d   40 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVSMALEEYLVC-------HGIPCYTLD   40 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHH-------TTCCEEEEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhh-------CCCcEEEEC
Confidence            3457899999999999999999987643       244566555

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=89.43  E-value=0.18  Score=49.84  Aligned_cols=26  Identities=12%  Similarity=0.101  Sum_probs=22.5

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ....++|+|++|+|||++++.|+..+
T Consensus         5 ~g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            5 KGLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            34578999999999999999998765

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=89.37  E-value=0.16  Score=48.26  Aligned_cols=23  Identities=9%  Similarity=0.013  Sum_probs=19.7

Q ss_pred             cCCceeecCCCCCHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~  249 (854)
                      .-+++|+|++|||||+++..+..
T Consensus         4 ~~ki~i~G~~~vGKSsl~~~l~~   26 (175)
T 2nzj_A            4 LYRVVLLGDPGVGKTSLASLFAG   26 (175)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEEEECCCCccHHHHHHHHhc
Confidence            45789999999999999987763

>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=89.34  E-value=0.3  Score=54.74  Aligned_cols=26  Identities=15%  Similarity=0.015  Sum_probs=22.1

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ...-++|+|+||+|||++++.|+++.
T Consensus       257 ~~~lIil~G~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          257 NPEVVVAVGFPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             SCCEEEEESCTTSSHHHHHHHHTGGG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhc
Confidence            45567899999999999999998753

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=89.32  E-value=0.24  Score=48.13  Aligned_cols=27  Identities=19%  Similarity=0.210  Sum_probs=22.7

Q ss_pred             eeEEEecCCCchHHHHHH------------HHHHHHhCC
Q 003038          658 TWLFFQGVDADAKEKIAK------------ELARLVFGS  684 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr------------~LA~~lfg~  684 (854)
                      ..+.++||+|+|||++++            .+...+|..
T Consensus        10 ei~~l~G~nGsGKSTl~~~~~~~~~~~~~d~~~g~~~~~   48 (171)
T 4gp7_A           10 SLVVLIGSSGSGKSTFAKKHFKPTEVISSDFCRGLMSDD   48 (171)
T ss_dssp             EEEEEECCTTSCHHHHHHHHSCGGGEEEHHHHHHHHCSS
T ss_pred             EEEEEECCCCCCHHHHHHHHccCCeEEccHHHHHHhcCc
Confidence            488999999999999999            666666654

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=89.23  E-value=1.1  Score=52.05  Aligned_cols=52  Identities=10%  Similarity=0.012  Sum_probs=33.4

Q ss_pred             CCCCCCCCC--cHHHHHHHHHHhh--c-cCcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          202 KPRVSLDPI--RNEDVMYVIENLM--S-KRKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       202 ~~~g~ldpv--r~~ei~~v~~~L~--r-~~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      .++|..-|-  .-.||-+++.-..  + +....++|+|.+|+|||++++.|+.++..
T Consensus       342 L~~g~~~p~~~~r~eV~~~lr~~~~~~~~~~~~I~l~G~~GsGKSTia~~La~~L~~  398 (546)
T 2gks_A          342 LKQGRKLPEWFTRPEVAEILAETYVPKHKQGFCVWLTGLPCAGKSTIAEILATMLQA  398 (546)
T ss_dssp             HTTTCCCCTTTSCHHHHHHHHHHSCCGGGCCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             hcCCCCCCccccchhHHHHHHHhhccccccceEEEccCCCCCCHHHHHHHHHHHhhh
Confidence            335655543  2234444444433  1 12346789999999999999999998753

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=89.16  E-value=0.2  Score=47.85  Aligned_cols=25  Identities=8%  Similarity=0.151  Sum_probs=21.4

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHH
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~  249 (854)
                      ++..+++|+|++|||||+++..+..
T Consensus         6 ~~~~~i~v~G~~~~GKssl~~~l~~   30 (178)
T 2lkc_A            6 ERPPVVTIMGHVDHGKTTLLDAIRH   30 (178)
T ss_dssp             CCCCEEEEESCTTTTHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhC
Confidence            3567899999999999999988763

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=89.15  E-value=3.4  Score=41.96  Aligned_cols=27  Identities=15%  Similarity=-0.027  Sum_probs=20.0

Q ss_pred             cCCceeecCCCCCHHHHHH-HHHHHHHc
Q 003038          227 KRNFVVVGECLASIEGVVR-GVIDKIEK  253 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~-~la~~i~~  253 (854)
                      .+|+++++|+|+|||.+.- .+..++..
T Consensus        66 g~~~l~~apTGsGKT~~~~l~~l~~l~~   93 (242)
T 3fe2_A           66 GLDMVGVAQTGSGKTLSYLLPAIVHINH   93 (242)
T ss_dssp             TCCEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CCCEEEECCCcCHHHHHHHHHHHHHHHh
Confidence            4799999999999997643 34455543

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=89.11  E-value=0.68  Score=53.26  Aligned_cols=27  Identities=7%  Similarity=-0.005  Sum_probs=23.4

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      .++++++|.||||||+++..||..+.+
T Consensus       101 ~~vI~ivG~~GvGKTTl~~kLA~~l~~  127 (504)
T 2j37_W          101 QNVIMFVGLQGSGKTTTCSKLAYYYQR  127 (504)
T ss_dssp             -EEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            457899999999999999999988765

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=89.08  E-value=0.32  Score=48.15  Aligned_cols=25  Identities=8%  Similarity=-0.001  Sum_probs=20.9

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      .+|+++++|+|+|||.++-.++...
T Consensus        48 ~~~~li~~~tGsGKT~~~~~~~~~~   72 (216)
T 3b6e_A           48 GKNIIICLPTGSGKTRVAVYIAKDH   72 (216)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCCHHHHHHHHHHHH
Confidence            4789999999999999887766543

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=89.05  E-value=1.9  Score=46.48  Aligned_cols=31  Identities=10%  Similarity=0.134  Sum_probs=22.5

Q ss_pred             HHHHhhccCcCCceeecCCCCCHHHHHHHHH
Q 003038          218 VIENLMSKRKRNFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       218 v~~~L~r~~k~n~vLvGe~GvGKta~v~~la  248 (854)
                      ++..+....++|+++++|+|+|||.++-..+
T Consensus        35 ~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~   65 (395)
T 3pey_A           35 ALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM   65 (395)
T ss_dssp             HHHHHHCSSCCCEEEECCTTSCHHHHHHHHH
T ss_pred             HHHHHHcCCCCeEEEECCCCCcHHHHHHHHH
Confidence            4444444566899999999999997665433

>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=89.00  E-value=0.2  Score=49.91  Aligned_cols=25  Identities=4%  Similarity=0.110  Sum_probs=21.7

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      ...+++|+|++|||||+++..+...
T Consensus        11 ~~~~i~~~G~~g~GKTsl~~~l~~~   35 (218)
T 1nrj_B           11 YQPSIIIAGPQNSGKTSLLTLLTTD   35 (218)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4567999999999999999988764

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=88.96  E-value=0.15  Score=50.40  Aligned_cols=34  Identities=18%  Similarity=0.108  Sum_probs=24.3

Q ss_pred             HHHHHHHhh-ccCcCCceeecCCCCCHHHHHHHHH
Q 003038          215 VMYVIENLM-SKRKRNFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       215 i~~v~~~L~-r~~k~n~vLvGe~GvGKta~v~~la  248 (854)
                      +..+++-+. ..+.-+++|+|++|||||+++..+.
T Consensus        12 ~~~~l~~~~~~~~~~ki~lvG~~~vGKSsLi~~l~   46 (198)
T 1f6b_A           12 FSSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLK   46 (198)
T ss_dssp             -CHHHHHHTCTTCCEEEEEEEETTSSHHHHHHHHS
T ss_pred             HHHHHHHhhccCCCcEEEEECCCCCCHHHHHHHHh
Confidence            344555542 2345579999999999999998775

>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=88.89  E-value=0.8  Score=45.47  Aligned_cols=28  Identities=11%  Similarity=0.090  Sum_probs=23.5

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhC
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFG  683 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg  683 (854)
                      ....++|+|++|+|||++...|....|.
T Consensus        11 ~~~~i~~~G~~g~GKTsl~~~l~~~~~~   38 (218)
T 1nrj_B           11 YQPSIIIAGPQNSGKTSLLTLLTTDSVR   38 (218)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHSSCC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            3458999999999999999999876553

>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=88.89  E-value=0.22  Score=49.88  Aligned_cols=24  Identities=17%  Similarity=0.247  Sum_probs=22.1

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      -.+.+.||+|+|||++++.|+.++
T Consensus        21 ei~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           21 RVVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            378899999999999999999987

>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=88.87  E-value=0.17  Score=48.27  Aligned_cols=22  Identities=5%  Similarity=0.143  Sum_probs=19.5

Q ss_pred             CCceeecCCCCCHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~  249 (854)
                      ..++|+|++|||||+++..++.
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            4689999999999999998864

>3iby_A Ferrous iron transport protein B; G protein, G domain, iron uptake, cell inner membrane, cell GTP-binding, ION transport, membrane; 2.50A {Legionella pneumophila}

Probab=88.84  E-value=0.29  Score=51.11  Aligned_cols=23  Identities=4%  Similarity=0.148  Sum_probs=20.3

Q ss_pred             CCceeecCCCCCHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      ++++|+|.||||||+++..|...
T Consensus         2 ~kI~lvG~~n~GKSTL~n~L~g~   24 (256)
T 3iby_A            2 THALLIGNPNCGKTTLFNALTNA   24 (256)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
Confidence            46899999999999999998754

>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=88.83  E-value=0.48  Score=53.43  Aligned_cols=27  Identities=11%  Similarity=-0.073  Sum_probs=23.9

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      .+.++++|++|||||+++..||..+..
T Consensus        97 ~~vI~lvG~~GsGKTTt~~kLA~~l~~  123 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAGKLAYFYKK  123 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            456889999999999999999988765

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=88.80  E-value=0.2  Score=46.91  Aligned_cols=24  Identities=13%  Similarity=0.131  Sum_probs=20.3

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      +-+++++|++|||||+++..+...
T Consensus         3 ~~~i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            3 EYKVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEEECCCCCCHHHHHHHHHcC
Confidence            347899999999999999887653

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=88.78  E-value=0.39  Score=49.36  Aligned_cols=38  Identities=8%  Similarity=0.002  Sum_probs=30.3

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      ...++|.|++|||||++|-.+|..+-......+-+++.
T Consensus         6 ~l~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v~d~D   43 (228)
T 2r8r_A            6 RLKVFLGAAPGVGKTYAMLQAAHAQLRQGVRVMAGVVE   43 (228)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHCCCCEEEEEeC
Confidence            45789999999999999999998876555566666654

>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=88.72  E-value=0.43  Score=53.49  Aligned_cols=32  Identities=13%  Similarity=0.144  Sum_probs=25.7

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      ..+++.|++|+|||++|+.|++.+     .+..++..
T Consensus       259 ~lIil~G~pGSGKSTla~~L~~~~-----~~~~i~~D  290 (416)
T 3zvl_A          259 EVVVAVGFPGAGKSTFIQEHLVSA-----GYVHVNRD  290 (416)
T ss_dssp             CEEEEESCTTSSHHHHHHHHTGGG-----TCEECCGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhc-----CcEEEccc
Confidence            478999999999999999999865     34555544

>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=88.72  E-value=0.2  Score=53.88  Aligned_cols=31  Identities=16%  Similarity=0.241  Sum_probs=26.4

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCC
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDV  256 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~v  256 (854)
                      +.+..+.|+||+|+|||++++.|+.-+ .|.|
T Consensus       124 ~~Ge~vaIvGpsGsGKSTLl~lL~gl~-~G~I  154 (305)
T 2v9p_A          124 PKKNCLAFIGPPNTGKSMLCNSLIHFL-GGSV  154 (305)
T ss_dssp             TTCSEEEEECSSSSSHHHHHHHHHHHH-TCEE
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhhhc-CceE
Confidence            466778999999999999999999877 6653

>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=88.69  E-value=0.25  Score=48.69  Aligned_cols=23  Identities=17%  Similarity=0.098  Sum_probs=21.3

Q ss_pred             eeEEEecCCCchHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARL  680 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~  680 (854)
                      ..+.+.|++|+|||++|+.||+.
T Consensus         9 ~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            9 IIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHC
Confidence            47899999999999999999995

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=88.63  E-value=0.26  Score=47.92  Aligned_cols=28  Identities=14%  Similarity=0.229  Sum_probs=24.8

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCC
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSH  685 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~  685 (854)
                      +..+|+||+|+|||++.++|.-.+++..
T Consensus        27 g~~~i~G~NGsGKStll~ai~~~l~~~~   54 (182)
T 3kta_A           27 GFTAIVGANGSGKSNIGDAILFVLGGLS   54 (182)
T ss_dssp             SEEEEEECTTSSHHHHHHHHHHHTTCCC
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHcCCc
Confidence            4789999999999999999999987643

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=88.60  E-value=0.21  Score=50.63  Aligned_cols=24  Identities=21%  Similarity=0.120  Sum_probs=21.8

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ..+.|+||+|+|||+|++.|+..+
T Consensus        24 ~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           24 YPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            368899999999999999999976

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=88.58  E-value=0.18  Score=48.77  Aligned_cols=23  Identities=4%  Similarity=0.138  Sum_probs=20.4

Q ss_pred             cCCceeecCCCCCHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~  249 (854)
                      +-+++|+|++|||||+++..++.
T Consensus         7 ~~~i~lvG~~gvGKStL~~~l~~   29 (188)
T 2wjg_A            7 SYEIALIGNPNVGKSTIFNALTG   29 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45799999999999999998874

>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=88.55  E-value=0.21  Score=47.01  Aligned_cols=24  Identities=17%  Similarity=0.217  Sum_probs=20.7

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      .-+++++|++|||||+++..+...
T Consensus         5 ~~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            5 AIKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            457899999999999999988753

>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=88.54  E-value=0.24  Score=49.52  Aligned_cols=34  Identities=12%  Similarity=0.101  Sum_probs=27.9

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      ..+.+.|++|+|||++|+.|++.+ |    +..+|+..+
T Consensus        13 ~iIgltG~~GSGKSTva~~L~~~l-g----~~vid~D~~   46 (192)
T 2grj_A           13 MVIGVTGKIGTGKSTVCEILKNKY-G----AHVVNVDRI   46 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHH-C----CEEEEHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc-C----CEEEECcHH
Confidence            478899999999999999999975 3    455666655

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=88.52  E-value=0.36  Score=48.97  Aligned_cols=37  Identities=11%  Similarity=0.097  Sum_probs=27.7

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      ..+++.||+|+|||+++..++..+.......+.++..
T Consensus        24 ~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~~e   60 (247)
T 2dr3_A           24 NVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVALE   60 (247)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEcc
Confidence            3789999999999999998887664444455555543

>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=88.52  E-value=0.17  Score=49.26  Aligned_cols=21  Identities=10%  Similarity=0.328  Sum_probs=18.6

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .++|+|++|||||+++..++.
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            589999999999999987764

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=88.38  E-value=3.3  Score=41.21  Aligned_cols=25  Identities=8%  Similarity=0.177  Sum_probs=18.9

Q ss_pred             cCCceeecCCCCCHHHH-HHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGV-VRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~-v~~la~~i  251 (854)
                      .+|+++++|+|+|||.+ +-.+..++
T Consensus        51 ~~~~lv~~pTGsGKT~~~~~~~l~~l   76 (224)
T 1qde_A           51 GHDVLAQAQSGTGKTGTFSIAALQRI   76 (224)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHHHH
Confidence            47899999999999976 33444444

>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=88.37  E-value=0.22  Score=49.57  Aligned_cols=21  Identities=19%  Similarity=0.124  Sum_probs=19.8

Q ss_pred             eEEEecCCCchHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELAR  679 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~  679 (854)
                      .+.+.||+|+|||++++.||.
T Consensus         4 ~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            578999999999999999998

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=88.36  E-value=0.22  Score=48.84  Aligned_cols=29  Identities=10%  Similarity=0.203  Sum_probs=21.9

Q ss_pred             hhccCcCCceeecCCCCCHHHHHHHHHHH
Q 003038          222 LMSKRKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       222 L~r~~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      +.+...-+++|+|++|||||+++..+...
T Consensus        23 ~~~~~~~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           23 MAKSAEVKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             ----CCEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             cCCCCceEEEEECCCCCCHHHHHHHHHhC
Confidence            34445678999999999999999988753

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=88.35  E-value=0.95  Score=51.41  Aligned_cols=96  Identities=11%  Similarity=0.036  Sum_probs=52.3

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCC-ch--HHH--------HHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSC-SY--IER--------FAE  726 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~--~e~--------L~e  726 (854)
                      ..++|+|.+|+|||++++.||+.++-.......++...+.....   .......+....+. ++  .+.        +..
T Consensus        40 ~~IvlvGlpGsGKSTia~~La~~l~~~~~~t~~~~~d~~r~~~~---g~~~~~~ifd~~g~~~~r~re~~~~~~l~~~~~  116 (469)
T 1bif_A           40 TLIVMVGLPARGKTYISKKLTRYLNFIGVPTREFNVGQYRRDMV---KTYKSFEFFLPDNEEGLKIRKQCALAALNDVRK  116 (469)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEHHHHHHHHH---CSCCCGGGGCTTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHhccCCCceEEecchhhhhhc---cCCCcccccCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            47899999999999999999998864433444444333220000   00000011122221 11  111        133


Q ss_pred             HHHcCCCEEEEEecCCCCCHHHHHHHHHhhh
Q 003038          727 AVSNNPHRVFLIEDVEQADYCSQKGFKRAIE  757 (854)
Q Consensus       727 av~~~p~~ViliDEieka~~~v~~~Ll~~le  757 (854)
                      .+......++++|.... ...-...+++.+.
T Consensus       117 ~l~~~~G~~vV~D~tn~-~~~~R~~~~~~~~  146 (469)
T 1bif_A          117 FLSEEGGHVAVFDATNT-TRERRAMIFNFGE  146 (469)
T ss_dssp             HHHTTCCSEEEEESCCC-SHHHHHHHHHHHH
T ss_pred             HHHhCCCCEEEEeCCCC-CHHHHHHHHHHHH
Confidence            34445566899998876 5555566666554

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=88.34  E-value=0.22  Score=46.67  Aligned_cols=24  Identities=8%  Similarity=0.084  Sum_probs=20.7

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      .-+++++|++|||||+++..+...
T Consensus         4 ~~~i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            4 LHKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhC
Confidence            457999999999999999988753

---

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	854
d1qvra3	315	c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus	3e-18
d1khya_	139	a.174.1.1 (A:) N-terminal domain of ClpB (heat sho	7e-12
d1qvra2	387	c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus	3e-07
d1r6bx3	315	c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, A	4e-06
d1qvra1	145	a.174.1.1 (A:4-148) N-terminal domain of ClpB (hea	3e-04
d1k6ka_	142	a.174.1.1 (A:) N-terminal, ClpS-binding domain of	0.001
d1r6bx2	268	c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, A	0.004

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]} Length = 315

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]

 Score = 84.4 bits (208), Expect = 3e-18
 Identities = 40/186 (21%), Positives = 72/186 (38%), Gaps = 16/186 (8%)

Query: 598 VHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEE 657
           V K  E   E L  L   L K+V  Q + +  +A+ + + R+G              +  
Sbjct: 3   VSKLLEGEREKLLRLEEELHKRVVGQDEAIRAVADAIRRARAGL---------KDPNRPI 53

Query: 658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADST--EDSRNKRSRDE 715
               F G     K ++AK LA  +F +    + I ++ +    A S            +E
Sbjct: 54  GSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEE 113

Query: 716 QSCSYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAI 775
                  +  EAV   P+ V L +++E+A         + ++ GR+  S G  V   + +
Sbjct: 114 GG-----QLTEAVRRRPYSVILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTV 168

Query: 776 VILSCE 781
           +IL+  
Sbjct: 169 IILTSN 174

>d1khya_ a.174.1.1 (A:) N-terminal domain of ClpB (heat shock protein F84.1) {Escherichia coli [TaxId: 562]} Length = 139

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Escherichia coli [TaxId: 562]

 Score = 61.7 bits (149), Expect = 7e-12
 Identities = 23/155 (14%), Positives = 51/155 (32%), Gaps = 19/155 (12%)

Query: 12  LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALEL 71
           LT +    +  A +LA    +  + PLH+ + +L    G +      +  +  Q +    
Sbjct: 3   LTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDIN 62

Query: 72  CFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIE 131
                          P + G       S  LV          ++              I 
Sbjct: 63  QAL---------NRLPQVEGTGGDVQPSQDLVRVLNLCDKLAQKRGDN---------FIS 104

Query: 132 LEQLIISILDDPS-VSRVMREAGFSSTQVKSNVEQ 165
            E  +++ L+    ++ +++ AG ++  +   +EQ
Sbjct: 105 SELFVLAALESRGTLADILKAAGATTANITQAIEQ 139

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]} Length = 387

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]

 Score = 51.2 bits (122), Expect = 3e-07
 Identities = 35/110 (31%), Positives = 58/110 (52%), Gaps = 15/110 (13%)

Query: 207 LDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGV-----VRGVIDKIEKGDVPEA 259
           LDP+  R+E++  VI+ L+ + K N V++GE      GV     V G+  +I KGDVPE 
Sbjct: 21  LDPVIGRDEEIRRVIQILLRRTKNNPVLIGE-----PGVGKTAIVEGLAQRIVKGDVPEG 75

Query: 260 LRDVKCLPLSISSF--RHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDL 307
           L+  + + L + S       R E E+R++ +   V    G  ++L + +L
Sbjct: 76  LKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGE-VILFIDEL 124

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]} Length = 315

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]

 Score = 47.1 bits (111), Expect = 4e-06
 Identities = 28/209 (13%), Positives = 71/209 (33%), Gaps = 18/209 (8%)

Query: 598 VHKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEE 657
                + + + L +L + L+  V  Q   +  +   +   R+G              K  
Sbjct: 2   EKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMARAGLGHEH---------KPV 52

Query: 658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQS 717
               F G     K ++  +L++ +       +   +S +     +    SR   +     
Sbjct: 53  GSFLFAGPTGVGKTEVTVQLSKALG---IELLRFDMSEYM----ERHTVSRLIGAPPGYV 105

Query: 718 CSYIERF-AEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIV 776
                    +AV  +PH V L++++E+A         + +++G +  ++G +    + ++
Sbjct: 106 GFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNVVL 165

Query: 777 ILSC-ESFSSRSRACSPPTKQKSDGCEEE 804
           +++         R       Q +     E
Sbjct: 166 VMTTNAGVRETERKSIGLIHQDNSTDAME 194

>d1qvra1 a.174.1.1 (A:4-148) N-terminal domain of ClpB (heat shock protein F84.1) {Thermus thermophilus [TaxId: 274]} Length = 145

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Thermus thermophilus [TaxId: 274]

 Score = 39.7 bits (92), Expect = 3e-04
 Identities = 16/83 (19%), Positives = 28/83 (33%)

Query: 12 LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALEL 71
           T  A   + QA  LA+R  H  +   H+   +L     L      ++ + P   K L+ 
Sbjct: 3  WTQAAREALAQAQVLAQRMKHQAIDLPHLWAVLLKDERSLAWRLLEKAGADPKALKELQE 62

Query: 72 CFNVALNRLPASTSTPMLGGHCQ 94
               L ++  +     L     
Sbjct: 63 RELARLPKVEGAEVGQYLTSRLS 85

>d1k6ka_ a.174.1.1 (A:) N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone {Escherichia coli [TaxId: 562]} Length = 142

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone
species: Escherichia coli [TaxId: 562]

 Score = 37.5 bits (86), Expect = 0.001
 Identities = 18/152 (11%), Positives = 45/152 (29%), Gaps = 19/152 (12%)

Query: 12  LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALEL 71
           L  E    +  A   AR   H  +T  H+   +L+  +              L+ +    
Sbjct: 2   LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAF 61

Query: 72  CFNVALNRLPASTSTPMLGGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIE 131
                   +  +T         +    + +     +RA  H +              ++ 
Sbjct: 62  --------IEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRN---------EVT 104

Query: 132 LEQLIISILDDPS--VSRVMREAGFSSTQVKS 161
              ++++I  +     + ++R+   S   V +
Sbjct: 105 GANVLVAIFSEQESQAAYLLRKHEVSRLDVVN 136

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]} Length = 268

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]

 Score = 37.7 bits (87), Expect = 0.004
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 2/69 (2%)

Query: 207 LDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVK 264
           +DP+  R +++   I+ L  +RK N ++VGE       +  G+  +I +GDVPE + D  
Sbjct: 17  IDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCT 76

Query: 265 CLPLSISSF 273
              L I S 
Sbjct: 77  IYSLDIGSL 85

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	854
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	100.0
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	100.0
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	100.0
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	100.0
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	100.0
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.89
d1khya_	139	N-terminal domain of ClpB (heat shock protein F84.	99.8
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.78
d1qvra1	145	N-terminal domain of ClpB (heat shock protein F84.	99.7
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.64
d1k6ka_	142	N-terminal, ClpS-binding domain of ClpA, an Hsp100	99.63
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.48
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	99.47
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.32
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.29
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.28
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	99.23
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.21
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.21
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.19
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.18
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.12
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.07
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.06
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.05
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.98
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	98.97
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	98.93
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.92
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.92
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	98.91
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.84
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.81
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.72
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	98.71
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	98.71
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.7
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	98.61
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.55
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.54
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.46
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.43
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	98.41
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.27
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.2
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.06
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.05
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.93
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.92
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	97.89
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	97.88
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.86
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.85
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	97.82
d1khya_	139	N-terminal domain of ClpB (heat shock protein F84.	97.82
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	97.78
d1k6ka_	142	N-terminal, ClpS-binding domain of ClpA, an Hsp100	97.77
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.77
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.74
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.74
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	97.66
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	97.58
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.55
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.48
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	97.4
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	97.21
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.21
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	97.21
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	97.11
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.09
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.01
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.92
d1qvra1	145	N-terminal domain of ClpB (heat shock protein F84.	96.68
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.65
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	96.51
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.43
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	96.36
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.35
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.35
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	96.33
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.3
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.28
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	96.24
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	96.24
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	96.21
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	96.18
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.08
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	96.02
d1tuea_	205	Replication protein E1 helicase domain {Human papi	96.02
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	95.98
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	95.91
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	95.83
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	95.81
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	95.78
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	95.77
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	95.75
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	95.75
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	95.73
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	95.72
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	95.69
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	95.69
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	95.65
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	95.45
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	95.43
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	95.42
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	95.42
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	95.41
d2qy9a2	211	GTPase domain of the signal recognition particle r	95.4
d1okkd2	207	GTPase domain of the signal recognition particle r	95.4
d2qy9a2	211	GTPase domain of the signal recognition particle r	95.3
d1vmaa2	213	GTPase domain of the signal recognition particle r	95.22
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.19
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	95.18
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	95.16
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	95.15
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.05
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.04
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	95.04
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	95.02
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	95.0
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	94.99
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	94.95
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	94.95
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	94.87
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	94.87
d1j8yf2	211	GTPase domain of the signal sequence recognition p	94.86
d1okkd2	207	GTPase domain of the signal recognition particle r	94.84
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	94.8
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	94.78
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	94.76
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	94.72
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	94.7
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	94.68
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	94.64
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.58
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	94.56
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	94.55
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	94.46
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	94.44
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	94.37
d1ls1a2	207	GTPase domain of the signal sequence recognition p	94.37
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	94.36
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	94.32
d1ls1a2	207	GTPase domain of the signal sequence recognition p	94.32
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	94.3
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	94.22
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	94.2
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	94.13
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	94.09
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	94.08
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	94.05
d2fh5b1	207	Signal recognition particle receptor beta-subunit	94.02
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	93.91
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	93.9
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	93.77
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	93.72
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	93.7
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	93.69
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	93.67
d1vmaa2	213	GTPase domain of the signal recognition particle r	93.51
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	93.38
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	93.35
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	93.22
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	93.15
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	93.12
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.08
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	92.84
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	92.83
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	92.78
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	92.54
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	92.51
d1j8yf2	211	GTPase domain of the signal sequence recognition p	92.38
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	92.33
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	92.27
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	92.23
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	92.11
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	92.02
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	91.99
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	91.87
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	91.66
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	91.65
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	91.63
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	91.31
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	91.24
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	91.23
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	90.93
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	90.82
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	90.81
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	90.79
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	90.79
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	90.75
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	90.74
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	90.73
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	90.7
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	90.59
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	90.5
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	90.5
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	90.41
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	90.37
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	90.28
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	90.13
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	90.1
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	90.05
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	89.97
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	89.96
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	89.93
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	89.93
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	89.91
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	89.9
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	89.74
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	89.74
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	89.7
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	89.61
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	89.6
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	89.59
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	89.53
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	89.53
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	89.5
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	89.48
d1tuea_	205	Replication protein E1 helicase domain {Human papi	89.47
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	89.38
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	89.36
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	89.34
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	89.17
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	89.08
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	88.96
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	88.93
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	88.9
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	88.87
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	88.77
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	88.76
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	88.75
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	88.67
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	88.61
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	88.6
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	88.6
d1nrjb_	209	Signal recognition particle receptor beta-subunit	88.56
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	88.55
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	88.33
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	88.3
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	88.25
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	88.2
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	88.09
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	88.05
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	88.02
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	87.96
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	87.96
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	87.9
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	87.88
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	87.85
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	87.79
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	87.78
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	87.77
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	87.73
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	87.62
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	87.3
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	87.25
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	87.2
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	87.13
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	87.02
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	86.92
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	86.91
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	86.83
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	86.69
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	86.56
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	86.46
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	86.35
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	86.26
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	86.2
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	86.17
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	86.06
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	85.94
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	85.64
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	85.58
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	85.55
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	85.42
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	85.37
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	85.21
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	84.98
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	84.96
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	84.86
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	84.73
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	84.34
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	84.32
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	84.23
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	84.09
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	84.07
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	84.07
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	84.02
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	84.01
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	83.85
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	83.69
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	83.62
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	83.49
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	83.46
d1xpua3	289	Transcription termination factor Rho, ATPase domai	83.41
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	83.36
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	82.93
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	82.83
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	82.69
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	82.06
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	81.73
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	81.73
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	81.66
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	81.48
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	81.43
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	81.28
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	81.21
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	81.19
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	81.02
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	80.82
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	80.63
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	80.44
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	80.39
d1g2912	240	Maltose transport protein MalK, N-terminal domain	80.35

>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=100.00  E-value=8.8e-50  Score=444.44  Aligned_cols=217  Identities=22%  Similarity=0.328  Sum_probs=172.2

Q ss_pred             cccccccccccccCCCCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEE
Q 003038          189 LVLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCL  266 (854)
Q Consensus       189 ~~~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~  266 (854)
                      .++++|+.|++..|++|+|||+  ||+||++++++|+|++||||||||||||||||||++||++|.+|+||+.|++.+||
T Consensus         3 ~~l~~~~~~l~~~a~~g~ld~~~gr~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~   82 (387)
T d1qvra2           3 NALEQYGIDLTRLAAEGKLDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIV   82 (387)
T ss_dssp             SHHHHHEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEE
T ss_pred             HHHHHHHHHHHHHHHcCCCCCCcCcHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEE
Confidence            4689999999999999999998  99999999999999999999999999999999999999999999999999999999


Q ss_pred             Eccccccccc--chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCC
Q 003038          267 PLSISSFRHM--NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGE  343 (854)
Q Consensus       267 ~l~~~~l~~~--~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g  343 (854)
                      +||+++|++|  |+|+||+|++.++.++... .+++||||||+|.+ ++|.+.             +.++++++|+|...
T Consensus        83 ~ld~~~l~ag~~~~g~~e~r~~~i~~~~~~~-~~~~ilfide~h~l~~~g~~~-------------g~~d~a~~Lkp~L~  148 (387)
T d1qvra2          83 SLQMGSLLAGAKYRGEFEERLKAVIQEVVQS-QGEVILFIDELHTVVGAGKAE-------------GAVDAGNMLKPALA  148 (387)
T ss_dssp             EECC-----------CHHHHHHHHHHHHHTT-CSSEEEEECCC--------------------------------HHHHH
T ss_pred             EeeHhhhhcccCcchhHHHHHHHHHHHhccC-CCceEEEeccHHHHhcCCCCC-------------CcccHHHHHHHHHh
Confidence            9999999997  8999999999999999876 56899999999999 988642             56899999999434


Q ss_pred             CceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHHHhh----------------cccch------hhhcccc
Q 003038          344 NARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLI----------------TTDSD------LQSQSTS  401 (854)
Q Consensus       344 ~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~al~----------------~~~s~------~~~~~~~  401 (854)
                      +|+|+|||+||++||++ +++||+|+|  +||.|.|.+|+...+++                +++.+      ++.||++
T Consensus       149 rg~~~~I~~tT~~ey~~-~e~d~al~r--rF~~v~v~ep~~~~~~~il~~~~~~~e~~h~v~~~~~ai~~~v~ls~ryi~  225 (387)
T d1qvra2         149 RGELRLIGATTLDEYRE-IEKDPALER--RFQPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYIT  225 (387)
T ss_dssp             TTCCCEEEEECHHHHHH-HTTCTTTCS--CCCCEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHCC
T ss_pred             CCCcceeeecCHHHHHH-hcccHHHHH--hcccccCCCCcHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHhcccccc
Confidence            44799999999999987 699999999  99999999998766543                33333      3459999


Q ss_pred             CCcCCCcccccccchhhhhhh
Q 003038          402 KKAESGVSWLLFEGEEENKQL  422 (854)
Q Consensus       402 ~~~~pdkaidlld~a~~~~~~  422 (854)
                      +|++|||||||||+|++++++
T Consensus       226 ~r~~PdKAidlld~a~a~~~i  246 (387)
T d1qvra2         226 ERRLPDKAIDLIDEAAARLRM  246 (387)
T ss_dssp             SSCTHHHHHHHHHHHHHHHHH
T ss_pred             cccChhhHHHHHHHHHHHHHh
Confidence            999999999999999888654

>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=100.00  E-value=1.2e-46  Score=398.65  Aligned_cols=214  Identities=18%  Similarity=0.248  Sum_probs=189.9

Q ss_pred             cccccccccccCCCCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEc
Q 003038          191 LSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPL  268 (854)
Q Consensus       191 ~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l  268 (854)
                      +++|+.|+++.|++|++||+  ||+||++++++|+|++|+||+|||||||||||+|++||++|.+|+||+.|++.+||++
T Consensus         1 L~~~~~dlt~~a~~~~ld~~igRd~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l   80 (268)
T d1r6bx2           1 LENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSL   80 (268)
T ss_dssp             CCSSSCBHHHHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEEC
T ss_pred             ChHHhHHHHHHHHcCCCCcccChHHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEe
Confidence            46799999999989999998  9999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccc--chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCc
Q 003038          269 SISSFRHM--NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENA  345 (854)
Q Consensus       269 ~~~~l~~~--~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g  345 (854)
                      |+++|++|  |+|+||+|++.+++++...  +++||||||+|.| ++|.+.            .+.++++++|+|...+|
T Consensus        81 ~~~~liag~~~~g~~e~r~~~i~~~~~~~--~~iIlfiDeih~l~~~g~~~------------g~~~d~a~~Lkp~L~rg  146 (268)
T d1r6bx2          81 DIGSLLAGTKYRGDFEKRFKALLKQLEQD--TNSILFIDEIHTIIGAGAAS------------GGQVDAANLIKPLLSSG  146 (268)
T ss_dssp             CCC---CCCCCSSCHHHHHHHHHHHHSSS--SCEEEEETTTTTTTTSCCSS------------SCHHHHHHHHSSCSSSC
T ss_pred             eechHhccCccchhHHHHHHHHHHHhhcc--CCceEEecchHHHhcCCCCC------------CccccHHHHhhHHHhCC
Confidence            99999997  9999999999999999876  6899999999999 887643            14679999999955556


Q ss_pred             eEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHHHhh----------------cccch------hhhccccCC
Q 003038          346 RFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLI----------------TTDSD------LQSQSTSKK  403 (854)
Q Consensus       346 ~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~al~----------------~~~s~------~~~~~~~~~  403 (854)
                      +|+|||+||++||++++++||+|.|  +|+.|.|.+|+.+.+++                +++.+      +..+|++++
T Consensus       147 ~i~vIgatT~eey~~~~e~d~al~r--rF~~I~V~Eps~e~t~~IL~~~~~~~e~~h~v~~~~~al~~~v~ls~ryi~~~  224 (268)
T d1r6bx2         147 KIRVIGSTTYQEFSNIFEKDRALAR--RFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDR  224 (268)
T ss_dssp             CCEEEEEECHHHHHCCCCCTTSSGG--GEEEEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTS
T ss_pred             CCeEEEeCCHHHHHHHHhhcHHHHh--hhcccccCCCCHHHHHHHHHHhhHHHhccCCEEeChHHHHHHHHHHHhhccCC
Confidence            8999999999999999999999999  99999999998665543                22222      345899999


Q ss_pred             cCCCcccccccchhhhh
Q 003038          404 AESGVSWLLFEGEEENK  420 (854)
Q Consensus       404 ~~pdkaidlld~a~~~~  420 (854)
                      ++|||||||||+|++++
T Consensus       225 ~~PdKAIdllDea~a~~  241 (268)
T d1r6bx2         225 HLPDKAIDVIDEAGARA  241 (268)
T ss_dssp             CTTHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHH
Confidence            99999999999997773

>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=100.00  E-value=3.9e-44  Score=360.27  Aligned_cols=184  Identities=21%  Similarity=0.317  Sum_probs=166.3

Q ss_pred             ccccccccccccCCCCCCCCC--cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEE
Q 003038          190 VLSQTASATKVSKPRVSLDPI--RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLP  267 (854)
Q Consensus       190 ~~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~  267 (854)
                      .+++|+.|+++.+++|++||+  ||+||++++++|+|++||||+|||||||||||+|++||++|.+|+||+.|++.+||+
T Consensus         4 ~l~~~~~dlt~~a~~g~ld~~igRd~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~   83 (195)
T d1jbka_           4 ALKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLA   83 (195)
T ss_dssp             HHHHHEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEE
T ss_pred             HHHHHHHHHHHHHHcCCCCCCcCcHHHHHHHHHHHhccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEE
Confidence            478999999999989999998  999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccccc--chHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCC
Q 003038          268 LSISSFRHM--NRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGEN  344 (854)
Q Consensus       268 l~~~~l~~~--~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~  344 (854)
                      +|+++|++|  |+|+||+|++.+++++.+. .+++||||||+|.+ +++.+.             +.++++++|+|...+
T Consensus        84 ld~~~LiAg~~~rG~~E~rl~~il~e~~~~-~~~iILfIDeih~l~~~g~~~-------------g~~d~~~~Lkp~L~r  149 (195)
T d1jbka_          84 LDMGALVAGAKYRGEFEERLKGVLNDLAKQ-EGNVILFIDELHTMVGAGKAD-------------GAMDAGNMLKPALAR  149 (195)
T ss_dssp             ECHHHHHTTTCSHHHHHHHHHHHHHHHHHS-TTTEEEEEETGGGGTT-------------------CCCCHHHHHHHHHT
T ss_pred             eeHHHHhccCCccHHHHHHHHHHHHHHhcC-CCcEEEEcchHHHHhcCCCCC-------------CcccHHHHHHHHHhC
Confidence            999999997  9999999999999999765 46899999999999 887642             346889999983334


Q ss_pred             ceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHHHhh
Q 003038          345 ARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSLSLI  389 (854)
Q Consensus       345 g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~al~  389 (854)
                      |+|+|||+||+++|++++++||+|.|  +||.|.|.+|+.+.+++
T Consensus       150 g~l~~IgatT~eey~~~~e~d~aL~r--rF~~I~V~Ep~~e~t~~  192 (195)
T d1jbka_         150 GELHCVGATTLDEYRQYIEKDAALER--RFQKVFVAEPSVEDTIA  192 (195)
T ss_dssp             TSCCEEEEECHHHHHHHTTTCHHHHT--TEEEEECCCCCHHHHHT
T ss_pred             CCceEEecCCHHHHHHHHHcCHHHHh--cCCEeecCCCCHHHHHH
Confidence            47999999999999999999999999  99999999999888764

>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=100.00  E-value=1.1e-34  Score=315.13  Aligned_cols=168  Identities=24%  Similarity=0.384  Sum_probs=152.1

Q ss_pred             hhhhhhhHHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHH
Q 003038          599 HKFKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELA  678 (854)
Q Consensus       599 ~~~~~~~~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA  678 (854)
                      +++.+.+.++|+.|++.|.++|+||++|++.|+.+|.++++|+.+++         ||.++|||+||+|||||++|+.||
T Consensus         4 ~~~~~~~~~~l~~l~~~L~~~v~GQ~~ai~~v~~~i~~~~~~l~~~~---------kp~~~~lf~Gp~G~GKt~lak~la   74 (315)
T d1qvra3           4 SKLLEGEREKLLRLEEELHKRVVGQDEAIRAVADAIRRARAGLKDPN---------RPIGSFLFLGPTGVGKTELAKTLA   74 (315)
T ss_dssp             HHTTCCHHHHHHSHHHHHHHHSCSCHHHHHHHHHHHHHHGGGCSCSS---------SCSEEEEEBSCSSSSHHHHHHHHH
T ss_pred             hhhhHHHHHHHHHHHHHhcCeEeCHHHHHHHHHHHHHHHhcCCCCCC---------CCceEEEEECCCcchHHHHHHHHH
Confidence            57788899999999999999999999999999999999999998874         889999999999999999999999


Q ss_pred             HHHhCCCCceEEEccccccCcCCCccccccccccC-CCCCC-chHH--HHHHHHHcCCCEEEEEecCCCCCHHHHHHHHH
Q 003038          679 RLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSR-DEQSC-SYIE--RFAEAVSNNPHRVFLIEDVEQADYCSQKGFKR  754 (854)
Q Consensus       679 ~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~-~~~g~-g~~e--~L~eav~~~p~~ViliDEieka~~~v~~~Ll~  754 (854)
                      +.|||.+.+|+++||++|+       +++..++++ .++|| ||.+  .|+++++++|++|||||||||||+++++.|++
T Consensus        75 ~~l~~~~~~~~~~~~~~~~-------~~~~~~~L~g~~~gyvG~~~~~~l~~~~~~~p~~Vvl~DEieK~~~~v~~~ll~  147 (315)
T d1qvra3          75 ATLFDTEEAMIRIDMTEYM-------EKHAVSRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDEIEKAHPDVFNILLQ  147 (315)
T ss_dssp             HHHHSSGGGEEEECTTTCC-------SSGGGGGC--------------CHHHHHHHCSSEEEEESSGGGSCHHHHHHHHH
T ss_pred             HHhcCCCcceEEEeccccc-------cchhhhhhcCCCCCCcCcccCChHHHHHHhCCCcEEEEehHhhcCHHHHHHHHH
Confidence            9999999999999999999       788899998 47888 8876  79999999999999999999999999999999


Q ss_pred             hhhcCeEecCCCceeecCCeEEEEecCC
Q 003038          755 AIESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       755 ~le~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      ++++|+++|.+|+.|+|+|+|||||||.
T Consensus       148 ~l~~g~~~~~~gr~v~~~~~i~i~tsnl  175 (315)
T d1qvra3         148 ILDDGRLTDSHGRTVDFRNTVIILTSNL  175 (315)
T ss_dssp             HHTTTEECCSSSCCEECTTEEEEEECCT
T ss_pred             HhccCceeCCCCcEecCcceEEEEeccc
Confidence            9999999999999999999999999994

>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=100.00  E-value=8e-33  Score=300.66  Aligned_cols=163  Identities=15%  Similarity=0.302  Sum_probs=152.3

Q ss_pred             hhhhhHHHHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHH
Q 003038          601 FKELNSENLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARL  680 (854)
Q Consensus       601 ~~~~~~e~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~  680 (854)
                      +++.|.++|++|++.|.++|+||++|++.|+.+|.+++.|+.+++         +|.++|||+||||||||+||+.||+.
T Consensus         5 ~~~~d~~~l~~l~~~L~~~viGQ~~a~~~v~~~v~~~~~~l~~~~---------~p~~~~lf~Gp~GvGKT~lak~la~~   75 (315)
T d1r6bx3           5 VSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMARAGLGHEH---------KPVGSFLFAGPTGVGKTEVTVQLSKA   75 (315)
T ss_dssp             SSSSHHHHHHHHHHHHTTTSCSCHHHHHHHHHHHHHHHTTCSCTT---------SCSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ccHhHHHHHHHHHHHhCCeecChHHHHHHHHHHHHHHHccCCCCC---------CCceEEEEECCCcchhHHHHHHHHhh
Confidence            445678899999999999999999999999999999999998864         88999999999999999999999999


Q ss_pred             HhCCCCceEEEccccccCcCCCccccccccccCC-CCCC-chHH--HHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhh
Q 003038          681 VFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRD-EQSC-SYIE--RFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAI  756 (854)
Q Consensus       681 lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~-~~g~-g~~e--~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~l  756 (854)
                      ++   .+|+++||++|+       +.|.++++++ ++|| ||.+  .+++.++++|++||+||||||+|++|++.|++++
T Consensus        76 l~---~~~i~~d~s~~~-------~~~~~~~l~g~~~gy~g~~~~~~l~~~~~~~~~~vvl~DeieKa~~~V~~~lLqil  145 (315)
T d1r6bx3          76 LG---IELLRFDMSEYM-------ERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNILLQVM  145 (315)
T ss_dssp             HT---CEEEEEEGGGCS-------SSSCCSSSCCCCSCSHHHHHTTHHHHHHHHCSSEEEEEETGGGSCHHHHHHHHHHH
T ss_pred             cc---CCeeEecccccc-------chhhhhhhcccCCCccccccCChhhHHHHhCccchhhhcccccccchHhhhhHHhh
Confidence            85   579999999999       7888889884 7788 8876  7999999999999999999999999999999999


Q ss_pred             hcCeEecCCCceeecCCeEEEEecCC
Q 003038          757 ESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       757 e~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      ++|+++|+.|+.++|+|+|||||||.
T Consensus       146 d~G~ltd~~Gr~vdf~n~iiI~Tsni  171 (315)
T d1r6bx3         146 DNGTLTDNNGRKADFRNVVLVMTTNA  171 (315)
T ss_dssp             HHSEEEETTTEEEECTTEEEEEEECS
T ss_pred             ccceecCCCCCccCccceEEEeccch
Confidence            99999999999999999999999985

>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=99.89  E-value=5.1e-24  Score=234.75  Aligned_cols=145  Identities=14%  Similarity=0.164  Sum_probs=102.4

Q ss_pred             HHHHHhhcCcccccHHHHHHHHHHHHHh------h---------------cCCCcccCCCcCCcccCcceeEEEecCCCc
Q 003038          610 TSLCNALEKKVPWQKDTVYDIANTVLKC------R---------------SGTMRRKGKFKDHSEVKEETWLFFQGVDAD  668 (854)
Q Consensus       610 ~~L~~~L~~~V~GQ~~av~~Ia~~v~~~------r---------------sgl~~~~~~~~~~~~~kp~~~lLf~Gp~Gv  668 (854)
                      +.|++.|.++|+||++|++.|+.||++.      +               .|+.++         .+|.++|||+|||||
T Consensus         9 ~ei~~~L~~~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~---------~~p~~niLfiGPTGv   79 (364)
T d1um8a_           9 KELKAVLDNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEV---------ELSKSNILLIGPTGS   79 (364)
T ss_dssp             HHHHHHHHTTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHT---------TCCCCCEEEECCTTS
T ss_pred             HHHHHHhCCeecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccc---------cCCCcceeeeCCCCc
Confidence            5789999999999999999999999532      1               112222         368889999999999


Q ss_pred             hHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCC-chHH--HHHHH-------HHcCCCEEEEE
Q 003038          669 AKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSC-SYIE--RFAEA-------VSNNPHRVFLI  738 (854)
Q Consensus       669 GKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~-g~~e--~L~ea-------v~~~p~~Vili  738 (854)
                      |||+|||+||+.+   +.+|+++||++|+       +          .|| ||+.  .+.+.       +++.|++||+|
T Consensus        80 GKTElAk~LA~~~---~~~~ir~D~s~~~-------e----------~gyvg~dv~~~i~~l~~~~~~~v~~~~~~iv~l  139 (364)
T d1um8a_          80 GKTLMAQTLAKHL---DIPIAISDATSLT-------E----------AGYVGEDVENILTRLLQASDWNVQKAQKGIVFI  139 (364)
T ss_dssp             SHHHHHHHHHHHT---TCCEEEEEGGGCC-------------------------CTHHHHHHHHHTTTCHHHHTTSEEEE
T ss_pred             cHHHHHHHHHhhc---ccceeehhhhhcc-------c----------chhhHhhhccchhhhhhhchhHHHHhhcccchh
Confidence            9999999999987   5689999999999       2          233 4432  34443       67789999999


Q ss_pred             ecCCC--------------CCHHHHHHHHHhhhc--CeEecCCCceeecCCeEEEEecCCC
Q 003038          739 EDVEQ--------------ADYCSQKGFKRAIES--GRIVTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       739 DEiek--------------a~~~v~~~Ll~~le~--G~l~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                      |||||              +|++||+.||+.||.  ++++++.|+.++|+|+|+|+|+|.+
T Consensus       140 DEieK~~~~s~~~~~~~d~a~~~V~~~lLqild~~~~~~~~~~gr~~~~~~~i~i~t~~i~  200 (364)
T d1um8a_         140 DEIDKISRLSENRSITRDVSGEGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDIL  200 (364)
T ss_dssp             ETGGGC--------------CHHHHHHHHHHHHCCEEC---------------CEECTTCE
T ss_pred             hhhhhhccccccccccccccchHHHHhhhhhhcCceeccCCCCCCcCCcceeEEEeehhhh
Confidence            99999              999999999999996  5577899999999999999999964

>d1khya_ a.174.1.1 (A:) N-terminal domain of ClpB (heat shock protein F84.1) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Escherichia coli [TaxId: 562]

Probab=99.80  E-value=3.3e-19  Score=169.35  Aligned_cols=137  Identities=22%  Similarity=0.289  Sum_probs=115.3

Q ss_pred             HhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCCCCCCCC
Q 003038           10 QGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTSTPML   89 (854)
Q Consensus        10 ~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~~~~~~~   89 (854)
                      ++||++++++|..|+++|++++|++|+|+|||++||.++++.+..+|..+|+++   +.++..+...+...|...+.+  
T Consensus         1 ~kfT~~~~~~l~~A~~~A~~~~h~~v~~eHlL~all~~~~~~~~~iL~~~g~d~---~~~~~~~~~~l~~~p~~~~~~--   75 (139)
T d1khya_           1 DRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINA---GQLRTDINQALNRLPQVEGTG--   75 (139)
T ss_dssp             CCBCHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHTCTTCSHHHHHHHHTCCH---HHHHHHHHHHHTTSCCC------
T ss_pred             CccCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCcccHHHHHHHHcCCcH---HHHHHHHHHHhhccccccCcc--
Confidence            489999999999999999999999999999999999999999999999999986   789999999999888765321  


Q ss_pred             CCCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC-hHHHHHHHhCCCHHHHHHHHH
Q 003038           90 GGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP-SVSRVMREAGFSSTQVKSNVE  164 (854)
Q Consensus        90 ~~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~-~~~~iL~~~Gi~~~~l~~~v~  164 (854)
                      ...+++|.+.++|..|.+.|..++    ++         +|+++|||+||++++ .++++|+++|++++.+++.++
T Consensus        76 ~~~~~s~~~~~vl~~A~~~a~~~~----d~---------~I~~ehlLlall~~~~~~~~~L~~~gi~~~~l~~~i~  138 (139)
T d1khya_          76 GDVQPSQDLVRVLNLCDKLAQKRG----DN---------FISSELFVLAALESRGTLADILKAAGATTANITQAIE  138 (139)
T ss_dssp             ---CBCHHHHHHHHHHHHHHHHHT----CS---------SBCHHHHHHHHHTSCHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             ccccccHHHHHHHHHHHHHHHHcC----CC---------eecHHHHHHHHHcCCcHHHHHHHHcCCCHHHHHHHhc
Confidence            234567777777777777777653    23         599999999999876 588999999999999998875

>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=99.78  E-value=1.2e-20  Score=203.66  Aligned_cols=151  Identities=17%  Similarity=0.189  Sum_probs=107.0

Q ss_pred             HHHHHhhcCcccccHHHHHHHHHHHHH--hhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc
Q 003038          610 TSLCNALEKKVPWQKDTVYDIANTVLK--CRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN  687 (854)
Q Consensus       610 ~~L~~~L~~~V~GQ~~av~~Ia~~v~~--~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~  687 (854)
                      +.+++.|.++|+||++|++.|+.+|.+  .|.++..+.+      +.+|.+.+||+||||||||+|||+||+.++   .+
T Consensus         6 ~~i~~~L~~~ViGQd~A~~~l~~av~~~~~r~~~~~~~~------~~~~~~~iLl~GPpG~GKT~lAkalA~~~~---~~   76 (309)
T d1ofha_           6 REIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLR------HEVTPKNILMIGPTGVGKTEIARRLAKLAN---AP   76 (309)
T ss_dssp             HHHHHHHHTTCCSCHHHHHHHHHHHHHHHHTTSSCHHHH------HHCCCCCEEEECCTTSSHHHHHHHHHHHHT---CC
T ss_pred             HHHHHHhcCcccChHHHHHHHHHHHHHHHHHhccCCCCc------cCCCCceEEEECCCCCCHHHHHHHHhhccc---cc
Confidence            588899999999999999999999965  4677765531      124668899999999999999999999984   58


Q ss_pred             eEEEccccccCcCCCccccccccccCC-CCCC-chHH-HHHHHHHcCCCEEEEEecCCCCCHH------------HHHHH
Q 003038          688 FVSIALSSFSSTRADSTEDSRNKRSRD-EQSC-SYIE-RFAEAVSNNPHRVFLIEDVEQADYC------------SQKGF  752 (854)
Q Consensus       688 ~i~id~s~~~~~~~~s~e~~~~~rl~~-~~g~-g~~e-~L~eav~~~p~~ViliDEieka~~~------------v~~~L  752 (854)
                      |++++|++|+       +.+.+.+... +++| ++.. ...+...  .++|||||||||+++.            +++.|
T Consensus        77 ~~~i~~s~~~-------~~~~~~~~~~~~~~~~f~~a~~~~~~~~--~~~IIf~DEIdki~~~~~~~~~~~~~~gv~~~L  147 (309)
T d1ofha_          77 FIKVEATKFT-------EVGYVGKEVDSIIRDLTDSAGGAIDAVE--QNGIVFIDEIDKICKKGEYSGADVSREGVQRDL  147 (309)
T ss_dssp             EEEEEGGGGS-------SCCSGGGSTTHHHHHHHHTTTTCHHHHH--HHCEEEEECGGGGSCCSSCCSSHHHHHHHHHHH
T ss_pred             hhcccccccc-------cceeEeeeccccccccchhhhccccccc--CCceEEehhhhhhhhhccCcccchhhhHHHHHh
Confidence            9999999998       4544443331 1222 1110 1111111  2479999999999865            66778


Q ss_pred             HHhhhcCeEecCCCceeecCCeEEEEe
Q 003038          753 KRAIESGRIVTSSGDEVSLGDAIVILS  779 (854)
Q Consensus       753 l~~le~G~l~d~~G~~v~~~~aIiIlT  779 (854)
                      +..+|...+.+. ...++++|.+||+|
T Consensus       148 L~~~dg~~~~~~-~~~i~~s~ilfi~~  173 (309)
T d1ofha_         148 LPLVEGSTVSTK-HGMVKTDHILFIAS  173 (309)
T ss_dssp             HHHHHCCEEEET-TEEEECTTCEEEEE
T ss_pred             hHHhcCCEEecC-CeEEEccceeEEec
Confidence            887864444332 34566777777765

>d1qvra1 a.174.1.1 (A:4-148) N-terminal domain of ClpB (heat shock protein F84.1) {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Thermus thermophilus [TaxId: 274]

Probab=99.70  E-value=3.2e-17  Score=157.05  Aligned_cols=130  Identities=19%  Similarity=0.220  Sum_probs=103.6

Q ss_pred             HhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCCCCCCCC
Q 003038           10 QGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTSTPML   89 (854)
Q Consensus        10 ~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~~~~~~~   89 (854)
                      ++||+.++++|..|+++|++++|.+|+|+|||++||.++++.+.++|+++|+++   +.|+..++..|.++|...+++  
T Consensus         1 dkfT~~a~~~l~~A~~~A~~~~~~~i~~~HlL~all~~~~~~~~~iL~~~gvd~---~~l~~~l~~~l~~~p~~~~~~--   75 (145)
T d1qvra1           1 ERWTQAAREALAQAQVLAQRMKHQAIDLPHLWAVLLKDERSLAWRLLEKAGADP---KALKELQERELARLPKVEGAE--   75 (145)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHCCSSSSHHHHHHHTTSSCH---HHHHHHHHHHHHTSCCCCGGG--
T ss_pred             CccCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHcCCcchHHHHHHHcCCCH---HHHHHHHHHHhhcccccCCCc--
Confidence            479999999999999999999999999999999999999999999999999986   899999999999999754321  


Q ss_pred             CCCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCChHHHHHHHhCCCHHHHHHHHH
Q 003038           90 GGHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDPSVSRVMREAGFSSTQVKSNVE  164 (854)
Q Consensus        90 ~~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~~~~~iL~~~Gi~~~~l~~~v~  164 (854)
                          ..+.+++.+..+|+.|+.++++.+++         +|+++|||+||+++..       .+.+...++..+.
T Consensus        76 ----~~~~~s~~l~~il~~A~~~a~~~gd~---------~Is~ehLllal~~~~~-------~~~~l~~l~~~i~  130 (145)
T d1qvra1          76 ----VGQYLTSRLSGALNRAEGLMEELKDR---------YVAVDTLVLALAEATP-------GLPGLEALKGALK  130 (145)
T ss_dssp             ----TTCEECHHHHHHHHHHHHHHHTTTCS---------SCCHHHHHHHHHHHST-------TSCCHHHHHHHHT
T ss_pred             ----ccCCCCHHHHHHHHHHHHHHHHcCCc---------cccHHHHHHHHHhccc-------chhhHHHHHHHHH
Confidence                23445666666666666665533334         5999999999998752       2334455666655

>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=99.64  E-value=9.8e-18  Score=179.87  Aligned_cols=175  Identities=9%  Similarity=-0.052  Sum_probs=116.8

Q ss_pred             ccccccccccccCCCCCCCCC--cHHHHHHHHHHh-hccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEE
Q 003038          190 VLSQTASATKVSKPRVSLDPI--RNEDVMYVIENL-MSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCL  266 (854)
Q Consensus       190 ~~~~~~~~~~~~~~~g~ldpv--r~~ei~~v~~~L-~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~  266 (854)
                      .+..+..+++..++++++||+  |..+..++.+.| +|..|++++|+||||||||++|++||..+..+        ..|+
T Consensus        83 ~~~~~~~~L~~~a~~~~~d~v~~~~~~~~~~~~~~~~~~~~g~~l~~G~pG~GKT~la~ala~~~~~~--------~~~~  154 (321)
T d1w44a_          83 VVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGK--------DKYA  154 (321)
T ss_dssp             EEEEETTEEEECCSEESSCSCTTCCSBCCEEEEETTEEEESEEEEEECSSSSCHHHHHHHHHHHHHTT--------SCCE
T ss_pred             hHHHHHhHHHHHHHhcCcchhccccccchHHHHHhhcccCCceEEEECCCCccHHHHHHHHHHHhcCC--------CCeE
Confidence            355667778888878999998  777777888888 56677777779999999999999999997542        4578


Q ss_pred             EcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcc-c-CCC
Q 003038          267 PLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVC-G-IGE  343 (854)
Q Consensus       267 ~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~-~-~~g  343 (854)
                      +++.+.+.++|+|++|+|++++|+++++    ++||||||||.+ +.++++...     ...++.+..+-.-+. . ...
T Consensus       155 ~~~~~~~~~~~~G~~e~~~~~~f~~a~~----~~ilf~DEid~~~~~r~~~~~~-----~~~~r~v~~lL~e~dg~~~~~  225 (321)
T d1w44a_         155 TVRFGEPLSGYNTDFNVFVDDIARAMLQ----HRVIVIDSLKNVIGAAGGNTTS-----GGISRGAFDLLSDIGAMAASR  225 (321)
T ss_dssp             EEEBSCSSTTCBCCHHHHHHHHHHHHHH----CSEEEEECCTTTC----------------CCHHHHHHHHHHHHHHHHH
T ss_pred             EEEhhHhhhcccchHHHHHHHHHHHHhh----ccEEEeehhhhhccccccCCCC-----CcchhhhhhhhhhccccccCC
Confidence            8999999999999999999999999984    579999999999 766432110     011233333222221 1 111


Q ss_pred             CceEEEEEecCHHHHHHhhccCCchhhh-hccCCCCCCCchHH
Q 003038          344 NARFWLMGIATFQSYMRCKSGHPSLETL-WSLHPLTIPAGSLS  385 (854)
Q Consensus       344 ~g~l~lIgatT~~ey~k~~~~~pale~~-~~~~~v~i~~~sl~  385 (854)
                        .|.+||||++.++...  .++++.|. ..+..|.|+.|+..
T Consensus       226 --~v~viaatN~~~~~~~--i~~~~~r~~Rf~~~v~v~~pd~~  264 (321)
T d1w44a_         226 --GCVVIASLNPTSNDDK--IVELVKEASRSNSTSLVISTDVD  264 (321)
T ss_dssp             --TCEEEEECCCCCCCHH--HHHHHHHHHHHSCSEEEEECSST
T ss_pred             --CeEEEEeCCCcccccc--hhhhhhccCcccceeecCCCChH
Confidence              3999999996432111  12333231 13355666655543

>d1k6ka_ a.174.1.1 (A:) N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone
species: Escherichia coli [TaxId: 562]

Probab=99.63  E-value=9.9e-16  Score=145.47  Aligned_cols=135  Identities=15%  Similarity=0.150  Sum_probs=103.0

Q ss_pred             hhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHHHHhccCCCCCC-CCCCC
Q 003038           12 LTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFNVALNRLPASTS-TPMLG   90 (854)
Q Consensus        12 fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~~~L~rlp~~~~-~~~~~   90 (854)
                      ||.++..+|..|+++|++++|+||+|||||+|||++++  ...++..+|++.   +.++..+...+...+...+ ....+
T Consensus         2 ~s~~l~~~l~~A~~~A~~~~h~~i~~EHLL~aLl~~~~--~~~~l~~~~~~~---~~l~~~~~~~~~~~~~~~~~~~~~~   76 (142)
T d1k6ka_           2 LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPS--AREALEACSVDL---VALRQELEAFIEQTTPVLPASEEER   76 (142)
T ss_dssp             BCHHHHHHHHHHHHHHHHHTBSEECHHHHHHHHTTCHH--HHHHHHHTTCCH---HHHHHHHHHHHHHHSCBCCSSCSCC
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhchh--HHHHHHHcCCch---hhhHHHHHHHHHhcCCCCCcccccc
Confidence            78999999999999999999999999999999998654  568899999886   7788888776654333211 01112


Q ss_pred             CCccChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC--hHHHHHHHhCCCHHHHHHHHH
Q 003038           91 GHCQFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP--SVSRVMREAGFSSTQVKSNVE  164 (854)
Q Consensus        91 ~~~~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~--~~~~iL~~~Gi~~~~l~~~v~  164 (854)
                      .++++|.+.+.|..|.+.|...    +++         +|+++|||+||+.++  .+.++|+++||+.+.+...+.
T Consensus        77 ~~~~s~~l~~il~~A~~~a~~~----~~~---------~i~~ehlLlall~~~~~~a~~lL~~~Gi~~~~l~~~Is  139 (142)
T d1k6ka_          77 DTQPTLSFQRVLQRAVFHVQSS----GRN---------EVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFIS  139 (142)
T ss_dssp             SCEECHHHHHHHHHHHHHHHSS----SCS---------CBCHHHHHHHHTTCTTSHHHHHHHHTTCCHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHHHHHHHc----CCC---------cchHHHHHHHHHHccCcHHHHHHHHCCCCHHHHHHHHh
Confidence            3445666666666666666544    223         599999999999864  689999999999988876654

>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=99.48  E-value=4.2e-14  Score=147.59  Aligned_cols=141  Identities=11%  Similarity=0.070  Sum_probs=103.7

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..++++|+||||||||.+|+.+|..+          +.+++.++.+.|.+.|.|+.|.+++.+++.++..  .|+|||||
T Consensus        44 ~~~~iLL~GppGtGKT~la~~iA~~~----------~~~~~~i~~~~l~~~~~g~~~~~l~~~f~~A~~~--~P~il~iD  111 (256)
T d1lv7a_          44 IPKGVLMVGPPGTGKTLLAKAIAGEA----------KVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKA--APCIIFID  111 (256)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHH----------TCCEEEECSCSSTTSCCCCCHHHHHHHHHHHHTT--CSEEEEET
T ss_pred             CCCeEEeeCCCCCCccHHHHHHHHHc----------CCCEEEEEhHHhhhcchhHHHHHHHHHHHHHHHc--CCEEEEEE
Confidence            35679999999999999999999875          6789999999999999999999999999999976  79999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCch
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGS  383 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~s  383 (854)
                      |++.+ ..+.....+   ........+..+-+.+....++..+.+||+|+.-+     .-||+|-|.=|| +.|.|+.|+
T Consensus       112 eiD~l~~~r~~~~~~---~~~~~~~~~~~ll~~~d~~~~~~~v~vIatTn~~~-----~ld~al~R~gRfd~~i~i~~P~  183 (256)
T d1lv7a_         112 EIDAVGRQRGAGLGG---GHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPD-----VLDPALLRPGRFDRQVVVGLPD  183 (256)
T ss_dssp             THHHHTCCCSTTSCC---TTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTT-----TSCGGGGSTTSSCEEEECCCCC
T ss_pred             ChhhhCccCCCCCCC---CcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCcc-----cCCHhHcCCCCCCEEEECCCcC
Confidence            99999 554332111   11112223333333342212233699999998654     468999764467 677777777


Q ss_pred             HHH
Q 003038          384 LSL  386 (854)
Q Consensus       384 l~~  386 (854)
                      ...
T Consensus       184 ~~~  186 (256)
T d1lv7a_         184 VRG  186 (256)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>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=99.47  E-value=4.6e-14  Score=146.57  Aligned_cols=155  Identities=15%  Similarity=0.119  Sum_probs=108.0

Q ss_pred             HHHHHHHHHhhcc---------CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHH
Q 003038          213 EDVMYVIENLMSK---------RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQ  283 (854)
Q Consensus       213 ~ei~~v~~~L~r~---------~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~  283 (854)
                      +.|+.++..|.++         ..++++|+||||||||.+|+++|..          .+.+++.++.+.|.+.|.|+.++
T Consensus        19 ~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~----------~~~~~~~i~~~~l~~~~~g~~~~   88 (247)
T d1ixza_          19 EELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE----------ARVPFITASGSDFVEMFVGVGAA   88 (247)
T ss_dssp             HHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHH----------TTCCEEEEEHHHHHHSCTTHHHH
T ss_pred             HHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHH----------cCCCEEEEEhHHhhhccccHHHH
Confidence            4466666655432         3567999999999999999999986          36799999999999999999999


Q ss_pred             HHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhh
Q 003038          284 RVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCK  362 (854)
Q Consensus       284 rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~  362 (854)
                      +++++++.++..  .|+||||||++.+ +.+.....+..   .........+-+.+..-..+..+.+||+|+.-+     
T Consensus        89 ~l~~~f~~a~~~--~p~Ii~iDeid~l~~~r~~~~~~~~---~~~~~~~~~ll~~~d~~~~~~~vivi~tTn~~~-----  158 (247)
T d1ixza_          89 RVRDLFETAKRH--APCIVFIDEIDAVGRKRGSGVGGGN---DEREQTLNQLLVEMDGFEKDTAIVVMAATNRPD-----  158 (247)
T ss_dssp             HHHHHHHHHTTS--SSEEEEEETHHHHHC---------C---HHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGG-----
T ss_pred             HHHHHHHHHHHc--CCEEEEEEChhhhCccCCCCCCCCc---HHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCcc-----
Confidence            999999999875  7999999999999 66543211100   111122333333332212233699999998754     


Q ss_pred             ccCCchhhhhcc-CCCCCCCchHHHH
Q 003038          363 SGHPSLETLWSL-HPLTIPAGSLSLS  387 (854)
Q Consensus       363 ~~~pale~~~~~-~~v~i~~~sl~~a  387 (854)
                      ..||+|-|.-|| +.+.|+.|+...-
T Consensus       159 ~ld~al~R~~Rf~~~i~~~~P~~~eR  184 (247)
T d1ixza_         159 ILDPALLRPGRFDRQIAIDAPDVKGR  184 (247)
T ss_dssp             GSCGGGGSTTSSCEEEECCSCCHHHH
T ss_pred             ccCHhHcCCCCCcEEEEECCcCHHHH
Confidence            468999764467 4778887776553

>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=99.32  E-value=4.4e-12  Score=129.69  Aligned_cols=128  Identities=12%  Similarity=0.090  Sum_probs=89.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +.|+||++++..|...+...+..             .++...+||+||||+|||++|++||+.+.   .+++.++.+...
T Consensus         9 ~divGqe~~~~~l~~~i~~~~~~-------------~~~~~~~L~~GPpGtGKT~lA~~la~~~~---~~~~~~~~~~~~   72 (238)
T d1in4a2           9 DEFIGQENVKKKLSLALEAAKMR-------------GEVLDHVLLAGPPGLGKTTLAHIIASELQ---TNIHVTSGPVLV   72 (238)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHH-------------TCCCCCEEEESSTTSSHHHHHHHHHHHHT---CCEEEEETTTCC
T ss_pred             HHcCChHHHHHHHHHHHHHHHhc-------------CCCCCeEEEECCCCCcHHHHHHHHHhccC---CCcccccCcccc
Confidence            45899999999999998765431             13455899999999999999999999984   245555544222


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHH-HcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCC-------cee
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAV-SNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSG-------DEV  769 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav-~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G-------~~v  769 (854)
                             ..               ..+...+ ....+.+++|||++++++.+++.++..++.+.+..-.+       ...
T Consensus        73 -------~~---------------~~~~~~~~~~~~~~~~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  130 (238)
T d1in4a2          73 -------KQ---------------GDMAAILTSLERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRI  130 (238)
T ss_dssp             -------SH---------------HHHHHHHHHCCTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC-------------
T ss_pred             -------cH---------------HHHHHHHHhhccCCchHHHHHHHhhhHHHhhcccceeeeeeeeeecCccccccccc
Confidence                   00               1122222 23567899999999999999999999999986542111       223


Q ss_pred             ecCCeEEEEecCCC
Q 003038          770 SLGDAIVILSCESF  783 (854)
Q Consensus       770 ~~~~aIiIlTsn~f  783 (854)
                      ...+++||++||.-
T Consensus       131 ~~~~~~~I~at~~~  144 (238)
T d1in4a2         131 DIQPFTLVGATTRS  144 (238)
T ss_dssp             --CCCEEEEEESCG
T ss_pred             CCCCeEEEEecCCC
Confidence            56788999998753

>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=99.29  E-value=2e-11  Score=124.92  Aligned_cols=127  Identities=11%  Similarity=0.056  Sum_probs=89.0

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .|+||+++++.+...|...+.+             .++...+||+||||+|||++|++||+.+.   .++..++.+... 
T Consensus        10 divGq~~~~~~L~~~i~~~~~~-------------~~~~~~~Ll~GPpG~GKTtla~~la~~~~---~~~~~~~~~~~~-   72 (239)
T d1ixsb2          10 EYIGQERLKQKLRVYLEAAKAR-------------KEPLEHLLLFGPPGLGKTTLAHVIAHELG---VNLRVTSGPAIE-   72 (239)
T ss_dssp             GSCSCHHHHHHHHHHHHHHTTS-------------SSCCCCEEEECCTTSCHHHHHHHHHHHHT---CCEEEEETTTCC-
T ss_pred             HhCCHHHHHHHHHHHHHHHHhc-------------CCCCCeEEEECCCCCCHHHHHHHHHHHhC---CCeEeccCCccc-
Confidence            5899999999999998776531             13445789999999999999999999984   345555544322 


Q ss_pred             cCCCccccccccccCCCCCCchHHHHHHHHHc--CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCC-----C--cee
Q 003038          699 TRADSTEDSRNKRSRDEQSCSYIERFAEAVSN--NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSS-----G--DEV  769 (854)
Q Consensus       699 ~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~--~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~-----G--~~v  769 (854)
                            ..            +.   ....+.+  ...+|++|||++++.+..+..++.+++++.+....     .  ...
T Consensus        73 ------~~------------~~---~~~~~~~~~~~~~i~~iDe~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~  131 (239)
T d1ixsb2          73 ------KP------------GD---LAAILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRL  131 (239)
T ss_dssp             ------SH------------HH---HHHHHHTTCCTTCEEEEETGGGCCHHHHHHHHHHHHHSEEEEECSCTTCCCEEEE
T ss_pred             ------cc------------hh---hHHHHHhhccCCCeeeeecccccchhHHHhhhhhhhhhhhhhhhccchhhhhccc
Confidence                  00            11   1112222  23579999999999999999999999987654321     1  233


Q ss_pred             ecCCeEEEEecCCC
Q 003038          770 SLGDAIVILSCESF  783 (854)
Q Consensus       770 ~~~~aIiIlTsn~f  783 (854)
                      ...+.+||++||..
T Consensus       132 ~~~~~~~i~~~~~~  145 (239)
T d1ixsb2         132 ELPRFTLIGATTRP  145 (239)
T ss_dssp             ECCCCEEEEEESCC
T ss_pred             CCCCEEEEeeccCc
Confidence            45667888888643

>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=99.28  E-value=5.7e-12  Score=131.36  Aligned_cols=138  Identities=12%  Similarity=0.111  Sum_probs=103.4

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      .+++++|+||||||||.+++++|..          .+.+++.++.+.+.+.+.|+.+..++.+++.++..  .|+|||||
T Consensus        37 ~~~giLL~GppGtGKT~l~~ala~~----------~~~~~~~i~~~~l~~~~~g~~~~~l~~~f~~A~~~--~p~il~iD  104 (258)
T d1e32a2          37 PPRGILLYGPPGTGKTLIARAVANE----------TGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKN--APAIIFID  104 (258)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHH----------TTCEEEEECHHHHTTSCTTHHHHHHHHHHHHHHHT--CSEEEEES
T ss_pred             CCceeEEecCCCCCchHHHHHHHHH----------hCCeEEEEEchhhcccccccHHHHHHHHHHHHHhc--CCeEEEeh
Confidence            4678999999999999999999987          36799999999999999999999999999999986  79999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCch
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGS  383 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~s  383 (854)
                      |++.+ +.+..+.++      ........+.+.+.....+..+.+||||+.-+     ..||++.|.-|| +.|.|+.|+
T Consensus       105 eid~l~~~r~~~~~~------~~~~~~~~~~~~~~~~~~~~~vlvi~tTn~~~-----~ld~al~r~gRfd~~i~~~~P~  173 (258)
T d1e32a2         105 ELDAIAPKREKTHGE------VERRIVSQLLTLMDGLKQRAHVIVMAATNRPN-----SIDPALRRFGRFDREVDIGIPD  173 (258)
T ss_dssp             SGGGTCCHHHHCCCT------THHHHHHHHHHHHHTCCCSSCEEEEEEESCGG-----GSCGGGTSTTSSCEEEECCCCC
T ss_pred             hhhhhccCCCCCCCc------hHHHHHHHhccccccccccCCccEEEeCCCcc-----ccchhhhhcccccceeECCCCC
Confidence            99999 554322111      11123333333332212223599999998665     469999874467 677777777


Q ss_pred             HHH
Q 003038          384 LSL  386 (854)
Q Consensus       384 l~~  386 (854)
                      ...
T Consensus       174 ~~~  176 (258)
T d1e32a2         174 ATG  176 (258)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            555

>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=99.23  E-value=2.1e-11  Score=122.83  Aligned_cols=134  Identities=8%  Similarity=0.141  Sum_probs=84.6

Q ss_pred             ccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc
Q 003038          620 VPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST  699 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~  699 (854)
                      .|||+++.+.+...+...                 +..+.+||+||+|+|||++|+.+|+.+++....-.. .+....++
T Consensus         4 yPw~~~~~~~l~~~~~~~-----------------~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~-~~~~~~~~   65 (207)
T d1a5ta2           4 YPWLRPDFEKLVASYQAG-----------------RGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHK-SCGHCRGC   65 (207)
T ss_dssp             CGGGHHHHHHHHHHHHTT-----------------CCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTB-CCSCSHHH
T ss_pred             CcccHHHHHHHHHHHHcC-----------------CcCeEEEEECCCCCcHHHHHHHHHHhcccccccccc-cccccchh
Confidence            389999999998887753                 334579999999999999999999999854321000 00000000


Q ss_pred             CCCccccc-cccccC-CC-CCC-chHH--HHHHHHHcC----CCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          700 RADSTEDS-RNKRSR-DE-QSC-SYIE--RFAEAVSNN----PHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       700 ~~~s~e~~-~~~rl~-~~-~g~-g~~e--~L~eav~~~----p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      .......+ .+..+. .. ... +..+  .+.+.+...    .++||+|||+|++..+.|+.|++.||+.          
T Consensus        66 ~~i~~~~~~~~~~~~~~~~~~~i~~~~ir~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep----------  135 (207)
T d1a5ta2          66 QLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEP----------  135 (207)
T ss_dssp             HHHHHTCCTTEEEECCCTTCSSBCHHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSC----------
T ss_pred             hhhhhccccccchhhhhhcccccccchhhHHhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHhh----------
Confidence            00000000 000000 01 111 2222  344444433    4679999999999999999999999973          


Q ss_pred             ecCCeEEEEecCC
Q 003038          770 SLGDAIVILSCES  782 (854)
Q Consensus       770 ~~~~aIiIlTsn~  782 (854)
                       -++++|||+|+.
T Consensus       136 -~~~~~fIl~t~~  147 (207)
T d1a5ta2         136 -PAETWFFLATRE  147 (207)
T ss_dssp             -CTTEEEEEEESC
T ss_pred             -cccceeeeeecC
Confidence             478899999964

>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=99.21  E-value=3.1e-11  Score=124.84  Aligned_cols=130  Identities=6%  Similarity=0.074  Sum_probs=89.3

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHH-HHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEV-EQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~-E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      .+.++|+||||||||++|++||...          +.+|+.++.+.+..|+.+.. .+.++.+++.++..  .|+|||||
T Consensus        40 ~~~vLL~GppGtGKT~la~alA~~~----------~~~~~~i~~~~~~~g~~~~~~~~~i~~if~~A~~~--~p~il~iD  107 (246)
T d1d2na_          40 LVSVLLEGPPHSGKTALAAKIAEES----------NFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKS--QLSCVVVD  107 (246)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHHH----------TCSEEEEECGGGCTTCCHHHHHHHHHHHHHHHHTS--SEEEEEEC
T ss_pred             CeEEEEECcCCCCHHHHHHHHhhcc----------cccccccccccccccccccchhhhhhhhhhhhhhc--ccceeehh
Confidence            3468999999999999999999874          67899999888777766654 47799999999986  68999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCCceEEEEEecCHHHHHHhhccCCchhhhhccC-CCCCCC
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGENARFWLMGIATFQSYMRCKSGHPSLETLWSLH-PLTIPA  381 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~-~v~i~~  381 (854)
                      ||+.+ +....+...       .+.....+..++..  ..++ ++.+||||+..+...    .+.+.+  +|+ .+.+|+
T Consensus       108 Eid~l~~~~~~~~~~-------~~~~~~~ll~~l~~~~~~~~-~v~vi~tTn~~~~ld----~~~~~~--rF~~~i~~P~  173 (246)
T d1d2na_         108 DIERLLDYVPIGPRF-------SNLVLQALLVLLKKAPPQGR-KLLIIGTTSRKDVLQ----EMEMLN--AFSTTIHVPN  173 (246)
T ss_dssp             CHHHHTTCBTTTTBC-------CHHHHHHHHHHTTCCCSTTC-EEEEEEEESCHHHHH----HTTCTT--TSSEEEECCC
T ss_pred             hhhhHhhhcccccch-------hHHHHHHHHHHhcCCCcccc-ceeeeeccCChhhcc----chhhcC--ccceEEecCC
Confidence            99999 654332110       01233344455532  2222 699999998755431    234555  553 345554


Q ss_pred             c
Q 003038          382 G  382 (854)
Q Consensus       382 ~  382 (854)
                      .
T Consensus       174 ~  174 (246)
T d1d2na_         174 I  174 (246)
T ss_dssp             E
T ss_pred             c
Confidence            3

>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=99.21  E-value=2.8e-11  Score=124.33  Aligned_cols=150  Identities=16%  Similarity=0.117  Sum_probs=92.9

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCce-----EEEc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNF-----VSIA  692 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~-----i~id  692 (854)
                      ..++||++++..+...+...                 +....+||+||+|+|||.+|+++++.+++....-     +..+
T Consensus        12 ~dlig~~~~~~~L~~~i~~~-----------------~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~   74 (239)
T d1njfa_          12 ADVVGQEHVLTALANGLSLG-----------------RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDN   74 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHTT-----------------CCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHH
T ss_pred             HHccChHHHHHHHHHHHHcC-----------------CCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchH
Confidence            46899999999988887642                 2234689999999999999999999997643110     0000


Q ss_pred             cccccCcCCCccccc-cccccCCCCCC-chHH--HHHHHHHc----CCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecC
Q 003038          693 LSSFSSTRADSTEDS-RNKRSRDEQSC-SYIE--RFAEAVSN----NPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTS  764 (854)
Q Consensus       693 ~s~~~~~~~~s~e~~-~~~rl~~~~g~-g~~e--~L~eav~~----~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~  764 (854)
                      +..+..      ..| .+.. +...+. +..+  .+.+.+..    .++.||+|||+|+++++.|+.|++.||++     
T Consensus        75 ~~~i~~------~~~~~~~~-~~~~~~~~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~~~~q~~Llk~lE~~-----  142 (239)
T d1njfa_          75 CREIEQ------GRFVDLIE-IDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEP-----  142 (239)
T ss_dssp             HHHHHH------TCCTTEEE-EETTCSSSHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSC-----
T ss_pred             HHHHHc------CCCCeEEE-ecchhcCCHHHHHHHHHHHHhccccCCCEEEEEECcccCCHHHHHHHHHHHhcC-----
Confidence            000000      000 0000 001111 2221  23333222    34689999999999999999999999963     


Q ss_pred             CCceeecCCeEEEEecCCCCCCCCCCCCCccCCCCCchhhcccccCCCCCceeeeccCC
Q 003038          765 SGDEVSLGDAIVILSCESFSSRSRACSPPTKQKSDGCEEEKGAAMEGTSPSVSLDLNIC  823 (854)
Q Consensus       765 ~G~~v~~~~aIiIlTsn~f~~~s~~~sp~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  823 (854)
                            -.+++|||+||..   +....+.                  .|+|..+.++.+
T Consensus       143 ------~~~~~~il~tn~~---~~i~~~i------------------~SRc~~i~~~~~  174 (239)
T d1njfa_         143 ------PEHVKFLLATTDP---QKLPVTI------------------LSRCLQFHLKAL  174 (239)
T ss_dssp             ------CTTEEEEEEESCG---GGSCHHH------------------HTTSEEEECCCC
T ss_pred             ------CCCeEEEEEcCCc---cccChhH------------------hhhhcccccccC
Confidence                  2567899999753   2233333                  667777766664

>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=99.19  E-value=8.1e-12  Score=129.30  Aligned_cols=137  Identities=9%  Similarity=0.066  Sum_probs=90.4

Q ss_pred             HHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEE
Q 003038          612 LCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSI  691 (854)
Q Consensus       612 L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~i  691 (854)
                      +.+++...|+|+.+.+..|..-.......+..+.        ..|...+||+||+|||||++|++||..+   ..+|+.+
T Consensus         3 ~~~~~~~~~i~~~~~i~~i~~~~~~~~~~~~~~~--------~~p~~~vLL~GppGtGKT~la~alA~~~---~~~~~~i   71 (246)
T d1d2na_           3 YASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSD--------RTPLVSVLLEGPPHSGKTALAAKIAEES---NFPFIKI   71 (246)
T ss_dssp             STTTCTTCCCCCSHHHHHHHHHHHHHHHHHHHCS--------SCSEEEEEEECSTTSSHHHHHHHHHHHH---TCSEEEE
T ss_pred             HHHhhccCCcCcCHHHHHHHHHHHHHHHHHhccC--------CCCCeEEEEECcCCCCHHHHHHHHhhcc---ccccccc
Confidence            3467778899987777666655554332222221        1455689999999999999999999987   4678888


Q ss_pred             ccccccCcCCCccccccccccCCCCCC---chHHHHHHHHHcCCCEEEEEecCCCC----------CHHHHHHHHHhhhc
Q 003038          692 ALSSFSSTRADSTEDSRNKRSRDEQSC---SYIERFAEAVSNNPHRVFLIEDVEQA----------DYCSQKGFKRAIES  758 (854)
Q Consensus       692 d~s~~~~~~~~s~e~~~~~rl~~~~g~---g~~e~L~eav~~~p~~ViliDEieka----------~~~v~~~Ll~~le~  758 (854)
                      ++++...       ..        .+.   .....+++..++++.+||||||||+.          ...+.+.|+..++.
T Consensus        72 ~~~~~~~-------g~--------~~~~~~~~i~~if~~A~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~ll~~l~~  136 (246)
T d1d2na_          72 CSPDKMI-------GF--------SETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKK  136 (246)
T ss_dssp             ECGGGCT-------TC--------CHHHHHHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTC
T ss_pred             ccccccc-------cc--------cccchhhhhhhhhhhhhhcccceeehhhhhhHhhhcccccchhHHHHHHHHHHhcC
Confidence            8764320       00        010   12224666677888899999999863          34456677777764


Q ss_pred             CeEecCCCceeecCCeEEEEecCC
Q 003038          759 GRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       759 G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      ..        -..++.+||.|||.
T Consensus       137 ~~--------~~~~~v~vi~tTn~  152 (246)
T d1d2na_         137 AP--------PQGRKLLIIGTTSR  152 (246)
T ss_dssp             CC--------STTCEEEEEEEESC
T ss_pred             CC--------ccccceeeeeccCC
Confidence            31        12346788999984

>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=99.18  E-value=2.2e-11  Score=127.35  Aligned_cols=139  Identities=14%  Similarity=0.144  Sum_probs=98.2

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                      ..++++|+||||+|||.+|+++|..+          +.+++.++.+.+.+.+.|+.+.+++.++..++..  .|+|||||
T Consensus        40 ~~~giLL~Gp~GtGKT~l~~ala~~~----------~~~~~~~~~~~l~~~~~~~~~~~l~~~f~~A~~~--~p~il~id  107 (265)
T d1r7ra3          40 PSKGVLFYGPPGCGKTLLAKAIANEC----------QANFISIKGPELLTMWFGESEANVREIFDKARQA--APCVLFFD  107 (265)
T ss_dssp             CCCEEEEBCCTTSSHHHHHHHHHHHT----------TCEEEEECHHHHHTSCTTTHHHHHHHHHHHHHHT--CSEEEEES
T ss_pred             CCCeEEEECCCCCcchhHHHHHHHHh----------CCcEEEEEHHHhhhccccchHHHHHHHHHHHHhc--CCcceeHH
Confidence            45689999999999999999999884          6899999999999999999999999999999986  79999999


Q ss_pred             ccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchhhhhcc-CCCCCCCch
Q 003038          306 DLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSL-HPLTIPAGS  383 (854)
Q Consensus       306 el~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~-~~v~i~~~s  383 (854)
                      |++.+ ..+.....   +.+...+.....+.+.+..-..+..+.+||+|+..+     ..||+|.|.-|| +.|.|+.|+
T Consensus       108 eid~l~~~~~~~~~---~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~-----~ld~al~r~gRf~~~i~~~~p~  179 (265)
T d1r7ra3         108 ELDSIAKARGGNIG---DGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPD-----IIDPAILRPGRLDQLIYIPLPD  179 (265)
T ss_dssp             SGGGTCCHHHHCCC---TTHHHHHHHHHHHHHTCC------CCEEEECCBSCT-----TTSCGGGSSTTSEEEEECCCCC
T ss_pred             hhhhccccCCCcCC---CCcHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCch-----hCCHHHhCCCCccEEEEecchH
Confidence            99999 54322110   111112223333434442211222588999998665     468999763345 355666555


Q ss_pred             H
Q 003038          384 L  384 (854)
Q Consensus       384 l  384 (854)
                      -
T Consensus       180 ~  180 (265)
T d1r7ra3         180 E  180 (265)
T ss_dssp             C
T ss_pred             H
Confidence            3

>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=99.12  E-value=9.4e-11  Score=118.71  Aligned_cols=117  Identities=15%  Similarity=0.230  Sum_probs=82.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCC--ceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHN--NFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~--~~i~id~s~  695 (854)
                      +.|+||++++..|...+...                  ....+||+||+|+|||++|++||+.+++...  .++.++.+.
T Consensus        14 ~divg~~~~~~~L~~~i~~~------------------~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~   75 (227)
T d1sxjc2          14 DEVYGQNEVITTVRKFVDEG------------------KLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASD   75 (227)
T ss_dssp             GGCCSCHHHHHHHHHHHHTT------------------CCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTS
T ss_pred             HHccCcHHHHHHHHHHHHcC------------------CCCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccc
Confidence            45899999999998887542                  1235899999999999999999999987532  223333332


Q ss_pred             ccCcCCCccccccccccCCCCCCchHH-HHHHHHH-----cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIE-RFAEAVS-----NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e-~L~eav~-----~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      +.                   +..+.. .+.....     ...+.||+|||+|.+....|+.|+.+|++.          
T Consensus        76 ~~-------------------~~~~~~~~~~~~~~~~~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~----------  126 (227)
T d1sxjc2          76 DR-------------------GIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERY----------  126 (227)
T ss_dssp             CC-------------------SHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHT----------
T ss_pred             cC-------------------CeeeeecchhhccccccccCCCeEEEEEeccccchhhHHHHHHHHhhhc----------
Confidence            21                   001111 1222222     234679999999999999999999999963          


Q ss_pred             ecCCeEEEEecCC
Q 003038          770 SLGDAIVILSCES  782 (854)
Q Consensus       770 ~~~~aIiIlTsn~  782 (854)
                       ..+++|+++||.
T Consensus       127 -~~~~~~~~~~~~  138 (227)
T d1sxjc2         127 -TKNTRFCVLANY  138 (227)
T ss_dssp             -TTTEEEEEEESC
T ss_pred             -ccceeeccccCc
Confidence             257899999874

>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=99.07  E-value=5.3e-11  Score=120.98  Aligned_cols=124  Identities=20%  Similarity=0.283  Sum_probs=85.6

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC--CceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH--NNFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~--~~~i~id~s~  695 (854)
                      ..|+||++++..|...+...                  ....+||+||+|+|||++|++||+.+++..  ..++.++.+.
T Consensus        24 ~diig~~~~~~~l~~~i~~~------------------~~~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e~n~s~   85 (231)
T d1iqpa2          24 DDIVGQEHIVKRLKHYVKTG------------------SMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASD   85 (231)
T ss_dssp             TTCCSCHHHHHHHHHHHHHT------------------CCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTC
T ss_pred             HHccCcHHHHHHHHHHHHcC------------------CCCeEEEECCCCCcHHHHHHHHHHHHHhcccCCCeeEEecCc
Confidence            45899999999999888642                  123689999999999999999999997642  3455666543


Q ss_pred             ccCcCCCccccccccccCCCCCCchHH-HHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCe
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIE-RFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDA  774 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e-~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~a  774 (854)
                      ..       ....+..       .+.+ ..........+.||+|||++++....++.|+..++++.           .++
T Consensus        86 ~~-------~~~~~~~-------~~~~~~~~~~~~~~~~~iilide~d~~~~~~~~~ll~~l~~~~-----------~~~  140 (231)
T d1iqpa2          86 ER-------GINVIRE-------KVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFS-----------SNV  140 (231)
T ss_dssp             HH-------HHHTTHH-------HHHHHHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTT-----------TTE
T ss_pred             cc-------chhHHHH-------HHHHHHhhhhccCCCceEEeehhhhhcchhHHHHHhhhcccCC-----------cce
Confidence            22       0000000       0101 01111123457899999999999999999999998642           467


Q ss_pred             EEEEecCCCC
Q 003038          775 IVILSCESFS  784 (854)
Q Consensus       775 IiIlTsn~f~  784 (854)
                      +||+++|..+
T Consensus       141 ~~i~~~n~~~  150 (231)
T d1iqpa2         141 RFILSCNYSS  150 (231)
T ss_dssp             EEEEEESCGG
T ss_pred             EEEeccCChh
Confidence            8999998654

>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=99.06  E-value=2.6e-10  Score=118.38  Aligned_cols=138  Identities=16%  Similarity=0.095  Sum_probs=89.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+|.+.+.+.|.+.|...+..-...+ .+     .++...+||+||+|||||.+|++||+.+   ..++++++++.+.
T Consensus        12 ~Di~Gl~~~k~~l~e~v~~~~~~~~~~~-~g-----~~~~~~iLL~GppGtGKT~la~~iA~~~---~~~~~~i~~~~l~   82 (256)
T d1lv7a_          12 ADVAGCDEAKEEVAELVEYLREPSRFQK-LG-----GKIPKGVLMVGPPGTGKTLLAKAIAGEA---KVPFFTISGSDFV   82 (256)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----------CCCCEEEEECCTTSCHHHHHHHHHHHH---TCCEEEECSCSST
T ss_pred             HHHhchHHHHHHHHHHHHHHHCHHHHHH-cC-----CCCCCeEEeeCCCCCCccHHHHHHHHHc---CCCEEEEEhHHhh
Confidence            3578888888888776654332111100 00     1233468999999999999999999988   4689999998776


Q ss_pred             CcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEEecCCCCC-----------H---HHHHHHHHhhhcCeEec
Q 003038          698 STRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLIEDVEQAD-----------Y---CSQKGFKRAIESGRIVT  763 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~ViliDEieka~-----------~---~v~~~Ll~~le~G~l~d  763 (854)
                             ..+     . +........+.+..+++..+||||||||++-           .   .+.+.|+..|+.-  . 
T Consensus        83 -------~~~-----~-g~~~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~--~-  146 (256)
T d1lv7a_          83 -------EMF-----V-GVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGF--E-  146 (256)
T ss_dssp             -------TSC-----C-CCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTC--C-
T ss_pred             -------hcc-----h-hHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCC--C-
Confidence                   211     1 1111233356777777888999999998731           1   2456778878732  1 


Q ss_pred             CCCceeecCCeEEEEecCCCCCC
Q 003038          764 SSGDEVSLGDAIVILSCESFSSR  786 (854)
Q Consensus       764 ~~G~~v~~~~aIiIlTsn~f~~~  786 (854)
                            +-++.+||.|||..+..
T Consensus       147 ------~~~~v~vIatTn~~~~l  163 (256)
T d1lv7a_         147 ------GNEGIIVIAATNRPDVL  163 (256)
T ss_dssp             ------SSSCEEEEEEESCTTTS
T ss_pred             ------CCCCEEEEEeCCCcccC
Confidence                  11457889899865544

>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=99.05  E-value=2.3e-10  Score=115.75  Aligned_cols=120  Identities=11%  Similarity=0.204  Sum_probs=82.8

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC--CceEEEcccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH--NNFVSIALSS  695 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~--~~~i~id~s~  695 (854)
                      ..++||++++..|...+...                  ....+||+||+|+|||++|+.||+.+.+..  ..++.++.++
T Consensus        15 ~d~ig~~~~~~~L~~~~~~~------------------~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~~   76 (224)
T d1sxjb2          15 SDIVGNKETIDRLQQIAKDG------------------NMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASD   76 (224)
T ss_dssp             GGCCSCTHHHHHHHHHHHSC------------------CCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTS
T ss_pred             HHhcCCHHHHHHHHHHHHcC------------------CCCeEEEECCCCCCchhhHHHHHHHHhccccccccccccccc
Confidence            45799999999988877531                  123689999999999999999999987642  2344444442


Q ss_pred             ccCcCCCccccccccccCCCCCCchHHHHHHHHH------cCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCcee
Q 003038          696 FSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVS------NNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEV  769 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~------~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v  769 (854)
                      ..          ...        -....+...+.      ...+.||++||+|.+....|+.|+..+++           
T Consensus        77 ~~----------~~~--------~i~~~~~~~~~~~~~~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~-----------  127 (224)
T d1sxjb2          77 DR----------GID--------VVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMEL-----------  127 (224)
T ss_dssp             CC----------SHH--------HHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHH-----------
T ss_pred             cC----------Cce--------ehhhHHHHHHHhhccCCCcceEEEEEecccccchhHHHHHhhhccc-----------
Confidence            21          000        00011222222      23467999999999999999999999985           


Q ss_pred             ecCCeEEEEecCCCC
Q 003038          770 SLGDAIVILSCESFS  784 (854)
Q Consensus       770 ~~~~aIiIlTsn~f~  784 (854)
                      .-.+++||++|+..+
T Consensus       128 ~~~~~~~i~~~~~~~  142 (224)
T d1sxjb2         128 YSNSTRFAFACNQSN  142 (224)
T ss_dssp             TTTTEEEEEEESCGG
T ss_pred             cccceeeeeccCchh
Confidence            335778999887543

>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=98.98  E-value=4.3e-10  Score=116.16  Aligned_cols=124  Identities=11%  Similarity=0.145  Sum_probs=80.7

Q ss_pred             cccccHHHHHHHHHHHHHh-------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEE
Q 003038          619 KVPWQKDTVYDIANTVLKC-------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSI  691 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~-------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~i  691 (854)
                      .|+|++++++.|.+.|.-.       +.|..             +...+||+||+|||||.+|++||+.+   ...++.+
T Consensus        10 di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~-------------~~~giLl~GppGtGKT~la~aia~~~---~~~~~~i   73 (247)
T d1ixza_          10 DVAGAEEAKEELKEIVEFLKNPSRFHEMGAR-------------IPKGVLLVGPPGVGKTHLARAVAGEA---RVPFITA   73 (247)
T ss_dssp             GCCSCHHHHHHHHHHHHHHHCHHHHHHTTCC-------------CCSEEEEECCTTSSHHHHHHHHHHHT---TCCEEEE
T ss_pred             HHccHHHHHHHHHHHHHHHHCHHHHHHcCCC-------------CCceEEEecCCCCChhHHHHHHHHHc---CCCEEEE
Confidence            4677777777766655321       22322             22368999999999999999999987   4679999


Q ss_pred             ccccccCcCCCccccccccccCCCCCC--chHHHHHHHHHcCCCEEEEEecCCCCC-----------H---HHHHHHHHh
Q 003038          692 ALSSFSSTRADSTEDSRNKRSRDEQSC--SYIERFAEAVSNNPHRVFLIEDVEQAD-----------Y---CSQKGFKRA  755 (854)
Q Consensus       692 d~s~~~~~~~~s~e~~~~~rl~~~~g~--g~~e~L~eav~~~p~~ViliDEieka~-----------~---~v~~~Ll~~  755 (854)
                      +++.+.       .++        .|.  .....+++..+.+..+||||||||.+-           .   .+.+.|+..
T Consensus        74 ~~~~l~-------~~~--------~g~~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~  138 (247)
T d1ixza_          74 SGSDFV-------EMF--------VGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVE  138 (247)
T ss_dssp             EHHHHH-------HSC--------TTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHH
T ss_pred             EhHHhh-------hcc--------ccHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHH
Confidence            988665       111        011  111245555666667999999998641           1   256677777


Q ss_pred             hhcCeEecCCCceeecCCeEEEEecCC
Q 003038          756 IESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       756 le~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      |+.  +.       .-.+.+||.|||.
T Consensus       139 ~d~--~~-------~~~~vivi~tTn~  156 (247)
T d1ixza_         139 MDG--FE-------KDTAIVVMAATNR  156 (247)
T ss_dssp             HHT--CC-------TTCCEEEEEEESC
T ss_pred             hhC--CC-------CCCCEEEEEeCCC
Confidence            773  11       1135678889985

>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=98.97  E-value=3.5e-10  Score=116.87  Aligned_cols=139  Identities=15%  Similarity=0.204  Sum_probs=97.4

Q ss_pred             ccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc
Q 003038          620 VPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST  699 (854)
Q Consensus       620 V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~  699 (854)
                      .|||+.+++.+...+.+.-.                ...++|+.|++|+||+.+|++|...-++....++.+++..+.  
T Consensus         2 ~v~~S~~~~~~~~~~~~~a~----------------~~~pvlI~Ge~GtGK~~~A~~ih~~s~~~~~~~~~~~~~~~~--   63 (247)
T d1ny5a2           2 YVFESPKMKEILEKIKKISC----------------AECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIP--   63 (247)
T ss_dssp             CCCCSHHHHHHHHHHHHHTT----------------CCSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSC--
T ss_pred             eEecCHHHHHHHHHHHHHhC----------------CCCCEEEECCCCcCHHHHHHHHHHhcCCcccccccchhhhhh--
Confidence            58999999999988887522                123578889999999999999999888888999999998765  


Q ss_pred             CCCccccccccccCC-CCCC--chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEE
Q 003038          700 RADSTEDSRNKRSRD-EQSC--SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIV  776 (854)
Q Consensus       700 ~~~s~e~~~~~rl~~-~~g~--g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIi  776 (854)
                           +......+.+ ..+.  +......+.+.......+||||||++++..|..|+++++++.++.-+|....-.++.|
T Consensus        64 -----~~~~~~~lfg~~~~~~~~~~~~~~g~l~~a~gGtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~~~~~~~~~~~Rl  138 (247)
T d1ny5a2          64 -----RDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRI  138 (247)
T ss_dssp             -----HHHHHHHHHCBCTTSSTTCCSCBCCHHHHTTTSEEEEESGGGCCHHHHHHHHHHHHHSEECCBTCCSBEECCCEE
T ss_pred             -----hcccHHHhcCcccCCcCCcccccCCHHHccCCCEEEEeChHhCCHHHHHHHHHHHHhCCEEECCCCCceecCeEE
Confidence                 2211111110 0000  0000001223445667899999999999999999999999988754443333446778


Q ss_pred             EEecC
Q 003038          777 ILSCE  781 (854)
Q Consensus       777 IlTsn  781 (854)
                      |+||+
T Consensus       139 I~~s~  143 (247)
T d1ny5a2         139 LAATN  143 (247)
T ss_dssp             EEEES
T ss_pred             EEecC
Confidence            88875

>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=98.93  E-value=1.1e-09  Score=117.57  Aligned_cols=142  Identities=13%  Similarity=0.093  Sum_probs=89.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..|+||++++..|.-+....                  ..+.+||.||+|+|||++||.||..|    ..+..+...++.
T Consensus         7 ~~I~Gq~~~kral~laa~~~------------------~~h~vLl~G~pG~GKT~lar~~~~iL----p~~~~~~~~~~~   64 (333)
T d1g8pa_           7 SAIVGQEDMKLALLLTAVDP------------------GIGGVLVFGDRGTGKSTAVRALAALL----PEIEAVEGCPVS   64 (333)
T ss_dssp             GGSCSCHHHHHHHHHHHHCG------------------GGCCEEEECCGGGCTTHHHHHHHHHS----CCEEEETTCTTC
T ss_pred             hhccCcHHHHHHHHHHHhcc------------------CCCeEEEECCCCccHHHHHHHHHHhC----CCchhhccCccc
Confidence            46899999998766544311                  12579999999999999999999988    345555544443


Q ss_pred             CcCCCcc-cccc------ccc--c-C-CCCCCchHHHHH------------------HHHHcCCCEEEEEecCCCCCHHH
Q 003038          698 STRADST-EDSR------NKR--S-R-DEQSCSYIERFA------------------EAVSNNPHRVFLIEDVEQADYCS  748 (854)
Q Consensus       698 ~~~~~s~-e~~~------~~r--l-~-~~~g~g~~e~L~------------------eav~~~p~~ViliDEieka~~~v  748 (854)
                      ....... +...      ..+  . . .+.+... ..+.                  ..+....+.|+||||++++++.+
T Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~l~G~~d~~~~~~~g~~~~~~G~l~~A~~gvl~iDEi~~~~~~~  143 (333)
T d1g8pa_          65 SPNVEMIPDWATVLSTNVIRKPTPVVDLPLGVSE-DRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLLEDHI  143 (333)
T ss_dssp             CSSGGGSCTTCCCSCCCEEEECCCEEEECTTCCH-HHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGSCHHH
T ss_pred             cCccccccchhhccccCcccccCceeeccCCCCc-ccccCcchhhhccccCcceeeccccccccccEeecccHHHHHHHH
Confidence            1100000 0000      000  0 0 0001000 0110                  12222346899999999999999


Q ss_pred             HHHHHHhhhcCeEecC-CCceeecC-CeEEEEecCC
Q 003038          749 QKGFKRAIESGRIVTS-SGDEVSLG-DAIVILSCES  782 (854)
Q Consensus       749 ~~~Ll~~le~G~l~d~-~G~~v~~~-~aIiIlTsn~  782 (854)
                      |+.|+++||+|.++-. .|..+.|. +.++|.|+|.
T Consensus       144 ~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~Np  179 (333)
T d1g8pa_         144 VDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNP  179 (333)
T ss_dssp             HHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECS
T ss_pred             HHHHhhhhcCCeEEecccCceecCCCCEEEEEecCc
Confidence            9999999999999864 46666664 7788888885

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.92  E-value=9e-11  Score=119.18  Aligned_cols=132  Identities=17%  Similarity=0.217  Sum_probs=84.2

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC---CCceEEEccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS---HNNFVSIALS  694 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~---~~~~i~id~s  694 (854)
                      ..|+||++++..|...+..                  +....++|+||+|+|||+++++||+.+++.   ......++.+
T Consensus        12 ~diig~~~~~~~l~~~i~~------------------~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~   73 (237)
T d1sxjd2          12 DEVTAQDHAVTVLKKTLKS------------------ANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNAS   73 (237)
T ss_dssp             TTCCSCCTTHHHHHHHTTC------------------TTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSS
T ss_pred             HHccCcHHHHHHHHHHHHc------------------CCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheecc
Confidence            3479999988887766532                  112358999999999999999999998653   2344556655


Q ss_pred             cccCcCCCccccccccccC-CCCCC-chHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecC
Q 003038          695 SFSSTRADSTEDSRNKRSR-DEQSC-SYIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLG  772 (854)
Q Consensus       695 ~~~~~~~~s~e~~~~~rl~-~~~g~-g~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~  772 (854)
                      ......... +  .+.... ..... ..  ...+.....++.||+|||+|+++.+.++.|+..++...           .
T Consensus        74 ~~~~~~~~~-~--~~~~~~~~~~~~~~~--~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~-----------~  137 (237)
T d1sxjd2          74 DERGISIVR-E--KVKNFARLTVSKPSK--HDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYS-----------G  137 (237)
T ss_dssp             SCCCHHHHT-T--HHHHHHHSCCCCCCT--THHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTT-----------T
T ss_pred             ccccchHHH-H--HHHHHhhhhhhhhhH--HHHhhccccCceEEEEecccccCHHHHHHHhhcccccc-----------c
Confidence            443100000 0  000000 00000 00  12333455678899999999999999999999998642           5


Q ss_pred             CeEEEEecCCC
Q 003038          773 DAIVILSCESF  783 (854)
Q Consensus       773 ~aIiIlTsn~f  783 (854)
                      +++||++++..
T Consensus       138 ~~~~i~~~~~~  148 (237)
T d1sxjd2         138 VTRFCLICNYV  148 (237)
T ss_dssp             TEEEEEEESCG
T ss_pred             ccccccccccc
Confidence            67788887643

>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=98.92  E-value=9.7e-10  Score=112.41  Aligned_cols=138  Identities=12%  Similarity=0.164  Sum_probs=76.6

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS  698 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~  698 (854)
                      .++||++++..|...+...                 +-...+||+||+|+|||++|+++|+.+++.......++...+..
T Consensus        12 diig~~~~~~~L~~~~~~~-----------------~~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~~~~~   74 (252)
T d1sxje2          12 ALSHNEELTNFLKSLSDQP-----------------RDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVT   74 (252)
T ss_dssp             GCCSCHHHHHHHHTTTTCT-----------------TCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC----------
T ss_pred             HccCcHHHHHHHHHHHHcC-----------------CCCCeEEEECCCCCCHHHHHHHHHHhhcCccccccccccccccc
Confidence            4899998888775543321                 11235899999999999999999999987554444444333221


Q ss_pred             cCCCcc--ccccccc--cCCCCCCchH-----HHHHH--------------HHHcCCCEEEEEecCCCCCHHHHHHHHHh
Q 003038          699 TRADST--EDSRNKR--SRDEQSCSYI-----ERFAE--------------AVSNNPHRVFLIEDVEQADYCSQKGFKRA  755 (854)
Q Consensus       699 ~~~~s~--e~~~~~r--l~~~~g~g~~-----e~L~e--------------av~~~p~~ViliDEieka~~~v~~~Ll~~  755 (854)
                      ......  .......  .+.....+..     .....              .....++.||+|||+|.++.+.++.|++.
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiide~d~l~~~~~~~l~~~  154 (252)
T d1sxje2          75 ASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRT  154 (252)
T ss_dssp             --------CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSCHHHHHHHHHH
T ss_pred             cccchhhhhhccCCccceeeecccccCCcceeeehhhhhhhhhhhhhhhcccccCCCceEEEeccccccccccchhhhcc
Confidence            000000  0000000  0000000100     01111              11134567999999999999999999999


Q ss_pred             hhcCeEecCCCceeecCCeEEEEecCCCC
Q 003038          756 IESGRIVTSSGDEVSLGDAIVILSCESFS  784 (854)
Q Consensus       756 le~G~l~d~~G~~v~~~~aIiIlTsn~f~  784 (854)
                      +++.           -.+++||++||..+
T Consensus       155 ~e~~-----------~~~~~~Il~tn~~~  172 (252)
T d1sxje2         155 MEKY-----------SKNIRLIMVCDSMS  172 (252)
T ss_dssp             HHHS-----------TTTEEEEEEESCSC
T ss_pred             cccc-----------cccccceeeecccc
Confidence            9952           35678999998654

>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=98.91  E-value=3.2e-09  Score=105.79  Aligned_cols=97  Identities=15%  Similarity=0.274  Sum_probs=71.9

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCC---CceEEEccccccCcCCCccccccccccCCCCCCchHH--HHHHHHHc
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSH---NNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIE--RFAEAVSN  730 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~---~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e--~L~eav~~  730 (854)
                      ...++||+||+|+|||.+|+.||+.+....   ..|+.++..                    +...|.++  .+.+.+..
T Consensus        14 ~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~--------------------~~~I~Id~IR~i~~~~~~   73 (198)
T d2gnoa2          14 EGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPE--------------------GENIGIDDIRTIKDFLNY   73 (198)
T ss_dssp             SSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCS--------------------SSCBCHHHHHHHHHHHTS
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCC--------------------cCCCCHHHHHHHHHHHhh
Confidence            346999999999999999999999885432   224444311                    01114444  46666665


Q ss_pred             CC----CEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCCC
Q 003038          731 NP----HRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCESF  783 (854)
Q Consensus       731 ~p----~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~f  783 (854)
                      .|    ++||+|||+|+++...||+||+.||+-           -.+++|||+|+.-
T Consensus        74 ~~~~~~~KviIId~ad~l~~~aqNaLLK~LEEP-----------p~~t~fiLit~~~  119 (198)
T d2gnoa2          74 SPELYTRKYVIVHDCERMTQQAANAFLKALEEP-----------PEYAVIVLNTRRW  119 (198)
T ss_dssp             CCSSSSSEEEEETTGGGBCHHHHHHTHHHHHSC-----------CTTEEEEEEESCG
T ss_pred             CcccCCCEEEEEeCccccchhhhhHHHHHHhCC-----------CCCceeeeccCCh
Confidence            55    579999999999999999999999972           2688999999753

>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=98.84  E-value=7.3e-09  Score=107.33  Aligned_cols=129  Identities=15%  Similarity=0.102  Sum_probs=85.3

Q ss_pred             CcccccHHHHHHHHHHHHHh--------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceE
Q 003038          618 KKVPWQKDTVYDIANTVLKC--------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFV  689 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~--------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i  689 (854)
                      ..|.|++.+++.|...|...        +.|+.             +...+||+||+|||||.+|+++|..+   ...|+
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~-------------~~~giLL~GppGtGKT~l~~ala~~~---~~~~~   67 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVK-------------PPRGILLYGPPGTGKTLIARAVANET---GAFFF   67 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCC-------------CCCEEEEECCTTSSHHHHHHHHHHHT---TCEEE
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCC-------------CCceeEEecCCCCCchHHHHHHHHHh---CCeEE
Confidence            35899999999998887531        22332             22358999999999999999999987   46788


Q ss_pred             EEccccccCcCCCccccccccccCCCCCC--chHHHHHHHHHcCCCEEEEEecCCCCCH-----------HHHHHHHHhh
Q 003038          690 SIALSSFSSTRADSTEDSRNKRSRDEQSC--SYIERFAEAVSNNPHRVFLIEDVEQADY-----------CSQKGFKRAI  756 (854)
Q Consensus       690 ~id~s~~~~~~~~s~e~~~~~rl~~~~g~--g~~e~L~eav~~~p~~ViliDEieka~~-----------~v~~~Ll~~l  756 (854)
                      .++++.+..       ..        .|.  .....+....+.+..+||||||+|..-+           .+.+.++..+
T Consensus        68 ~i~~~~l~~-------~~--------~g~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~  132 (258)
T d1e32a2          68 LINGPEIMS-------KL--------AGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLM  132 (258)
T ss_dssp             EECHHHHTT-------SC--------TTHHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHH
T ss_pred             EEEchhhcc-------cc--------cccHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCCCCchHHHHHHHhcccc
Confidence            888775541       10        011  1112455566667779999999998742           2445555555


Q ss_pred             hcCeEecCCCceeecCCeEEEEecCCCCCC
Q 003038          757 ESGRIVTSSGDEVSLGDAIVILSCESFSSR  786 (854)
Q Consensus       757 e~G~l~d~~G~~v~~~~aIiIlTsn~f~~~  786 (854)
                      +.-         ..-.+.+||+|||.-+..
T Consensus       133 ~~~---------~~~~~vlvi~tTn~~~~l  153 (258)
T d1e32a2         133 DGL---------KQRAHVIVMAATNRPNSI  153 (258)
T ss_dssp             HTC---------CCSSCEEEEEEESCGGGS
T ss_pred             ccc---------cccCCccEEEeCCCcccc
Confidence            421         122457889999865444

>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=98.81  E-value=3.1e-09  Score=110.71  Aligned_cols=129  Identities=12%  Similarity=0.121  Sum_probs=82.1

Q ss_pred             cccccHHHHHHHHHHHHHh--------hcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEE
Q 003038          619 KVPWQKDTVYDIANTVLKC--------RSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVS  690 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~--------rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~  690 (854)
                      .|.|.++++..|...|...        ..|+.             +...+||+||+|+|||.+|++||..+   ..+|+.
T Consensus         8 di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~-------------~~~giLL~Gp~GtGKT~l~~ala~~~---~~~~~~   71 (265)
T d1r7ra3           8 DIGGLEDVKRELQELVQYPVEHPDKFLKFGMT-------------PSKGVLFYGPPGCGKTLLAKAIANEC---QANFIS   71 (265)
T ss_dssp             SCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCC-------------CCCEEEEBCCTTSSHHHHHHHHHHHT---TCEEEE
T ss_pred             HhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCC-------------CCCeEEEECCCCCcchhHHHHHHHHh---CCcEEE
Confidence            4667777666666655321        12332             23368999999999999999999998   467888


Q ss_pred             EccccccCcCCCccccccccccCCCCCC--chHHHHHHHHHcCCCEEEEEecCCCCCHH--------------HHHHHHH
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSC--SYIERFAEAVSNNPHRVFLIEDVEQADYC--------------SQKGFKR  754 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~--g~~e~L~eav~~~p~~ViliDEieka~~~--------------v~~~Ll~  754 (854)
                      ++++.+..       ..        .+.  .....++...+.+..+||+|||+|.+-..              +.+.|+.
T Consensus        72 ~~~~~l~~-------~~--------~~~~~~~l~~~f~~A~~~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~  136 (265)
T d1r7ra3          72 IKGPELLT-------MW--------FGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILT  136 (265)
T ss_dssp             ECHHHHHT-------SC--------TTTHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHH
T ss_pred             EEHHHhhh-------cc--------ccchHHHHHHHHHHHHhcCCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHH
Confidence            88776541       00        011  12224555556666699999999977432              4567777


Q ss_pred             hhhcCeEecCCCceeecCCeEEEEecCCCCCCC
Q 003038          755 AIESGRIVTSSGDEVSLGDAIVILSCESFSSRS  787 (854)
Q Consensus       755 ~le~G~l~d~~G~~v~~~~aIiIlTsn~f~~~s  787 (854)
                      .|+. .        ..-.+.+||+|||.-+...
T Consensus       137 ~l~~-~--------~~~~~v~vi~ttn~~~~ld  160 (265)
T d1r7ra3         137 EMDG-M--------STKKNVFIIGATNRPDIID  160 (265)
T ss_dssp             TCC---------------CCEEEECCBSCTTTS
T ss_pred             HhhC-c--------CCCCCEEEEEeCCCchhCC
Confidence            7752 1        1223578999998765543

>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=98.72  E-value=1e-08  Score=104.85  Aligned_cols=134  Identities=13%  Similarity=0.063  Sum_probs=77.1

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +.++||+++++.|...|................ ....+...+||+||+|+|||++|++||+.+.   ..++.+++++..
T Consensus        14 ~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~-~~~~~~~~lll~GPpG~GKTt~a~~la~~~~---~~~~~~~~~~~~   89 (253)
T d1sxja2          14 QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGK-DGSGVFRAAMLYGPPGIGKTTAAHLVAQELG---YDILEQNASDVR   89 (253)
T ss_dssp             GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCT-TSTTSCSEEEEECSTTSSHHHHHHHHHHHTT---CEEEEECTTSCC
T ss_pred             HHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcc-cCCCCCceEEEECCCCCCHHHHHHHHHHHHH---hhhhccccccch
Confidence            568999999999988876432110000000000 0012334799999999999999999999984   357788877654


Q ss_pred             CcCCCccccccccccCCCC-CCc-hHHHHHHHHHcCCCEEEEEecCCCCCHHHHHHHHHhhhc
Q 003038          698 STRADSTEDSRNKRSRDEQ-SCS-YIERFAEAVSNNPHRVFLIEDVEQADYCSQKGFKRAIES  758 (854)
Q Consensus       698 ~~~~~s~e~~~~~rl~~~~-g~g-~~e~L~eav~~~p~~ViliDEieka~~~v~~~Ll~~le~  758 (854)
                      .....   .......+... ... +...........++.|+++||++.+....+..+...++.
T Consensus        90 ~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~~~~~~~~~~~~~  149 (253)
T d1sxja2          90 SKTLL---NAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQF  149 (253)
T ss_dssp             CHHHH---HHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHH
T ss_pred             hhHHH---HHHHHHHhhcchhhhhhhhhhhcccccccceEEEeeeccccccchhhhhHHHhhh
Confidence            20000   00011111000 000 000111112345678999999999999988887777764

>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=98.71  E-value=8.7e-09  Score=114.71  Aligned_cols=80  Identities=16%  Similarity=0.227  Sum_probs=62.3

Q ss_pred             HHHHHhhcCcccccHHHHHHHHHHHHHhh--cCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc
Q 003038          610 TSLCNALEKKVPWQKDTVYDIANTVLKCR--SGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN  687 (854)
Q Consensus       610 ~~L~~~L~~~V~GQ~~av~~Ia~~v~~~r--sgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~  687 (854)
                      +.+.++|.+.|+||++|.+.|+-+|..+.  ..+....+.      .-..-.+||.||||||||+|||.||+.+   .-+
T Consensus         6 ~~i~~~Ld~yVvGQ~~AKk~lsvav~nhyrR~~~~~~~~~------ei~ksNILliGPTGvGKTlLAr~LAk~l---~VP   76 (443)
T d1g41a_           6 REIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLRH------EVTPKNILMIGPTGVGKTEIARRLAKLA---NAP   76 (443)
T ss_dssp             HHHHHHHHTTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTT------TCCCCCEEEECCTTSSHHHHHHHHHHHT---TCC
T ss_pred             HHHHHHhcCcccCcHHHHHHHHHHHHHHHHHhhccccccc------ccccccEEEECCCCCCHHHHHHHHHHHh---CCC
Confidence            57899999999999999999999996542  211111100      0111279999999999999999999988   689


Q ss_pred             eEEEccccccC
Q 003038          688 FVSIALSSFSS  698 (854)
Q Consensus       688 ~i~id~s~~~~  698 (854)
                      |+.+|++.|++
T Consensus        77 Fv~~daT~fTe   87 (443)
T d1g41a_          77 FIKVEATKFTE   87 (443)
T ss_dssp             EEEEEGGGGC-
T ss_pred             EEEeecceeee
Confidence            99999999994

>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=98.71  E-value=1.1e-08  Score=108.86  Aligned_cols=99  Identities=14%  Similarity=0.227  Sum_probs=68.1

Q ss_pred             cceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHH---HHHHHHHcCC
Q 003038          656 EETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIE---RFAEAVSNNP  732 (854)
Q Consensus       656 p~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e---~L~eav~~~p  732 (854)
                      |.+.+||+||||||||.+|++||..+ |...+|+.++++++.       .++.        | .+.+   .+++..++  
T Consensus       122 ~~g~~l~~G~pG~GKT~la~ala~~~-~~~~~~~~~~~~~~~-------~~~~--------G-~~e~~~~~~f~~a~~--  182 (321)
T d1w44a_         122 ASGMVIVTGKGNSGKTPLVHALGEAL-GGKDKYATVRFGEPL-------SGYN--------T-DFNVFVDDIARAMLQ--  182 (321)
T ss_dssp             ESEEEEEECSSSSCHHHHHHHHHHHH-HTTSCCEEEEBSCSS-------TTCB--------C-CHHHHHHHHHHHHHH--
T ss_pred             CCceEEEECCCCccHHHHHHHHHHHh-cCCCCeEEEEhhHhh-------hccc--------c-hHHHHHHHHHHHHhh--
Confidence            55789999999999999999999998 445688999988776       2111        1 1222   45555554  


Q ss_pred             CEEEEEecCCCCCH------------HHHHHHHHhhhcCeEecCCCceeecCCeEEEEecCC
Q 003038          733 HRVFLIEDVEQADY------------CSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCES  782 (854)
Q Consensus       733 ~~ViliDEieka~~------------~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn~  782 (854)
                      .+||||||||.+.+            .+.|.||.-||.-         .+.++.|||.++|.
T Consensus       183 ~~ilf~DEid~~~~~r~~~~~~~~~~r~v~~lL~e~dg~---------~~~~~v~viaatN~  235 (321)
T d1w44a_         183 HRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAM---------AASRGCVVIASLNP  235 (321)
T ss_dssp             CSEEEEECCTTTC-----------CCHHHHHHHHHHHHH---------HHHHTCEEEEECCC
T ss_pred             ccEEEeehhhhhccccccCCCCCcchhhhhhhhhhcccc---------ccCCCeEEEEeCCC
Confidence            46999999998743            2444555555410         12357889999984

>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=98.70  E-value=8.5e-09  Score=106.11  Aligned_cols=161  Identities=8%  Similarity=0.039  Sum_probs=92.3

Q ss_pred             cHHHHHHHHHHhhcc-----CcCC----ceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccccc-----
Q 003038          211 RNEDVMYVIENLMSK-----RKRN----FVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHM-----  276 (854)
Q Consensus       211 r~~ei~~v~~~L~r~-----~k~n----~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~-----  276 (854)
                      |++|++++..+|.+.     ...|    .+|+||||||||++++.++..+.....+ .....+++.++.......     
T Consensus        21 Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~   99 (287)
T d1w5sa2          21 RRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAK-EGLTVKQAYVNAFNAPNLYTILS   99 (287)
T ss_dssp             SCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHH-TTCCEEEEEEEGGGCCSHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhccc-ccCCceeeeeccccccchhhHHH
Confidence            999999999987543     2222    2457999999999999999987542211 112244554544333221     


Q ss_pred             -----------chHHHHHHHH-HHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCC
Q 003038          277 -----------NRVEVEQRVE-EIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGE  343 (854)
Q Consensus       277 -----------~rge~E~rl~-~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g  343 (854)
                                 +.|.....+. .+....+.. +.+.++++||++.+ .......        ...+..+.+.+++.+..+
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~iide~d~l~~~~~~~~--------~~~~~l~~l~~~l~~~~~  170 (287)
T d1w5sa2         100 LIVRQTGYPIQVRGAPALDILKALVDNLYVE-NHYLLVILDEFQSMLSSPRIAA--------EDLYTLLRVHEEIPSRDG  170 (287)
T ss_dssp             HHHHHHTCCCCCTTCCHHHHHHHHHHHHHHH-TCEEEEEEESTHHHHSCTTSCH--------HHHHHHHTHHHHSCCTTS
T ss_pred             HHhhhcccccccccchHHHHHHHHHHHHHhc-cCccccceeEEEEeccccccch--------hHHHHHHHHHHhcchhhc
Confidence                       2233333333 344444443 66889999999999 6544210        111233334444544223


Q ss_pred             CceEEEEEecCHHHHHHhh-ccCCchhhhhccCCCCCCCc
Q 003038          344 NARFWLMGIATFQSYMRCK-SGHPSLETLWSLHPLTIPAG  382 (854)
Q Consensus       344 ~g~l~lIgatT~~ey~k~~-~~~pale~~~~~~~v~i~~~  382 (854)
                      ...+++|++++..+|...+ ...|.+.+++ .+.+.++..
T Consensus       171 ~~~~~~i~i~~~~~~~~~~~~~~~~~~~r~-~~~i~f~~y  209 (287)
T d1w5sa2         171 VNRIGFLLVASDVRALSYMREKIPQVESQI-GFKLHLPAY  209 (287)
T ss_dssp             CCBEEEEEEEEETHHHHHHHHHCHHHHTTC-SEEEECCCC
T ss_pred             ccceeEEeecccHHHHHHHHhhccchhccc-ceeeeccCC
Confidence            3479999999887776543 3456655421 234444443

>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=98.61  E-value=1.1e-08  Score=108.72  Aligned_cols=78  Identities=8%  Similarity=0.203  Sum_probs=64.4

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc--cchHHHHHHHHHHHHHHHhhh---CCCe
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH--MNRVEVEQRVEEIKNLVRSCL---GRGI  300 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~--~~rge~E~rl~~l~~~~~~~~---~~~~  300 (854)
                      .+.+++|+||||||||.+|++||..+          +..++.++++.+..  .+.|+.+..+..++..+....   ..++
T Consensus        48 ~~~~iLl~GPpG~GKT~lAkalA~~~----------~~~~~~i~~s~~~~~~~~~~~~~~~~~~~f~~a~~~~~~~~~~~  117 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIARRLAKLA----------NAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNG  117 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHH----------TCCEEEEEGGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHC
T ss_pred             CCceEEEECCCCCCHHHHHHHHhhcc----------ccchhcccccccccceeEeeeccccccccchhhhcccccccCCc
Confidence            46899999999999999999999874          45799999999974  378999999999998875421   1368


Q ss_pred             EEEeCccccc-ccc
Q 003038          301 VLNLGDLEWA-EFR  313 (854)
Q Consensus       301 ILfidel~~l-~~~  313 (854)
                      |||||||+.+ ..+
T Consensus       118 IIf~DEIdki~~~~  131 (309)
T d1ofha_         118 IVFIDEIDKICKKG  131 (309)
T ss_dssp             EEEEECGGGGSCCS
T ss_pred             eEEehhhhhhhhhc
Confidence            9999999999 543

>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=98.55  E-value=1.7e-07  Score=95.48  Aligned_cols=150  Identities=10%  Similarity=-0.034  Sum_probs=94.3

Q ss_pred             cHHHHHHHHHHhhcc------CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc---------
Q 003038          211 RNEDVMYVIENLMSK------RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH---------  275 (854)
Q Consensus       211 r~~ei~~v~~~L~r~------~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~---------  275 (854)
                      ||++|+.+.+.|.+.      ..++++|+||||||||++++.++..+...      .+.+++.++......         
T Consensus        21 Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~------~~~~~~~~~~~~~~~~~~~~~~~~   94 (276)
T d1fnna2          21 REQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDK------TTARFVYINGFIYRNFTAIIGEIA   94 (276)
T ss_dssp             CHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTS------CCCEEEEEETTTCCSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcc------cCCcEEEecchhhhhhhhhhhhhH
Confidence            999999999999753      33689999999999999999999988543      234555554332211         


Q ss_pred             -------cchHH-HHHHHHHHHHHHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhccc--CCCC
Q 003038          276 -------MNRVE-VEQRVEEIKNLVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCG--IGEN  344 (854)
Q Consensus       276 -------~~rge-~E~rl~~l~~~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~--~~g~  344 (854)
                             .+.+. ...-+..+.+.+... ....++++|+++.+ ....                 .....++..  ....
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~d~~~~~~~-----------------~~~~~~~~~~~~~~~  156 (276)
T d1fnna2          95 RSLNIPFPRRGLSRDEFLALLVEHLRER-DLYMFLVLDDAFNLAPDIL-----------------STFIRLGQEADKLGA  156 (276)
T ss_dssp             HHTTCCCCSSCCCHHHHHHHHHHHHHHT-TCCEEEEEETGGGSCHHHH-----------------HHHHHHTTCHHHHSS
T ss_pred             HhhhhhhhhhccchhHHHHHHHHHHhhc-ccccccchhHHHHhhhhhh-----------------hhHHHHHhccccccc
Confidence                   11111 223344455555554 45778888888777 4321                 112223321  1122


Q ss_pred             ceEEEEEecCHHHHHHhhccCCchhhhhccCCCCCCCchHHH
Q 003038          345 ARFWLMGIATFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSL  386 (854)
Q Consensus       345 g~l~lIgatT~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~  386 (854)
                      ..+.+|++++...+..  ..+|.+.+++..+.|.++..+...
T Consensus       157 ~~~~~i~~~~~~~~~~--~~~~~~~~r~~~~~i~~~~~~~~e  196 (276)
T d1fnna2         157 FRIALVIVGHNDAVLN--NLDPSTRGIMGKYVIRFSPYTKDQ  196 (276)
T ss_dssp             CCEEEEEEESSTHHHH--TSCHHHHHHHTTCEEECCCCBHHH
T ss_pred             cceEEeecCCchhhhh--hcchhhhhhhcchhccccchhHHH
Confidence            2599999998877664  357778775555667777766544

>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=98.54  E-value=9.8e-08  Score=94.06  Aligned_cols=111  Identities=11%  Similarity=0.195  Sum_probs=77.8

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC-------CCceEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS-------HNNFVS  690 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-------~~~~i~  690 (854)
                      ..++|.++-+..+...+.+.                  .....+|+||+|||||.++..||+.+-..       ...++.
T Consensus        22 d~~igRd~Ei~~l~~iL~r~------------------~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~   83 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQRR------------------TKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLA   83 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSS------------------SSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEE
T ss_pred             CCCcCcHHHHHHHHHHHhcc------------------CCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEE
Confidence            35799998888887766542                  12367899999999999999999877532       244566


Q ss_pred             EccccccCcCCCccccccccccCCCCCC--chHHHHH---HHH-HcCCCEEEEEecCCCC--------CHHHHHHHHHhh
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSC--SYIERFA---EAV-SNNPHRVFLIEDVEQA--------DYCSQKGFKRAI  756 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~--g~~e~L~---eav-~~~p~~ViliDEieka--------~~~v~~~Ll~~l  756 (854)
                      +|++.                ++++..|  .+.+++.   +.+ ...+.-|+||||++.+        ..++-+.|+.+|
T Consensus        84 ld~~~----------------LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L  147 (195)
T d1jbka_          84 LDMGA----------------LVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPAL  147 (195)
T ss_dssp             ECHHH----------------HHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHH
T ss_pred             eeHHH----------------HhccCCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHH
Confidence            66543                3344444  4555443   333 3345679999999976        225779999999


Q ss_pred             hcCeEe
Q 003038          757 ESGRIV  762 (854)
Q Consensus       757 e~G~l~  762 (854)
                      +.|.+.
T Consensus       148 ~rg~l~  153 (195)
T d1jbka_         148 ARGELH  153 (195)
T ss_dssp             HTTSCC
T ss_pred             hCCCce
Confidence            999888

>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=98.46  E-value=2e-07  Score=96.50  Aligned_cols=110  Identities=13%  Similarity=0.198  Sum_probs=78.9

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC-------CCceEEE
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS-------HNNFVSI  691 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-------~~~~i~i  691 (854)
                      .++|.++-+..+...+.+.                  .....+++||+|||||.++..||+.+...       ...++.+
T Consensus        19 ~~igRd~Ei~~l~~iL~r~------------------~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l   80 (268)
T d1r6bx2          19 PLIGREKELERAIQVLCRR------------------RKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSL   80 (268)
T ss_dssp             CCCSCHHHHHHHHHHHTSS------------------SSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEEC
T ss_pred             cccChHHHHHHHHHHHhcC------------------ccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEe
Confidence            5799998888888877542                  12367899999999999999999876532       2344555


Q ss_pred             ccccccCcCCCccccccccccCCCCCC--chHHH---HHHHHHcCCCEEEEEecCCCC---------CHHHHHHHHHhhh
Q 003038          692 ALSSFSSTRADSTEDSRNKRSRDEQSC--SYIER---FAEAVSNNPHRVFLIEDVEQA---------DYCSQKGFKRAIE  757 (854)
Q Consensus       692 d~s~~~~~~~~s~e~~~~~rl~~~~g~--g~~e~---L~eav~~~p~~ViliDEieka---------~~~v~~~Ll~~le  757 (854)
                      |++.                ++++..|  .+.++   +.+.+.+++..|+||||++.+         +.++-+.|+.++.
T Consensus        81 ~~~~----------------liag~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~  144 (268)
T d1r6bx2          81 DIGS----------------LLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS  144 (268)
T ss_dssp             CCC-------------------CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS
T ss_pred             eech----------------HhccCccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHh
Confidence            5443                3333334  45553   455566788899999999987         2478999999999


Q ss_pred             cCeEe
Q 003038          758 SGRIV  762 (854)
Q Consensus       758 ~G~l~  762 (854)
                      .|.+.
T Consensus       145 rg~i~  149 (268)
T d1r6bx2         145 SGKIR  149 (268)
T ss_dssp             SCCCE
T ss_pred             CCCCe
Confidence            99888

>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=98.43  E-value=4.8e-07  Score=92.04  Aligned_cols=145  Identities=11%  Similarity=0.033  Sum_probs=90.0

Q ss_pred             cCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC-CCceEEEcccc
Q 003038          617 EKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS-HNNFVSIALSS  695 (854)
Q Consensus       617 ~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-~~~~i~id~s~  695 (854)
                      -++++|++..++.|...|....   .++.         .+...+||+||+|+|||++++.|++.+++. ...++.+++..
T Consensus        15 p~~l~~Re~ei~~l~~~l~~~l---~~~~---------~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~   82 (276)
T d1fnna2          15 PKRLPHREQQLQQLDILLGNWL---RNPG---------HHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFI   82 (276)
T ss_dssp             CSCCTTCHHHHHHHHHHHHHHH---HSTT---------SSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTT
T ss_pred             CCCCCCHHHHHHHHHHHHHHHH---hCCC---------CCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecchh
Confidence            3678999999999988886532   2221         345689999999999999999999999754 34566666655


Q ss_pred             ccCcCCCcccccccccc---CCCCCCchHH---HHHHHH-HcCCCEEEEEecCCCCCHHHHHHHHHhhhcCeEecCCCce
Q 003038          696 FSSTRADSTEDSRNKRS---RDEQSCSYIE---RFAEAV-SNNPHRVFLIEDVEQADYCSQKGFKRAIESGRIVTSSGDE  768 (854)
Q Consensus       696 ~~~~~~~s~e~~~~~rl---~~~~g~g~~e---~L~eav-~~~p~~ViliDEieka~~~v~~~Ll~~le~G~l~d~~G~~  768 (854)
                      +.......  .......   ....+....+   .+.+.+ ......++++|+++..+...++.+...+.....       
T Consensus        83 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~-------  153 (276)
T d1fnna2          83 YRNFTAII--GEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADK-------  153 (276)
T ss_dssp             CCSHHHHH--HHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHH-------
T ss_pred             hhhhhhhh--hhhHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhhhhhhHHHHHhcccc-------
Confidence            44100000  0000000   0111222222   344444 345678899999999999998888877764321       


Q ss_pred             eecCCeEEEEecCC
Q 003038          769 VSLGDAIVILSCES  782 (854)
Q Consensus       769 v~~~~aIiIlTsn~  782 (854)
                      ..-.+.+||++++.
T Consensus       154 ~~~~~~~~i~~~~~  167 (276)
T d1fnna2         154 LGAFRIALVIVGHN  167 (276)
T ss_dssp             HSSCCEEEEEEESS
T ss_pred             ccccceEEeecCCc
Confidence            22235567777764

>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=98.41  E-value=1.2e-08  Score=110.75  Aligned_cols=71  Identities=20%  Similarity=0.246  Sum_probs=53.0

Q ss_pred             HHHHHHHhhcCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc
Q 003038          608 NLTSLCNALEKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN  687 (854)
Q Consensus       608 ~l~~L~~~L~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~  687 (854)
                      ..+..-..|+..+.|+++++..+...+.+   |.  |          ++ ..++|+||||+|||++|++||+.+.+   .
T Consensus       121 ~~~~il~~l~~~~~~~~~~i~~~l~~~~~---~~--~----------~~-~~~~~~g~~~~gk~~~~~~~~~~~~~---~  181 (362)
T d1svma_         121 EWMAGVAWLHCLLPKMDSVVYDFLKCMVY---NI--P----------KK-RYWLFKGPIDSGKTTLAAALLELCGG---K  181 (362)
T ss_dssp             HHHHHHHHHTTTSTTHHHHHHHHHHHHHH---CC--T----------TC-CEEEEECSTTSSHHHHHHHHHHHHCC---E
T ss_pred             HHHHHHHHHHhcccchHHHHHHHHHHHHh---CC--C----------Cc-CeEEEECCCCCCHHHHHHHHHHHcCC---C
Confidence            33455577888899999888766555443   22  1          22 27899999999999999999999954   6


Q ss_pred             eEEEcccccc
Q 003038          688 FVSIALSSFS  697 (854)
Q Consensus       688 ~i~id~s~~~  697 (854)
                      |+++++++..
T Consensus       182 ~i~in~s~~r  191 (362)
T d1svma_         182 ALNVNLPLDR  191 (362)
T ss_dssp             EECCSSCTTT
T ss_pred             EEEEECcchh
Confidence            8889888654

>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=98.27  E-value=9.5e-07  Score=96.17  Aligned_cols=111  Identities=16%  Similarity=0.243  Sum_probs=66.0

Q ss_pred             CcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC-------CCceEE
Q 003038          618 KKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS-------HNNFVS  690 (854)
Q Consensus       618 ~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~-------~~~~i~  690 (854)
                      ..++|.++-|..+...+.+.+                |  ...+++||+|||||.++..||+.+...       ...++.
T Consensus        22 d~~~gr~~ei~~~~~~L~r~~----------------k--~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~   83 (387)
T d1qvra2          22 DPVIGRDEEIRRVIQILLRRT----------------K--NNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVS   83 (387)
T ss_dssp             CCCCSCHHHHHHHHHHHHCSS----------------C--CCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEE
T ss_pred             CCCcCcHHHHHHHHHHHhcCC----------------C--CCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEE
Confidence            357999988888888876421                1  134788999999999999999866432       234666


Q ss_pred             EccccccCcCCCccccccccccCCCCCC--chHHHHHH---HHHc-CCCEEEEEecCCCC--------CHHHHHHHHHhh
Q 003038          691 IALSSFSSTRADSTEDSRNKRSRDEQSC--SYIERFAE---AVSN-NPHRVFLIEDVEQA--------DYCSQKGFKRAI  756 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~~~~rl~~~~g~--g~~e~L~e---av~~-~p~~ViliDEieka--------~~~v~~~Ll~~l  756 (854)
                      +|++.+                +++..|  .+.+++..   .+.. ++.-|+||||++.+        ..++-|.|+.+|
T Consensus        84 ld~~~l----------------~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L  147 (387)
T d1qvra2          84 LQMGSL----------------LAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPAL  147 (387)
T ss_dssp             ECC---------------------------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHH
T ss_pred             eeHhhh----------------hcccCcchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHH
Confidence            665543                334444  45554433   3333 45678999999987        357889999999


Q ss_pred             hcCeEe
Q 003038          757 ESGRIV  762 (854)
Q Consensus       757 e~G~l~  762 (854)
                      ..|.++
T Consensus       148 ~rg~~~  153 (387)
T d1qvra2         148 ARGELR  153 (387)
T ss_dssp             HTTCCC
T ss_pred             hCCCcc
Confidence            999988

>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=98.20  E-value=9.7e-07  Score=88.68  Aligned_cols=142  Identities=7%  Similarity=-0.023  Sum_probs=86.9

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKN  290 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~  290 (854)
                      .++-+..+...+..++..|.+|+||||+|||++|+.+|..+...     ..+..++.++.++....  ..+.....+...
T Consensus        29 ~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak~l~~~-----~~~~~~~e~n~s~~~~~--~~~~~~~~~~~~  101 (231)
T d1iqpa2          29 QEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGE-----NWRHNFLELNASDERGI--NVIREKVKEFAR  101 (231)
T ss_dssp             CHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGG-----GHHHHEEEEETTCHHHH--HTTHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHHhc-----ccCCCeeEEecCcccch--hHHHHHHHHHHh
Confidence            56777888888888888899999999999999999999987532     12345666665543321  111122222111


Q ss_pred             HHHhhhCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHHHhhccCCchh
Q 003038          291 LVRSCLGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYMRCKSGHPSLE  369 (854)
Q Consensus       291 ~~~~~~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~k~~~~~pale  369 (854)
                      ........+.|++|||++.+ ....                 .-+..++.....  .+.+|.+|+...     ...++|.
T Consensus       102 ~~~~~~~~~~iilide~d~~~~~~~-----------------~~ll~~l~~~~~--~~~~i~~~n~~~-----~i~~~l~  157 (231)
T d1iqpa2         102 TKPIGGASFKIIFLDEADALTQDAQ-----------------QALRRTMEMFSS--NVRFILSCNYSS-----KIIEPIQ  157 (231)
T ss_dssp             SCCGGGCSCEEEEEETGGGSCHHHH-----------------HHHHHHHHHTTT--TEEEEEEESCGG-----GSCHHHH
T ss_pred             hhhccCCCceEEeehhhhhcchhHH-----------------HHHhhhcccCCc--ceEEEeccCChh-----hchHhHh
Confidence            11111135789999999988 4321                 123334421123  377787776432     3567787


Q ss_pred             hhhccCCCCCCCchHH
Q 003038          370 TLWSLHPLTIPAGSLS  385 (854)
Q Consensus       370 ~~~~~~~v~i~~~sl~  385 (854)
                      .  |++.+.++.+.-.
T Consensus       158 s--R~~~i~~~~~~~~  171 (231)
T d1iqpa2         158 S--RCAIFRFRPLRDE  171 (231)
T ss_dssp             H--TEEEEECCCCCHH
T ss_pred             C--ccccccccccchh
Confidence            7  7777777776543

>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=98.06  E-value=3.8e-06  Score=84.54  Aligned_cols=64  Identities=13%  Similarity=0.096  Sum_probs=44.2

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhhCCCeEEEeCc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCLGRGIVLNLGD  306 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~~~~~ILfide  306 (854)
                      .+|.+|+||||||||++|+.+|..+          +..++.++...+.  ..++    +..++.   .. ..+.++||||
T Consensus        35 ~~~~L~~GPpGtGKT~lA~~la~~~----------~~~~~~~~~~~~~--~~~~----~~~~~~---~~-~~~~~~~ide   94 (238)
T d1in4a2          35 LDHVLLAGPPGLGKTTLAHIIASEL----------QTNIHVTSGPVLV--KQGD----MAAILT---SL-ERGDVLFIDE   94 (238)
T ss_dssp             CCCEEEESSTTSSHHHHHHHHHHHH----------TCCEEEEETTTCC--SHHH----HHHHHH---HC-CTTCEEEEET
T ss_pred             CCeEEEECCCCCcHHHHHHHHHhcc----------CCCcccccCcccc--cHHH----HHHHHH---hh-ccCCchHHHH
Confidence            4689999999999999999999875          3455555544332  2222    222222   22 4578999999


Q ss_pred             cccc
Q 003038          307 LEWA  310 (854)
Q Consensus       307 l~~l  310 (854)
                      +|.+
T Consensus        95 ~~~~   98 (238)
T d1in4a2          95 IHRL   98 (238)
T ss_dssp             GGGC
T ss_pred             HHHh
Confidence            9999

>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=98.05  E-value=4.1e-06  Score=84.42  Aligned_cols=81  Identities=9%  Similarity=0.108  Sum_probs=52.3

Q ss_pred             cHHHHHHHHHHhhc------cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHH
Q 003038          211 RNEDVMYVIENLMS------KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQR  284 (854)
Q Consensus       211 r~~ei~~v~~~L~r------~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~r  284 (854)
                      ..+++.+.+..+..      ....|++|+||||||||++|+.+|...          +..+..++.+.+.  ..+.....
T Consensus        13 Gq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~----------~~~~~~~~~~~~~--~~~~~~~~   80 (239)
T d1ixsb2          13 GQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL----------GVNLRVTSGPAIE--KPGDLAAI   80 (239)
T ss_dssp             SCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHH----------TCCEEEEETTTCC--SHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHh----------CCCeEeccCCccc--cchhhHHH
Confidence            44555554444432      135689999999999999999999874          4456666655443  33333333


Q ss_pred             HHHHHHHHHhhhCCCeEEEeCccccc
Q 003038          285 VEEIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       285 l~~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                      +.       .....+.|+||||+|.+
T Consensus        81 ~~-------~~~~~~~i~~iDe~~~~   99 (239)
T d1ixsb2          81 LA-------NSLEEGDILFIDEIHRL   99 (239)
T ss_dssp             HH-------TTCCTTCEEEEETGGGC
T ss_pred             HH-------hhccCCCeeeeeccccc
Confidence            22       21134678999999999

>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=97.93  E-value=4.9e-06  Score=83.03  Aligned_cols=138  Identities=11%  Similarity=0.091  Sum_probs=76.0

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKN  290 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~  290 (854)
                      .++.+..+-..+..++..|.+|+||||+|||++|+.+|+.+......     ..++.++.+.....  ......+.....
T Consensus        19 ~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~-----~~~~e~~~~~~~~~--~~~~~~~~~~~~   91 (227)
T d1sxjc2          19 QNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNYS-----NMVLELNASDDRGI--DVVRNQIKDFAS   91 (227)
T ss_dssp             CHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTSHH-----HHEEEECTTSCCSH--HHHHTHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHHhhcCCCc-----ceeEEecccccCCe--eeeecchhhccc
Confidence            45566666666666677789999999999999999999987643211     12344444333221  111111111111


Q ss_pred             HHHhhh-CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhc-ccCCCCceEEEEEecCHHHHHHhhccCCc
Q 003038          291 LVRSCL-GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CGIGENARFWLMGIATFQSYMRCKSGHPS  367 (854)
Q Consensus       291 ~~~~~~-~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~~~g~g~l~lIgatT~~ey~k~~~~~pa  367 (854)
                       ..... .+..|++|||++.+ ....                 ..+.+.+ ++ ..  ...++.+|+..     ....|+
T Consensus        92 -~~~~~~~~~kiiiiDe~d~~~~~~~-----------------~~Ll~~le~~-~~--~~~~~~~~~~~-----~~i~~~  145 (227)
T d1sxjc2          92 -TRQIFSKGFKLIILDEADAMTNAAQ-----------------NALRRVIERY-TK--NTRFCVLANYA-----HKLTPA  145 (227)
T ss_dssp             -BCCSSSCSCEEEEETTGGGSCHHHH-----------------HHHHHHHHHT-TT--TEEEEEEESCG-----GGSCHH
T ss_pred             -cccccCCCeEEEEEeccccchhhHH-----------------HHHHHHhhhc-cc--ceeeccccCcH-----HHhHHH
Confidence             01100 34579999999998 4321                 1233444 22 12  25556555532     135677


Q ss_pred             hhhhhccCCCCCCCch
Q 003038          368 LETLWSLHPLTIPAGS  383 (854)
Q Consensus       368 le~~~~~~~v~i~~~s  383 (854)
                      +.+  |++.+.+..++
T Consensus       146 i~s--r~~~i~~~~~~  159 (227)
T d1sxjc2         146 LLS--QCTRFRFQPLP  159 (227)
T ss_dssp             HHT--TSEEEECCCCC
T ss_pred             HHH--HHhhhcccccc
Confidence            777  55555555443

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.92  E-value=1.8e-05  Score=79.95  Aligned_cols=141  Identities=10%  Similarity=0.019  Sum_probs=81.6

Q ss_pred             cHHHHHHHHHHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCCCc-ccC-------------CceEEEcccccccc
Q 003038          211 RNEDVMYVIENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDVPE-ALR-------------DVKCLPLSISSFRH  275 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~vp~-~L~-------------~~~~~~l~~~~l~~  275 (854)
                      .++-+..+...+...+-.+ .+|+||||+|||++|+.++..+....... .-.             ...++.++.+... 
T Consensus        17 ~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~-   95 (239)
T d1njfa_          17 QEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRT-   95 (239)
T ss_dssp             CHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHHTCCTTEEEEETTCSS-
T ss_pred             hHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchHHHHHHcCCCCeEEEecchhcC-
Confidence            4555666666665444344 78899999999999999999876532110 000             0124444433211 


Q ss_pred             cchHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhc-ccCCCCceEEEEE
Q 003038          276 MNRVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CGIGENARFWLMG  351 (854)
Q Consensus       276 ~~rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~~~g~g~l~lIg  351 (854)
                       ...    -++++++.+....  ++..|++|||++.+ ...                 ...+-..+ .+ ..  ...+|+
T Consensus        96 -~i~----~ir~~~~~~~~~~~~~~~kviiIde~d~l~~~~-----------------q~~Llk~lE~~-~~--~~~~il  150 (239)
T d1njfa_          96 -KVE----DTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHS-----------------FNALLKTLEEP-PE--HVKFLL  150 (239)
T ss_dssp             -SHH----HHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHH-----------------HHHHHHHHHSC-CT--TEEEEE
T ss_pred             -CHH----HHHHHHHHHHhccccCCCEEEEEECcccCCHHH-----------------HHHHHHHHhcC-CC--CeEEEE
Confidence             111    2344555543321  44579999999999 331                 12344444 22 22  478888


Q ss_pred             ecCHHHHHHhhccCCchhhhhccCCCCCCCchH
Q 003038          352 IATFQSYMRCKSGHPSLETLWSLHPLTIPAGSL  384 (854)
Q Consensus       352 atT~~ey~k~~~~~pale~~~~~~~v~i~~~sl  384 (854)
                      +|+...     ...|++.+  |++.+.++.++.
T Consensus       151 ~tn~~~-----~i~~~i~S--Rc~~i~~~~~~~  176 (239)
T d1njfa_         151 ATTDPQ-----KLPVTILS--RCLQFHLKALDV  176 (239)
T ss_dssp             EESCGG-----GSCHHHHT--TSEEEECCCCCH
T ss_pred             EcCCcc-----ccChhHhh--hhcccccccCcH
Confidence            887522     35677877  667777766553

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.89  E-value=1.3e-05  Score=81.57  Aligned_cols=133  Identities=8%  Similarity=-0.041  Sum_probs=73.0

Q ss_pred             cCcccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCC------CCceEE
Q 003038          617 EKKVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGS------HNNFVS  690 (854)
Q Consensus       617 ~~~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~------~~~~i~  690 (854)
                      -.+++|.+.-++.|+..+.+....-..+         ..+...++|+||+|+|||.+++++++.+...      ...++.
T Consensus        15 P~~~~~Re~e~~~l~~~l~~~~~~~~~~---------~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~   85 (287)
T d1w5sa2          15 PPELRVRRGEAEALARIYLNRLLSGAGL---------SDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAY   85 (287)
T ss_dssp             CSSCSSSCHHHHHHHHHHHHHHHTSSCB---------CCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHcCCCC---------CCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeee
Confidence            4678888888888888876654321111         1344567889999999999999999988531      233444


Q ss_pred             EccccccCcCCCccccc-cccccCCCCCCchH---HHHHHHHH-cCCCEEEEEecCCCC------CHHHHHHHHHhhhc
Q 003038          691 IALSSFSSTRADSTEDS-RNKRSRDEQSCSYI---ERFAEAVS-NNPHRVFLIEDVEQA------DYCSQKGFKRAIES  758 (854)
Q Consensus       691 id~s~~~~~~~~s~e~~-~~~rl~~~~g~g~~---e~L~eav~-~~p~~ViliDEieka------~~~v~~~Ll~~le~  758 (854)
                      +++.........-.... .........+....   +.+.+..+ .....++++||++..      ..++...|.+.++.
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~  164 (287)
T d1w5sa2          86 VNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEE  164 (287)
T ss_dssp             EEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHH
T ss_pred             eccccccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEeccccccchhHHHHHHHHHHh
Confidence            55444331000000000 00000011122111   13444444 345678889999854      44566667666653

>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=97.88  E-value=6.8e-06  Score=82.19  Aligned_cols=144  Identities=11%  Similarity=0.059  Sum_probs=80.7

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKN  290 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~  290 (854)
                      .++-+..+...+...+..|.+|+||||+|||++|+.+|+.+...+.    .....+.++.+.....  ..+...+++...
T Consensus        17 ~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~----~~~~~~~~~~~~~~~~--~~~~~~~~~~~~   90 (237)
T d1sxjd2          17 QDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDL----MKSRILELNASDERGI--SIVREKVKNFAR   90 (237)
T ss_dssp             CCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHH----HTTSEEEECSSSCCCH--HHHTTHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHHHcCCcc----cccchhheeccccccc--hHHHHHHHHHhh
Confidence            5556777777777777788999999999999999999998754321    1234444444332211  011111222111


Q ss_pred             ---------HHHhhh-CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhcccCCCCceEEEEEecCHHHHH
Q 003038          291 ---------LVRSCL-GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLVCGIGENARFWLMGIATFQSYM  359 (854)
Q Consensus       291 ---------~~~~~~-~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~g~g~l~lIgatT~~ey~  359 (854)
                               .+.... +..-|+||||++.+ ....                 ..+..++.....  ...+|.+++...  
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~viiiDe~d~l~~~~~-----------------~~l~~~~~~~~~--~~~~i~~~~~~~--  149 (237)
T d1sxjd2          91 LTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQ-----------------SALRRTMETYSG--VTRFCLICNYVT--  149 (237)
T ss_dssp             SCCCCCCTTHHHHSCCCSCEEEEETTGGGSCHHHH-----------------HHHHHHHHHTTT--TEEEEEEESCGG--
T ss_pred             hhhhhhhHHHHhhccccCceEEEEecccccCHHHH-----------------HHHhhccccccc--cccccccccccc--
Confidence                     011110 23458999999999 4321                 122233311112  255555544221  


Q ss_pred             HhhccCCchhhhhccCCCCCCCchHHH
Q 003038          360 RCKSGHPSLETLWSLHPLTIPAGSLSL  386 (854)
Q Consensus       360 k~~~~~pale~~~~~~~v~i~~~sl~~  386 (854)
                         ...+++..  |++.|.+..++...
T Consensus       150 ---~~~~~l~s--r~~~i~f~~~~~~~  171 (237)
T d1sxjd2         150 ---RIIDPLAS--QCSKFRFKALDASN  171 (237)
T ss_dssp             ---GSCHHHHH--HSEEEECCCCCHHH
T ss_pred             ---cccccccc--hhhhhccccccccc
Confidence               34567777  77888888776544

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.86  E-value=1.5e-05  Score=80.39  Aligned_cols=43  Identities=12%  Similarity=0.225  Sum_probs=32.0

Q ss_pred             cHHHHHHHHHHhhccCc--CCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          211 RNEDVMYVIENLMSKRK--RNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k--~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ..+++.+.+..+....+  +|.+|+||||+|||++|+.+|+.+..
T Consensus        15 g~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~~l~~   59 (252)
T d1sxje2          15 HNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFG   59 (252)
T ss_dssp             SCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSC
T ss_pred             CcHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHhhcC
Confidence            34556666655554433  36799999999999999999998744

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.85  E-value=1.3e-05  Score=79.82  Aligned_cols=99  Identities=14%  Similarity=0.190  Sum_probs=65.6

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLI  738 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vili  738 (854)
                      .++++||+|+|||.|+.+++..+......++.+++..+.       .... ..+.    .+....+.+.++  ...+|+|
T Consensus        38 ~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~~~-------~~~~-~~~~----~~~~~~~~~~~~--~~dll~i  103 (213)
T d1l8qa2          38 PIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFA-------QAMV-EHLK----KGTINEFRNMYK--SVDLLLL  103 (213)
T ss_dssp             SEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHHH-------HHHH-HHHH----HTCHHHHHHHHH--TCSEEEE
T ss_pred             cEEEECCCCCcHHHHHHHHHHHhccCccceEEechHHHH-------HHHH-HHHH----ccchhhHHHHHh--hccchhh
Confidence            488999999999999999999987777778888776554       1110 0000    012223444444  3579999


Q ss_pred             ecCCCC--CHHHHHHHHHhhhcCeEecCCCceeecCCeEEEEecC
Q 003038          739 EDVEQA--DYCSQKGFKRAIESGRIVTSSGDEVSLGDAIVILSCE  781 (854)
Q Consensus       739 DEieka--~~~v~~~Ll~~le~G~l~d~~G~~v~~~~aIiIlTsn  781 (854)
                      ||||..  ++..+..|...+..          +.-.+.-+|+||+
T Consensus       104 DDi~~i~~~~~~~~~lf~lin~----------~~~~~~~iiits~  138 (213)
T d1l8qa2         104 DDVQFLSGKERTQIEFFHIFNT----------LYLLEKQIILASD  138 (213)
T ss_dssp             ECGGGGTTCHHHHHHHHHHHHH----------HHHTTCEEEEEES
T ss_pred             hhhhhhcCchHHHHHHHHHHHH----------HhhccceEEEecC
Confidence            999976  57778888887763          1123334677775

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=97.82  E-value=7.2e-06  Score=83.43  Aligned_cols=57  Identities=11%  Similarity=0.147  Sum_probs=42.1

Q ss_pred             HHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          628 YDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       628 ~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      ..+...+.....|....         .+|. .+||+||||+|||++|++||..++   .+|+.+++++|.
T Consensus        13 ~~~~~~~~~~~~~~~~~---------~~P~-~ilL~GpPGtGKT~la~~la~~~~---~~~~~i~~d~~~   69 (273)
T d1gvnb_          13 NRLNDNLEELIQGKKAV---------ESPT-AFLLGGQPGSGKTSLRSAIFEETQ---GNVIVIDNDTFK   69 (273)
T ss_dssp             HHHHHHHHHHHTTCCCC---------SSCE-EEEEECCTTSCTHHHHHHHHHHTT---TCCEEECTHHHH
T ss_pred             HHHHHHHHHHHhcccCC---------CCCE-EEEEECCCCCCHHHHHHHHHHHhh---cceEEEecHHHH
Confidence            34445555555555443         2444 589999999999999999999985   468999998886

>d1khya_ a.174.1.1 (A:) N-terminal domain of ClpB (heat shock protein F84.1) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Escherichia coli [TaxId: 562]

Probab=97.82  E-value=1.9e-05  Score=72.86  Aligned_cols=62  Identities=13%  Similarity=0.163  Sum_probs=54.1

Q ss_pred             HHhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHHH
Q 003038            9 QQGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCFN   74 (854)
Q Consensus         9 ~~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l~   74 (854)
                      ...|++.+.++|+.|..+|+.+|+.+|+++|||+||+.+ ++.+.++|.++|+++   +.|+..++
T Consensus        77 ~~~~s~~~~~vl~~A~~~a~~~~d~~I~~ehlLlall~~-~~~~~~~L~~~gi~~---~~l~~~i~  138 (139)
T d1khya_          77 DVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALES-RGTLADILKAAGATT---ANITQAIE  138 (139)
T ss_dssp             --CBCHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHHTS-CHHHHHHHHHTTCCH---HHHHHHHH
T ss_pred             cccccHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHcC-CcHHHHHHHHcCCCH---HHHHHHhc
Confidence            346999999999999999999999999999999999974 568899999999997   67776654

>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=97.78  E-value=9e-06  Score=89.88  Aligned_cols=73  Identities=8%  Similarity=0.160  Sum_probs=53.8

Q ss_pred             cHHHHHHHHHHhhcc---------------CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccccc-
Q 003038          211 RNEDVMYVIENLMSK---------------RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFR-  274 (854)
Q Consensus       211 r~~ei~~v~~~L~r~---------------~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~-  274 (854)
                      .+++-++++-+-.++               .|+|+||+||+|||||-+|+.||+.+          ++.|+..|...|. 
T Consensus        18 GQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk~l----------~VPFv~~daT~fTe   87 (443)
T d1g41a_          18 GQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA----------NAPFIKVEATKFTE   87 (443)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHT----------TCCEEEEEGGGGC-
T ss_pred             CcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHHHh----------CCCEEEeecceeee
Confidence            556666666664432               38899999999999999999999763          6789999999996 


Q ss_pred             ccchHH-HHHHHHHHHHHHH
Q 003038          275 HMNRVE-VEQRVEEIKNLVR  293 (854)
Q Consensus       275 ~~~rge-~E~rl~~l~~~~~  293 (854)
                      +||.|+ +|.=+.+|+..+.
T Consensus        88 aGYvG~DVesii~~L~~~a~  107 (443)
T d1g41a_          88 VGYVGKEVDSIIRDLTDSAM  107 (443)
T ss_dssp             ---CCCCTHHHHHHHHHHHH
T ss_pred             cceeecchhHHHHHHHHHHh
Confidence            578776 7777777665443

>d1k6ka_ a.174.1.1 (A:) N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone
species: Escherichia coli [TaxId: 562]

Probab=97.77  E-value=1.8e-05  Score=73.19  Aligned_cols=61  Identities=11%  Similarity=0.049  Sum_probs=55.1

Q ss_pred             HhhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcCCcHHHHHHHHcCCChhhHHHHHHHH
Q 003038           10 QGLTAEAASVVKQAMTLARRRGHAQVTPLHVANTMLAASTGLLRTACLQSHSHPLQCKALELCF   73 (854)
Q Consensus        10 ~~fT~~a~~aL~~A~~~A~~~gh~~Vt~eHLLlaLL~~~~s~l~~iL~~~gvd~~~~~aL~~~l   73 (854)
                      ..+|+.+.++++.|..+|..+|+.+|+++|||++|+.++++.+.++|.+.|++.   +++.+.+
T Consensus        78 ~~~s~~l~~il~~A~~~a~~~~~~~i~~ehlLlall~~~~~~a~~lL~~~Gi~~---~~l~~~I  138 (142)
T d1k6ka_          78 TQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSR---LDVVNFI  138 (142)
T ss_dssp             CEECHHHHHHHHHHHHHHHSSSCSCBCHHHHHHHHTTCTTSHHHHHHHHTTCCH---HHHHHHH
T ss_pred             cccCHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHHccCcHHHHHHHHCCCCH---HHHHHHH
Confidence            468999999999999999999999999999999999999999999999999986   4554433

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.77  E-value=3e-05  Score=76.72  Aligned_cols=144  Identities=8%  Similarity=0.008  Sum_probs=84.6

Q ss_pred             HHHHHHHHHhhccCcCC-ceeecCCCCCHHHHHHHHHHHHHcCCC--Cc-c-----------cCCceEEEcccccccccc
Q 003038          213 EDVMYVIENLMSKRKRN-FVVVGECLASIEGVVRGVIDKIEKGDV--PE-A-----------LRDVKCLPLSISSFRHMN  277 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n-~vLvGe~GvGKta~v~~la~~i~~~~v--p~-~-----------L~~~~~~~l~~~~l~~~~  277 (854)
                      +-++++...+...+-.+ .+|+||||+|||++++.+|..+..-+-  .. .           .....++.+....-....
T Consensus         9 ~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~i   88 (207)
T d1a5ta2           9 PDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTL   88 (207)
T ss_dssp             HHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSB
T ss_pred             HHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhccccc
Confidence            45777888888777666 788999999999999999998753211  10 0           001122222111000000


Q ss_pred             hHHHHHHHHHHHHHHHhhh--CCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhc-ccCCCCceEEEEEec
Q 003038          278 RVEVEQRVEEIKNLVRSCL--GRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CGIGENARFWLMGIA  353 (854)
Q Consensus       278 rge~E~rl~~l~~~~~~~~--~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~~~g~g~l~lIgat  353 (854)
                      .   -..++++++.+....  ++.-|++|||+|.+ ...                 ...+-+++ .| ..  .+++|.+|
T Consensus        89 ~---~~~ir~l~~~~~~~~~~~~~kviIide~d~l~~~a-----------------~n~Llk~lEep-~~--~~~fIl~t  145 (207)
T d1a5ta2          89 G---VDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAA-----------------ANALLKTLEEP-PA--ETWFFLAT  145 (207)
T ss_dssp             C---HHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCHHH-----------------HHHHHHHHTSC-CT--TEEEEEEE
T ss_pred             c---cchhhHHhhhhhhccccCccceEEechhhhhhhhh-----------------hHHHHHHHHhh-cc--cceeeeee
Confidence            0   122455666554321  44669999999999 431                 22344555 23 22  37778777


Q ss_pred             CHHHHHHhhccCCchhhhhccCCCCCCCchHHH
Q 003038          354 TFQSYMRCKSGHPSLETLWSLHPLTIPAGSLSL  386 (854)
Q Consensus       354 T~~ey~k~~~~~pale~~~~~~~v~i~~~sl~~  386 (854)
                      +...     ...|++.+  |.+.|.++.++-..
T Consensus       146 ~~~~-----~ll~tI~S--Rc~~i~~~~~~~~~  171 (207)
T d1a5ta2         146 REPE-----RLLATLRS--RCRLHYLAPPPEQY  171 (207)
T ss_dssp             SCGG-----GSCHHHHT--TSEEEECCCCCHHH
T ss_pred             cChh-----hhhhhhcc--eeEEEecCCCCHHH
Confidence            6432     35788888  77888887766443

>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=97.74  E-value=2.2e-05  Score=79.28  Aligned_cols=73  Identities=12%  Similarity=0.099  Sum_probs=47.2

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHH------------HHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKN------------LVR  293 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~------------~~~  293 (854)
                      ..++.+|+||||||||++|+.+|..+          +..++.++.+.+..++  .++..++..+.            ...
T Consensus        51 ~~~~lll~GPpG~GKTt~a~~la~~~----------~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~  118 (253)
T d1sxja2          51 VFRAAMLYGPPGIGKTTAAHLVAQEL----------GYDILEQNASDVRSKT--LLNAGVKNALDNMSVVGYFKHNEEAQ  118 (253)
T ss_dssp             SCSEEEEECSTTSSHHHHHHHHHHHT----------TCEEEEECTTSCCCHH--HHHHTGGGGTTBCCSTTTTTC----C
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHH----------HhhhhccccccchhhH--HHHHHHHHHhhcchhhhhhhhhhhcc
Confidence            45689999999999999999999874          4577777776554431  11111111111            011


Q ss_pred             hhhCCCeEEEeCccccc
Q 003038          294 SCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       294 ~~~~~~~ILfidel~~l  310 (854)
                      ...+...|+++||++.+
T Consensus       119 ~~~~~~~vi~ide~~~~  135 (253)
T d1sxja2         119 NLNGKHFVIIMDEVDGM  135 (253)
T ss_dssp             CSSTTSEEEEECSGGGC
T ss_pred             cccccceEEEeeecccc
Confidence            11145789999999999

>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=97.74  E-value=2.1e-05  Score=78.34  Aligned_cols=142  Identities=9%  Similarity=-0.022  Sum_probs=80.5

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKN  290 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~  290 (854)
                      .++-+..+...+...+..|.+|+||||+|||++|+.+|+.+....     ....++.++.+...+.  ......+.....
T Consensus        20 ~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~-----~~~~~~~~n~~~~~~~--~~i~~~~~~~~~   92 (224)
T d1sxjb2          20 NKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRS-----YADGVLELNASDDRGI--DVVRNQIKHFAQ   92 (224)
T ss_dssp             CTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGG-----HHHHEEEECTTSCCSH--HHHHTHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHHHHHhccc-----cccccccccccccCCc--eehhhHHHHHHH
Confidence            345566666666766777899999999999999999999876432     2234666665544331  111112221111


Q ss_pred             HHHhh-hCCCeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhc-ccCCCCceEEEEEecCHHHHHHhhccCCc
Q 003038          291 LVRSC-LGRGIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CGIGENARFWLMGIATFQSYMRCKSGHPS  367 (854)
Q Consensus       291 ~~~~~-~~~~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~~~g~g~l~lIgatT~~ey~k~~~~~pa  367 (854)
                      ..... ....-|++|||+|.+ +....                 -+...+ .+ ..  ...+|.+|+...     ...++
T Consensus        93 ~~~~~~~~~~kviiiDe~d~~~~~~~~-----------------~ll~~~e~~-~~--~~~~i~~~~~~~-----~i~~~  147 (224)
T d1sxjb2          93 KKLHLPPGKHKIVILDEADSMTAGAQQ-----------------ALRRTMELY-SN--STRFAFACNQSN-----KIIEP  147 (224)
T ss_dssp             BCCCCCTTCCEEEEEESGGGSCHHHHH-----------------TTHHHHHHT-TT--TEEEEEEESCGG-----GSCHH
T ss_pred             hhccCCCcceEEEEEecccccchhHHH-----------------HHhhhcccc-cc--ceeeeeccCchh-----hhhhH
Confidence            11000 034579999999999 44221                 011122 22 12  244555544221     34677


Q ss_pred             hhhhhccCCCCCCCchHHH
Q 003038          368 LETLWSLHPLTIPAGSLSL  386 (854)
Q Consensus       368 le~~~~~~~v~i~~~sl~~  386 (854)
                      |.+  |++.+.++.++...
T Consensus       148 l~s--r~~~i~~~~~~~~~  164 (224)
T d1sxjb2         148 LQS--QCAILRYSKLSDED  164 (224)
T ss_dssp             HHT--TSEEEECCCCCHHH
T ss_pred             HHH--HHHHhhhcccchhh
Confidence            877  67777887776444

>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=97.66  E-value=6.4e-05  Score=75.76  Aligned_cols=37  Identities=14%  Similarity=0.182  Sum_probs=32.7

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      |++||+++.+.    .+++++|+||+|+|||++++.++..+
T Consensus        17 R~~el~~l~~~----~~~~i~i~G~~G~GKTsLl~~~~~~~   53 (283)
T d2fnaa2          17 REKEIEKLKGL----RAPITLVLGLRRTGKSSIIKIGINEL   53 (283)
T ss_dssp             CHHHHHHHHHT----CSSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             hHHHHHHHHhc----cCCEEEEEcCCCCcHHHHHHHHHHHC
Confidence            99999998753    56789999999999999999998875

>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=97.58  E-value=1.9e-06  Score=93.06  Aligned_cols=41  Identities=15%  Similarity=0.191  Sum_probs=34.6

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH  275 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~  275 (854)
                      .++++++|+||||||||+++.+||..+          +..|++++.+...+
T Consensus       152 ~~~~~~~~~g~~~~gk~~~~~~~~~~~----------~~~~i~in~s~~rs  192 (362)
T d1svma_         152 PKKRYWLFKGPIDSGKTTLAAALLELC----------GGKALNVNLPLDRL  192 (362)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHH----------CCEEECCSSCTTTH
T ss_pred             CCcCeEEEECCCCCCHHHHHHHHHHHc----------CCCEEEEECcchhh
Confidence            477899999999999999999999774          55899998776544

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.55  E-value=5.6e-05  Score=79.69  Aligned_cols=71  Identities=11%  Similarity=0.128  Sum_probs=48.5

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc------------cchHHHHHHHHHHHHHHHhhh
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH------------MNRVEVEQRVEEIKNLVRSCL  296 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~------------~~rge~E~rl~~l~~~~~~~~  296 (854)
                      +.+|+||+|||||.+|+.||+.+-..       +..++.++++.+..            ||.|.-+  -..|.+.+++. 
T Consensus        55 ~~lf~Gp~G~GKt~lak~la~~l~~~-------~~~~~~~~~~~~~~~~~~~~L~g~~~gyvG~~~--~~~l~~~~~~~-  124 (315)
T d1qvra3          55 SFLFLGPTGVGKTELAKTLAATLFDT-------EEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEE--GGQLTEAVRRR-  124 (315)
T ss_dssp             EEEEBSCSSSSHHHHHHHHHHHHHSS-------GGGEEEECTTTCCSSGGGGGC----------------CHHHHHHHC-
T ss_pred             EEEEECCCcchHHHHHHHHHHHhcCC-------CcceEEEeccccccchhhhhhcCCCCCCcCccc--CChHHHHHHhC-
Confidence            56788999999999999999987432       34788898876642            4666422  13355666665 


Q ss_pred             CCCeEEEeCccccc
Q 003038          297 GRGIVLNLGDLEWA  310 (854)
Q Consensus       297 ~~~~ILfidel~~l  310 (854)
                       +..|+++|||+-+
T Consensus       125 -p~~Vvl~DEieK~  137 (315)
T d1qvra3         125 -PYSVILFDEIEKA  137 (315)
T ss_dssp             -SSEEEEESSGGGS
T ss_pred             -CCcEEEEehHhhc
Confidence             5789999999877

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.48  E-value=9.5e-05  Score=77.87  Aligned_cols=68  Identities=16%  Similarity=0.153  Sum_probs=49.6

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc------------cchHHHHHHHHHHHHHHHhhh
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH------------MNRVEVEQRVEEIKNLVRSCL  296 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~------------~~rge~E~rl~~l~~~~~~~~  296 (854)
                      +.+|+||||||||.+|+.||+.+          +..++.+|++.+..            ||.|--+..+  +...+... 
T Consensus        54 ~~lf~Gp~GvGKT~lak~la~~l----------~~~~i~~d~s~~~~~~~~~~l~g~~~gy~g~~~~~~--l~~~~~~~-  120 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVTVQLSKAL----------GIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGL--LTDAVIKH-  120 (315)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH----------TCEEEEEEGGGCSSSSCCSSSCCCCSCSHHHHHTTH--HHHHHHHC-
T ss_pred             EEEEECCCcchhHHHHHHHHhhc----------cCCeeEeccccccchhhhhhhcccCCCccccccCCh--hhHHHHhC-
Confidence            67899999999999999999864          34799999887631            3666544332  33344443 


Q ss_pred             CCCeEEEeCccccc
Q 003038          297 GRGIVLNLGDLEWA  310 (854)
Q Consensus       297 ~~~~ILfidel~~l  310 (854)
                       ...|+++||++-+
T Consensus       121 -~~~vvl~DeieKa  133 (315)
T d1r6bx3         121 -PHAVLLLDEIEKA  133 (315)
T ss_dssp             -SSEEEEEETGGGS
T ss_pred             -ccchhhhcccccc
Confidence             5689999999877

>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=97.40  E-value=0.00013  Score=78.38  Aligned_cols=74  Identities=12%  Similarity=0.147  Sum_probs=51.9

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc-cchHH-HHHHHHHHHHH----HHhhhCC
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH-MNRVE-VEQRVEEIKNL----VRSCLGR  298 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~-~~rge-~E~rl~~l~~~----~~~~~~~  298 (854)
                      +.+.|.+++||+|||||-+|+.||+.+          +..|+.+|++.+.- ||.|. .+.-+.+++..    ++..  .
T Consensus        66 ~p~~niLfiGPTGvGKTElAk~LA~~~----------~~~~ir~D~s~~~e~gyvg~dv~~~i~~l~~~~~~~v~~~--~  133 (364)
T d1um8a_          66 LSKSNILLIGPTGSGKTLMAQTLAKHL----------DIPIAISDATSLTEAGYVGEDVENILTRLLQASDWNVQKA--Q  133 (364)
T ss_dssp             CCCCCEEEECCTTSSHHHHHHHHHHHT----------TCCEEEEEGGGCC--------CTHHHHHHHHHTTTCHHHH--T
T ss_pred             CCCcceeeeCCCCccHHHHHHHHHhhc----------ccceeehhhhhcccchhhHhhhccchhhhhhhchhHHHHh--h
Confidence            368899999999999999999999652          45799999998864 57765 34445555543    3332  4


Q ss_pred             CeEEEeCccccc
Q 003038          299 GIVLNLGDLEWA  310 (854)
Q Consensus       299 ~~ILfidel~~l  310 (854)
                      ..|+|+||+.-+
T Consensus       134 ~~iv~lDEieK~  145 (364)
T d1um8a_         134 KGIVFIDEIDKI  145 (364)
T ss_dssp             TSEEEEETGGGC
T ss_pred             cccchhhhhhhh
Confidence            568999999877

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=97.21  E-value=0.00013  Score=73.71  Aligned_cols=72  Identities=10%  Similarity=0.151  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHhhcc-----CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc---cchHHHHH
Q 003038          212 NEDVMYVIENLMSK-----RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH---MNRVEVEQ  283 (854)
Q Consensus       212 ~~ei~~v~~~L~r~-----~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~---~~rge~E~  283 (854)
                      .+.+.+.++.|...     ..++++|+||||||||++++.||..+          +..++.++.+.+..   .+.+....
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~P~~ilL~GpPGtGKT~la~~la~~~----------~~~~~~i~~d~~~~~~~~~~~~~~~   81 (273)
T d1gvnb_          12 ENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEET----------QGNVIVIDNDTFKQQHPNFDELVKL   81 (273)
T ss_dssp             HHHHHHHHHHHHTTCCCCSSCEEEEEECCTTSCTHHHHHHHHHHT----------TTCCEEECTHHHHTTSTTHHHHHHH
T ss_pred             HHHHHHHHHHHHhcccCCCCCEEEEEECCCCCCHHHHHHHHHHHh----------hcceEEEecHHHHHHhccCcccchh
Confidence            34555656656433     33458999999999999999999874          34577777766643   24444443


Q ss_pred             HHHHHHHHHH
Q 003038          284 RVEEIKNLVR  293 (854)
Q Consensus       284 rl~~l~~~~~  293 (854)
                      ..+.....++
T Consensus        82 ~~~~~~~~~~   91 (273)
T d1gvnb_          82 YEKDVVKHVT   91 (273)
T ss_dssp             HGGGCHHHHH
T ss_pred             hhHHHHHHHH
Confidence            3333333333

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.21  E-value=0.00017  Score=71.56  Aligned_cols=74  Identities=14%  Similarity=0.192  Sum_probs=51.6

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHH-HHHHHHHHHHHHhhhCCCeEEEeCc
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEV-EQRVEEIKNLVRSCLGRGIVLNLGD  306 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~-E~rl~~l~~~~~~~~~~~~ILfide  306 (854)
                      |.++|+||||+|||.++.+++....+.       +..++.++...+...+...+ +....++.+..+.    --+|+|||
T Consensus        37 n~l~l~G~~G~GKTHLl~A~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~dll~iDD  105 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHLLQAAGNEAKKR-------GYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKS----VDLLLLDD  105 (213)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHHHHHT-------TCCEEEEEHHHHHHHHHHHHHHTCHHHHHHHHHT----CSEEEEEC
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHhccC-------ccceEEechHHHHHHHHHHHHccchhhHHHHHhh----ccchhhhh
Confidence            457899999999999999999998763       45677777766654322221 2234445555554    34899999


Q ss_pred             cccc-cc
Q 003038          307 LEWA-EF  312 (854)
Q Consensus       307 l~~l-~~  312 (854)
                      ||.+ +.
T Consensus       106 i~~i~~~  112 (213)
T d1l8qa2         106 VQFLSGK  112 (213)
T ss_dssp             GGGGTTC
T ss_pred             hhhhcCc
Confidence            9999 54

>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=97.21  E-value=0.00047  Score=69.83  Aligned_cols=84  Identities=18%  Similarity=0.145  Sum_probs=51.0

Q ss_pred             HHHHHHHHhhc--cCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHH------
Q 003038          214 DVMYVIENLMS--KRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRV------  285 (854)
Q Consensus       214 ei~~v~~~L~r--~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl------  285 (854)
                      -++++++-+.+  ..+.+++|.||+|+|||.+|+.+...-.       -....++.++...+.   ...++..+      
T Consensus         8 ~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~~s~-------~~~~~~~~~~~~~~~---~~~~~~~lfg~~~~   77 (247)
T d1ny5a2           8 KMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSD-------RSKEPFVALNVASIP---RDIFEAELFGYEKG   77 (247)
T ss_dssp             HHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHHST-------TTTSCEEEEETTTSC---HHHHHHHHHCBCTT
T ss_pred             HHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhcC-------Ccccccccchhhhhh---hcccHHHhcCcccC
Confidence            34444444433  3566788889999999999999976421       134467777766553   22233322      


Q ss_pred             ---------HHHHHHHHhhhCCCeEEEeCccccc-cc
Q 003038          286 ---------EEIKNLVRSCLGRGIVLNLGDLEWA-EF  312 (854)
Q Consensus       286 ---------~~l~~~~~~~~~~~~ILfidel~~l-~~  312 (854)
                               ..+++.+.     +-.||||||+.+ ..
T Consensus        78 ~~~~~~~~~~g~l~~a~-----gGtL~l~~i~~L~~~  109 (247)
T d1ny5a2          78 AFTGAVSSKEGFFELAD-----GGTLFLDEIGELSLE  109 (247)
T ss_dssp             SSTTCCSCBCCHHHHTT-----TSEEEEESGGGCCHH
T ss_pred             CcCCcccccCCHHHccC-----CCEEEEeChHhCCHH
Confidence                     12333322     236999999999 44

>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=97.11  E-value=0.0012  Score=71.63  Aligned_cols=98  Identities=12%  Similarity=0.221  Sum_probs=71.7

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc-cccccCcCCCccccccccccCC-CCCCchHHHHHHHHHcCC
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA-LSSFSSTRADSTEDSRNKRSRD-EQSCSYIERFAEAVSNNP  732 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id-~s~~~~~~~~s~e~~~~~rl~~-~~g~g~~e~L~eav~~~p  732 (854)
                      ++.|.+||.||+|+|||++..++-+.+.....+++.+. --||.-       .+.....+. ..+..|.+-|..++|..|
T Consensus       156 ~~~GliLvtGpTGSGKSTTl~~~l~~~~~~~~~i~tiEdPiE~~~-------~~~~q~~v~~~~~~~~~~~l~~~lR~dP  228 (401)
T d1p9ra_         156 RPHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEFDI-------DGIGQTQVNPRVDMTFARGLRAILRQDP  228 (401)
T ss_dssp             SSSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCSCC-------SSSEEEECBGGGTBCHHHHHHHHGGGCC
T ss_pred             hhhceEEEEcCCCCCccHHHHHHhhhhcCCCceEEEeccCccccc-------CCCCeeeecCCcCCCHHHHHHHHHhhcC
Confidence            46789999999999999999998888866556777663 233331       111000111 122367778888899988


Q ss_pred             CEEEEEecCCCCCHHHHHHHHHhhhcCeEe
Q 003038          733 HRVFLIEDVEQADYCSQKGFKRAIESGRIV  762 (854)
Q Consensus       733 ~~ViliDEieka~~~v~~~Ll~~le~G~l~  762 (854)
                       .||++.||-  ++......+++-.+|++.
T Consensus       229 -Dvi~igEiR--d~~ta~~a~~aa~tGhlV  255 (401)
T d1p9ra_         229 -DVVMVGEIR--DLETAQIAVQASLTGHLV  255 (401)
T ss_dssp             -SEEEESCCC--SHHHHHHHHHHHHTTCEE
T ss_pred             -CEEEecCcC--ChHHHHHHHHHHhcCCeE
Confidence             799999999  888889999999999876

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=97.09  E-value=0.00011  Score=67.67  Aligned_cols=25  Identities=28%  Similarity=0.379  Sum_probs=23.4

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      |+|++|+|+|||||||+++.||.++
T Consensus         2 ~k~I~l~G~~GsGKSTvak~La~~L   26 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQLAQQL   26 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHh
Confidence            6799999999999999999999884

>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=97.01  E-value=0.00055  Score=64.30  Aligned_cols=32  Identities=19%  Similarity=0.289  Sum_probs=28.3

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcc
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLS  269 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~  269 (854)
                      +|++|+|+||+|||++++.||+++          |..++.+|
T Consensus         1 k~I~liG~~GsGKsTi~k~La~~l----------~~~~~d~d   32 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLARALAKDL----------DLVFLDSD   32 (161)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHH----------TCEEEEHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHh----------CCCEEecC
Confidence            479999999999999999999985          67888765

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.92  E-value=0.001  Score=62.46  Aligned_cols=23  Identities=13%  Similarity=0.221  Sum_probs=21.6

Q ss_pred             EEEecCCCchHHHHHHHHHHHHh
Q 003038          660 LFFQGVDADAKEKIAKELARLVF  682 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lf  682 (854)
                      +++.||+|+|||+|++.|+..+-
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~l~   25 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHG
T ss_pred             EEEECCCCcHHHHHHHHHHhcCC
Confidence            78999999999999999999884

>d1qvra1 a.174.1.1 (A:4-148) N-terminal domain of ClpB (heat shock protein F84.1) {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Thermus thermophilus [TaxId: 274]

Probab=96.68  E-value=0.0015  Score=60.34  Aligned_cols=62  Identities=24%  Similarity=0.267  Sum_probs=52.8

Q ss_pred             cChhHHHHHHHHHHHHHHHhhhCCcccccccccccccCHHHHHHHhccCC--hHHHHHHHhCCCHHHHHHHHHHHhh
Q 003038           94 QFPTISNALVAAFKRAQAHQRRGSIENQQQPLLAVKIELEQLIISILDDP--SVSRVMREAGFSSTQVKSNVEQAVS  168 (854)
Q Consensus        94 ~~p~~s~~L~~al~~A~~~~~~~~~~~~~~~~~~~~I~~eHLLLALL~d~--~~~~iL~~~Gi~~~~l~~~v~~~l~  168 (854)
                      |++.+.++|..|.+.|..+++    .         +|+++|||+|||+++  .+.++|..+|++...++..+...+.
T Consensus         3 fT~~a~~~l~~A~~~A~~~~~----~---------~i~~~HlL~all~~~~~~~~~iL~~~gvd~~~l~~~l~~~l~   66 (145)
T d1qvra1           3 WTQAAREALAQAQVLAQRMKH----Q---------AIDLPHLWAVLLKDERSLAWRLLEKAGADPKALKELQERELA   66 (145)
T ss_dssp             SCHHHHHHHHHHHHHHHHTTC----S---------EECHHHHHHHHCCSSSSHHHHHHHTTSSCHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHHHcCC----C---------cccHHHHHHHHHcCCcchHHHHHHHcCCCHHHHHHHHHHHhh
Confidence            788888899999988887632    2         599999999999875  5899999999999999999887664

>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=96.65  E-value=0.00057  Score=63.62  Aligned_cols=25  Identities=12%  Similarity=0.068  Sum_probs=23.1

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      -.|++|+|+||+||||+++.||+++
T Consensus         4 ~~~I~i~G~pGsGKTTia~~La~~l   28 (173)
T d1rkba_           4 LPNILLTGTPGVGKTTLGKELASKS   28 (173)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999999985

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=96.51  E-value=0.00082  Score=63.42  Aligned_cols=33  Identities=12%  Similarity=0.151  Sum_probs=28.4

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLS  269 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~  269 (854)
                      .++++|+|+||+|||++++.||+++          |..++..|
T Consensus         2 ~~~Iil~G~~GsGKSTia~~LA~~L----------g~~~id~D   34 (170)
T d1e6ca_           2 TEPIFMVGARGCGMTTVGRELARAL----------GYEFVDTD   34 (170)
T ss_dssp             CCCEEEESCTTSSHHHHHHHHHHHH----------TCEEEEHH
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHh----------CCCEEehh
Confidence            3678999999999999999999985          66777765

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.43  E-value=0.0009  Score=62.79  Aligned_cols=32  Identities=19%  Similarity=0.125  Sum_probs=27.8

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcc
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLS  269 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~  269 (854)
                      .|+||+|+||||||++.+.||.++          |..|+.+|
T Consensus         2 p~IvliG~~G~GKSTig~~La~~l----------~~~fiD~D   33 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTIGRRLAKAL----------GVGLLDTD   33 (165)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHH----------TCCEEEHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHh----------CCCeEeec
Confidence            479999999999999999999986          56777665

>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=96.36  E-value=0.00069  Score=61.99  Aligned_cols=23  Identities=26%  Similarity=0.432  Sum_probs=21.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.||+|+|||++|+.||+.|
T Consensus         4 ~I~l~G~~GsGKSTvak~La~~L   26 (169)
T d1kaga_           4 NIFLVGPMGAGKSTIGRQLAQQL   26 (169)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            47888999999999999999998

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.35  E-value=0.0016  Score=61.15  Aligned_cols=25  Identities=16%  Similarity=0.421  Sum_probs=22.3

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHc
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      +++|+||||+|||++++.++..+..
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            4789999999999999999987753

>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=96.35  E-value=0.0068  Score=58.83  Aligned_cols=127  Identities=11%  Similarity=0.016  Sum_probs=75.2

Q ss_pred             HhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccccchHHHHHHHHHHHHHHHhhh--CC
Q 003038          221 NLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRHMNRVEVEQRVEEIKNLVRSCL--GR  298 (854)
Q Consensus       221 ~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~~~rge~E~rl~~l~~~~~~~~--~~  298 (854)
                      ++.++.-.+.+|+||||+|||+++..++..+..-.-    +..-|+.+....-. -...    .++++.+.+....  ++
T Consensus         9 ~i~~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~----~h~D~~~i~~~~~~-I~Id----~IR~i~~~~~~~~~~~~   79 (198)
T d2gnoa2           9 IIEKSEGISILINGEDLSYPREVSLELPEYVEKFPP----KASDVLEIDPEGEN-IGID----DIRTIKDFLNYSPELYT   79 (198)
T ss_dssp             HHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCC----CTTTEEEECCSSSC-BCHH----HHHHHHHHHTSCCSSSS
T ss_pred             HHhcCCCceEEEECCCCCCHHHHHHHHHHHHhcccc----CCCCEEEEeCCcCC-CCHH----HHHHHHHHHhhCcccCC
Confidence            334567778999999999999999999988765422    12235555432100 0112    3455666665432  44


Q ss_pred             CeEEEeCccccc-cccccccccccccchhhhHHHHHHHhhc-ccCCCCceEEEEEecCHHHHHHhhccCCchhhhhccCC
Q 003038          299 GIVLNLGDLEWA-EFRASSSEQVRGYYCSIEHIIMEIGKLV-CGIGENARFWLMGIATFQSYMRCKSGHPSLETLWSLHP  376 (854)
Q Consensus       299 ~~ILfidel~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ll-~~~~g~g~l~lIgatT~~ey~k~~~~~pale~~~~~~~  376 (854)
                      .=|++|||+|.+ ...                 ..-+-+.| .| .++  ..+|-+|+..+     .--|++..  |.|.
T Consensus        80 ~KviIId~ad~l~~~a-----------------qNaLLK~LEEP-p~~--t~fiLit~~~~-----~ll~TI~S--RC~~  132 (198)
T d2gnoa2          80 RKYVIVHDCERMTQQA-----------------ANAFLKALEEP-PEY--AVIVLNTRRWH-----YLLPTIKS--RVFR  132 (198)
T ss_dssp             SEEEEETTGGGBCHHH-----------------HHHTHHHHHSC-CTT--EEEEEEESCGG-----GSCHHHHT--TSEE
T ss_pred             CEEEEEeCccccchhh-----------------hhHHHHHHhCC-CCC--ceeeeccCChh-----hCHHHHhc--ceEE
Confidence            469999999999 432                 12233444 23 222  44444555432     24577877  7777


Q ss_pred             CCCCCch
Q 003038          377 LTIPAGS  383 (854)
Q Consensus       377 v~i~~~s  383 (854)
                      +.++.+.
T Consensus       133 i~~~~p~  139 (198)
T d2gnoa2         133 VVVNVPK  139 (198)
T ss_dssp             EECCCCH
T ss_pred             EeCCCch
Confidence            7777554

>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=96.33  E-value=0.0028  Score=58.47  Aligned_cols=24  Identities=4%  Similarity=0.243  Sum_probs=21.6

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +-++|+|+||+||||+++.|++.+
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            458999999999999999999874

>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=96.30  E-value=0.00094  Score=62.41  Aligned_cols=27  Identities=7%  Similarity=0.149  Sum_probs=24.4

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHcC
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEKG  254 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~~  254 (854)
                      +|++|+||||+|||++++.++..+.+.
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            689999999999999999999887653

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=96.28  E-value=0.0013  Score=61.32  Aligned_cols=27  Identities=7%  Similarity=0.139  Sum_probs=24.0

Q ss_pred             cCcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          225 KRKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       225 ~~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      .+..|++|.|+|||||||+++.||.++
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            356789999999999999999999873

>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=96.24  E-value=0.00078  Score=63.02  Aligned_cols=35  Identities=14%  Similarity=0.106  Sum_probs=27.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      .++|.||+|+|||++|++||+.+ |  ..++..++..+
T Consensus         9 ~I~i~G~~GsGKTTla~~La~~~-~--~~~i~~~~~~~   43 (192)
T d1lw7a2           9 TVAILGGESSGKSVLVNKLAAVF-N--TTSAWEYGREF   43 (192)
T ss_dssp             EEEEECCTTSHHHHHHHHHHHHT-T--CEEECCTTHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh-C--CCeEeeehHHH
Confidence            58999999999999999999976 3  34555554443

>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=96.24  E-value=0.0013  Score=62.65  Aligned_cols=36  Identities=8%  Similarity=0.157  Sum_probs=28.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      .++|.|++|+|||++|++||+.+.-.......++..
T Consensus        21 vI~L~G~pGSGKTTiAk~La~~l~~~~~~~~~~~~d   56 (195)
T d1x6va3          21 TVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGD   56 (195)
T ss_dssp             EEEEESSCHHHHHHHHHHHHHHHHHTTCCEEEECHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCCccchhHH
Confidence            678999999999999999999986544555555443

>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=96.21  E-value=0.00083  Score=62.83  Aligned_cols=26  Identities=8%  Similarity=0.080  Sum_probs=23.6

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      -.++++++|+|||||||+++.||.+.
T Consensus         6 ~~K~I~i~G~~GsGKTTla~~La~~~   31 (192)
T d1lw7a2           6 FAKTVAILGGESSGKSVLVNKLAAVF   31 (192)
T ss_dssp             TCEEEEEECCTTSHHHHHHHHHHHHT
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHHh
Confidence            45689999999999999999999984

>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=96.18  E-value=0.0015  Score=60.81  Aligned_cols=26  Identities=23%  Similarity=0.287  Sum_probs=23.3

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHh
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVF  682 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lf  682 (854)
                      ...++|.|++|+|||++|++||+.|.
T Consensus         6 g~~I~l~G~~GsGKTTia~~La~~L~   31 (183)
T d1m8pa3           6 GFTIFLTGYMNSGKDAIARALQVTLN   31 (183)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            34788999999999999999999883

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=96.08  E-value=0.0033  Score=58.40  Aligned_cols=37  Identities=5%  Similarity=0.051  Sum_probs=28.6

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSF  273 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l  273 (854)
                      .+-++|+|+||+|||++++.|++++          +..++.++...+
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~l----------g~~~~~~~~d~~   40 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANLP----------GVPKVHFHSDDL   40 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTCS----------SSCEEEECTTHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh----------CCCEEEecHHHH
Confidence            4457899999999999999998753          556777765433

>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=96.02  E-value=0.0028  Score=66.34  Aligned_cols=40  Identities=15%  Similarity=0.130  Sum_probs=30.0

Q ss_pred             cHHHHHHHHHH-hhccCcCCceeecCCCCCHHHHHHHHHHH
Q 003038          211 RNEDVMYVIEN-LMSKRKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       211 r~~ei~~v~~~-L~r~~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      ..+++++-+.+ +......|++|+|+||||||++++.++.-
T Consensus        11 Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~lar~~~~i   51 (333)
T d1g8pa_          11 GQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAAL   51 (333)
T ss_dssp             SCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHhccCCCeEEEECCCCccHHHHHHHHHHh
Confidence            55677764443 33224469999999999999999999974

>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=96.02  E-value=0.0041  Score=60.40  Aligned_cols=94  Identities=15%  Similarity=0.240  Sum_probs=56.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFLI  738 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vili  738 (854)
                      .++|+||+++|||.+|.+|.+.+.|.   .+.     |..  ..  ..+-+..+.                  ..+|+++
T Consensus        55 ~i~~~GP~~TGKS~f~~sl~~~l~G~---vis-----~~N--~~--s~F~Lq~l~------------------~~kv~l~  104 (205)
T d1tuea_          55 CLVFCGPANTGKSYFGMSFIHFIQGA---VIS-----FVN--ST--SHFWLEPLT------------------DTKVAML  104 (205)
T ss_dssp             EEEEESCGGGCHHHHHHHHHHHHTCE---ECC-----CCC--SS--SCGGGGGGT------------------TCSSEEE
T ss_pred             EEEEECCCCccHHHHHHHHHHHhCCE---EEe-----ccC--CC--CCccccccc------------------CCeEEEE
Confidence            78999999999999999999999652   111     110  00  011111110                  1369999


Q ss_pred             ecCCCCCHHHHHHHHH-hhhcCeEe-cCCC-ceeecCCeEEEEecCC
Q 003038          739 EDVEQADYCSQKGFKR-AIESGRIV-TSSG-DEVSLGDAIVILSCES  782 (854)
Q Consensus       739 DEieka~~~v~~~Ll~-~le~G~l~-d~~G-~~v~~~~aIiIlTsn~  782 (854)
                      ||+........+..++ +++-..++ |.++ ..+.++-+-+|+|||.
T Consensus       105 dD~t~~~~~~~d~~lK~ll~G~~vsvd~KhK~~vqi~~pPliITsN~  151 (205)
T d1tuea_         105 DDATTTCWTYFDTYMRNALDGNPISIDRKHKPLIQLKCPPILLTTNI  151 (205)
T ss_dssp             EEECHHHHHHHHHHCHHHHHTCCEEEC----CCEEECCCCEEEEESS
T ss_pred             eccccchHHHHHHHHHhccCCCeeeeecccCCcccccCCCEEEEcCC
Confidence            9998776666666544 44433333 3433 3456666667888983

>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=95.98  E-value=0.0077  Score=61.42  Aligned_cols=40  Identities=18%  Similarity=0.129  Sum_probs=33.4

Q ss_pred             cHHHHHHHHHHhhcc-CcC--CceeecCCCCCHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSK-RKR--NFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       211 r~~ei~~v~~~L~r~-~k~--n~vLvGe~GvGKta~v~~la~~  250 (854)
                      |+.|++++++-|... .+.  -+.|+|.+|+|||++|+.+.+.
T Consensus        25 R~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~   67 (277)
T d2a5yb3          25 REYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSK   67 (277)
T ss_dssp             CHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHh
Confidence            999999999998653 222  3579999999999999999875

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=95.91  E-value=0.0024  Score=59.32  Aligned_cols=25  Identities=24%  Similarity=0.383  Sum_probs=22.9

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHH
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ...++|.||+|+|||++|+.||+.+
T Consensus         6 ~~iivl~G~~GsGKsT~a~~La~~l   30 (171)
T d1knqa_           6 HHIYVLMGVSGSGKSAVASEVAHQL   30 (171)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4578889999999999999999988

>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=95.83  E-value=0.0023  Score=59.30  Aligned_cols=23  Identities=26%  Similarity=0.343  Sum_probs=21.5

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+++.||+|+|||++|+.||+.+
T Consensus         6 ~I~i~G~pGsGKTTia~~La~~l   28 (173)
T d1rkba_           6 NILLTGTPGVGKTTLGKELASKS   28 (173)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            57899999999999999999987

>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=95.81  E-value=0.031  Score=56.73  Aligned_cols=47  Identities=15%  Similarity=0.159  Sum_probs=38.0

Q ss_pred             cccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHH
Q 003038          619 KVPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARL  680 (854)
Q Consensus       619 ~V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~  680 (854)
                      .++|.+.-+..|...+.....               +....+.++|..|+|||+||+.+.+.
T Consensus        21 ~~~gR~~~~~~i~~~L~~~~~---------------~~~~~v~I~GmgGiGKTtLA~~v~~~   67 (277)
T d2a5yb3          21 TCYIREYHVDRVIKKLDEMCD---------------LDSFFLFLHGRAGSGKSVIASQALSK   67 (277)
T ss_dssp             CSCCCHHHHHHHHHHHHHHTT---------------SSSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ceeCcHHHHHHHHHHHHhccC---------------CCceEEEEECCCCCCHHHHHHHHHHh
Confidence            478999888888888876422               34568899999999999999998765

>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=95.78  E-value=0.0021  Score=59.60  Aligned_cols=34  Identities=15%  Similarity=0.343  Sum_probs=27.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      .++|.||+|+|||++|++||+.+ +  ..++.++...
T Consensus         5 iI~l~G~~GsGKsTva~~L~~~l-~--~~~~~~~~d~   38 (178)
T d1qhxa_           5 MIILNGGSSAGKSGIVRCLQSVL-P--EPWLAFGVDS   38 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHS-S--SCEEEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc-C--CCeEEeecch
Confidence            68899999999999999999987 3  3566665443

>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=95.77  E-value=0.0064  Score=63.64  Aligned_cols=92  Identities=10%  Similarity=0.142  Sum_probs=61.5

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEE-ccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSI-ALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~i-d~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      .+++.||+|+|||++.++|...+ ....+++.| |-.|+.-.+     ......+....+..+.+-+..++|.+|. .|+
T Consensus       168 nili~G~tgSGKTT~l~al~~~i-~~~~rivtiEd~~El~l~~-----~~~~~~~~~~~~~~~~~ll~~~lR~~pd-~ii  240 (323)
T d1g6oa_         168 NVIVCGGTGSGKTTYIKSIMEFI-PKEERIISIEDTEEIVFKH-----HKNYTQLFFGGNITSADCLKSCLRMRPD-RII  240 (323)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGGS-CTTCCEEEEESSCCCCCSS-----CSSEEEEECBTTBCHHHHHHHHTTSCCS-EEE
T ss_pred             CEEEEeeccccchHHHHHHhhhc-ccccceeeccchhhhhccc-----ccccceeccccchhHHHHHHHHhccCCC-ccc
Confidence            58999999999999999999877 556677777 444443100     0111111122233555667788888885 567


Q ss_pred             EecCCCCCHHHHHHHHHhhhcCe
Q 003038          738 IEDVEQADYCSQKGFKRAIESGR  760 (854)
Q Consensus       738 iDEieka~~~v~~~Ll~~le~G~  760 (854)
                      +.|+-  ++++.. +++++..|.
T Consensus       241 vgEiR--~~ea~~-~l~a~~tGh  260 (323)
T d1g6oa_         241 LGELR--SSEAYD-FYNVLCSGH  260 (323)
T ss_dssp             ESCCC--STHHHH-HHHHHHTTC
T ss_pred             CCccC--chhHHH-HHHHHHhcC
Confidence            99997  567775 678998873

>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=95.75  E-value=0.0052  Score=58.93  Aligned_cols=35  Identities=9%  Similarity=0.015  Sum_probs=26.7

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcc
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLS  269 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~  269 (854)
                      ++|+|.||+|||++++.|++.+....     ..+.+++.|
T Consensus         5 i~l~GlpgsGKSTla~~L~~~l~~~~-----~~~~~~~~D   39 (213)
T d1bifa1           5 IVMVGLPARGKTYISKKLTRYLNFIG-----VPTREFNVG   39 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHTT-----CCEEEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhcC-----CCCeEEccc
Confidence            57899999999999999999876532     234555555

>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=95.75  E-value=0.0023  Score=61.23  Aligned_cols=35  Identities=17%  Similarity=0.269  Sum_probs=29.2

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      || ..+++.||+|+|||++|+.||+.+     .++++++.+
T Consensus         5 kp-~iI~i~G~pGSGKsT~a~~La~~~-----g~~~i~~g~   39 (194)
T d1qf9a_           5 KP-NVVFVLGGPGSGKGTQCANIVRDF-----GWVHLSAGD   39 (194)
T ss_dssp             CC-EEEEEEESTTSSHHHHHHHHHHHH-----CCEEEEHHH
T ss_pred             CC-cEEEEECCCCCCHHHHHHHHHHHH-----CCceEchhh
Confidence            55 478999999999999999999987     467777654

>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=95.73  E-value=0.0024  Score=59.33  Aligned_cols=23  Identities=17%  Similarity=0.292  Sum_probs=21.5

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.||+|+|||++|+.||+.+
T Consensus         7 ~I~i~G~~GsGKTT~~~~La~~l   29 (174)
T d1y63a_           7 NILITGTPGTGKTSMAEMIAAEL   29 (174)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHh
Confidence            78888999999999999999987

>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=95.72  E-value=0.0023  Score=59.51  Aligned_cols=26  Identities=8%  Similarity=0.175  Sum_probs=22.8

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      -.++|+|.||+||||+++.||.++..
T Consensus         7 ~~I~l~G~~GsGKTTia~~La~~L~~   32 (183)
T d1m8pa3           7 FTIFLTGYMNSGKDAIARALQVTLNQ   32 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            34779999999999999999999854

>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=95.69  E-value=0.0018  Score=60.30  Aligned_cols=35  Identities=26%  Similarity=0.271  Sum_probs=28.7

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      .++|.||+|+|||++|++||+.+   ..+++.++...+
T Consensus         6 iI~l~G~~GsGKSTia~~La~~l---g~~~~~~~~d~~   40 (176)
T d1zp6a1           6 ILLLSGHPGSGKSTIAEALANLP---GVPKVHFHSDDL   40 (176)
T ss_dssp             EEEEEECTTSCHHHHHHHHHTCS---SSCEEEECTTHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh---CCCEEEecHHHH
Confidence            68899999999999999999976   346777776544

>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=95.69  E-value=0.0021  Score=59.26  Aligned_cols=23  Identities=22%  Similarity=0.247  Sum_probs=21.5

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+++.||+|+|||++|+.||+.+
T Consensus         4 lI~i~G~~GsGKTTva~~L~~~~   26 (176)
T d2bdta1           4 LYIITGPAGVGKSTTCKRLAAQL   26 (176)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            57899999999999999999987

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.65  E-value=0.0026  Score=61.05  Aligned_cols=34  Identities=18%  Similarity=0.281  Sum_probs=28.5

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      ...++|.||+|+|||++|+.||+.+     .+.+|++.+
T Consensus         8 ~~iI~i~GppGSGKsT~a~~La~~~-----g~~~is~gd   41 (196)
T d1ukza_           8 VSVIFVLGGPGAGKGTQCEKLVKDY-----SFVHLSAGD   41 (196)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHS-----SCEEEEHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh-----CCeEEehhH
Confidence            4578889999999999999999987     567777654

>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=95.45  E-value=0.0095  Score=56.15  Aligned_cols=57  Identities=14%  Similarity=0.213  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          625 DTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       625 ~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      +.+..|+..+.....              .+| ..+.+.||+|+|||++|+.|++.+-...-....+++..|
T Consensus         5 ~~~~~~~~~~~~~~~--------------~~~-~iIgI~G~~GSGKSTla~~L~~~l~~~~~~~~~~~~~~~   61 (198)
T d1rz3a_           5 DRIDFLCKTILAIKT--------------AGR-LVLGIDGLSRSGKTTLANQLSQTLREQGISVCVFHMDDH   61 (198)
T ss_dssp             HHHHHHHHHHHTSCC--------------SSS-EEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEGGGG
T ss_pred             HHHHHHHHHHHhccC--------------CCC-EEEEEECCCCCCHHHHHHHHHHHhccccccceecccccc
Confidence            455667777754322              123 367799999999999999999887544444455554443

>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=95.43  E-value=0.003  Score=60.36  Aligned_cols=36  Identities=11%  Similarity=0.147  Sum_probs=28.6

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      +|. .++|.||+|+|||++|+.||+.+     .+.+++++++
T Consensus         2 ~Pm-~I~i~GppGsGKsT~a~~La~~~-----~~~~is~~~~   37 (189)
T d1zaka1           2 DPL-KVMISGAPASGKGTQCELIKTKY-----QLAHISAGDL   37 (189)
T ss_dssp             CSC-CEEEEESTTSSHHHHHHHHHHHH-----CCEECCHHHH
T ss_pred             CCe-EEEEECCCCCCHHHHHHHHHHHH-----CCcEEehhHH
Confidence            454 47789999999999999999988     4666666543

>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=95.42  E-value=0.0041  Score=58.08  Aligned_cols=22  Identities=23%  Similarity=0.447  Sum_probs=20.5

Q ss_pred             EEEecCCCchHHHHHHHHHHHH
Q 003038          660 LFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ++|.|++|+|||++|+.||+.+
T Consensus         4 IvliG~~G~GKSTig~~La~~l   25 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKAL   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5677999999999999999998

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.42  E-value=0.0044  Score=57.54  Aligned_cols=35  Identities=11%  Similarity=0.126  Sum_probs=27.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIAL  693 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~  693 (854)
                      .+++.||+|+|||++++++++.+......+..+.+
T Consensus         3 ~v~ItG~~GtGKTtl~~~i~~~l~~~~~~v~~~~~   37 (189)
T d2i3ba1           3 HVFLTGPPGVGKTTLIHKASEVLKSSGVPVDGFYT   37 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHHHHTTCCCEEEEC
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEe
Confidence            47899999999999999999998655444444433

>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=95.41  E-value=0.0039  Score=58.52  Aligned_cols=22  Identities=27%  Similarity=0.520  Sum_probs=20.3

Q ss_pred             EEEecCCCchHHHHHHHHHHHH
Q 003038          660 LFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ++|.|++|+|||++|+.||+.|
T Consensus         5 Iil~G~~GsGKSTia~~LA~~L   26 (170)
T d1e6ca_           5 IFMVGARGCGMTTVGRELARAL   26 (170)
T ss_dssp             EEEESCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4677999999999999999998

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=95.40  E-value=0.023  Score=55.49  Aligned_cols=99  Identities=14%  Similarity=0.147  Sum_probs=55.3

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccc-cccccCC------CCCCchHH---HH
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDS-RNKRSRD------EQSCSYIE---RF  724 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~-~~~rl~~------~~g~g~~e---~L  724 (854)
                      +.+.+++|+||+|+|||+.+--||..+-....++.-+.+..|...   ..++- ...+.++      ..+.....   +.
T Consensus         7 ~~p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt~R~g---A~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~~   83 (211)
T d2qy9a2           7 KAPFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAA---AVEQLQVWGQRNNIPVIAQHTGADSASVIFDA   83 (211)
T ss_dssp             CTTEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEECCCTTCHH---HHHHHHHHHHHTTCCEECCSTTCCHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeccccccc---chhhhhhhhhhcCCcccccccCCCHHHHHHHH
Confidence            345689999999999998877788766555556666666655410   00111 0111111      11111111   23


Q ss_pred             HHHHHcCCCEEEEEecCCCCCHHH--HHHHHHhh
Q 003038          725 AEAVSNNPHRVFLIEDVEQADYCS--QKGFKRAI  756 (854)
Q Consensus       725 ~eav~~~p~~ViliDEieka~~~v--~~~Ll~~l  756 (854)
                      .+..+.+.+.+||||=.-+.+.+.  .+.|.+..
T Consensus        84 ~~~a~~~~~d~ilIDTaGr~~~d~~~~~el~~l~  117 (211)
T d2qy9a2          84 IQAAKARNIDVLIADTAGRLQNKSHLMEELKKIV  117 (211)
T ss_dssp             HHHHHHTTCSEEEECCCCCGGGHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCEEEeccCCCccccHHHHHHHHHHH
Confidence            333445778999999998876543  34444443

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=95.40  E-value=0.018  Score=56.12  Aligned_cols=40  Identities=13%  Similarity=0.011  Sum_probs=29.6

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccc
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSI  270 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~  270 (854)
                      +++-++||||+|||||+.+--||.++.+..     +.+-+++.|.
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~~~~~~g-----~kV~lit~Dt   44 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGRYYQNLG-----KKVMFCAGDT   44 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHTTT-----CCEEEECCCC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCC-----CcEEEEEecc
Confidence            455678899999999999999998886531     2355666654

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=95.30  E-value=0.016  Score=56.64  Aligned_cols=36  Identities=11%  Similarity=0.097  Sum_probs=27.6

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccc
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSI  270 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~  270 (854)
                      ++||||+|||||+.+--||.++.+..     +.+-++..|.
T Consensus        12 i~lvGptGvGKTTTiAKLA~~~~~~g-----~kV~lit~Dt   47 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLARQFEQQG-----KSVMLAAGDT   47 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTTT-----CCEEEECCCT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCC-----CcEEEEeccc
Confidence            56899999999999999999887532     3456666654

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=95.22  E-value=0.0086  Score=58.81  Aligned_cols=43  Identities=19%  Similarity=0.288  Sum_probs=29.4

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      +++.+++|+||+|+|||+.+--||..+-....++.-+.+..|-
T Consensus         9 ~~p~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit~Dt~R   51 (213)
T d1vmaa2           9 EPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADTFR   51 (213)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEECTTC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEeecccc
Confidence            4557999999999999987777776554444455444444443

>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=95.19  E-value=0.0046  Score=59.40  Aligned_cols=36  Identities=6%  Similarity=0.139  Sum_probs=28.1

Q ss_pred             cCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          654 VKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       654 ~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      .|.. -+++.||||+|||++|+.||+.+     .+..+++++
T Consensus         4 ~r~m-rIiliG~PGSGKtT~a~~La~~~-----g~~~is~gd   39 (189)
T d2ak3a1           4 ARLL-RAAIMGAPGSGKGTVSSRITKHF-----ELKHLSSGD   39 (189)
T ss_dssp             SCCC-EEEEECCTTSSHHHHHHHHHHHB-----CCEEEEHHH
T ss_pred             Ccce-eEEEECCCCCCHHHHHHHHHHHH-----CCeEEcHHH
Confidence            4555 45566999999999999999986     467777654

>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=95.18  E-value=0.0058  Score=58.19  Aligned_cols=24  Identities=8%  Similarity=0.005  Sum_probs=22.0

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      -+++|.||||+||||+++.|+++.
T Consensus         4 m~I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            468999999999999999999885

>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=95.16  E-value=0.0053  Score=57.21  Aligned_cols=22  Identities=27%  Similarity=0.478  Sum_probs=20.7

Q ss_pred             EEEecCCCchHHHHHHHHHHHH
Q 003038          660 LFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ++|.|++|+|||++|+.||+.+
T Consensus         3 I~liG~~GsGKsTi~k~La~~l   24 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKDL   24 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5777999999999999999998

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=95.15  E-value=0.0047  Score=57.17  Aligned_cols=22  Identities=18%  Similarity=0.338  Sum_probs=20.5

Q ss_pred             ceeecCCCCCHHHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ++|+|+||+|||++++.|+.++
T Consensus         9 ivl~G~~GsGKsT~a~~La~~l   30 (171)
T d1knqa_           9 YVLMGVSGSGKSAVASEVAHQL   30 (171)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6889999999999999999885

>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=95.05  E-value=0.0058  Score=58.64  Aligned_cols=24  Identities=8%  Similarity=0.001  Sum_probs=21.9

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      .-+++|+|+||+|||++++-||++
T Consensus         6 ~mrIiliG~PGSGKtT~a~~La~~   29 (189)
T d2ak3a1           6 LLRAAIMGAPGSGKGTVSSRITKH   29 (189)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             ceeEEEECCCCCCHHHHHHHHHHH
Confidence            447899999999999999999987

>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=95.04  E-value=0.0055  Score=58.36  Aligned_cols=32  Identities=19%  Similarity=0.160  Sum_probs=26.0

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      -++|.||||+|||++|+.||+.+     .+.++++++
T Consensus         5 riil~G~pGSGKsT~a~~La~~~-----g~~~i~~gd   36 (190)
T d1ak2a1           5 RAVLLGPPGAGKGTQAPKLAKNF-----CVCHLATGD   36 (190)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH-----TCEEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh-----CCeEEeHHH
Confidence            34567999999999999999987     467777653

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=95.04  E-value=0.0058  Score=57.80  Aligned_cols=23  Identities=22%  Similarity=0.225  Sum_probs=21.3

Q ss_pred             CceeecCCCCCHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +++|+|+||+|||++++-||++.
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47999999999999999999885

>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=95.02  E-value=0.0046  Score=59.10  Aligned_cols=27  Identities=15%  Similarity=0.140  Sum_probs=22.2

Q ss_pred             cCc-CCceeecCCCCCHHHHHHHHHHHH
Q 003038          225 KRK-RNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       225 ~~k-~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +.| +-++|+||||+|||++++-||++.
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            344 456889999999999999999874

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.00  E-value=0.0045  Score=58.54  Aligned_cols=32  Identities=19%  Similarity=0.216  Sum_probs=26.1

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      .++|.||||+|||++|+.||+.+     .|..+++++
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~-----g~~~i~~~~   33 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKL-----GIPQISTGE   33 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH-----TCCEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH-----CCceEchHH
Confidence            36788999999999999999988     356666544

>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=94.99  E-value=0.0052  Score=57.72  Aligned_cols=23  Identities=17%  Similarity=0.153  Sum_probs=21.3

Q ss_pred             CceeecCCCCCHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      |++|+|+||+||||+++.||.+.
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            58999999999999999999884

>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=94.95  E-value=0.0046  Score=64.78  Aligned_cols=91  Identities=12%  Similarity=0.185  Sum_probs=57.5

Q ss_pred             CCCCCCC-cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcc-cccc--------
Q 003038          204 RVSLDPI-RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLS-ISSF--------  273 (854)
Q Consensus       204 ~g~ldpv-r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~-~~~l--------  273 (854)
                      .|-++.. ..+++...+..+.+ .+.|++++|++|+|||++..+|+..|-..        .+++.+. ...+        
T Consensus       143 ~g~~~~~~~~~~~~~~l~~~v~-~~~nili~G~tgSGKTT~l~al~~~i~~~--------~rivtiEd~~El~l~~~~~~  213 (323)
T d1g6oa_         143 QGFYNLLDNKEQAISAIKDGIA-IGKNVIVCGGTGSGKTTYIKSIMEFIPKE--------ERIISIEDTEEIVFKHHKNY  213 (323)
T ss_dssp             TTTTTTCSSHHHHHHHHHHHHH-HTCCEEEEESTTSSHHHHHHHHGGGSCTT--------CCEEEEESSCCCCCSSCSSE
T ss_pred             HhhhcccccHHHHHHHHHHHHH-hCCCEEEEeeccccchHHHHHHhhhcccc--------cceeeccchhhhhccccccc
Confidence            4555544 56777778887775 66779999999999999999998776332        2333321 1000        


Q ss_pred             cc-cchHHHHHHHHHHHHHHHhhhCCCeEEEeCcc
Q 003038          274 RH-MNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDL  307 (854)
Q Consensus       274 ~~-~~rge~E~rl~~l~~~~~~~~~~~~ILfidel  307 (854)
                      .. .+.+++  .+.+++..+...  .|-.++|+|+
T Consensus       214 ~~~~~~~~~--~~~~ll~~~lR~--~pd~iivgEi  244 (323)
T d1g6oa_         214 TQLFFGGNI--TSADCLKSCLRM--RPDRIILGEL  244 (323)
T ss_dssp             EEEECBTTB--CHHHHHHHHTTS--CCSEEEESCC
T ss_pred             ceeccccch--hHHHHHHHHhcc--CCCcccCCcc
Confidence            00 022222  345555555543  5889999998

>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=94.95  E-value=0.0059  Score=55.45  Aligned_cols=33  Identities=18%  Similarity=0.193  Sum_probs=25.0

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      .+++.||+|+|||++|+.|++...    .+..++...
T Consensus         4 lIii~G~pGsGKTTla~~L~~~~~----~~~~~~~d~   36 (152)
T d1ly1a_           4 IILTIGCPGSGKSTWAREFIAKNP----GFYNINRDD   36 (152)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHST----TEEEECHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhCC----CCEEechHH
Confidence            578899999999999999987653    355555443

>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=94.87  E-value=0.0083  Score=56.69  Aligned_cols=23  Identities=13%  Similarity=0.176  Sum_probs=21.0

Q ss_pred             CceeecCCCCCHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      .++|+|+||+|||++++.||++.
T Consensus         4 rIvl~G~pGSGKtT~a~~La~~~   26 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999884

>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=94.87  E-value=0.0057  Score=55.54  Aligned_cols=23  Identities=17%  Similarity=0.130  Sum_probs=19.9

Q ss_pred             CCceeecCCCCCHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      +-++|+|+||+|||++++.|++.
T Consensus         3 klIii~G~pGsGKTTla~~L~~~   25 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAK   25 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            45789999999999999988764

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=94.86  E-value=0.011  Score=57.99  Aligned_cols=43  Identities=16%  Similarity=0.109  Sum_probs=24.8

Q ss_pred             cCcceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          654 VKEETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       654 ~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      .|.+.+++|.||+|+|||+++--||..+-....++.-+.+..|
T Consensus         9 ~k~p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt~   51 (211)
T d1j8yf2           9 DKIPYVIMLVGVQGTGKATTAGKLAYFYKKKGFKVGLVGADVY   51 (211)
T ss_dssp             SSSSEEEEEECSCCC----HHHHHHHHHHHTTCCEEEEECCCS
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEEeecc
Confidence            4566799999999999998777677544333334444444444

>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=94.84  E-value=0.038  Score=53.76  Aligned_cols=87  Identities=9%  Similarity=0.067  Sum_probs=48.3

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccc-cccccCC------CCCCchHHHHHH---H
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDS-RNKRSRD------EQSCSYIERFAE---A  727 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~-~~~rl~~------~~g~g~~e~L~e---a  727 (854)
                      ..++|+||+|+|||+++--||..+-....++.-+.+..|-.   ...++- ...+..+      ..+..-...+.+   .
T Consensus         7 ~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~lit~Dt~R~---gA~eQL~~~a~~l~i~~~~~~~~~d~~~~~~~~~~~   83 (207)
T d1okkd2           7 RVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTFRA---AGGTQLSEWGKRLSIPVIQGPEGTDPAALAYDAVQA   83 (207)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEECCCCSST---THHHHHHHHHHHHTCCEECCCTTCCHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEeccccc---cchhhHhhcccccCceEEeccCCccHHHHHHHHHHH
Confidence            58899999999999887778876654445555555554441   111111 0111111      111111112222   2


Q ss_pred             HHcCCCEEEEEecCCCCCHH
Q 003038          728 VSNNPHRVFLIEDVEQADYC  747 (854)
Q Consensus       728 v~~~p~~ViliDEieka~~~  747 (854)
                      .+.+.+.+||||=.-+.+.+
T Consensus        84 ~~~~~~d~ilIDTaGr~~~d  103 (207)
T d1okkd2          84 MKARGYDLLFVDTAGRLHTK  103 (207)
T ss_dssp             HHHHTCSEEEECCCCCCTTC
T ss_pred             HHHCCCCEEEcCccccchhh
Confidence            24456899999999987654

>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=94.80  E-value=0.0062  Score=56.27  Aligned_cols=25  Identities=24%  Similarity=0.379  Sum_probs=21.7

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ++=++|.|+||+|||++++.|++++
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l   27 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHc
Confidence            4456788999999999999999985

>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=94.78  E-value=0.0055  Score=57.55  Aligned_cols=31  Identities=16%  Similarity=0.249  Sum_probs=25.6

Q ss_pred             EEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          660 LFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      +++.||||+|||++|+.||+.+     .+..+++++
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~-----~~~~i~~~~   33 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAAY-----GIPHISTGD   33 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH-----CCCEEEHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH-----CCceechhH
Confidence            6789999999999999999987     455665543

>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=94.76  E-value=0.0064  Score=57.52  Aligned_cols=31  Identities=16%  Similarity=0.183  Sum_probs=25.6

Q ss_pred             EEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          660 LFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      ++|.||+|+|||++|+.||+.+     .+..|++.+
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~-----g~~~i~~~d   35 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERF-----HAAHLATGD   35 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH-----CCEEEEHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh-----CCceEeccc
Confidence            5677999999999999999987     456676654

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=94.72  E-value=0.0058  Score=58.53  Aligned_cols=34  Identities=9%  Similarity=0.260  Sum_probs=28.6

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      ..++|.||||+||+++|+.||+.+     .|..|++++.
T Consensus         9 ~iI~l~G~pGSGKsT~a~~La~~~-----g~~~is~g~l   42 (194)
T d3adka_           9 KIIFVVGGPGSGKGTQCEKIVQKY-----GYTHLSTGDL   42 (194)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHT-----CCEEEEHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh-----CCeeEeccHH
Confidence            478889999999999999999976     5777877654

>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=94.70  E-value=0.007  Score=57.10  Aligned_cols=23  Identities=13%  Similarity=0.124  Sum_probs=21.5

Q ss_pred             CceeecCCCCCHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      |++|.|+||+|||++++.||++.
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            68999999999999999999885

>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=94.68  E-value=0.0061  Score=57.69  Aligned_cols=31  Identities=13%  Similarity=0.187  Sum_probs=25.6

Q ss_pred             EEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          660 LFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      ++|.||||+|||++|+.||+.+     .++++++..
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~-----g~~~is~gd   33 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEKY-----GTPHISTGD   33 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH-----CCCEEEHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH-----CCceeeHHH
Confidence            6788999999999999999988     456666543

>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=94.64  E-value=0.015  Score=54.80  Aligned_cols=24  Identities=17%  Similarity=0.026  Sum_probs=19.9

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~  249 (854)
                      ...=+||+|+||+|||++++.++.
T Consensus        13 ~p~liil~G~pGsGKST~a~~l~~   36 (172)
T d1yj5a2          13 NPEVVVAVGFPGAGKSTFIQEHLV   36 (172)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHTG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            344578999999999999998864

>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=94.58  E-value=0.0086  Score=56.94  Aligned_cols=25  Identities=12%  Similarity=-0.008  Sum_probs=22.4

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      .-++||+||||+|||++++-||++.
T Consensus         3 ~~riil~G~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHHh
Confidence            4578999999999999999999884

>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=94.56  E-value=0.0064  Score=57.28  Aligned_cols=32  Identities=13%  Similarity=0.174  Sum_probs=25.9

Q ss_pred             EEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccc
Q 003038          660 LFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSF  696 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~  696 (854)
                      ++|.||||+|||++|+.||+.+     .+..++++++
T Consensus         3 I~i~G~pGSGKsT~~~~La~~~-----~~~~i~~~~l   34 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEKY-----GIPQISTGDM   34 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH-----CCCEEEHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh-----CCceechhhH
Confidence            5788999999999999999987     3556665543

>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=94.55  E-value=0.0095  Score=56.96  Aligned_cols=25  Identities=32%  Similarity=0.449  Sum_probs=22.8

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHh
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVF  682 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lf  682 (854)
                      +.++++|.||+|||++|+.||+.+-
T Consensus         3 ~li~l~GlpgsGKSTla~~L~~~l~   27 (213)
T d1bifa1           3 TLIVMVGLPARGKTYISKKLTRYLN   27 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHH
Confidence            5789999999999999999998773

>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=94.46  E-value=0.01  Score=56.40  Aligned_cols=32  Identities=9%  Similarity=0.187  Sum_probs=27.1

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSS  695 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~  695 (854)
                      .+++.||+|+|||++|+.||+.+     .+.+++...
T Consensus         3 iI~i~GppGSGKsT~a~~La~~~-----g~~~i~~g~   34 (194)
T d1teva_           3 VVFVLGGPGAGKGTQCARIVEKY-----GYTHLSAGE   34 (194)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH-----CCEEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh-----CCceEcHHH
Confidence            67899999999999999999987     467776543

>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=94.44  E-value=0.011  Score=54.78  Aligned_cols=26  Identities=19%  Similarity=0.107  Sum_probs=23.0

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHcC
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEKG  254 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~~  254 (854)
                      -+++.|+||+|||++++.|+.++...
T Consensus         3 iI~i~G~~GsGKsT~~~~L~~~l~~~   28 (190)
T d1khta_           3 VVVVTGVPGVGSTTSSQLAMDNLRKE   28 (190)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            46888999999999999999998653

>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=94.37  E-value=0.011  Score=54.85  Aligned_cols=34  Identities=9%  Similarity=0.040  Sum_probs=26.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      .++|.|++|+|||++++.|++.+-.....+..+.
T Consensus         3 iI~i~G~~GsGKsT~~~~L~~~l~~~~~~~~~~~   36 (190)
T d1khta_           3 VVVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMVS   36 (190)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTTTCCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEe
Confidence            5789999999999999999998844444444443

>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=94.37  E-value=0.022  Score=55.53  Aligned_cols=28  Identities=7%  Similarity=-0.048  Sum_probs=23.2

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcC
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKG  254 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~  254 (854)
                      ++=++|+||+|||||+.+--||.++.+.
T Consensus        10 ~~vi~lvGp~GvGKTTTiaKLA~~~~~~   37 (207)
T d1ls1a2          10 RNLWFLVGLQGSGKTTTAAKLALYYKGK   37 (207)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            3335779999999999999999988763

>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=94.36  E-value=0.0052  Score=58.11  Aligned_cols=26  Identities=12%  Similarity=-0.043  Sum_probs=22.4

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHcC
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEKG  254 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~~  254 (854)
                      .++|+|.||+|||++++.||.++...
T Consensus        21 vI~L~G~pGSGKTTiAk~La~~l~~~   46 (195)
T d1x6va3          21 TVWLTGLSGAGKTTVSMALEEYLVCH   46 (195)
T ss_dssp             EEEEESSCHHHHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            45588999999999999999987553

>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=94.32  E-value=0.041  Score=52.02  Aligned_cols=25  Identities=16%  Similarity=0.272  Sum_probs=21.7

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ++-+||+||+|+||++|.+.|+++.
T Consensus         3 ~k~ivl~Gpsg~GK~tl~~~L~~~~   27 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIKNTLITKH   27 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhC
Confidence            3468999999999999999998763

>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=94.32  E-value=0.019  Score=56.05  Aligned_cols=98  Identities=15%  Similarity=0.119  Sum_probs=52.4

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccc-cccccCCCC------CCchHH---HHHH
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDS-RNKRSRDEQ------SCSYIE---RFAE  726 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~-~~~rl~~~~------g~g~~e---~L~e  726 (854)
                      ..+++|.||+|+|||+++--||..+-....+..-+.+..|-..   ..++. ...+..+-+      .....+   ....
T Consensus        10 ~~vi~lvGp~GvGKTTTiaKLA~~~~~~g~kV~lit~Dt~R~g---A~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~~~~   86 (207)
T d1ls1a2          10 RNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPA---AREQLRLLGEKVGVPVLEVMDGESPESIRRRVEE   86 (207)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEECCSSCHH---HHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEecccccch---HHHHHHHHHHhcCCccccccccchhhHHHHHHHH
Confidence            3589999999999998888788665444455555655544410   00110 000000101      001111   1122


Q ss_pred             HHHcCCCEEEEEecCCCCCHH--HHHHHHHhhh
Q 003038          727 AVSNNPHRVFLIEDVEQADYC--SQKGFKRAIE  757 (854)
Q Consensus       727 av~~~p~~ViliDEieka~~~--v~~~Ll~~le  757 (854)
                      ..+.+.+.+||+|=.-+.+.+  ....|....+
T Consensus        87 ~~~~~~~d~vlIDTaGr~~~d~~~~~el~~~~~  119 (207)
T d1ls1a2          87 KARLEARDLILVDTAGRLQIDEPLMGELARLKE  119 (207)
T ss_dssp             HHHHHTCCEEEEECCCCSSCCHHHHHHHHHHHH
T ss_pred             HHhhccCcceeecccccchhhhhhHHHHHHHHh
Confidence            334567889999998877653  3444444443

>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=94.30  E-value=0.011  Score=56.47  Aligned_cols=24  Identities=13%  Similarity=0.256  Sum_probs=21.7

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +.+||+||+|||||+|++.|+++.
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~   25 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhC
Confidence            458999999999999999999875

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=94.22  E-value=0.016  Score=53.19  Aligned_cols=25  Identities=4%  Similarity=-0.021  Sum_probs=22.2

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHc
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      .+.++|+||+||||+++.|+.++..
T Consensus         4 vi~itG~~GSGKTTL~~~L~~~l~~   28 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKKLIPALCA   28 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            4689999999999999999988754

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=94.20  E-value=0.019  Score=52.68  Aligned_cols=34  Identities=18%  Similarity=0.093  Sum_probs=27.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      .+.|.|++|+|||+|++.|++.+......+..+.
T Consensus         4 vi~itG~~GSGKTTL~~~L~~~l~~~g~~v~v~~   37 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKKLIPALCARGIRPGLIK   37 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEec
Confidence            7889999999999999999998865544444443

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=94.13  E-value=0.026  Score=54.87  Aligned_cols=73  Identities=15%  Similarity=0.172  Sum_probs=44.6

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc------c----chHHHHHHHHHHHHHHHhh
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH------M----NRVEVEQRVEEIKNLVRSC  295 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~------~----~rge~E~rl~~l~~~~~~~  295 (854)
                      +..-+.|.|.||+|||++++.|+.++.+.      .+..++.||...+..      +    .|.+.-.|+..+...... 
T Consensus        23 kg~vIwltGlsGsGKTTia~~L~~~l~~~------~~~~~~~ldgD~iR~~l~~~l~ys~~~r~~~~~r~~~~a~~~~~-   95 (208)
T d1m7ga_          23 RGLTIWLTGLSASGKSTLAVELEHQLVRD------RRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFAD-   95 (208)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHHHHH------HCCCEEEECHHHHTTTTTTTCCSSHHHHHHHHHHHHHHHHHHHH-
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHh------cCceEEEEcchHHHHhhcCCCCCChhHHHHHHHHHHHHHHHHhc-
Confidence            33458899999999999999999887431      234667777665543      1    233333444444444443 


Q ss_pred             hCCCeEEEeCcc
Q 003038          296 LGRGIVLNLGDL  307 (854)
Q Consensus       296 ~~~~~ILfidel  307 (854)
                        .+.++.++=+
T Consensus        96 --~g~~viv~~i  105 (208)
T d1m7ga_          96 --SNSIAITSFI  105 (208)
T ss_dssp             --TTCEEEEECC
T ss_pred             --cCCceeeecc
Confidence              3555555544

>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=94.09  E-value=0.01  Score=55.72  Aligned_cols=23  Identities=13%  Similarity=0.260  Sum_probs=21.1

Q ss_pred             CceeecCCCCCHHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +++|+|+||+|||++++.||.+.
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999999999874

>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=94.08  E-value=0.012  Score=56.26  Aligned_cols=24  Identities=17%  Similarity=0.246  Sum_probs=21.7

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      |.+||+||+|||||+|++.|++..
T Consensus         1 rpIvl~GPsGsGK~tl~~~L~~~~   24 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTLLKKLFQEH   24 (190)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhC
Confidence            458999999999999999999875

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=94.05  E-value=0.0098  Score=58.09  Aligned_cols=40  Identities=15%  Similarity=0.228  Sum_probs=32.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCC-CCceEEEcccccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGS-HNNFVSIALSSFS  697 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~-~~~~i~id~s~~~  697 (854)
                      ..++|.|.+|+|||++|++|++.++.. ..+++.+|+..+-
T Consensus        25 ~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ldgD~iR   65 (208)
T d1m7ga_          25 LTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIR   65 (208)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEcchHHH
Confidence            489999999999999999999887532 3467888877543

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.02  E-value=0.018  Score=55.36  Aligned_cols=22  Identities=18%  Similarity=0.297  Sum_probs=19.8

Q ss_pred             CCceeecCCCCCHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~  249 (854)
                      +|++|+|+||||||+++..+..
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~   22 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLT   22 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHc
Confidence            6899999999999999987764

>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=93.91  E-value=0.012  Score=56.21  Aligned_cols=25  Identities=16%  Similarity=0.195  Sum_probs=22.0

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      +.+-++|+||||+|||++++.||++
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~   31 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQK   31 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4556788999999999999999987

>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=93.90  E-value=0.033  Score=54.92  Aligned_cols=36  Identities=17%  Similarity=0.216  Sum_probs=28.2

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      .++++||+|+|||+|++.+++.+ +  ..+..+++..+.
T Consensus        31 ~i~i~G~~G~GKTsLl~~~~~~~-~--~~~~~i~~~~~~   66 (283)
T d2fnaa2          31 ITLVLGLRRTGKSSIIKIGINEL-N--LPYIYLDLRKFE   66 (283)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH-T--CCEEEEEGGGGT
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHC-C--CCeEEEEecccc
Confidence            57899999999999999999887 2  345666665544

>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=93.77  E-value=0.023  Score=52.93  Aligned_cols=34  Identities=12%  Similarity=0.075  Sum_probs=26.7

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      .++|.|++|+|||++++.||+.|-.....+..+.
T Consensus         3 iivi~G~~GsGKTT~~~~La~~L~~~~~~~~~~~   36 (194)
T d1nksa_           3 IGIVTGIPGVGKSTVLAKVKEILDNQGINNKIIN   36 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEE
Confidence            5689999999999999999999854444444443

>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=93.72  E-value=0.015  Score=55.55  Aligned_cols=25  Identities=12%  Similarity=0.033  Sum_probs=21.7

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ..-++|+||||+|||++++.||++.
T Consensus         8 ~~iI~i~GppGSGKsT~a~~La~~~   32 (196)
T d1ukza_           8 VSVIFVLGGPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            3457899999999999999999873

>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=93.70  E-value=0.094  Score=54.47  Aligned_cols=87  Identities=15%  Similarity=0.059  Sum_probs=54.3

Q ss_pred             HHHHHHHHhhccCcCC--ceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccc-------------------
Q 003038          214 DVMYVIENLMSKRKRN--FVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISS-------------------  272 (854)
Q Consensus       214 ei~~v~~~L~r~~k~n--~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~-------------------  272 (854)
                      ..++++.-|...++|.  +=++|+||+|||+++..|+..+....     ..+-++.+|.++                   
T Consensus        39 ~~~~ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~~~~~~g-----~~vavlavDpss~~~ggailgdr~rm~~~~~  113 (327)
T d2p67a1          39 LSTQLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGMLLIREG-----LKVAVIAVDPSSPVTGGSILGDKTRMNDLAR  113 (327)
T ss_dssp             HHHHHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHHHHHHTT-----CCEEEEEECCC---------------CTTTT
T ss_pred             HHHHHHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHHHHHhcC-----CceeeecCCCceeeeccccccchhHHHHhcc
Confidence            3456666666555554  56789999999999999998776521     123344444321                   


Q ss_pred             ----cc-c----cchHHHHHHHHHHHHHHHhhhCCCeEEEeCcc
Q 003038          273 ----FR-H----MNRVEVEQRVEEIKNLVRSCLGRGIVLNLGDL  307 (854)
Q Consensus       273 ----l~-~----~~rge~E~rl~~l~~~~~~~~~~~~ILfidel  307 (854)
                          ++ +    +..|.+.....+.+..+...  +-.++||+-+
T Consensus       114 ~~~~~ir~~~~~g~lgg~~~~~~~~~~~~~~~--g~d~iliEtv  155 (327)
T d2p67a1         114 AEAAFIRPVPSSGHLGGASQRARELMLLCEAA--GYDVVIVETV  155 (327)
T ss_dssp             CTTEEEEEECC-----CHHHHHHHHHHHHHHT--TCSEEEEEEE
T ss_pred             cccccccccccccccccchhhhhHHHHHHHhc--CCCeEEEeec
Confidence                11 1    25677888888888888875  4566777644

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=93.69  E-value=0.043  Score=48.91  Aligned_cols=23  Identities=4%  Similarity=-0.205  Sum_probs=18.3

Q ss_pred             CcCCceeecCCCCCHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la  248 (854)
                      ..+..+|++|+|+|||.++-.++
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~~~   29 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPAAY   29 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHH
Confidence            56678999999999998775443

>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=93.67  E-value=0.16  Score=52.54  Aligned_cols=86  Identities=15%  Similarity=0.093  Sum_probs=58.7

Q ss_pred             HHHHHHHHHhhccCcCC--ceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc---------------
Q 003038          213 EDVMYVIENLMSKRKRN--FVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH---------------  275 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n--~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~---------------  275 (854)
                      +..+.+++-+..++++.  +=+.|+||+|||+++..|+..+.+-.     ..+-|+.+|.++=..               
T Consensus        35 ~~~~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~~~~~~g-----~~vaViavDpss~~~gg~llgdr~rm~~~~  109 (323)
T d2qm8a1          35 AAVRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLLTAAG-----HKVAVLAVDPSSTRTGGSILGDKTRMARLA  109 (323)
T ss_dssp             HHHHHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHHHHTT-----CCEEEEEECGGGGSSCCCSSCCGGGSTTGG
T ss_pred             HHHHHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHHHHhhcC-----CceeeeecccccHHHHhccccchhhHHHHh
Confidence            34566666666556555  55789999999999999998765421     345666666543321               


Q ss_pred             -------------cchHHHHHHHHHHHHHHHhhhCCCeEEEeC
Q 003038          276 -------------MNRVEVEQRVEEIKNLVRSCLGRGIVLNLG  305 (854)
Q Consensus       276 -------------~~rge~E~rl~~l~~~~~~~~~~~~ILfid  305 (854)
                                   +..|.+...+.+.+..++..  +-.++||.
T Consensus       110 ~~~~~~ir~~~~~~~~gg~~~~~~~~i~~~~~~--g~d~iiiE  150 (323)
T d2qm8a1         110 IDRNAFIRPSPSSGTLGGVAAKTRETMLLCEAA--GFDVILVE  150 (323)
T ss_dssp             GCTTEEEECCCCCSSHHHHHHHHHHHHHHHHHT--TCCEEEEE
T ss_pred             cccceeeccccccccccchhHHHHHHHHhhccC--CCCeEEEe
Confidence                         14477888888888888865  34566765

>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=93.51  E-value=0.037  Score=54.05  Aligned_cols=39  Identities=10%  Similarity=-0.026  Sum_probs=29.0

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccc
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSI  270 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~  270 (854)
                      .+-++||||+|||||+.+--||.++.+..     +.+-+++.|.
T Consensus        11 p~vi~lvGptGvGKTTTiAKLAa~~~~~~-----~kV~lit~Dt   49 (213)
T d1vmaa2          11 PFVIMVVGVNGTGKTTSCGKLAKMFVDEG-----KSVVLAAADT   49 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTT-----CCEEEEEECT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCC-----CceEEEeecc
Confidence            33457899999999999999998886532     3456666654

>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=93.38  E-value=0.15  Score=53.64  Aligned_cols=27  Identities=11%  Similarity=0.132  Sum_probs=23.2

Q ss_pred             CCCEEEEEecCCCCCHHHHHHHHHhhh
Q 003038          731 NPHRVFLIEDVEQADYCSQKGFKRAIE  757 (854)
Q Consensus       731 ~p~~ViliDEieka~~~v~~~Ll~~le  757 (854)
                      .++.+|++||+-.++......++.++.
T Consensus       260 l~~d~lIIDEaSmv~~~l~~~ll~~~~  286 (359)
T d1w36d1         260 LHLDVLVVDEASMIDLPMMSRLIDALP  286 (359)
T ss_dssp             CSCSEEEECSGGGCBHHHHHHHHHTCC
T ss_pred             cccceeeehhhhccCHHHHHHHHHHhc
Confidence            357899999999999988888888775

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

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: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=93.35  E-value=0.072  Score=53.78  Aligned_cols=93  Identities=12%  Similarity=0.150  Sum_probs=57.0

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      -.++|+||+++|||.++.+|+..+ |.+..   ++-+  .       ..+.+..+.                  ..+|++
T Consensus       105 n~~~l~G~~~tGKS~f~~~i~~~l-g~~~~---~~~~--~-------~~f~l~~l~------------------~k~~~~  153 (267)
T d1u0ja_         105 NTIWLFGPATTGKTNIAEAIAHTV-PFYGC---VNWT--N-------ENFPFNDCV------------------DKMVIW  153 (267)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHS-SCEEE---CCTT--C-------SSCTTGGGS------------------SCSEEE
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHh-cchhh---cccc--C-------CCccccccC------------------CCEEEE
Confidence            378899999999999999999987 75421   1111  0       111122111                  247999


Q ss_pred             EecCCCCCHHHHHHHHHhhhcCeEec-C-CCceeecC-CeEEEEecCC
Q 003038          738 IEDVEQADYCSQKGFKRAIESGRIVT-S-SGDEVSLG-DAIVILSCES  782 (854)
Q Consensus       738 iDEieka~~~v~~~Ll~~le~G~l~d-~-~G~~v~~~-~aIiIlTsn~  782 (854)
                      +||...-.. ....+++++.-..++- . +...+.|. .+++|+|+|.
T Consensus       154 ~~e~~~~~~-~~~~~K~l~gGd~i~v~~K~k~~~~~~~~p~li~s~n~  200 (267)
T d1u0ja_         154 WEEGKMTAK-VVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTN  200 (267)
T ss_dssp             ECSCCEETT-THHHHHHHHTTCCEEC------CCEECCCCEEEEESSC
T ss_pred             EeCCCcccc-HHHHHHHhcCCCceEeecccCCCcEeeCCeEEEEeCCC
Confidence            999986554 4456777777545542 2 34566765 4577777764

>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=93.22  E-value=0.035  Score=51.83  Aligned_cols=22  Identities=9%  Similarity=0.155  Sum_probs=19.5

Q ss_pred             CceeecCCCCCHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~  250 (854)
                      .++|+|.||||||+++..|..+
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999988753

>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=93.15  E-value=0.022  Score=54.01  Aligned_cols=22  Identities=18%  Similarity=0.166  Sum_probs=20.2

Q ss_pred             ceeecCCCCCHHHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ++|+||||+||||+++-||.+.
T Consensus         4 I~i~GppGSGKsT~a~~La~~~   25 (194)
T d1teva_           4 VFVLGGPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6899999999999999999874

>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=93.12  E-value=0.092  Score=52.13  Aligned_cols=35  Identities=26%  Similarity=0.527  Sum_probs=27.7

Q ss_pred             HHHHHHHcCCCEEEEEecCCC-CCHHHHHHHHHhhhc
Q 003038          723 RFAEAVSNNPHRVFLIEDVEQ-ADYCSQKGFKRAIES  758 (854)
Q Consensus       723 ~L~eav~~~p~~ViliDEiek-a~~~v~~~Ll~~le~  758 (854)
                      .|..++-.+| .|++|||.-- +|+.....+++.|.+
T Consensus       149 alARal~~~p-~ililDEpts~LD~~~~~~i~~~l~~  184 (241)
T d2pmka1         149 AIARALVNNP-KILIFDEATSALDYESEHVIMRNMHK  184 (241)
T ss_dssp             HHHHHHTTCC-SEEEECCCCSCCCHHHHHHHHHHHHH
T ss_pred             hhhhhhhccc-chhhhhCCccccCHHHHHHHHHHHHH
Confidence            4677777777 7999999875 688888888888764

>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=93.08  E-value=0.028  Score=50.77  Aligned_cols=21  Identities=14%  Similarity=0.055  Sum_probs=18.6

Q ss_pred             ceeecCCCCCHHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~  250 (854)
                      ++|+|+||||||+++..+...
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999987654

>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=92.84  E-value=0.24  Score=51.89  Aligned_cols=37  Identities=14%  Similarity=0.037  Sum_probs=26.0

Q ss_pred             HHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          213 EDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      +....+..+|.   ++-.+|.|+||+|||+++..+...+.
T Consensus       152 ~Q~~A~~~al~---~~~~vI~G~pGTGKTt~i~~~l~~l~  188 (359)
T d1w36d1         152 WQKVAAAVALT---RRISVISGGPGTGKTTTVAKLLAALI  188 (359)
T ss_dssp             HHHHHHHHHHT---BSEEEEECCTTSTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHc---CCeEEEEcCCCCCceehHHHHHHHHH
Confidence            44445555553   56889999999999998876554443

>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=92.83  E-value=0.025  Score=52.55  Aligned_cols=24  Identities=17%  Similarity=0.098  Sum_probs=21.3

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHc
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      +|+.|.||||||++++.|+.++..
T Consensus         4 ivi~G~~GsGKTT~~~~La~~L~~   27 (194)
T d1nksa_           4 GIVTGIPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH
Confidence            467899999999999999999754

>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=92.78  E-value=0.025  Score=53.30  Aligned_cols=22  Identities=27%  Similarity=0.382  Sum_probs=20.0

Q ss_pred             ceeecCCCCCHHHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +||+||||+|||++++.|+.+.
T Consensus         5 ivl~GpsG~GK~tl~~~L~~~~   26 (182)
T d1znwa1           5 VVLSGPSAVGKSTVVRCLRERI   26 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhhC
Confidence            6899999999999999998774

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=92.54  E-value=0.063  Score=49.85  Aligned_cols=21  Identities=5%  Similarity=0.158  Sum_probs=18.8

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .++|+|.||||||+++..|..
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~   22 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTG   22 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            478999999999999999864

>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=92.51  E-value=0.027  Score=52.95  Aligned_cols=75  Identities=11%  Similarity=0.168  Sum_probs=44.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCccccccccccCCCCCCchHHHHHHHHHcCCCEEEE
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTEDSRNKRSRDEQSCSYIERFAEAVSNNPHRVFL  737 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~~~~~rl~~~~g~g~~e~L~eav~~~p~~Vil  737 (854)
                      ..++++|++|+|||++|+.|+...     .+++++..++.       ..+           .....+.+++.+..  -|+
T Consensus        15 ~liil~G~pGsGKST~a~~l~~~~-----~~~~i~~D~~~-------~~~-----------~~~~~~~~~l~~g~--~vI   69 (172)
T d1yj5a2          15 EVVVAVGFPGAGKSTFIQEHLVSA-----GYVHVNRDTLG-------SWQ-----------RCVSSCQAALRQGK--RVV   69 (172)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTGGG-----TCEEEEHHHHC-------SHH-----------HHHHHHHHHHHTTC--CEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhc-----CCEEEchHHHH-------HHH-----------HHHHHHHHHHHCCC--Cce
Confidence            589999999999999999887643     34555544332       000           11223445555433  355


Q ss_pred             EecCCCCCHHHHHHHHHhhhc
Q 003038          738 IEDVEQADYCSQKGFKRAIES  758 (854)
Q Consensus       738 iDEieka~~~v~~~Ll~~le~  758 (854)
                      +|... ........+++..++
T Consensus        70 iD~t~-~~~~~R~~~~~~a~~   89 (172)
T d1yj5a2          70 IDNTN-PDVPSRARYIQCAKD   89 (172)
T ss_dssp             EESCC-CSHHHHHHHHHHHHH
T ss_pred             eeCcC-CCHHHHHHHHHHHHh
Confidence            78665 445555566665553

>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=92.38  E-value=0.061  Score=52.41  Aligned_cols=38  Identities=11%  Similarity=-0.035  Sum_probs=24.6

Q ss_pred             CceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccc
Q 003038          229 NFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSIS  271 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~  271 (854)
                      -++||||+|||||+.+--||.+..+..     +.+-|+..|.-
T Consensus        14 vi~lvGptGvGKTTTiAKLA~~~~~~g-----~kV~lit~Dt~   51 (211)
T d1j8yf2          14 VIMLVGVQGTGKATTAGKLAYFYKKKG-----FKVGLVGADVY   51 (211)
T ss_dssp             EEEEECSCCC----HHHHHHHHHHHTT-----CCEEEEECCCS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCC-----CceEEEEeecc
Confidence            367799999999999999998886532     34566666654

>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=92.33  E-value=0.11  Score=50.52  Aligned_cols=78  Identities=9%  Similarity=0.076  Sum_probs=51.1

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccc--cc-----c-------------------chH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSF--RH-----M-------------------NRV  279 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l--~~-----~-------------------~rg  279 (854)
                      .+.-.+|.||||+|||.++..+|....+..     ..+-+++++.+.-  ..     +                   ...
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~~~~~~-----~~~~~is~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVENACANK-----ERAILFAYEESRAQLLRNAYSWGMDFEEMERQNLLKIVCAYPESA   99 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHHHTTT-----CCEEEEESSSCHHHHHHHHHTTSCCHHHHHHTTSEEECCCCGGGS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhc-----cccceeeccCCHHHHHHHHHHcCCChHHHhhcCceEEEEeecchh
Confidence            577889999999999999999999876543     1234555443210  00     0                   012


Q ss_pred             HHHHHHHHHHHHHHhhhCCCeEEEeCccccc
Q 003038          280 EVEQRVEEIKNLVRSCLGRGIVLNLGDLEWA  310 (854)
Q Consensus       280 e~E~rl~~l~~~~~~~~~~~~ILfidel~~l  310 (854)
                      ..+..+..+...+++.  ++-+++||.+..+
T Consensus       100 ~~~~~~~~i~~~i~~~--~~~~vviDs~~~~  128 (242)
T d1tf7a2         100 GLEDHLQIIKSEINDF--KPARIAIDSLSAL  128 (242)
T ss_dssp             CHHHHHHHHHHHHHTT--CCSEEEEECHHHH
T ss_pred             hHHHHHHHHHHHHHhc--CCceeeeecchhh
Confidence            2345556666666664  5778899999888

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=92.27  E-value=0.025  Score=49.79  Aligned_cols=34  Identities=3%  Similarity=-0.143  Sum_probs=22.0

Q ss_pred             eeEEEecCCCchHHHHHH-HHHHHHhCCCCceEEE
Q 003038          658 TWLFFQGVDADAKEKIAK-ELARLVFGSHNNFVSI  691 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr-~LA~~lfg~~~~~i~i  691 (854)
                      ...++.+|||+|||.+|- ++.+........++.+
T Consensus         8 ~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~vli~   42 (140)
T d1yksa1           8 MTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVL   42 (140)
T ss_dssp             CEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEE
T ss_pred             CcEEEEcCCCCChhHHHHHHHHHHhhhcCceeeee
Confidence            367899999999997774 4444444434444433

>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=92.23  E-value=0.035  Score=51.30  Aligned_cols=31  Identities=16%  Similarity=0.094  Sum_probs=22.4

Q ss_pred             HHHHhhcc-CcCCceeecCCCCCHHHHHHHHH
Q 003038          218 VIENLMSK-RKRNFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       218 v~~~L~r~-~k~n~vLvGe~GvGKta~v~~la  248 (854)
                      +++-|... +...++|||+||||||+++..|.
T Consensus         3 ~~~~~~~~~k~~kI~lvG~~~vGKTsLl~~l~   34 (186)
T d1f6ba_           3 VLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLK   34 (186)
T ss_dssp             HHHHHTCTTCCEEEEEEEETTSSHHHHHHHHS
T ss_pred             hHHhccccCCCCEEEEECCCCCCHHHHHHHHh
Confidence            34444433 34469999999999999998664

>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=92.11  E-value=0.047  Score=52.50  Aligned_cols=38  Identities=16%  Similarity=0.222  Sum_probs=28.5

Q ss_pred             eecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcc
Q 003038          232 VVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLS  269 (854)
Q Consensus       232 LvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~  269 (854)
                      |.|++|+||||+++.|++.+....++..-.++.+++.|
T Consensus         7 I~G~~gSGKSTla~~L~~~l~~~~~~~~~~~~~vi~~D   44 (213)
T d1uj2a_           7 VSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQD   44 (213)
T ss_dssp             EECSTTSSHHHHHHHHHHHTTGGGSCGGGCSEEEEEGG
T ss_pred             EECCCCCCHHHHHHHHHHHhchhccccCCCceEEEecc
Confidence            55999999999999999988665555444455565554

>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=92.02  E-value=0.049  Score=52.46  Aligned_cols=30  Identities=20%  Similarity=0.296  Sum_probs=24.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIAL  693 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~  693 (854)
                      .+.+-||+|+|||++|+.||+.+     .|..++.
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~l-----g~~~ist   34 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDF-----GFTYLDT   34 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHH-----CCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh-----CCcEECH
Confidence            35566999999999999999998     4555653

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=91.99  E-value=0.083  Score=47.92  Aligned_cols=21  Identities=14%  Similarity=0.243  Sum_probs=18.7

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .++|+|+|+||||+++..|..
T Consensus         3 kI~lvG~~nvGKSsLin~l~~   23 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAG   23 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            478999999999999998874

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=91.87  E-value=0.15  Score=45.12  Aligned_cols=27  Identities=11%  Similarity=0.282  Sum_probs=21.6

Q ss_pred             CCCEEEEEecCCCCCHHHHHHHHHhhh
Q 003038          731 NPHRVFLIEDVEQADYCSQKGFKRAIE  757 (854)
Q Consensus       731 ~p~~ViliDEieka~~~v~~~Ll~~le  757 (854)
                      ..+++|+|||+|..+......+..+++
T Consensus        93 ~~~~~vIiDE~H~~~~~~~~~~~~~l~  119 (136)
T d1a1va1          93 GAYDIIICDECHSTDATSILGIGTVLD  119 (136)
T ss_dssp             CCCSEEEEETTTCCSHHHHHHHHHHHH
T ss_pred             hcCCEEEEecccccCHHHHHHHHHHHH
Confidence            457899999999999987666666655

>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=91.66  E-value=0.13  Score=51.41  Aligned_cols=35  Identities=20%  Similarity=0.394  Sum_probs=28.0

Q ss_pred             HHHHHHHcCCCEEEEEecCCC-CCHHHHHHHHHhhhc
Q 003038          723 RFAEAVSNNPHRVFLIEDVEQ-ADYCSQKGFKRAIES  758 (854)
Q Consensus       723 ~L~eav~~~p~~ViliDEiek-a~~~v~~~Ll~~le~  758 (854)
                      .|..++-.+| .|++|||.-- +|+.....+++.|..
T Consensus       164 ~iARal~~~p-~ililDEpts~LD~~t~~~i~~~l~~  199 (255)
T d2hyda1         164 SIARIFLNNP-PILILDEATSALDLESESIIQEALDV  199 (255)
T ss_dssp             HHHHHHHHCC-SEEEEESTTTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCC-CEEEEeCccccCCHHHHHHHHHHHHH
Confidence            4677887777 6999999985 588888888888864

>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=91.65  E-value=0.057  Score=51.65  Aligned_cols=31  Identities=13%  Similarity=0.239  Sum_probs=25.9

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      .+.+.||+|+||+++|+.||+.+     .|.+++..
T Consensus         5 iI~I~GppGSGKgT~ak~La~~~-----gl~~iStG   35 (225)
T d1ckea_           5 VITIDGPSGAGKGTLCKAMAEAL-----QWHLLDSG   35 (225)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH-----TCEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh-----CCcEECHH
Confidence            67788999999999999999998     46666543

>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=91.63  E-value=0.076  Score=53.03  Aligned_cols=52  Identities=2%  Similarity=0.086  Sum_probs=43.5

Q ss_pred             HHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccc
Q 003038          213 EDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSIS  271 (854)
Q Consensus       213 ~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~  271 (854)
                      .++..|.+-|.|..++=+++.|--|||||+++-.||..+.+       +|.+++-+|..
T Consensus         6 ~~~~~~~~~~~~~~~~iii~sGKGGVGKTT~a~nLA~~lA~-------~G~rVllvD~D   57 (279)
T d1ihua2           6 PSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLAD-------MGFDVHLTTSD   57 (279)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEECSTTSSHHHHHHHHHHHHHH-------TTCCEEEEESC
T ss_pred             ccHHHHHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHHHH-------CCCcEEEEeCC
Confidence            36888999999988888999999999999999999988876       35566666654

>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=91.31  E-value=0.16  Score=52.18  Aligned_cols=43  Identities=21%  Similarity=0.177  Sum_probs=32.3

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhC--CCCceEEEcccccc
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFG--SHNNFVSIALSSFS  697 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg--~~~~~i~id~s~~~  697 (854)
                      |.+-.+-+.|++|+|||++|+.|+..|-.  .......|.|..|-
T Consensus        78 k~P~iIGIaG~sgSGKSTla~~L~~lL~~~~~~~~v~~Is~D~F~  122 (308)
T d1sq5a_          78 RIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFL  122 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGGB
T ss_pred             CCCEEEEEeCCCCCCCcHHHHHHHHHHhhhcCCCceEEEeeeeeE
Confidence            33458899999999999999999998831  23456666666664

>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=91.24  E-value=0.063  Score=50.15  Aligned_cols=23  Identities=4%  Similarity=0.085  Sum_probs=20.2

Q ss_pred             eecCCCCCHHHHHHHHHHHHHcC
Q 003038          232 VVGECLASIEGVVRGVIDKIEKG  254 (854)
Q Consensus       232 LvGe~GvGKta~v~~la~~i~~~  254 (854)
                      +.|++|+|||++++.|+..+...
T Consensus        27 I~G~~GSGKSTla~~L~~~l~~~   49 (198)
T d1rz3a_          27 IDGLSRSGKTTLANQLSQTLREQ   49 (198)
T ss_dssp             EEECTTSSHHHHHHHHHHHHHHT
T ss_pred             EECCCCCCHHHHHHHHHHHhccc
Confidence            66999999999999999887653

>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=91.23  E-value=0.076  Score=49.93  Aligned_cols=37  Identities=14%  Similarity=0.340  Sum_probs=28.7

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccc
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSI  270 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~  270 (854)
                      +||+|++|||||+++..+  ++....+|.  .|..+..++.
T Consensus         5 ivllG~~~vGKTsll~r~--~f~~~~~pT--iG~~~~~~~~   41 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQM--RIIHGQDPT--KGIHEYDFEI   41 (200)
T ss_dssp             EEEECSTTSSHHHHHHHH--HHHHSCCCC--SSEEEEEEEE
T ss_pred             EEEECCCCCCHHHHHHHH--hcCCCCCCe--eeeEEEEEee
Confidence            789999999999999998  577777774  2555555544

>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=90.93  E-value=0.05  Score=49.29  Aligned_cols=21  Identities=10%  Similarity=0.047  Sum_probs=18.4

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      +++|+|+||||||+++..+..
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~   27 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQV   27 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999987653

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.82  E-value=0.054  Score=49.84  Aligned_cols=21  Identities=10%  Similarity=0.376  Sum_probs=18.3

Q ss_pred             ceeecCCCCCHHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~  250 (854)
                      ++|+|+||||||++++.+...
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999877643

>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=90.81  E-value=0.059  Score=51.56  Aligned_cols=20  Identities=10%  Similarity=0.197  Sum_probs=18.0

Q ss_pred             eecCCCCCHHHHHHHHHHHH
Q 003038          232 VVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       232 LvGe~GvGKta~v~~la~~i  251 (854)
                      +.||||+||+|+++-||.+.
T Consensus         8 I~GppGSGKgT~ak~La~~~   27 (225)
T d1ckea_           8 IDGPSGAGKGTLCKAMAEAL   27 (225)
T ss_dssp             EECCTTSSHHHHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHHHh
Confidence            33999999999999999985

>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=90.79  E-value=0.06  Score=51.17  Aligned_cols=22  Identities=18%  Similarity=0.274  Sum_probs=20.4

Q ss_pred             EEEecCCCchHHHHHHHHHHHH
Q 003038          660 LFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      +.+.||+|+||+++++.|++..
T Consensus         3 Ivl~GPsGsGK~tl~~~L~~~~   24 (190)
T d1lvga_           3 VVLSGPSGAGKSTLLKKLFQEH   24 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHhC
Confidence            6799999999999999999876

>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=90.79  E-value=0.056  Score=52.30  Aligned_cols=24  Identities=8%  Similarity=0.205  Sum_probs=20.9

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +=+||+||+|||||+|.+.|..+.
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~~   26 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKTQ   26 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhC
Confidence            347899999999999999998773

>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=90.75  E-value=0.14  Score=51.32  Aligned_cols=86  Identities=7%  Similarity=0.003  Sum_probs=52.4

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCc-CCCccccccccccC-CCCCCchHH---HHHHHHHcCC
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSST-RADSTEDSRNKRSR-DEQSCSYIE---RFAEAVSNNP  732 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~-~~~s~e~~~~~rl~-~~~g~g~~e---~L~eav~~~p  732 (854)
                      .+..|+||+|+|||.+|..++...-......+.+|.-.-... .... -.....+++ ..+. ..++   .+...+++++
T Consensus        55 ~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyidtE~~~~~~~a~~-~Gvd~d~v~~~~~~-~~E~~~~~i~~l~~~~~  132 (263)
T d1u94a1          55 RIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARK-LGVDIDNLLCSQPD-TGEQALEICDALARSGA  132 (263)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHH-TTCCGGGCEEECCS-SHHHHHHHHHHHHHHTC
T ss_pred             eEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEccccccCHHHHHH-hCCCHHHEEEecCC-CHHHHHHHHHHHHhcCC
Confidence            488999999999999999998877666677888885432210 0000 000112222 1221 2222   3445566788


Q ss_pred             CEEEEEecCCCCC
Q 003038          733 HRVFLIEDVEQAD  745 (854)
Q Consensus       733 ~~ViliDEieka~  745 (854)
                      ..+|++|-|--+-
T Consensus       133 ~~liViDSi~al~  145 (263)
T d1u94a1         133 VDVIVVDSVAALT  145 (263)
T ss_dssp             CSEEEEECGGGCC
T ss_pred             CCEEEEECccccc
Confidence            8999999996553

>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=90.74  E-value=0.088  Score=51.00  Aligned_cols=37  Identities=16%  Similarity=0.126  Sum_probs=28.0

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEccccc
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISS  272 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~  272 (854)
                      ++++|++|+||||+++.|.+....+      +.+-++.+|.+.
T Consensus         3 i~v~G~~GsGKTTLl~~ll~~~~~~------~~~~ivn~d~~~   39 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGRYLEDN------YKVAYVNLDTGV   39 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTTT------SCEEEEECCSSC
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHhhC------CeEEEEecCccc
Confidence            5789999999999999998765433      345667766553

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.73  E-value=0.056  Score=50.19  Aligned_cols=19  Identities=5%  Similarity=0.270  Sum_probs=17.1

Q ss_pred             ceeecCCCCCHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la  248 (854)
                      ++++|+||||||+++..+.
T Consensus         6 ivvvG~~~vGKTsli~r~~   24 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFT   24 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHh
Confidence            7899999999999998665

>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=90.70  E-value=0.38  Score=51.03  Aligned_cols=42  Identities=5%  Similarity=0.023  Sum_probs=32.1

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      .++.+..+-+++. +.+--+|+.||.|+|||+...++.+.+.+
T Consensus       143 ~~~~~~~l~~l~~-~~~GliLvtGpTGSGKSTTl~~~l~~~~~  184 (401)
T d1p9ra_         143 TAHNHDNFRRLIK-RPHGIILVTGPTGSGKSTTLYAGLQELNS  184 (401)
T ss_dssp             CHHHHHHHHHHHT-SSSEEEEEECSTTSCHHHHHHHHHHHHCC
T ss_pred             cHHHHHHHHHHHh-hhhceEEEEcCCCCCccHHHHHHhhhhcC
Confidence            4455555555544 56667899999999999999999998854

>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=90.59  E-value=0.06  Score=49.54  Aligned_cols=21  Identities=14%  Similarity=0.177  Sum_probs=18.4

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .++|+|++|||||+++..+..
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~   25 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVT   25 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999987654

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.50  E-value=0.057  Score=49.58  Aligned_cols=21  Identities=19%  Similarity=0.310  Sum_probs=17.9

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .++|+|+||||||+++..+..
T Consensus         4 Kv~liG~~~vGKSsLi~rl~~   24 (164)
T d1z2aa1           4 KMVVVGNGAVGKSSMIQRYCK   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            378999999999999986653

>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=90.50  E-value=0.067  Score=51.45  Aligned_cols=21  Identities=10%  Similarity=0.150  Sum_probs=18.6

Q ss_pred             eeecCCCCCHHHHHHHHHHHH
Q 003038          231 VVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       231 vLvGe~GvGKta~v~~la~~i  251 (854)
                      .+-||||+||||+++.||.++
T Consensus         7 aIdGp~GsGKgT~ak~La~~l   27 (223)
T d1q3ta_           7 AIDGPASSGKSTVAKIIAKDF   27 (223)
T ss_dssp             EEECSSCSSHHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHh
Confidence            344999999999999999985

>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=90.41  E-value=0.062  Score=50.81  Aligned_cols=22  Identities=18%  Similarity=0.261  Sum_probs=20.3

Q ss_pred             EEEecCCCchHHHHHHHHHHHH
Q 003038          660 LFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      ++|.||+|+||++|++.|++..
T Consensus         4 Ivl~GpsG~GK~tl~~~L~~~~   25 (186)
T d1gkya_           4 IVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHHhC
Confidence            6899999999999999998875

>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=90.37  E-value=0.084  Score=48.57  Aligned_cols=32  Identities=9%  Similarity=0.086  Sum_probs=24.3

Q ss_pred             HHHHHHhhccCcCCceeecCCCCCHHHHHHHHH
Q 003038          216 MYVIENLMSKRKRNFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       216 ~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la  248 (854)
                      .++..++. ++.-+++|+|.||||||+++..+.
T Consensus         5 ~~~~~~~~-~k~~kI~vvG~~~~GKSsLi~rl~   36 (177)
T d1zj6a1           5 TRIWRLFN-HQEHKVIIVGLDNAGKTTILYQFS   36 (177)
T ss_dssp             HHHHHHHT-TSCEEEEEEESTTSSHHHHHHHHH
T ss_pred             HHHHHHhC-CCeEEEEEECCCCCCHHHHHHHHh
Confidence            34555555 455679999999999999998654

>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=90.28  E-value=0.053  Score=50.26  Aligned_cols=27  Identities=7%  Similarity=0.186  Sum_probs=21.4

Q ss_pred             hhccCcCCceeecCCCCCHHHHHHHHH
Q 003038          222 LMSKRKRNFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       222 L~r~~k~n~vLvGe~GvGKta~v~~la  248 (854)
                      |..+++-.++|+|+||||||+++..+.
T Consensus         7 ~~~~k~~kIvlvG~~~vGKTSli~rl~   33 (173)
T d1e0sa_           7 IFGNKEMRILMLGLDAAGKTTILYKLK   33 (173)
T ss_dssp             HHTTCCEEEEEEEETTSSHHHHHHHTT
T ss_pred             hhCCCeEEEEEECCCCCCHHHHHHHHh
Confidence            334556679999999999999997543

>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=90.13  E-value=0.14  Score=51.97  Aligned_cols=39  Identities=5%  Similarity=-0.001  Sum_probs=28.3

Q ss_pred             HHHHHHHhhccCcCCceee---cCCCCCHHHHHHHHHHHHHc
Q 003038          215 VMYVIENLMSKRKRNFVVV---GECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       215 i~~v~~~L~r~~k~n~vLv---Ge~GvGKta~v~~la~~i~~  253 (854)
                      +.+.++.-.+..++.|+||   |++|+|||+++..|+..+..
T Consensus        12 ~~~~~~~~~~~~~~~P~iIGi~G~qGSGKSTl~~~l~~~L~~   53 (286)
T d1odfa_          12 LDKYIPEWFETGNKCPLFIFFSGPQGSGKSFTSIQIYNHLME   53 (286)
T ss_dssp             HHHHHHHHHTTTCCSCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCCEEEEeECCCCCCHHHHHHHHHHHHHH
Confidence            3444555445566678777   89999999999988877644

>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=90.10  E-value=0.13  Score=52.10  Aligned_cols=41  Identities=2%  Similarity=0.070  Sum_probs=28.7

Q ss_pred             HHHHHHHHhhccCcCCceeecCCCCCHHH-HHHHHHHHHHcCCCCc
Q 003038          214 DVMYVIENLMSKRKRNFVVVGECLASIEG-VVRGVIDKIEKGDVPE  258 (854)
Q Consensus       214 ei~~v~~~L~r~~k~n~vLvGe~GvGKta-~v~~la~~i~~~~vp~  258 (854)
                      |=+++++-    ...+.++.|+||+|||+ +++.+++.+..+.+|+
T Consensus        15 eQ~~~v~~----~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p   56 (318)
T d1pjra1          15 EQQEAVRT----TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAP   56 (318)
T ss_dssp             HHHHHHHC----CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCG
T ss_pred             HHHHHHhC----CCCCEEEEecCCccHHHHHHHHHHHHHHcCCCCH
Confidence            44556652    35678899999999995 4556777777776553

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {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: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=90.05  E-value=0.36  Score=45.65  Aligned_cols=27  Identities=11%  Similarity=0.122  Sum_probs=19.5

Q ss_pred             cCCceeecCCCCCHHHHHH-HHHHHHHc
Q 003038          227 KRNFVVVGECLASIEGVVR-GVIDKIEK  253 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~-~la~~i~~  253 (854)
                      .+|++|.+|+|+|||.++. .+...+.+
T Consensus        40 ~~~~il~apTGsGKT~~a~l~i~~~~~~   67 (202)
T d2p6ra3          40 GKNLLLAMPTAAGKTLLAEMAMVREAIK   67 (202)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHHHHHT
T ss_pred             CCCEEEEcCCCCchhHHHHHHHHHHhhc
Confidence            5689999999999998763 23334433

>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=89.97  E-value=0.076  Score=49.75  Aligned_cols=23  Identities=17%  Similarity=0.261  Sum_probs=20.9

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.||+|+||+++++.|.+..
T Consensus         4 iivl~GpsG~GK~tl~~~L~~~~   26 (182)
T d1znwa1           4 VVVLSGPSAVGKSTVVRCLRERI   26 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            68899999999999999998765

>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=89.96  E-value=0.19  Score=46.44  Aligned_cols=30  Identities=10%  Similarity=0.320  Sum_probs=25.7

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHHhCCC
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLVFGSH  685 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~  685 (854)
                      +|...++|.|+=|+|||+++|.+++.+ |-.
T Consensus        31 ~~g~ii~L~G~LGaGKTtfvr~~~~~l-g~~   60 (158)
T d1htwa_          31 EKAIMVYLNGDLGAGKTTLTRGMLQGI-GHQ   60 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHT-TCC
T ss_pred             CCCeEEEEecCCCccHHHHHHHHHhhc-ccc
Confidence            455589999999999999999999998 543

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.93  E-value=0.25  Score=48.57  Aligned_cols=79  Identities=13%  Similarity=0.197  Sum_probs=46.1

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHcCC----CCcccCCceEEEccc--cccc---c--cchHHHHHHHHHHHHHHHh
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEKGD----VPEALRDVKCLPLSI--SSFR---H--MNRVEVEQRVEEIKNLVRS  294 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~~~----vp~~L~~~~~~~l~~--~~l~---~--~~rge~E~rl~~l~~~~~~  294 (854)
                      .++..||.||...|||++.+.++.-+.=.+    ||..  .+.+-.+|-  .++.   +  ....-|...++++-..++.
T Consensus        40 ~~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~--~a~~~~~d~I~~~~~~~d~~~~~~S~F~~E~~~~~~il~~  117 (234)
T d1wb9a2          40 QRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQ--KVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHN  117 (234)
T ss_dssp             SSCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSS--EEEECCCCEEEEEEC-----------CHHHHHHHHHHHHH
T ss_pred             CceEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecC--ceecccchhheeEEccCcccccchhHHHHHHHHHHHHHHh
Confidence            567789999999999999998887665433    5522  222222221  1111   1  1122355555555555555


Q ss_pred             hhCCCeEEEeCcc
Q 003038          295 CLGRGIVLNLGDL  307 (854)
Q Consensus       295 ~~~~~~ILfidel  307 (854)
                      . .++.++.|||+
T Consensus       118 ~-~~~sLvliDE~  129 (234)
T d1wb9a2         118 A-TEYSLVLMDEI  129 (234)
T ss_dssp             C-CTTEEEEEESC
T ss_pred             c-ccccEEeeccc
Confidence            4 45789999999

>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=89.93  E-value=0.049  Score=50.90  Aligned_cols=33  Identities=9%  Similarity=0.075  Sum_probs=25.3

Q ss_pred             HHHHHH-HhhccCcCCceeecCCCCCHHHHHHHH
Q 003038          215 VMYVIE-NLMSKRKRNFVVVGECLASIEGVVRGV  247 (854)
Q Consensus       215 i~~v~~-~L~r~~k~n~vLvGe~GvGKta~v~~l  247 (854)
                      +.++++ .+.+++.-.++|+|+||||||+++..+
T Consensus         4 ~~~~~~~l~~~~k~~KI~lvG~~~vGKTsLi~~l   37 (182)
T d1moza_           4 FSSMFDKLWGSNKELRILILGLDGAGKTTILYRL   37 (182)
T ss_dssp             HHHHHGGGTTCSSCEEEEEEEETTSSHHHHHHHT
T ss_pred             HHHHHHHHhCCCceEEEEEECCCCCCHHHHHHHH
Confidence            445554 346667778999999999999999754

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.91  E-value=0.073  Score=48.97  Aligned_cols=20  Identities=20%  Similarity=0.252  Sum_probs=17.5

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++|+|++|||||+++..+..
T Consensus         6 ivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999986653

>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=89.90  E-value=0.051  Score=51.38  Aligned_cols=26  Identities=8%  Similarity=0.123  Sum_probs=23.1

Q ss_pred             CcceeEEEecCCCchHHHHHHHHHHHH
Q 003038          655 KEETWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       655 kp~~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      || -.+.|.|++|+|||++++.|++.+
T Consensus         8 kp-~~I~ieG~~GsGKTTl~~~L~~~l   33 (197)
T d2vp4a1           8 QP-FTVLIEGNIGSGKTTYLNHFEKYK   33 (197)
T ss_dssp             CC-EEEEEECSTTSCHHHHHHTTGGGT
T ss_pred             Cc-eEEEEECCCCCCHHHHHHHHHHHh
Confidence            45 478899999999999999999977

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.74  E-value=0.077  Score=48.97  Aligned_cols=20  Identities=10%  Similarity=0.212  Sum_probs=17.7

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++|+|++|||||+++..+..
T Consensus         5 i~lvG~~~vGKTsli~r~~~   24 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLT   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            78999999999999987654

>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=89.74  E-value=0.15  Score=49.52  Aligned_cols=36  Identities=8%  Similarity=0.172  Sum_probs=29.2

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIAL  693 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~  693 (854)
                      ...++.||+|+|||.+|..+|..........+.+..
T Consensus        27 sl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is~   62 (242)
T d1tf7a2          27 SIILATGATGTGKTLLVSRFVENACANKERAILFAY   62 (242)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEES
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHHhccccceeec
Confidence            478999999999999999999887665556655554

>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=89.70  E-value=0.061  Score=50.05  Aligned_cols=22  Identities=14%  Similarity=0.193  Sum_probs=18.3

Q ss_pred             CCceeecCCCCCHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~  249 (854)
                      ..+||+|++|||||+++..+..
T Consensus         3 ~KivvvG~~~vGKTsLi~~~~~   24 (177)
T d1kmqa_           3 KKLVIVGDGACGKTCLLIVNSK   24 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            4489999999999999976553

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.61  E-value=0.074  Score=49.12  Aligned_cols=21  Identities=24%  Similarity=0.230  Sum_probs=18.7

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .++|+|+||||||++++.+..
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~   27 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQ   27 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999997764

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {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: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=89.60  E-value=0.32  Score=46.44  Aligned_cols=38  Identities=13%  Similarity=0.029  Sum_probs=26.7

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      |+-..+.+-.++   ..++.+|++|+|+|||.++-.++.++
T Consensus        72 r~yQ~eav~~~~---~~~~~ll~~~tG~GKT~~a~~~~~~~  109 (206)
T d2fz4a1          72 RDYQEKALERWL---VDKRGCIVLPTGSGKTHVAMAAINEL  109 (206)
T ss_dssp             CHHHHHHHHHHT---TTSEEEEEESSSTTHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHH---hCCCcEEEeCCCCCceehHHhHHHHh
Confidence            655555444443   23467899999999999887777664

>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=89.59  E-value=0.27  Score=48.61  Aligned_cols=29  Identities=14%  Similarity=-0.030  Sum_probs=26.0

Q ss_pred             cCCceeecCCCCCHHHHHHHHHHHHHcCC
Q 003038          227 KRNFVVVGECLASIEGVVRGVIDKIEKGD  255 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~~i~~~~  255 (854)
                      .+-.+|+|+||+|||+++-.+|..|..|.
T Consensus        29 g~~~~i~G~~G~GKS~l~l~la~~ia~g~   57 (274)
T d1nlfa_          29 GTVGALVSPGGAGKSMLALQLAAQIAGGP   57 (274)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHTCC
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHcCC
Confidence            45688999999999999999999998874

>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=89.53  E-value=0.082  Score=47.32  Aligned_cols=20  Identities=10%  Similarity=0.092  Sum_probs=17.3

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++|+|+||||||+++..+..
T Consensus         3 I~liG~~nvGKSSLln~l~~   22 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKN   22 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            68999999999999986553

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=89.53  E-value=0.08  Score=48.83  Aligned_cols=20  Identities=10%  Similarity=0.230  Sum_probs=17.8

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++++|++|||||+++..+..
T Consensus         8 i~vvG~~~vGKTsLi~~l~~   27 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYAD   27 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            78999999999999987754

>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=89.50  E-value=0.081  Score=48.64  Aligned_cols=21  Identities=14%  Similarity=0.221  Sum_probs=18.0

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .++|+|++|||||++++.+..
T Consensus         5 KivvvG~~~vGKTsli~r~~~   25 (167)
T d1c1ya_           5 KLVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            389999999999999986653

>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=89.48  E-value=0.076  Score=48.55  Aligned_cols=20  Identities=15%  Similarity=0.255  Sum_probs=17.7

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++|+|++|||||+++..+..
T Consensus         3 v~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999987653

>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=89.47  E-value=0.1  Score=50.20  Aligned_cols=26  Identities=19%  Similarity=0.121  Sum_probs=23.6

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      +||.++|+|||++|||.++.+|+.-+
T Consensus        52 Kkn~i~~~GP~~TGKS~f~~sl~~~l   77 (205)
T d1tuea_          52 KKNCLVFCGPANTGKSYFGMSFIHFI   77 (205)
T ss_dssp             TCSEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             CceEEEEECCCCccHHHHHHHHHHHh
Confidence            88889999999999999999998654

>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=89.38  E-value=0.37  Score=47.34  Aligned_cols=65  Identities=14%  Similarity=0.156  Sum_probs=44.8

Q ss_pred             HHHHHHhhcCc-ccccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCCCc
Q 003038          609 LTSLCNALEKK-VPWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSHNN  687 (854)
Q Consensus       609 l~~L~~~L~~~-V~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~  687 (854)
                      .+.+++.+.-. -..|..++..|.+.+...                 +|. ..|++|.+|+|||+++-..+...+.....
T Consensus        45 ~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~-----------------~~~-~~LL~GdvGsGKT~V~~~a~~~~~~~g~q  106 (233)
T d2eyqa3          45 YQLFCDSFPFETTPDQAQAINAVLSDMCQP-----------------LAM-DRLVCGDVGFGKTEVAMRAAFLAVDNHKQ  106 (233)
T ss_dssp             HHHHHHTCCSCCCHHHHHHHHHHHHHHHSS-----------------SCC-EEEEECCCCTTTHHHHHHHHHHHHTTTCE
T ss_pred             HHhhhhccccccchhHHHHHHHHHHHHhcc-----------------Ccc-CeEEEcCCCCCcHHHHHHHHHHHHHcCCc
Confidence            34555555333 366898888888876642                 333 67888999999999999888777655544


Q ss_pred             eEEE
Q 003038          688 FVSI  691 (854)
Q Consensus       688 ~i~i  691 (854)
                      .+-+
T Consensus       107 v~~l  110 (233)
T d2eyqa3         107 VAVL  110 (233)
T ss_dssp             EEEE
T ss_pred             eEEE
Confidence            4443

>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=89.36  E-value=0.13  Score=47.29  Aligned_cols=23  Identities=13%  Similarity=0.078  Sum_probs=20.9

Q ss_pred             eeecCCCCCHHHHHHHHHHHHHc
Q 003038          231 VVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       231 vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      -++|.+|+||||+++.|+.++.+
T Consensus         5 ~I~G~~gSGKTTli~~l~~~L~~   27 (165)
T d1xjca_           5 QVVGYKHSGKTTLMEKWVAAAVR   27 (165)
T ss_dssp             EEECCTTSSHHHHHHHHHHHHHH
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHh
Confidence            48999999999999999998875

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.34  E-value=0.084  Score=48.66  Aligned_cols=21  Identities=19%  Similarity=0.376  Sum_probs=18.0

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .++++|++|||||+++..+..
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~   28 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999986653

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.17  E-value=0.09  Score=48.30  Aligned_cols=21  Identities=5%  Similarity=0.254  Sum_probs=18.2

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .++|+|++|||||+++..+..
T Consensus         6 Ki~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           6 KVCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999986653

>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=89.08  E-value=0.093  Score=47.92  Aligned_cols=20  Identities=10%  Similarity=0.185  Sum_probs=17.8

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++|+|++|||||+++..+..
T Consensus         5 v~liG~~~vGKTsLl~~~~~   24 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCA   24 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999987653

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.96  E-value=0.087  Score=48.36  Aligned_cols=20  Identities=25%  Similarity=0.278  Sum_probs=17.8

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++|+|++|||||+++..+..
T Consensus         6 i~viG~~~vGKTsli~~l~~   25 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQ   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            79999999999999987654

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.93  E-value=0.074  Score=48.88  Aligned_cols=22  Identities=9%  Similarity=0.220  Sum_probs=19.0

Q ss_pred             CCceeecCCCCCHHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~  249 (854)
                      ..++|+|++|||||+++..+..
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~   26 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVE   26 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHh
Confidence            4689999999999999987754

>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=88.90  E-value=0.15  Score=49.13  Aligned_cols=34  Identities=15%  Similarity=0.283  Sum_probs=27.1

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      -+.|.|++|+|||++++.|++.|-....+.+.+.
T Consensus         5 lI~ieG~dGsGKsT~~~~L~~~L~~~g~~v~~~~   38 (209)
T d1nn5a_           5 LIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLR   38 (209)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            4678899999999999999999865555555543

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.87  E-value=0.096  Score=48.21  Aligned_cols=21  Identities=19%  Similarity=0.403  Sum_probs=17.7

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .++|+|++|||||+++..+..
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~   25 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVS   25 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            378999999999999986653

>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=88.77  E-value=0.094  Score=48.24  Aligned_cols=19  Identities=16%  Similarity=0.144  Sum_probs=17.0

Q ss_pred             ceeecCCCCCHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la  248 (854)
                      ++|+|++|||||+++..+.
T Consensus         5 i~viG~~~vGKTsLi~r~~   23 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFV   23 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            7899999999999998665

>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=88.76  E-value=0.093  Score=48.64  Aligned_cols=21  Identities=24%  Similarity=0.238  Sum_probs=18.1

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .++|+|++|||||+++..+..
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~   28 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQ   28 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999986653

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.75  E-value=0.097  Score=48.91  Aligned_cols=21  Identities=19%  Similarity=0.200  Sum_probs=18.6

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .++|+|++|||||+++..+..
T Consensus         7 KivviG~~~vGKTsli~~~~~   27 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTT   27 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999998765

>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=88.67  E-value=0.096  Score=48.98  Aligned_cols=19  Identities=5%  Similarity=0.095  Sum_probs=16.6

Q ss_pred             ceeecCCCCCHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la  248 (854)
                      ++|+|+||||||++++.+.
T Consensus         8 i~ivG~~~vGKTsLi~~l~   26 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYT   26 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHh
Confidence            7899999999999987553

>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=88.61  E-value=0.24  Score=44.10  Aligned_cols=23  Identities=26%  Similarity=0.317  Sum_probs=19.9

Q ss_pred             EEEecCCCchHHHHHHHHHHHHh
Q 003038          660 LFFQGVDADAKEKIAKELARLVF  682 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lf  682 (854)
                      ++|+|++|||||+|...|...-|
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~~~   25 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLGEI   25 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhcCCC
Confidence            68999999999999999876544

>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=88.60  E-value=0.095  Score=48.35  Aligned_cols=20  Identities=20%  Similarity=0.310  Sum_probs=17.9

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++|+|++|||||++++.+..
T Consensus         8 i~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999987764

>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=88.60  E-value=0.12  Score=48.50  Aligned_cols=22  Identities=9%  Similarity=0.128  Sum_probs=17.6

Q ss_pred             CCceee---cCCCCCHHHHHHHHHH
Q 003038          228 RNFVVV---GECLASIEGVVRGVID  249 (854)
Q Consensus       228 ~n~vLv---Ge~GvGKta~v~~la~  249 (854)
                      +||+++   |.+|+|||++++-|..
T Consensus         1 k~p~IIgitG~~gSGKstva~~l~~   25 (191)
T d1uf9a_           1 KHPIIIGITGNIGSGKSTVAALLRS   25 (191)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            356655   8999999999998753

>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=88.56  E-value=0.1  Score=49.37  Aligned_cols=23  Identities=4%  Similarity=0.138  Sum_probs=20.1

Q ss_pred             cCCceeecCCCCCHHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la~  249 (854)
                      ...++|+|+|+||||+++..|..
T Consensus         3 ~p~V~lvG~~n~GKTSLln~l~~   25 (209)
T d1nrjb_           3 QPSIIIAGPQNSGKTSLLTLLTT   25 (209)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45789999999999999998864

>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=88.55  E-value=0.097  Score=47.98  Aligned_cols=20  Identities=5%  Similarity=0.265  Sum_probs=17.7

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++++|+||||||++++.+..
T Consensus         5 i~vvG~~~vGKTSli~~l~~   24 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVE   24 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999987653

>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=88.33  E-value=0.1  Score=48.84  Aligned_cols=21  Identities=19%  Similarity=0.314  Sum_probs=17.8

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .+||+|++|||||+++..+..
T Consensus         4 KivliG~~~vGKTsli~r~~~   24 (179)
T d1m7ba_           4 KIVVVGDSQCGKTALLHVFAK   24 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999986653

>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=88.30  E-value=0.39  Score=48.57  Aligned_cols=40  Identities=15%  Similarity=0.361  Sum_probs=28.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHh---CCCCceEEEcccccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVF---GSHNNFVSIALSSFS  697 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lf---g~~~~~i~id~s~~~  697 (854)
                      -.+-+.|++|+|||++|..|...|.   +....++.+.+..|.
T Consensus        28 ~iIGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~DdfY   70 (286)
T d1odfa_          28 LFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFY   70 (286)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGB
T ss_pred             EEEEeECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCCC
Confidence            4677999999999999998876652   233455555565553

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.25  E-value=0.13  Score=49.22  Aligned_cols=38  Identities=21%  Similarity=0.378  Sum_probs=28.1

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCC------CceEEEccccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSH------NNFVSIALSSF  696 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~------~~~i~id~s~~  696 (854)
                      -.+-+.||+|+|||++|+.|++.+ +..      .....+.|..|
T Consensus         3 ~iIgI~G~~gSGKSTla~~L~~~l-~~~~~~~~~~~~~vi~~D~y   46 (213)
T d1uj2a_           3 FLIGVSGGTASGKSSVCAKIVQLL-GQNEVDYRQKQVVILSQDSF   46 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT-TGGGSCGGGCSEEEEEGGGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHh-chhccccCCCceEEEecccc
Confidence            367789999999999999999986 321      23455666655

>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=88.20  E-value=0.11  Score=47.77  Aligned_cols=20  Identities=5%  Similarity=0.318  Sum_probs=17.6

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++|+|+||||||+++..+..
T Consensus         5 i~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            78999999999999987653

>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=88.09  E-value=0.17  Score=47.95  Aligned_cols=33  Identities=18%  Similarity=0.362  Sum_probs=26.0

Q ss_pred             EEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          660 LFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      +.|.|++|+|||++++.|++.|-....+++.+.
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~g~~v~~~~   35 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLA   35 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEe
Confidence            568899999999999999998855444555543

>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=88.05  E-value=0.1  Score=48.94  Aligned_cols=21  Identities=19%  Similarity=0.243  Sum_probs=17.9

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .++|+|++|||||+++..+..
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~   31 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAN   31 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhh
Confidence            478999999999999987653

>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=88.02  E-value=0.12  Score=47.79  Aligned_cols=20  Identities=5%  Similarity=0.225  Sum_probs=17.9

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++|+|+||||||+++..+..
T Consensus         9 I~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            79999999999999987764

>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=87.96  E-value=0.11  Score=48.98  Aligned_cols=20  Identities=20%  Similarity=0.197  Sum_probs=17.4

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++|+|++|||||+++..+..
T Consensus         6 vvllG~~~vGKTSli~r~~~   25 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTT   25 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            79999999999999976653

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=87.96  E-value=0.11  Score=47.44  Aligned_cols=21  Identities=14%  Similarity=0.177  Sum_probs=18.3

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      +++|+|++|||||+++..+..
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~   24 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIAS   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            578999999999999987654

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.90  E-value=0.12  Score=47.55  Aligned_cols=20  Identities=15%  Similarity=0.194  Sum_probs=17.5

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++++|++|||||++++.+..
T Consensus         9 i~vvG~~~vGKTsli~~~~~   28 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKD   28 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            79999999999999986653

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=87.88  E-value=0.12  Score=48.19  Aligned_cols=20  Identities=5%  Similarity=0.313  Sum_probs=17.5

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++|+|++|||||+++..+..
T Consensus         5 v~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999986653

>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=87.85  E-value=0.11  Score=47.89  Aligned_cols=19  Identities=21%  Similarity=0.410  Sum_probs=17.1

Q ss_pred             ceeecCCCCCHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la  248 (854)
                      ++|+|.||||||++++.+.
T Consensus         8 I~lvG~~~vGKTsll~~~~   26 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFI   26 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHH
Confidence            8999999999999998664

>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=87.79  E-value=0.12  Score=47.61  Aligned_cols=19  Identities=11%  Similarity=0.027  Sum_probs=16.9

Q ss_pred             ceeecCCCCCHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la  248 (854)
                      ++|+|++|||||+++..+.
T Consensus         4 i~lvG~~~vGKTsLi~~~~   22 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFG   22 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHh
Confidence            6899999999999998664

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.78  E-value=1.1  Score=43.78  Aligned_cols=24  Identities=17%  Similarity=0.310  Sum_probs=21.2

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHh
Q 003038          659 WLFFQGVDADAKEKIAKELARLVF  682 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lf  682 (854)
                      .+++.||...|||.+.|.+|-.++
T Consensus        43 ~~iiTGpN~~GKSt~lk~i~l~~~   66 (234)
T d1wb9a2          43 MLIITGPNMGGKSTYMRQTALIAL   66 (234)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEeccCchhhHHHHHHHHHHHH
Confidence            689999999999999998886654

>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=87.77  E-value=0.12  Score=47.77  Aligned_cols=19  Identities=11%  Similarity=0.253  Sum_probs=17.0

Q ss_pred             ceeecCCCCCHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la  248 (854)
                      ++++|++|||||+++..+.
T Consensus         7 i~vvG~~~vGKTsLi~~~~   25 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFT   25 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHH
Confidence            7899999999999997664

>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=87.73  E-value=0.11  Score=47.45  Aligned_cols=20  Identities=10%  Similarity=0.142  Sum_probs=17.6

Q ss_pred             CceeecCCCCCHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la  248 (854)
                      +++++|+||||||+++..+.
T Consensus         4 ki~ivG~~~~GKTsLi~~l~   23 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFN   23 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHc
Confidence            58999999999999998653

>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=87.62  E-value=1.2  Score=44.84  Aligned_cols=36  Identities=11%  Similarity=0.233  Sum_probs=27.1

Q ss_pred             HHHHHhhc-cCcCCceeecCCCCCHHHHHHHHHHHHH
Q 003038          217 YVIENLMS-KRKRNFVVVGECLASIEGVVRGVIDKIE  252 (854)
Q Consensus       217 ~v~~~L~r-~~k~n~vLvGe~GvGKta~v~~la~~i~  252 (854)
                      ++|+.|.- .+.....|+|++|||||+++..++....
T Consensus        57 raID~l~pig~GQr~~If~~~g~GKt~ll~~~~~~~~   93 (285)
T d2jdia3          57 KAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQK   93 (285)
T ss_dssp             HHHHHHSCCBTTCBCEEEESTTSSHHHHHHHHHHHTH
T ss_pred             eEEecccCccCCCEEEeecCCCCChHHHHHHHHHhHH
Confidence            56666542 3666788889999999999988876543

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=87.30  E-value=0.14  Score=47.21  Aligned_cols=20  Identities=10%  Similarity=0.104  Sum_probs=17.5

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++|+|++|||||+++..+..
T Consensus         7 ivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           7 VIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999987653

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=87.25  E-value=0.98  Score=46.40  Aligned_cols=91  Identities=12%  Similarity=0.061  Sum_probs=49.0

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHhCCCC--ceEEEccccccCcCCCccccccc----------cccCCCCCC--chHH
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVFGSHN--NFVSIALSSFSSTRADSTEDSRN----------KRSRDEQSC--SYIE  722 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~--~~i~id~s~~~~~~~~s~e~~~~----------~rl~~~~g~--g~~e  722 (854)
                      ...+-+.||||+|||+|...|++.+-....  .++.+|.+.-.+..+.-.+...+          -|..+..++  |...
T Consensus        54 ~~~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss~~~ggailgdr~rm~~~~~~~~~~ir~~~~~g~lgg~~~  133 (327)
T d2p67a1          54 TLRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSSPVTGGSILGDKTRMNDLARAEAAFIRPVPSSGHLGGASQ  133 (327)
T ss_dssp             SEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC---------------CTTTTCTTEEEEEECC-----CHHH
T ss_pred             ceEEEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCceeeeccccccchhHHHHhcccccccccccccccccccchh
Confidence            457899999999999999999988875443  44666654322111000011110          111111122  2222


Q ss_pred             ---HHHHHHHcCCCEEEEEecCCCCCHH
Q 003038          723 ---RFAEAVSNNPHRVFLIEDVEQADYC  747 (854)
Q Consensus       723 ---~L~eav~~~p~~ViliDEieka~~~  747 (854)
                         .....+....+.+||++-|--.-.+
T Consensus       134 ~~~~~~~~~~~~g~d~iliEtvG~gq~e  161 (327)
T d2p67a1         134 RARELMLLCEAAGYDVVIVETVGVGQSE  161 (327)
T ss_dssp             HHHHHHHHHHHTTCSEEEEEEECCTTHH
T ss_pred             hhhHHHHHHHhcCCCeEEEeeccccccc
Confidence               3444556678899999998754433

>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=87.20  E-value=0.15  Score=47.88  Aligned_cols=23  Identities=17%  Similarity=0.192  Sum_probs=20.1

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++|.||+|+||++|++.|.+..
T Consensus         5 ~ivl~Gpsg~GK~tl~~~L~~~~   27 (178)
T d1kgda_           5 TLVLLGAHGVGRRHIKNTLITKH   27 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHC
T ss_pred             cEEEECCCCCCHHHHHHHHHHhC
Confidence            37889999999999999998753

>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=87.13  E-value=0.2  Score=49.07  Aligned_cols=22  Identities=5%  Similarity=0.016  Sum_probs=19.3

Q ss_pred             cCCceeecCCCCCHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la  248 (854)
                      .+-.+|+|+||||||+++..|.
T Consensus        95 ~kt~~~~G~SGVGKSTLiN~L~  116 (225)
T d1u0la2          95 GKISTMAGLSGVGKSSLLNAIN  116 (225)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHS
T ss_pred             CCeEEEECCCCCCHHHHHHhhc
Confidence            4567899999999999999885

>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=87.02  E-value=0.15  Score=49.08  Aligned_cols=23  Identities=9%  Similarity=0.150  Sum_probs=20.8

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+++.||+|+||++|.+.|.+..
T Consensus         4 livi~GPSG~GK~tl~~~L~~~~   26 (205)
T d1s96a_           4 LYIVSAPSGAGKSSLIQALLKTQ   26 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            68899999999999999998864

>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=86.92  E-value=2.3  Score=43.36  Aligned_cols=39  Identities=21%  Similarity=0.221  Sum_probs=30.8

Q ss_pred             ceeEEEecCCCchHHHHHHHHHHHHh--CCCCceEEEcccc
Q 003038          657 ETWLFFQGVDADAKEKIAKELARLVF--GSHNNFVSIALSS  695 (854)
Q Consensus       657 ~~~lLf~Gp~GvGKt~lAr~LA~~lf--g~~~~~i~id~s~  695 (854)
                      ...+-+.||||+|||++.-.|.+.+-  |..-.++.+|.+.
T Consensus        51 ~~~igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss   91 (323)
T d2qm8a1          51 AIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSS   91 (323)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGG
T ss_pred             ceEEeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeeccccc
Confidence            45789999999999999999998654  4455667788664

>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=86.91  E-value=0.26  Score=45.02  Aligned_cols=34  Identities=6%  Similarity=0.002  Sum_probs=26.6

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIA  692 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id  692 (854)
                      .+-+.|++|+|||+|+..|++.|-........+.
T Consensus         3 ii~I~G~~gSGKTTli~~l~~~L~~~g~~v~vik   36 (165)
T d1xjca_           3 VWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVK   36 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            5679999999999999999998865444554443

>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=86.83  E-value=0.15  Score=47.25  Aligned_cols=20  Identities=15%  Similarity=0.310  Sum_probs=17.7

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++|+|++|||||+++..+..
T Consensus        10 i~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999987654

>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=86.69  E-value=0.12  Score=47.54  Aligned_cols=19  Identities=11%  Similarity=0.193  Sum_probs=17.0

Q ss_pred             CceeecCCCCCHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGV  247 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~l  247 (854)
                      .++++|+||||||+++..+
T Consensus        18 kI~vvG~~~vGKSsLi~~l   36 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQL   36 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            5899999999999999755

>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=86.56  E-value=0.15  Score=46.78  Aligned_cols=21  Identities=10%  Similarity=0.221  Sum_probs=18.5

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      .++|+|+||||||++++.|..
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~   22 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVK   22 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            378999999999999998863

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.46  E-value=0.17  Score=46.68  Aligned_cols=20  Identities=20%  Similarity=0.245  Sum_probs=17.9

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++|+|++|||||+++..++.
T Consensus         7 i~lvG~~~vGKTsll~~~~~   26 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQ   26 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999987765

>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=86.35  E-value=0.29  Score=45.13  Aligned_cols=28  Identities=21%  Similarity=0.318  Sum_probs=23.1

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHcC-CCC
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEKG-DVP  257 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~~-~vp  257 (854)
                      ++|.|+=|+|||++|+++++.+--. .|+
T Consensus        36 i~L~G~LGaGKTtfvr~~~~~lg~~~~V~   64 (158)
T d1htwa_          36 VYLNGDLGAGKTTLTRGMLQGIGHQGNVK   64 (158)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTTCCSCCC
T ss_pred             EEEecCCCccHHHHHHHHHhhcccccccC
Confidence            6789999999999999999987543 354

>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=86.26  E-value=0.15  Score=51.01  Aligned_cols=31  Identities=10%  Similarity=0.022  Sum_probs=22.5

Q ss_pred             cCCceeecCCCCCHHHH-HHHHHHHHHcCCCC
Q 003038          227 KRNFVVVGECLASIEGV-VRGVIDKIEKGDVP  257 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~-v~~la~~i~~~~vp  257 (854)
                      ..+.+++|+||+|||++ ++-++..+..+.++
T Consensus        14 ~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~   45 (306)
T d1uaaa1          14 TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQ   45 (306)
T ss_dssp             SSEEEECCCTTSCHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCEEEEeeCCccHHHHHHHHHHHHHHhcCCC
Confidence            45688899999999965 56666666654444

>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=86.20  E-value=0.16  Score=46.85  Aligned_cols=19  Identities=16%  Similarity=0.113  Sum_probs=17.0

Q ss_pred             ceeecCCCCCHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la  248 (854)
                      ++|+|++|||||+++..+.
T Consensus         6 v~lvG~~~vGKTsLi~~~~   24 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFA   24 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHH
Confidence            7899999999999997654

>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=86.17  E-value=0.18  Score=48.22  Aligned_cols=24  Identities=8%  Similarity=0.295  Sum_probs=21.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHh
Q 003038          659 WLFFQGVDADAKEKIAKELARLVF  682 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lf  682 (854)
                      -+.|-|++|+|||++++.|++.|-
T Consensus         4 fIviEG~dGsGKsT~~~~L~~~L~   27 (210)
T d4tmka_           4 YIVIEGLEGAGKTTARNVVVETLE   27 (210)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            367889999999999999999873

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.06  E-value=0.16  Score=47.30  Aligned_cols=22  Identities=5%  Similarity=0.102  Sum_probs=18.8

Q ss_pred             CceeecCCCCCHHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~~  250 (854)
                      .+||+|++|||||+++..+...
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4799999999999999987543

>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=85.94  E-value=0.19  Score=46.77  Aligned_cols=24  Identities=21%  Similarity=0.090  Sum_probs=21.6

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+.++.||+|+|||.+|..||...
T Consensus        24 ~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          24 SITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHHH
Confidence            489999999999999999998765

>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=85.64  E-value=0.11  Score=48.04  Aligned_cols=20  Identities=10%  Similarity=0.202  Sum_probs=8.6

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++|+|.+|||||++++.+..
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEECCCCC-----------
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            79999999999999987763

>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=85.58  E-value=0.54  Score=47.07  Aligned_cols=84  Identities=8%  Similarity=0.024  Sum_probs=51.3

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccCcCCCcccc--ccccccC-CCCCCchHH---HHHHHHHcCC
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSSTRADSTED--SRNKRSR-DEQSCSYIE---RFAEAVSNNP  732 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~~~~~s~e~--~~~~rl~-~~~g~g~~e---~L~eav~~~p  732 (854)
                      +..|+||+|+|||.+|..++...-......+.||.-.-.+. . -.+.  ....+++ ..+. ..++   .+...++..+
T Consensus        59 itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDtE~~~~~-~-~a~~~Gvd~d~i~~~~~~-~~E~~~~~~~~l~~~~~  135 (268)
T d1xp8a1          59 ITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALDP-V-YARALGVNTDELLVSQPD-NGEQALEIMELLVRSGA  135 (268)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCH-H-HHHHTTCCGGGCEEECCS-SHHHHHHHHHHHHTTTC
T ss_pred             EEEEecCCccchHHHHHHHHHHHHhCCCEEEEEECCccCCH-H-HHHHhCCCchhEEEEcCC-CHHHHHHHHHHHHhcCC
Confidence            78899999999999999988877666667888885421110 0 0000  0112222 2222 2333   3344455678


Q ss_pred             CEEEEEecCCCCC
Q 003038          733 HRVFLIEDVEQAD  745 (854)
Q Consensus       733 ~~ViliDEieka~  745 (854)
                      ..+|++|=+--+-
T Consensus       136 ~~liIiDSi~al~  148 (268)
T d1xp8a1         136 IDVVVVDSVAALT  148 (268)
T ss_dssp             CSEEEEECTTTCC
T ss_pred             CcEEEEecccccc
Confidence            9999999886654

>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=85.55  E-value=0.2  Score=46.54  Aligned_cols=28  Identities=7%  Similarity=-0.026  Sum_probs=23.7

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ..+-++|.||||+|||+++-.+|.....
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~~~~   49 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVTCQL   49 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTS
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            5667899999999999999999876543

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {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: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=85.42  E-value=0.65  Score=44.14  Aligned_cols=22  Identities=9%  Similarity=-0.077  Sum_probs=19.0

Q ss_pred             EEEecCCCchHHHHHHHHHHHH
Q 003038          660 LFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       660 lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .++.+|+|.|||.+|-.++..+
T Consensus        88 ~ll~~~tG~GKT~~a~~~~~~~  109 (206)
T d2fz4a1          88 GCIVLPTGSGKTHVAMAAINEL  109 (206)
T ss_dssp             EEEEESSSTTHHHHHHHHHHHS
T ss_pred             cEEEeCCCCCceehHHhHHHHh
Confidence            3677899999999999888776

>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=85.37  E-value=0.8  Score=45.77  Aligned_cols=87  Identities=8%  Similarity=-0.023  Sum_probs=52.8

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccccccC-cCCCccccccccccC-CCCCCchHH---HHHHHHHcCC
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFSS-TRADSTEDSRNKRSR-DEQSCSYIE---RFAEAVSNNP  732 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~~-~~~~s~e~~~~~rl~-~~~g~g~~e---~L~eav~~~p  732 (854)
                      .+..|+||+|+|||.+|..++...-......+.||.-.-.+ .+.... .....+++ ..+. ..++   .+-..++..+
T Consensus        61 ~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDtE~~~~~e~a~~~-GvD~d~il~~~~~-~~E~~~~~~~~l~~~~~  138 (269)
T d1mo6a1          61 RVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKL-GVDTDSLLVSQPD-TGEQALEIADMLIRSGA  138 (269)
T ss_dssp             SEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEESSCCCCHHHHHHH-TCCGGGCEEECCS-SHHHHHHHHHHHHHTTC
T ss_pred             eeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEECCccCCHHHHHHh-CCCHHHeEEecCC-CHHHHHHHHHHHHhcCC
Confidence            38899999999999999988877766667788888543211 000000 00112222 2222 2222   2333456788


Q ss_pred             CEEEEEecCCCCCH
Q 003038          733 HRVFLIEDVEQADY  746 (854)
Q Consensus       733 ~~ViliDEieka~~  746 (854)
                      ..+|++|-+--+-|
T Consensus       139 ~~liIiDSi~al~~  152 (269)
T d1mo6a1         139 LDIVVIDSVAALVP  152 (269)
T ss_dssp             EEEEEEECSTTCCC
T ss_pred             CCEEEEeccccccc
Confidence            89999999987764

>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=85.21  E-value=0.19  Score=47.43  Aligned_cols=20  Identities=10%  Similarity=0.200  Sum_probs=17.8

Q ss_pred             ceeecCCCCCHHHHHHHHHH
Q 003038          230 FVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~  249 (854)
                      ++++|++|||||+++..+..
T Consensus         9 ivvvG~~~vGKTsli~~l~~   28 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSD   28 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHhh
Confidence            78999999999999987764

>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=84.98  E-value=0.38  Score=46.39  Aligned_cols=37  Identities=22%  Similarity=0.188  Sum_probs=27.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHh------CCCCceEEEccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVF------GSHNNFVSIALS  694 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lf------g~~~~~i~id~s  694 (854)
                      .+.++.||+|+|||.+|..+|....      +.....+.++..
T Consensus        37 ~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~   79 (254)
T d1pzna2          37 AITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTE   79 (254)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESS
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEecc
Confidence            4899999999999999998887653      223455555543

>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=84.96  E-value=0.13  Score=47.49  Aligned_cols=20  Identities=20%  Similarity=0.302  Sum_probs=17.1

Q ss_pred             CceeecCCCCCHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la  248 (854)
                      .++++|++|||||+++..+.
T Consensus         5 Ki~vvG~~~vGKTsli~~~~   24 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHL   24 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC
T ss_pred             EEEEECCCCcCHHHHHHHHH
Confidence            47899999999999997554

>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=84.86  E-value=0.61  Score=45.66  Aligned_cols=58  Identities=9%  Similarity=0.017  Sum_probs=43.0

Q ss_pred             cHHHHHHHHHHhhccCcCCceeecCCCCCHHHHHHHHHHHHHcCCCCcccCCceEEEcccccccc
Q 003038          211 RNEDVMYVIENLMSKRKRNFVVVGECLASIEGVVRGVIDKIEKGDVPEALRDVKCLPLSISSFRH  275 (854)
Q Consensus       211 r~~ei~~v~~~L~r~~k~n~vLvGe~GvGKta~v~~la~~i~~~~vp~~L~~~~~~~l~~~~l~~  275 (854)
                      ...-+..|.+-|.+....+.+|.|+.|+|||-|+-..+.....       +|.+++-|-.....+
T Consensus        60 Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~-------~g~qv~~l~Pt~~La  117 (233)
T d2eyqa3          60 QAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD-------NHKQVAVLVPTTLLA  117 (233)
T ss_dssp             HHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT-------TTCEEEEECSSHHHH
T ss_pred             HHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHH-------cCCceEEEccHHHhH
Confidence            4466777888888888889999999999999999877766544       355666665544433

>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=84.73  E-value=0.21  Score=48.24  Aligned_cols=23  Identities=17%  Similarity=0.348  Sum_probs=21.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      -+.|-|++|+|||++++.|++.|
T Consensus         5 ~I~iEG~DGsGKST~~~~L~~~L   27 (214)
T d1tmka_           5 LILIEGLDRTGKTTQCNILYKKL   27 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCcHHHHHHHHHHHH
Confidence            57799999999999999999987

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase 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: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=84.34  E-value=0.39  Score=48.05  Aligned_cols=47  Identities=19%  Similarity=0.091  Sum_probs=35.0

Q ss_pred             cccHHHHHHHHHHHHHhhcCCCcccCCCcCCcccCcceeEEEecCCCchHHHHHHHHHHHHhCCC
Q 003038          621 PWQKDTVYDIANTVLKCRSGTMRRKGKFKDHSEVKEETWLFFQGVDADAKEKIAKELARLVFGSH  685 (854)
Q Consensus       621 ~GQ~~av~~Ia~~v~~~rsgl~~~~~~~~~~~~~kp~~~lLf~Gp~GvGKt~lAr~LA~~lfg~~  685 (854)
                      ..|..|+.+|..-+...                 +|. ..|++|.+|+|||.+|-..+.....+.
T Consensus        86 ~~Q~~ai~ei~~d~~~~-----------------~~m-~rLL~GdvGSGKT~Va~~a~~~~~~~g  132 (264)
T d1gm5a3          86 NAQKRAHQEIRNDMISE-----------------KPM-NRLLQGDVGSGKTVVAQLAILDNYEAG  132 (264)
T ss_dssp             HHHHHHHHHHHHHHHSS-----------------SCC-CCEEECCSSSSHHHHHHHHHHHHHHHT
T ss_pred             chHHHHHHHHHHHhhcc-----------------Ccc-eeeeeccccccccHHHHHHHHHHHhcc
Confidence            55999999888776642                 333 468999999999999997776655433

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=84.32  E-value=0.19  Score=51.04  Aligned_cols=39  Identities=13%  Similarity=0.167  Sum_probs=26.8

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcccccc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALSSFS  697 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s~~~  697 (854)
                      .+-+.|++|+|||+++++|++.+-...-+.+.+.+..|-
T Consensus         6 IIgIaG~SGSGKTTva~~l~~i~~~~~v~~~iI~~Dsfy   44 (288)
T d1a7ja_           6 IISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAFH   44 (288)
T ss_dssp             EEEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGGGGB
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHhhcCCCeEEEeCCCCC
Confidence            789999999999999999998774333344556666663

>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=84.23  E-value=0.26  Score=47.62  Aligned_cols=24  Identities=13%  Similarity=-0.010  Sum_probs=21.6

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      .+.++.||+|+|||.+|..+|...
T Consensus        38 ~~~~i~G~~GsGKT~lalq~~~~~   61 (258)
T d1v5wa_          38 AITEAFGEFRTGKTQLSHTLCVTA   61 (258)
T ss_dssp             EEEEEECCTTCTHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
Confidence            489999999999999999998754

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=84.09  E-value=0.99  Score=43.76  Aligned_cols=77  Identities=10%  Similarity=0.107  Sum_probs=46.9

Q ss_pred             CCceeecCCCCCHHHHHHHHHHHHHcC----CCCcccCCceEEEccc--cccc-----ccchHHHHHHHHHHHHHHHhhh
Q 003038          228 RNFVVVGECLASIEGVVRGVIDKIEKG----DVPEALRDVKCLPLSI--SSFR-----HMNRVEVEQRVEEIKNLVRSCL  296 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la~~i~~~----~vp~~L~~~~~~~l~~--~~l~-----~~~rge~E~rl~~l~~~~~~~~  296 (854)
                      +-.||.||...|||++.+.++.-+.=.    -||..  ...+-.+|.  ..+.     .....-|...++++...++.. 
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~--~~~i~~~d~I~~~~~~~d~~~~~~StF~~el~~~~~il~~~-  112 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAE--EAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKEA-  112 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSS--EEEECCCSEEEEECCC------CCSHHHHHHHHHHHHHHHC-
T ss_pred             cEEEEECCCccccchhhhhhHHHHHHHhccceeecC--ceEEeecceEEEEECCCccccCCccHHHHhHHHHHHHhccC-
Confidence            347999999999999999877654432    35531  122222221  1111     112344666677776666654 


Q ss_pred             CCCeEEEeCcc
Q 003038          297 GRGIVLNLGDL  307 (854)
Q Consensus       297 ~~~~ILfidel  307 (854)
                      ..+.++.|||+
T Consensus       113 ~~~sLvliDE~  123 (224)
T d1ewqa2         113 TENSLVLLDEV  123 (224)
T ss_dssp             CTTEEEEEEST
T ss_pred             CCCcEEeeccc
Confidence            56788999999

>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=84.07  E-value=0.42  Score=47.49  Aligned_cols=37  Identities=19%  Similarity=0.264  Sum_probs=31.0

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHhCCCCceEEEccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVFGSHNNFVSIALS  694 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~s  694 (854)
                      .+++|.|.-|||||++|-.||..+=....+..-+|+.
T Consensus         9 ~~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD~D   45 (296)
T d1ihua1           9 PYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVSTD   45 (296)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             eEEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEeCC
Confidence            4889999999999999999998886656677777765

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=84.07  E-value=0.52  Score=48.15  Aligned_cols=32  Identities=13%  Similarity=0.151  Sum_probs=24.4

Q ss_pred             hhccCcCCceee---cCCCCCHHHHHHHHHHHHHc
Q 003038          222 LMSKRKRNFVVV---GECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       222 L~r~~k~n~vLv---Ge~GvGKta~v~~la~~i~~  253 (854)
                      |....++.|++|   |++|+|||++++.|+..+.+
T Consensus        72 l~~~~~k~P~iIGIaG~sgSGKSTla~~L~~lL~~  106 (308)
T d1sq5a_          72 LGTNGQRIPYIISIAGSVAVGKSTTARVLQALLSR  106 (308)
T ss_dssp             HTCC-CCCCEEEEEEECTTSSHHHHHHHHHHHHTT
T ss_pred             hcccCCCCCEEEEEeCCCCCCCcHHHHHHHHHHhh
Confidence            445566677665   69999999999999988754

>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=84.02  E-value=0.21  Score=45.90  Aligned_cols=21  Identities=10%  Similarity=0.167  Sum_probs=18.8

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      +++|+|.|+||||+++..|..
T Consensus         7 ~I~iiG~~nvGKSSLin~L~~   27 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLLG   27 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            478999999999999999863

>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=84.01  E-value=0.22  Score=46.09  Aligned_cols=20  Identities=10%  Similarity=0.272  Sum_probs=17.1

Q ss_pred             CceeecCCCCCHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la  248 (854)
                      .+||+|..|||||++++.+.
T Consensus         4 KivllG~~~vGKTsl~~r~~   23 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMK   23 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            37999999999999998553

>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=83.85  E-value=0.21  Score=47.81  Aligned_cols=37  Identities=16%  Similarity=0.156  Sum_probs=26.5

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHH-----hC-CCCceEEEccc
Q 003038          658 TWLFFQGVDADAKEKIAKELARLV-----FG-SHNNFVSIALS  694 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~l-----fg-~~~~~i~id~s  694 (854)
                      .+.+|.||+|+|||.+|..+|...     ++ .....+.++..
T Consensus        35 ~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~   77 (251)
T d1szpa2          35 SITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE   77 (251)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESS
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeec
Confidence            389999999999999999887532     11 23456666644

>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=83.69  E-value=0.34  Score=46.50  Aligned_cols=24  Identities=17%  Similarity=0.156  Sum_probs=21.0

Q ss_pred             ceeecCCCCCHHHHHHHHHHHHHc
Q 003038          230 FVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       230 ~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ++|-|+.|+||||.++.|++.+..
T Consensus         6 I~ieG~dGsGKsT~~~~L~~~L~~   29 (209)
T d1nn5a_           6 IVLEGVDRAGKSTQSRKLVEALCA   29 (209)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH
Confidence            455599999999999999999865

>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=83.62  E-value=0.1  Score=50.52  Aligned_cols=23  Identities=22%  Similarity=0.208  Sum_probs=21.2

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      -+.|-|++|+|||++++.|++.|
T Consensus         4 ~I~ieG~dGsGKST~~~~L~~~l   26 (241)
T d1p5zb_           4 KISIEGNIAAGKSTFVNILKQLC   26 (241)
T ss_dssp             EEEEECSTTSSHHHHHTTTGGGC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999999999976

>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=83.46  E-value=0.23  Score=48.11  Aligned_cols=23  Identities=26%  Similarity=0.188  Sum_probs=21.4

Q ss_pred             eEEEecCCCchHHHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELARLV  681 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~l  681 (854)
                      -+.|-|++|+|||++++.|++.+
T Consensus         4 ~IviEG~~GsGKST~~~~L~~~l   26 (241)
T d2ocpa1           4 RLSIEGNIAVGKSTFVKLLTKTY   26 (241)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHC
T ss_pred             EEEEECCCCCcHHHHHHHHHHHH
Confidence            57899999999999999999987

>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=83.41  E-value=0.96  Score=45.58  Aligned_cols=37  Identities=14%  Similarity=0.100  Sum_probs=30.6

Q ss_pred             HHHHHhhcc-CcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          217 YVIENLMSK-RKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       217 ~v~~~L~r~-~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      |+|+.|.-= +.....|+|++|||||+++..++..+..
T Consensus        32 r~ID~l~PigrGQr~~I~g~~g~GKT~l~~~i~~~~~~   69 (289)
T d1xpua3          32 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAY   69 (289)
T ss_dssp             HHHHHHSCCBTTCEEEEEECSSSSHHHHHHHHHHHHHH
T ss_pred             eeeeecccccCCCeeeEeCCCCCCHHHHHHHHHHHHhh
Confidence            789988633 6677889999999999999999987654

>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=83.36  E-value=0.26  Score=45.80  Aligned_cols=21  Identities=10%  Similarity=0.306  Sum_probs=18.0

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      +++++|++|||||+++..+..
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~   27 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLT   27 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            578999999999999986653

>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=82.93  E-value=0.22  Score=47.72  Aligned_cols=25  Identities=8%  Similarity=-0.020  Sum_probs=21.2

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDK  250 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~  250 (854)
                      ..+-++|+||||+|||+++-.+|..
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~   57 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVT   57 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            5667899999999999999887643

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=82.83  E-value=0.56  Score=44.93  Aligned_cols=34  Identities=18%  Similarity=0.363  Sum_probs=26.6

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHhCCCCceEEEcc
Q 003038          659 WLFFQGVDADAKEKIAKELARLVFGSHNNFVSIAL  693 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lfg~~~~~i~id~  693 (854)
                      +++|.||.|+|||+|.+.|.+.+ +.......++.
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~-~~~~~~~ivn~   35 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYL-EDNYKVAYVNL   35 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH-TTTSCEEEEEC
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHH-hhCCeEEEEec
Confidence            57899999999999999999877 34445555543

>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=82.69  E-value=0.23  Score=46.60  Aligned_cols=20  Identities=10%  Similarity=0.280  Sum_probs=18.8

Q ss_pred             CceeecCCCCCHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la  248 (854)
                      .++|+|.||||||+++..|.
T Consensus        25 ~I~lvG~~n~GKSTLin~L~   44 (195)
T d1svia_          25 EIALAGRSNVGKSSFINSLI   44 (195)
T ss_dssp             EEEEEEBTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHhc
Confidence            59999999999999999986

>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=82.06  E-value=0.28  Score=47.32  Aligned_cols=22  Identities=9%  Similarity=0.246  Sum_probs=18.8

Q ss_pred             cCCceeecCCCCCHHHHHHHHH
Q 003038          227 KRNFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       227 k~n~vLvGe~GvGKta~v~~la  248 (854)
                      .-.+||+|++|||||++++.+.
T Consensus         6 ~~KilllG~~~vGKTsll~~~~   27 (221)
T d1azta2           6 THRLLLLGAGESGKSTIVKQMR   27 (221)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHH
T ss_pred             cCEEEEECCCCCCHHHHHHHHh
Confidence            3458999999999999998774

>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=81.73  E-value=0.25  Score=45.76  Aligned_cols=20  Identities=15%  Similarity=0.017  Sum_probs=17.9

Q ss_pred             CceeecCCCCCHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la  248 (854)
                      ++.|+|+|+||||+++..|.
T Consensus         3 ~VaiiG~~nvGKSSLin~L~   22 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVS   22 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSE
T ss_pred             eEEEECCCCCCHHHHHHHHh
Confidence            68899999999999998764

>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=81.66  E-value=0.29  Score=46.79  Aligned_cols=28  Identities=4%  Similarity=-0.019  Sum_probs=24.3

Q ss_pred             CcCCceeecCCCCCHHHHHHHHHHHHHc
Q 003038          226 RKRNFVVVGECLASIEGVVRGVIDKIEK  253 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la~~i~~  253 (854)
                      ...-++|.|+||+|||.++-.+|..+..
T Consensus        33 ~G~l~~i~G~~G~GKT~~~l~~a~~~~~   60 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIMHQSCVNLQN   60 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTC
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            5677899999999999999999987654

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

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: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=81.48  E-value=0.52  Score=47.14  Aligned_cols=33  Identities=6%  Similarity=0.213  Sum_probs=26.1

Q ss_pred             HHHhhcc--CcCCceeecCCCCCHHHHHHHHHHHH
Q 003038          219 IENLMSK--RKRNFVVVGECLASIEGVVRGVIDKI  251 (854)
Q Consensus       219 ~~~L~r~--~k~n~vLvGe~GvGKta~v~~la~~i  251 (854)
                      ..+|.++  ++|.++|+|||++|||.++..++.-+
T Consensus        94 ~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~l  128 (267)
T d1u0ja_          94 LGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3446444  56678999999999999999998764

>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=81.43  E-value=0.36  Score=45.30  Aligned_cols=21  Identities=24%  Similarity=0.265  Sum_probs=19.0

Q ss_pred             eEEEecCCCchHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELAR  679 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~  679 (854)
                      -+||.|++|+|||++|.+|.+
T Consensus        16 gvl~~G~sG~GKStlal~l~~   36 (176)
T d1kkma_          16 GVLITGDSGVGKSETALELVQ   36 (176)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHH
Confidence            689999999999999988776

>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=81.28  E-value=0.39  Score=47.00  Aligned_cols=25  Identities=12%  Similarity=0.195  Sum_probs=22.4

Q ss_pred             eeEEEecCCCchHHHHHHHHHHHHh
Q 003038          658 TWLFFQGVDADAKEKIAKELARLVF  682 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA~~lf  682 (854)
                      -.+.+.||+|+|||++.+.|+.++-
T Consensus        27 e~~~liGpsGaGKSTll~~l~Gl~~   51 (229)
T d3d31a2          27 EYFVILGPTGAGKTLFLELIAGFHV   51 (229)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhcCcC
Confidence            4889999999999999999998763

>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=81.21  E-value=0.33  Score=44.88  Aligned_cols=21  Identities=10%  Similarity=0.267  Sum_probs=18.8

Q ss_pred             CceeecCCCCCHHHHHHHHHH
Q 003038          229 NFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       229 n~vLvGe~GvGKta~v~~la~  249 (854)
                      ++.++|.+|||||+++.+|..
T Consensus        10 kV~iiG~~~~GKSTLin~l~~   30 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILN   30 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHC
Confidence            588999999999999998863

>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=81.19  E-value=0.3  Score=45.89  Aligned_cols=21  Identities=19%  Similarity=0.226  Sum_probs=19.0

Q ss_pred             eEEEecCCCchHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELAR  679 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~  679 (854)
                      -+||.||+|.|||++|.+|.+
T Consensus        17 gvli~G~sG~GKS~lal~l~~   37 (177)
T d1knxa2          17 GVLLTGRSGIGKSECALDLIN   37 (177)
T ss_dssp             EEEEEESSSSSHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHH
Confidence            689999999999999988865

>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=81.02  E-value=0.56  Score=46.38  Aligned_cols=38  Identities=16%  Similarity=0.289  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHhhcc--CcCCceeecCCCCCHHHHHHHHHH
Q 003038          212 NEDVMYVIENLMSK--RKRNFVVVGECLASIEGVVRGVID  249 (854)
Q Consensus       212 ~~ei~~v~~~L~r~--~k~n~vLvGe~GvGKta~v~~la~  249 (854)
                      ..++..++.-|...  ..-|++|+|.||||||+++..|..
T Consensus        15 ~~~l~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~ilg   54 (257)
T d1h65a_          15 QTKLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIG   54 (257)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHhC
Confidence            35555555555433  334899999999999999998874

>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=80.82  E-value=0.44  Score=42.16  Aligned_cols=21  Identities=29%  Similarity=0.449  Sum_probs=18.5

Q ss_pred             eEEEecCCCchHHHHHHHHHH
Q 003038          659 WLFFQGVDADAKEKIAKELAR  679 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~  679 (854)
                      -++|+|++|||||+|...|..
T Consensus         2 KI~liG~~nvGKSSLln~l~~   22 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKN   22 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            478999999999999988765

>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=80.63  E-value=0.27  Score=45.13  Aligned_cols=21  Identities=29%  Similarity=0.430  Sum_probs=18.1

Q ss_pred             eeEEEecCCCchHHHHHHHHH
Q 003038          658 TWLFFQGVDADAKEKIAKELA  678 (854)
Q Consensus       658 ~~lLf~Gp~GvGKt~lAr~LA  678 (854)
                      --++++|++|||||+|.+.|.
T Consensus        13 ~kIvlvG~~~vGKTSli~rl~   33 (173)
T d1e0sa_          13 MRILMLGLDAAGKTTILYKLK   33 (173)
T ss_dssp             EEEEEEEETTSSHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHh
Confidence            468899999999999988764

>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=80.44  E-value=0.29  Score=45.23  Aligned_cols=21  Identities=14%  Similarity=0.116  Sum_probs=18.6

Q ss_pred             CCceeecCCCCCHHHHHHHHH
Q 003038          228 RNFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       228 ~n~vLvGe~GvGKta~v~~la  248 (854)
                      .|+.|+|.|+||||+++..|.
T Consensus         2 ~~VaivG~~nvGKSTLin~L~   22 (180)
T d1udxa2           2 ADVGLVGYPNAGKSSLLAAMT   22 (180)
T ss_dssp             CSEEEECCGGGCHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHh
Confidence            368999999999999998874

>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=80.39  E-value=0.2  Score=45.91  Aligned_cols=23  Identities=9%  Similarity=0.079  Sum_probs=19.4

Q ss_pred             CcCCceeecCCCCCHHHHHHHHH
Q 003038          226 RKRNFVVVGECLASIEGVVRGVI  248 (854)
Q Consensus       226 ~k~n~vLvGe~GvGKta~v~~la  248 (854)
                      .+..++|+|.|+||||+++..|.
T Consensus        15 ~~~~I~lvG~~NvGKSSL~n~L~   37 (188)
T d1puia_          15 TGIEVAFAGRSNAGKSSALNTLT   37 (188)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHh
Confidence            35669999999999999997663

>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=80.35  E-value=0.41  Score=47.21  Aligned_cols=24  Identities=17%  Similarity=0.216  Sum_probs=21.7

Q ss_pred             eEEEecCCCchHHHHHHHHHHHHh
Q 003038          659 WLFFQGVDADAKEKIAKELARLVF  682 (854)
Q Consensus       659 ~lLf~Gp~GvGKt~lAr~LA~~lf  682 (854)
                      .+-+.||+|+|||++.+.|+.++-
T Consensus        31 ~~~liG~sGaGKSTll~~i~gl~~   54 (240)
T d1g2912          31 FMILLGPSGCGKTTTLRMIAGLEE   54 (240)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             EEEEECCCCChHHHHHHHHhcCCC
Confidence            788999999999999999997663