Psyllid ID: psy13846

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------930-------940-------950-------960-------970-------980-------990------1000------1010------1020------1030------1040------1050------1060------1070------1080------1090------1100------1110------1120------1130------1140------1150------1160------1170------1180------1190------1200------1210------1220------1230------1240------1250------1260------1270------1280------1290------1300------1310------1320------1330------1340------1350------1360------1370------1380------1390------1400------1410------1420---
Protein Sequence
MKNSVIGTLTLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHTNTLAAVP
Secondary Structure (PSIPRED)
ccccccccHHHHHHHHHHHHHHHccccccccccccccEEEEHHHHccccHHcccccccccHHHHHHHHHHHHcccccccccEEEEccccHHHHHcccEEEEEccccccccccccccccccccccccccccccccccccccccccccccEEEEccccEEEEccHHHHHHHHHHHccccccccccccHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccHHHccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccEEEEccccccEEEEEccccccccccccEEEEEccccccccccccccccccccccccccccccccHHHHHHcccccHHHHHHHHHHHHHHccccccccccccccEEEEEHHHHHHHHHcccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccHHHHHHHccccccccccEEEEEEccccccccccccccccEEEEEccEEEEEEEccccccccccccEEEEHHHHccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccHHHHHHHHHccccccEEEEEEcccccHHHHHHHHHHHccccHHHHHHHEEEEEEccccEEEEEEEHHHHHHHHccccHHHHHHHHHHHcccccEEEEccccEEEEccccccHHHHHHHHHHHHHcccccccccccccEEEEEcccccccEEEEEEEccccHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHcccccccccccccEEEccccccccEEEHHHHHHHcccccccccccccEEEEEccHHHHHHHHccccHHHHHHHHHHHcccccEEEEccccEEEEccccccHHHHHHHHHHHHcccccEEEccccccEEEEEcccccccEEEEEEEEcccHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHccccccccEEEEEccccccccccccccccHHHHHHHHHHHHHHcccccccccccccEEccccccccccEEEEEccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcccccHccEEEEccccHHHHHHHcEEEEEccHHHccccccccccccccccccccccccccccccccccccccccccEEEccccEEHHHHHHHHHHHHHHHHHcccccEEEcccccHHHHHHHHHccccccccHHHHHHHHHHHHccccEcccccccccccccccccccccccccccccccccccccHHHHHHHccccccccHHHHHHHHccccccHHHHHHHHHccccccccccccccccccccEEEEEccccccccccHHHHHHcccccEEEEEccccHHHcccccccEEEEcccEEEEEEEEEcccccccccccccccccccHHHHHHHHHccccccEEEEEHHHHHccccccccccccccEEEEHHHHHHHHHHHHcccccccHHHHHHHHHHcccccccEEEEcccccccccccccEEcccccccccEEEEEEcccccccEEEEEEccccccccccccccccccEEEEEccEEEEEEEEcccccccccccEEEEEEHcccHHHHHHHHHHHHHHHHHHHHHcccEEEcccccccccHHHHHHHccccHHHHHHHHcccccccEcHHHHHHHHHHHHHHHHHHHHHHHHHccccEEcccccEEEEEEccccccHHHHHccccccHHHHHHHcccccHHHHHHHHccccccHHHHHHHcccccccEEEEccccEEEEccccccccccccccHHHHHHHHHccccccEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEcHHHHHHHHHcccHHHHHHHHHHHccccccEEEccccEEEEEcccccHHHHHHHHHHHHccccEEEEcccccEEEEEEccccccccEEEEEEcccHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcccEccccccccHHHHHHHHHHHccccccccccHHHHHHHHHHHcccHHHHcccHHHHHHHHHHHHHcHHHHHHHHHHccccccHHHHHHHHHHHccccHcHHHHHHHHHHHHHHHHHHHHHHccccccHHHEEHHccccccccHHEEEccccccEcccccccccccccEEEEEEccccHHHHHHcccHHHHHHHHHHHcccccEEEEccccEEEEEccccccccHHHHHHHHHHHHcccccccccccEEEEEEcccccccHEEEEccHHHHHHHHcccccccEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHccHHHHHHcccccccccHHHHccHHHHHHHHHHHHHHHcccccccccHHEEEccccccccccHHHEccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MKNSVIGTLTLYYATRNCWQVLMANksnlvtprngELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLiegtvtkedrVQQQSHIQIVSknlycqdpqrtpiphglldrrmgtnqkeancttcgqnlsdcvghfgyidlplpvfhiGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETtkkvsvcphcgeingvVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEavkfnpeieahkkfgliqtlnplevlqlfeaiplediplllmnaelskpsdliltrllvppncirpsvisdlksdndvvlfnrqpslhklSIMAHRAkvlphrtfrfnecvctpynadfdgdemnvhlpqtEEARAEALPSLHKLSIMAHRAKVLMAnksnlvtprngELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRfswrswnpvVFVRTAVIWTGKQIFSLilkpnrdcpvnanlktkgraytaneefchrdSYVILRNSEllagsmdkstlgsggkaNVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNrgfsigigdvtpgqgfvqnsffsgltptefffhtmggreglVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSfdaafygqtdcisgVSECiimglpmnvGTGLIKLLqavprsepvprtllfdnpefhfpqvyyerrrdySVKVTASVKVTLElwnpgdyklsqdgvpRIKEIINASRNISTPIItayldkdtdlDYARIVKGRLERTTLGEVCEYIeevfvpddsfiLIKLDMDRIRLLHLEVDIDSIRYCIERtrgisghltvsghsflilkpkdssksfNSKMYQMKQLLPSVVIKGVQginraviheedvegvTKYKLLVEGDNLRDVMATYGvkgvkcssnntYEVYKTLGIEAARSTIMTEIKLVMEnhgmsidfrhPMLVADLMtskgevlgngtpVELKRLLDDIIaknssrsdpslsAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSkkesvtshqdkvsqPLREQILSHqdkighgresnpfpsackAEACREKYVRAQIEPATAVGALAaqsigepgtqmtlKTFHFAGEVCEYIEevfvpddsfiLIKLDMDRIRLLHLEVDIDSIRYCIERtrgisghltvsghsflilkpkdssksfNSKMYQMKQLLPSVVIKGVQginraviheedvegvTKYKLLVEGDNLRDVMATYGvkgvkcssnntYEVYKTLGIEAARSTIMTEIKLVMEnhgmsidfrhPMLVADLMTskgevlgiTRHGLAKMKESVLNLasfentsdhlfdaafygqtdcisgVSECiimglpmnvGTGLIKLLqavprsepvprtllfdnpefhtntlaavp
Flexible Loop (DISEMBL)
MKNSVIGTLTLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIvsknlycqdpqRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAgfraklrnpalsylVRKSLKKKILettkkvsvcphcgeingvvkkcgllkishekyknrtkkkdAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPsvisdlksdnDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKrfswrswnpVVFVRTAVIWTGKQIFslilkpnrdcpVNANLKtkgraytaneefchrdSYVILRNSELLAGsmdkstlgsgGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEpvprtllfdnpeFHFPQVYYERRRDYSVKVTASVKvtlelwnpgdyklsqdgVPRIKEIinasrnistpiitayldkdtdlDYARIVKGrlerttlgevCEYIEevfvpddsfiLIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRaviheedvegvTKYKLLVEGDNLRDVMATYgvkgvkcssnntYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKnssrsdpslsaQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEfskkesvtshqdkvsqplREQILSHQdkighgresnpFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRaviheedvegvTKYKLLVEGDNLRDVMATYgvkgvkcssnntYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVprtllfdnpefhtntlaavp
Low Complexity Region (SEG)
MKNSVIGTLTLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIkkfleefskkesVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHTNTLAAVP
Disordered region (IsUnstruct)
****VIGTLTLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLD*******KEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNV***************LHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILK***********MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDII*******************************************************************************************EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILK***********MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFD*************
Disordered Region (DISOPRED)
***SVIGTLTLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET*****************************************EDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAV*******************************YG*TDCISGVSECIIMGLPMNVGTGLIKL************TLLFDNPEFHFPQVYYERR**Y**KVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV***********FDNPEFHT*******
Disordered Region (DISEMBL)
MKNSVIGTLTLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNS********AQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFS*************QPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHTNTLAAVP
Disordered Region (DISPRO)
**NSVIGTLTLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCG*********************RTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR*****RTLLFDNP***********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MKNSVIGTLTLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHTNTLAAVP
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	1423	2.2.26 [Sep-21-2011]
Q5ZL98	1390	DNA-directed RNA polymera	yes	N/A	0.289	0.296	0.496	1e-115
A4IF62	1390	DNA-directed RNA polymera	yes	N/A	0.289	0.296	0.448	1e-100
O14802	1390	DNA-directed RNA polymera	yes	N/A	0.289	0.296	0.442	2e-98
Q6BI69	1457	DNA-directed RNA polymera	yes	N/A	0.177	0.172	0.508	4e-75
O94666	1405	DNA-directed RNA polymera	yes	N/A	0.175	0.177	0.503	7e-74
Q86AQ5	1450	DNA-directed RNA polymera	yes	N/A	0.174	0.171	0.485	2e-73
P04051	1460	DNA-directed RNA polymera	yes	N/A	0.177	0.172	0.496	2e-73
P27625	2339	DNA-directed RNA polymera	yes	N/A	0.175	0.106	0.434	1e-60
P08968	1530	DNA-directed RNA polymera	N/A	N/A	0.172	0.160	0.428	4e-56
P41556	889	DNA-directed RNA polymera	yes	N/A	0.172	0.275	0.380	1e-45

>sp|Q5ZL98|RPC1_CHICK DNA-directed RNA polymerase III subunit RPC1 OS=Gallus gallus GN=POLR3A PE=2 SV=1

 Score =  417 bits (1071), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 238/479 (49%), Positives = 305/479 (63%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    RS+P+LS  E++  S   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIRAVYPCRSEPALSKNELVLTSESIMKKNEFLC-CRDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQLEKFLETCRDKYMRAQ 1026

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFH-------------------------------- 1142
            +EP +AVGAL AQSIGEPGTQMTLKTFH                                
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                      FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  CI + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICISKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQSLKEELPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K SSNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTKTSSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FDN EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKESTPPRRPLIFDNNEFH 1385

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol III. A bridging helix emanates from RPC1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol III by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition.
Gallus gallus (taxid: 9031)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6

>sp|A4IF62|RPC1_BOVIN DNA-directed RNA polymerase III subunit RPC1 OS=Bos taurus GN=POLR3A PE=2 SV=1

 Score =  369 bits (946), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 215/479 (44%), Positives = 289/479 (60%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    RS+P+LS  E+L  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCRSEPALSKNELLLSAESIMKKNEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++E S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKEVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPSPPRRPLIFDTNEFH 1385

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol III. A bridging helix emanates from RPC1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol III by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts induce type I interferon and NF- Kappa-B through the RIG-I pathway.

Bos taurus (taxid: 9913)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|O14802|RPC1_HUMAN DNA-directed RNA polymerase III subunit RPC1 OS=Homo sapiens GN=POLR3A PE=1 SV=2

 Score =  362 bits (928), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 212/479 (44%), Positives = 286/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMKKSEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQVEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1385

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol III. A bridging helix emanates from RPC1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol III by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition (By similarity). Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts, such as Epstein-Barr virus-encoded RNAs (EBERs) induce type I interferon and NF- Kappa-B through the RIG-I pathway.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q6BI69|RPC1_DEBHA DNA-directed RNA polymerase III subunit RPC1 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=RPC1 PE=3 SV=2

 Score =  284 bits (727), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 143/281 (50%), Positives = 187/281 (66%), Gaps = 29/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 465 DGDIVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNIHVPQTEEA 524

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 525 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLVSHKDSFFDR 570

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++   +    +DI   I         P    +  ++WTGKQ+FSL++KPN+   V 
Sbjct: 571 ASLVQLLCMM--SDADIQFDIP--------PPAIFKPVMLWTGKQVFSLLIKPNKKSNVV 620

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + YT        E    D +VI+R S++L+G MDKSTLG G K +VFY +LRD
Sbjct: 621 INLDAKNKTYTPPAKGFPNEMSPNDGFVIIRGSQILSGVMDKSTLGDGKKHSVFYTILRD 680

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +G D A  AM R++++ + YL NRGFSIGI DV PG    Q
Sbjct: 681 YGPDEAANAMNRMAKLCARYLGNRGFSIGINDVIPGSDLKQ 721

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol III. A bridging helix emanates from RPC1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol III by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition.

Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) (taxid: 284592)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|O94666|RPC1_SCHPO DNA-directed RNA polymerase III subunit rpc1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc1 PE=2 SV=1

 Score =  280 bits (715), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 140/278 (50%), Positives = 182/278 (65%), Gaps = 28/278 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVVLFNRQPSLHKLSIMAH  KV P RT RFNECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 450 DNDVVLFNRQPSLHKLSIMAHLVKVRPWRTLRFNECVCGPYNADFDGDEMNLHVPQTEEA 509

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           + EAL               LM  K+NLV+PRNGE +IAATQDFIT  YLL+ K+ F +R
Sbjct: 510 KTEALE--------------LMGIKNNLVSPRNGEPIIAATQDFITAAYLLSLKDTFLDR 555

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I   ++  ++ I             P   ++   +WTGKQ+F++++KPNR   V 
Sbjct: 556 KSISNICCYMMDASTHI----------DLPPPAIIKPRCLWTGKQVFTVLMKPNRFSKVL 605

Query: 521 ANLKTKGRAY----TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  K R++    +   E C +D Y+++RNSE++AG +DKS +G G K ++FY++LRD+
Sbjct: 606 VNLDAKTRSFSRIKSKTPEMCPKDGYLMIRNSEIIAGVVDKSVVGDGKKDSLFYVILRDY 665

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGF 614
           G   A  A+ RLS+M + +L NRGFSIGI DV PG+  
Sbjct: 666 GALEAAEAITRLSKMCARFLGNRGFSIGIEDVQPGKSL 703

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol III. A bridging helix emanates from RPC1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol III by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q86AQ5|RPC1_DICDI DNA-directed RNA polymerase III subunit rpc1 OS=Dictyostelium discoideum GN=polr3a PE=3 SV=1

 Score =  278 bits (711), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 132/272 (48%), Positives = 183/272 (67%), Gaps = 24/272 (8%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D++LFNRQPSLHKLSIM+H+A+V+P RT RFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 448 DGDIMLFNRQPSLHKLSIMSHKARVMPWRTLRFNECVCTPYNADFDGDEMNIHLPQTEEA 507

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A +LM   +NL+TPRNGE L+AATQDF+T  YL+++++AF+ R
Sbjct: 508 RAE--------------ATILMGVTNNLITPRNGEPLVAATQDFLTASYLISRRDAFYER 553

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   +  T  AD ++   +          P   ++   +WTGKQIF ++L+P+    V 
Sbjct: 554 YR-FALMCTHFADANEHIDL---------PPPAILKPVELWTGKQIFEVLLRPSVKSHVL 603

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N +T+ R Y+ N   C +D YV  RNSEL+ GS+DKS +G G K ++F+IL+RDF   +
Sbjct: 604 CNFETRSRTYSKNLYMCPKDGYVYFRNSELMCGSIDKSIIGGGNKNSLFHILMRDFSPTI 663

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           A   M RL+++ + +L ++GFSIGI D+ P +
Sbjct: 664 AANCMTRLAKLCARFLGDQGFSIGIPDIKPAE 695

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol III. A bridging helix emanates from RPC1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol III by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition.

Dictyostelium discoideum (taxid: 44689)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P04051|RPC1_YEAST DNA-directed RNA polymerase III subunit RPC1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPO31 PE=1 SV=1

 Score =  278 bits (711), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 140/282 (49%), Positives = 188/282 (66%), Gaps = 30/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 468 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++R
Sbjct: 528 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDR 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S +++D       I+ F      P   ++   +WTGKQ+FSL++KPN + PV 
Sbjct: 574 ATLTQLLS-MMSDG------IEHF---DIPPPAIMKPYYLWTGKQVFSLLIKPNHNSPVV 623

Query: 521 ANLKTKGRAYTANE------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + +   +      E    D +VI+R S++L+G MDKS LG G K +VFY +LR
Sbjct: 624 INLDAKNKVFVPPKSKSLPNEMSQNDGFVIIRGSQILSGVMDKSVLGDGKKHSVFYTILR 683

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           D+G   A  AM R++++ + +L NRGFSIGI DVTP     Q
Sbjct: 684 DYGPQEAANAMNRMAKLCARFLGNRGFSIGINDVTPADDLKQ 725

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol III. A bridging helix emanates from RPC1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol III by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P27625|RPC1_PLAFA DNA-directed RNA polymerase III subunit RPC1 OS=Plasmodium falciparum PE=3 SV=1

 Score =  236 bits (601), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 122/281 (43%), Positives = 170/281 (60%), Gaps = 31/281 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM H+AK++  +TFRFNECVC+PYNADFDGDEMN+ +PQTEEA
Sbjct: 568 DGDIVLFNRQPSLHRMSIMCHKAKIMDFKTFRFNECVCSPYNADFDGDEMNLDVPQTEEA 627

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 628 RAEAL--------------YLMNVKHNLITPKNGEVIIALTQDFLSASYIITNKDTFLDR 673

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
             T  +  +  +D S    +          P+   ++   +WTGKQ+ S+++KPN+    
Sbjct: 674 -DTFCLLCSYFSDASLYIEL----------PIPAILKPKELWTGKQLISVLIKPNKKENT 722

Query: 520 NANLKTKGRAYTAN----EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             N + + R Y+      +  C  DSYV    SEL+ GS+ K  LGS  K  +FY L+  
Sbjct: 723 IINFEIQEREYSNKFGDLKHLCLNDSYVCFYKSELICGSLGKKVLGS-SKYGLFYYLIHH 781

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
               +A+  M RLS++TS Y  N+G +IGI DV P Q   +
Sbjct: 782 NSSHIALKIMNRLSKLTSRYFSNKGMTIGIDDVRPSQTLTE 822

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol III. A bridging helix emanates from RPC1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol III by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition.

Plasmodium falciparum (taxid: 5833)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P08968|RPC1_TRYBB DNA-directed RNA polymerase III subunit RPC1 OS=Trypanosoma brucei brucei PE=3 SV=1

 Score =  221 bits (562), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 116/271 (42%), Positives = 164/271 (60%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLH++S+MAHRA+VLP RTFRFNEC C PYNADFDGDEMNVH  QTE+A
Sbjct: 460 NGDLVLFNRQPSLHRVSMMAHRARVLPFRTFRFNECCCAPYNADFDGDEMNVHFVQTEKA 519

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM+   N+++ +NGE +IA TQDF+   YL+T ++ FF+R
Sbjct: 520 RAEALQ--------------LMSTARNIISAKNGEPIIACTQDFLAAAYLVTSRDVFFDR 565

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++ S  +       G + +F  R   P + ++   +WTGKQ+F LI++P+ +  V 
Sbjct: 566 GEFSQMVSHWL-------GPVTQF--RLPIPAI-LKPVELWTGKQLFELIVRPSPEVDVL 615

Query: 521 ANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            + +   + YT   +  C  + YV   +S  ++G +DK  LG G K  +F  L    G  
Sbjct: 616 LSFEAPTKFYTRKGKHDCAEEGYVAFLDSCFISGRLDKKLLGGGAKDGLFARLHTIAGGG 675

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
                M R+++ TS YL N GFS+G+GDV P
Sbjct: 676 YTARVMSRIAQFTSRYLTNYGFSLGLGDVAP 706

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol III. A bridging helix emanates from RPC1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol III by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition.

Trypanosoma brucei brucei (taxid: 5702)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P41556|RPOA1_METVS DNA-directed RNA polymerase subunit A' OS=Methanococcus vannielii (strain SB / ATCC 35089 / DSM 1224) GN=rpoA1 PE=3 SV=1

 Score =  186 bits (473), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 108/284 (38%), Positives = 152/284 (53%), Gaps = 39/284 (13%)

Query: 328 NCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDG 387
           N +   V+     D DVVL+NRQPSLH++SIMAH+ KVLP+RTFR N CVC PYNADFDG
Sbjct: 410 NIVDGMVVERHLGDGDVVLYNRQPSLHRMSIMAHKVKVLPYRTFRHNLCVCPPYNADFDG 469

Query: 388 DEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITG 447
           DEMNVH+PQ+EEARAE              A+ LM  + ++++PR G  +I A  DF++G
Sbjct: 470 DEMNVHVPQSEEARAE--------------AETLMLVEKHIISPRYGGPIIGAIHDFVSG 515

Query: 448 GYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIF 507
            Y+LT  N   + A T+  +S               F      P         ++GK +F
Sbjct: 516 AYVLTSSNFIKDEALTLLKSSG--------------FGSELGEPDFVENGIEYYSGKSLF 561

Query: 508 SLILKPNRDCPVNANLKTKGRA----YTANEEFCHRDSYVILRNSELLAGSMDKSTLGSG 563
           S  L      P   NL+ K +          E C  D++VI+RN  L+ G +DK+  G+ 
Sbjct: 562 SKTL------PKGLNLQYKAKVCKKCVQCKREECENDAFVIIRNGRLVQGVIDKNGFGA- 614

Query: 564 GKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
               V   +++DFG + A T +   ++M+   +M RGF+ GI D
Sbjct: 615 ETGVVLNTIVKDFGSEDARTFLDSATKMSVKSMMLRGFTTGIDD 658

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Methanococcus vannielii (strain SB / ATCC 35089 / DSM 1224) (taxid: 406327)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

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	1423
441657982	1275	PREDICTED: DNA-directed RNA polymerase I	0.354	0.395	0.495	1e-149
449269147	1375	DNA-directed RNA polymerase III subunit	0.289	0.299	0.498	1e-114
57529842	1390	DNA-directed RNA polymerase III subunit	0.289	0.296	0.496	1e-113
345489196	1355	PREDICTED: DNA-directed RNA polymerase I	0.283	0.298	0.480	1e-113
326923517	641	PREDICTED: DNA-directed RNA polymerase I	0.287	0.638	0.493	1e-113
449504974	1369	PREDICTED: DNA-directed RNA polymerase I	0.289	0.300	0.492	1e-112
224052370	1390	PREDICTED: DNA-directed RNA polymerase I	0.289	0.296	0.492	1e-112
451770412	1390	DNA-directed RNA polymerase III subunit	0.289	0.296	0.486	1e-112
345309868	1489	PREDICTED: DNA-directed RNA polymerase I	0.289	0.276	0.486	1e-111
410895601	1390	PREDICTED: DNA-directed RNA polymerase I	0.286	0.292	0.481	1e-111

>gi|441657982|ref|XP_003274523.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Nomascus leucogenys]

 Score =  537 bits (1384), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 282/569 (49%), Positives = 365/569 (64%), Gaps = 65/569 (11%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD Q  P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIE----------------------AHKKFGLIQTLNPLEVLQL--------FEAIPL 300
           N E+E                      +     +I+   P +VL L        F    +
Sbjct: 204 NKEVEPLLGRAQVSLRIDRVSPCWPGSSRSPDRVIRPPQPPKVLGLQVNNANINFLRKLV 263

Query: 301 EDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS---------DNDVVLFNRQP 351
           ++ P +   A   +     + R L   N  R  +  +LK          D DVVLFNRQP
Sbjct: 264 QNGPEVHPGANFIQQRHTQMKRFLKYGN--REKMAQELKYGDIVERHLIDGDVVLFNRQP 321

Query: 352 SLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKL 411
           SLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA+AEAL      
Sbjct: 322 SLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEAKAEAL------ 375

Query: 412 SIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 471
                   VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++
Sbjct: 376 --------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASIL 427

Query: 472 ADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYT 531
                  G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV ANL+TKG+ Y 
Sbjct: 428 V------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSNDNPVRANLRTKGKQYC 480

Query: 532 A-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSR 590
              E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++ A  AM RL+R
Sbjct: 481 GKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQNEAADAMSRLAR 540

Query: 591 MTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
           +   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 541 LAPVYLSNRGFSIGIGDVTPGQGLLKAKY 569

Source: Nomascus leucogenys

Species: Nomascus leucogenys

Genus: Nomascus

Family: Hylobatidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|449269147|gb|EMC79953.1| DNA-directed RNA polymerase III subunit RPC1, partial [Columba livia]

 Score =  419 bits (1076), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 239/479 (49%), Positives = 305/479 (63%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    RS+P+LS  E++  S   +   EFL    ++F+++IKKF
Sbjct: 899  GKDEPLEFKRVLDNIRAVYPCRSEPALSKNELVLTSESIMKKNEFLC-CRDSFLQEIKKF 957

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       Q+L   D+I       P       E CR+KY+RAQ
Sbjct: 958  IKGVSEKIKKTRDKYGINDNGTTEPQVLYQLDRI------TPTQLEKFLETCRDKYMRAQ 1011

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFH-------------------------------- 1142
            +EP +AVGAL AQSIGEPGTQMTLKTFH                                
Sbjct: 1012 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1071

Query: 1143 ----------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                      FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1072 AQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1131

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  CI + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1132 ETVRYSICISKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQSLKEELPKVVVQGIPE 1191

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K SSNNTYEV KTLGIEAAR+T
Sbjct: 1192 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTKTSSNNTYEVEKTLGIEAARTT 1251

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1252 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1311

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FDN EFH
Sbjct: 1312 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKESTPPRRPLVFDNNEFH 1370

Source: Columba livia

Species: Columba livia

Genus: Columba

Family: Columbidae

Order: Columbiformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|57529842|ref|NP_001006500.1| DNA-directed RNA polymerase III subunit RPC1 [Gallus gallus] gi|75571385|sp|Q5ZL98.1|RPC1_CHICK RecName: Full=DNA-directed RNA polymerase III subunit RPC1; Short=RNA polymerase III subunit C1; AltName: Full=DNA-directed RNA polymerase III subunit A gi|53130332|emb|CAG31495.1| hypothetical protein RCJMB04_7b9 [Gallus gallus]

 Score =  417 bits (1071), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 238/479 (49%), Positives = 305/479 (63%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    RS+P+LS  E++  S   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIRAVYPCRSEPALSKNELVLTSESIMKKNEFLC-CRDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQLEKFLETCRDKYMRAQ 1026

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFH-------------------------------- 1142
            +EP +AVGAL AQSIGEPGTQMTLKTFH                                
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                      FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  CI + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICISKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQSLKEELPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K SSNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTKTSSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FDN EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKESTPPRRPLIFDNNEFH 1385

Source: Gallus gallus

Species: Gallus gallus

Genus: Gallus

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|345489196|ref|XP_001602571.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like [Nasonia vitripennis]

 Score =  417 bits (1071), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 231/481 (48%), Positives = 305/481 (63%), Gaps = 77/481 (16%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   PV+ KR+LDD+ ++++  ++  L    I+  ++  LDS++F    S+ F +++ +F
Sbjct: 885  GKDCPVDYKRVLDDVKSRSTHITEDPLDGPGIMKATSLLLDSEDF-ACLSDEFKQELAQF 943

Query: 1057 LEEFSKK-ESVTSH-QDKVSQPLREQI----LSHQDKIGHGRESNPFPSACKAEACREKY 1110
            L+  + K   V  H +   +QP+ + I    +S   +  H               C+EKY
Sbjct: 944  LKAVAIKIARVRQHIKSNDNQPVYKYIERLTVSQLAEFIH--------------TCKEKY 989

Query: 1111 VRAQIEPATAVGALAAQSIGEPGTQMTLKTFH---------------------------- 1142
            ++A+IEP TAVGALAAQSIGEPGTQMTLKTFH                            
Sbjct: 990  MKAKIEPGTAVGALAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINANPKIST 1049

Query: 1143 --------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHL 1176
                          FA            GE+ EYIEEV++PDD F+L+K+D+DR++LL L
Sbjct: 1050 PIITAALENDTDPEFARRVKGRIEKTTLGEITEYIEEVYLPDDCFLLLKIDIDRVKLLKL 1109

Query: 1177 EVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKG 1234
            EVD++SIRY  C  + +    ++ + G S + + P     + +  + Q+K  +P+V++KG
Sbjct: 1110 EVDVNSIRYSLCTSKLKLNPKNVVIQGDSIITIYPSKQKHNLSVTLTQLKDSIPNVIVKG 1169

Query: 1235 VQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 1294
            +  ++RAVIH +D  G T+YKL VEGDN+RDVMAT GVKG K +SNNT EV+KTLGIEAA
Sbjct: 1170 IASVSRAVIHNDDSSGKTRYKLFVEGDNMRDVMATLGVKGPKTTSNNTIEVFKTLGIEAA 1229

Query: 1295 RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFEN 1354
            R+TIMTEIKLVMENHGMSID RHPMLVADLMTS+GEVLGITR GLAKMKESVLNLASFE 
Sbjct: 1230 RATIMTEIKLVMENHGMSIDRRHPMLVADLMTSRGEVLGITRQGLAKMKESVLNLASFEK 1289

Query: 1355 TSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEF 1414
            T+DHLFDAA+YGQ D ISGVSE IIMG+P+ VGTG+ KLL    +     RTLLFD+P  
Sbjct: 1290 TADHLFDAAYYGQKDAISGVSESIIMGIPVPVGTGIFKLLHKSEKDPLKTRTLLFDSPNH 1349

Query: 1415 H 1415
            H
Sbjct: 1350 H 1350

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|326923517|ref|XP_003207982.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like, partial [Meleagris gallopavo]

 Score =  416 bits (1070), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 238/482 (49%), Positives = 307/482 (63%), Gaps = 73/482 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    RS+P+LS  E++  S   +   EFL    ++F+++IKKF
Sbjct: 165  GKDEPLEFKRVLDNIRAVYPCRSEPALSKNELVLTSESIMKKNEFLC-CRDSFLQEIKKF 223

Query: 1057 LEEFSKKESVTS-----HQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYV 1111
            ++  S+K   T      + +  ++P   ++L   D+I       P       E CR+KY+
Sbjct: 224  IKGVSEKIKKTRDKYGINDNGTTEP---RVLYQLDRI------TPTQLEKFLETCRDKYM 274

Query: 1112 RAQIEPATAVGALAAQSIGEPGTQMTLKTFH----------------------------- 1142
            RAQ+EP +AVGAL AQSIGEPGTQMTLKTFH                             
Sbjct: 275  RAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTP 334

Query: 1143 -------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLE 1177
                         FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL LE
Sbjct: 335  IITAQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLE 394

Query: 1178 VDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKG 1234
            V+ +++RY  CI + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G
Sbjct: 395  VNAETVRYSICISKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQSLKEELPKVVVQG 454

Query: 1235 VQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 1294
            +  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K SSNNTYEV KTLGIEAA
Sbjct: 455  IPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTKTSSNNTYEVEKTLGIEAA 514

Query: 1295 RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFEN 1354
            R+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE 
Sbjct: 515  RTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEK 574

Query: 1355 TSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPE 1413
            T+DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FDN +
Sbjct: 575  TADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKESTPPRRPLVFDNND 634

Query: 1414 FH 1415
            FH
Sbjct: 635  FH 636

Source: Meleagris gallopavo

Species: Meleagris gallopavo

Genus: Meleagris

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|449504974|ref|XP_004174828.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 isoform 2 [Taeniopygia guttata]

 Score =  415 bits (1066), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 236/479 (49%), Positives = 305/479 (63%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    RS+P+LS  E++  S   +   EFL    ++F+++IKKF
Sbjct: 893  GKDEPLEFKRVLDNIRAVYPCRSEPALSKNELVLTSESIMKKNEFLC-CQDSFLQEIKKF 951

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 952  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQLEKFLETCRDKYMRAQ 1005

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFH-------------------------------- 1142
            +EP +AVGAL AQSIGEPGTQMTLKTFH                                
Sbjct: 1006 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1065

Query: 1143 ----------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                      FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1066 AQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1125

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1126 ETVRYSICVSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQSLKEELPKVVVQGIPE 1185

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K SSNNTYEV KTLGIEAAR+T
Sbjct: 1186 VSRAVIHVDEQSGKEKYKLLVEGDNLRAVMATHGVKGTKTSSNNTYEVEKTLGIEAARTT 1245

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1246 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1305

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FD+ EFH
Sbjct: 1306 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHRADKESTPPRRPLIFDHNEFH 1364

Source: Taeniopygia guttata

Species: Taeniopygia guttata

Genus: Taeniopygia

Family: Estrildidae

Order: Passeriformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|224052370|ref|XP_002195476.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 isoform 1 [Taeniopygia guttata]

 Score =  415 bits (1066), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 236/479 (49%), Positives = 305/479 (63%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    RS+P+LS  E++  S   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIRAVYPCRSEPALSKNELVLTSESIMKKNEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQLEKFLETCRDKYMRAQ 1026

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFH-------------------------------- 1142
            +EP +AVGAL AQSIGEPGTQMTLKTFH                                
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                      FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICVSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQSLKEELPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K SSNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHVDEQSGKEKYKLLVEGDNLRAVMATHGVKGTKTSSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FD+ EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHRADKESTPPRRPLIFDHNEFH 1385

Source: Taeniopygia guttata

Species: Taeniopygia guttata

Genus: Taeniopygia

Family: Estrildidae

Order: Passeriformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|451770412|ref|NP_001263425.1| DNA-directed RNA polymerase III subunit RPC1 [Danio rerio]

 Score =  414 bits (1064), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 233/479 (48%), Positives = 304/479 (63%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A  S   +P+LS  E+L  S+  +  K+FL    + F+ +I+KF
Sbjct: 914  GKDEPLEFKRVLDNIRAVYSCTGEPALSRNELLLTSDSIMKRKDFLC-CKDTFLEEIRKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKTVSEKVKKTRDKYGINDNGTTEPKVLYQLDRI------TPTQLEKFLETCRDKYMRAQ 1026

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFH-------------------------------- 1142
            +EP +AVGAL AQSIGEPGTQMTLKTFH                                
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIIS 1086

Query: 1143 ----------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                      FA            GE+ EYIEEVF+PDD+FIL+KL +DRIRLL LEV+ 
Sbjct: 1087 ANLDTNDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDDTFILVKLSLDRIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +KQ LP VV++G+  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVQVHGEAVVCVSPRENSKSSMYYVLQSLKQDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  K+KLLVEGDN+R VMAT+GV G K +SNNTYEV KTLGIEAARST
Sbjct: 1207 VSRAVIHIDEQSGKQKFKLLVEGDNMRSVMATHGVNGSKTTSNNTYEVEKTLGIEAARST 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML+ADLM+ KGE+LGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLADLMSYKGEILGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR-SEPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R ++P  R LLFD+P+FH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHRSNREADPPRRPLLFDSPDFH 1385

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|345309868|ref|XP_001514706.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Ornithorhynchus anatinus]

 Score =  410 bits (1054), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 233/479 (48%), Positives = 302/479 (63%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 1013 GKDEPLEFKRVLDNIKAVFPCQSEPALSKNELVLTTESIMKKNEFLC-CQDSFLQEIKKF 1071

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 1072 IKVVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQLEKFLETCRDKYMRAQ 1125

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFH-------------------------------- 1142
            +EP +AVGAL AQSIGEPGTQMTLKTFH                                
Sbjct: 1126 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1185

Query: 1143 ----------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                      FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1186 AQLDSDDDSDFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1245

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + L + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1246 ETVRYSICMSKLRVKPGDVAVHGEAVLCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1305

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K +SNNTYEV KTLGIEAAR+T
Sbjct: 1306 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTKTTSNNTYEVEKTLGIEAARTT 1365

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1366 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1425

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1426 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPERPLVFDTSEFH 1484

Source: Ornithorhynchus anatinus

Species: Ornithorhynchus anatinus

Genus: Ornithorhynchus

Family: Ornithorhynchidae

Order: Monotremata

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|410895601|ref|XP_003961288.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like [Takifugu rubripes]

 Score =  409 bits (1052), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 233/484 (48%), Positives = 304/484 (62%), Gaps = 77/484 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A  +   +P+LS  E++  ++      +FL    ++F+ +IKKF
Sbjct: 914  GKDEPLEFKRVLDNIRAVYTCSDEPALSQNELVLTADAITKRADFLC-CRDSFLEEIKKF 972

Query: 1057 LEEFSKKESVTSHQDK-------VSQPLREQILSHQDKIGHGRESNPFPSACKAEACREK 1109
            ++ FS  E +   +DK        S+P   ++L   D+I       P       E CR+K
Sbjct: 973  VKGFS--ERIKKTRDKYGINDNGTSEP---KVLYQLDRI------TPTQLERFLETCRDK 1021

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH--------------------------- 1142
            Y+RAQ+EP +AVGAL AQSIGEPGTQMTLKTFH                           
Sbjct: 1022 YMRAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNIS 1081

Query: 1143 ---------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLH 1175
                           FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL 
Sbjct: 1082 TPIITAHLDVEDDADFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLR 1141

Query: 1176 LEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVI 1232
            LEV+ +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV+
Sbjct: 1142 LEVNAETVRYSICMSKLRVKPGDIAVHGEAVVCVSPRENSKSSMYYVLQSLKEDLPKVVV 1201

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            +G+  + RAVIH ++  G  KYKLLVEGDNLR VMAT+GV G + +SNNT+EV KTLGIE
Sbjct: 1202 QGIPEVARAVIHIDEQSGRNKYKLLVEGDNLRAVMATHGVNGSRTTSNNTFEVEKTLGIE 1261

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AARSTI+ EI+  M NHGMSID RH ML+ADLM+ KGE+LGITR GLAKMKESVL LASF
Sbjct: 1262 AARSTIINEIQYTMVNHGMSIDRRHVMLLADLMSYKGEILGITRFGLAKMKESVLMLASF 1321

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDN 1411
            E T+DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A     P  R LLFDN
Sbjct: 1322 EKTADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKAEKEPSPAKRPLLFDN 1381

Query: 1412 PEFH 1415
            P+FH
Sbjct: 1382 PDFH 1385

Source: Takifugu rubripes

Species: Takifugu rubripes

Genus: Takifugu

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

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	1423
UNIPROTKB|F1NIK7	1390	POLR3A "DNA-directed RNA polym	0.190	0.194	0.629	2.2e-261
UNIPROTKB|Q5ZL98	1390	POLR3A "DNA-directed RNA polym	0.190	0.194	0.629	9.6e-261
UNIPROTKB|O14802	1390	POLR3A "DNA-directed RNA polym	0.190	0.194	0.610	6.9e-257
UNIPROTKB|A4IF62	1390	POLR3A "DNA-directed RNA polym	0.190	0.194	0.610	6.9e-257
UNIPROTKB|F1S2E6	1390	POLR3A "DNA-directed RNA polym	0.190	0.194	0.614	1.1e-256
UNIPROTKB|J9P629	1390	POLR3A "DNA-directed RNA polym	0.190	0.194	0.610	2.2e-256
ZFIN|ZDB-GENE-050208-103	1390	polr3a "polymerase (RNA) III (	0.190	0.194	0.614	9.9e-255
UNIPROTKB|E2QXD8	1376	POLR3A "DNA-directed RNA polym	0.190	0.196	0.610	8.3e-246
UNIPROTKB|E9PTB6	1342	Polr3a "DNA-directed RNA polym	0.209	0.222	0.508	5.2e-239
FB|FBgn0030687	1383	CG17209 [Drosophila melanogast	0.180	0.185	0.515	4.2e-204

UNIPROTKB|F1NIK7 POLR3A "DNA-directed RNA polymerase" [Gallus gallus (taxid:9031)]

 Score = 854 (305.7 bits), Expect = 2.2e-261, Sum P(6) = 2.2e-261
 Identities = 173/275 (62%), Positives = 214/275 (77%)

Query:  1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGH 1202
             GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ +++RY  CI + R   G + V G 
Sbjct:  1111 GEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNAETVRYSICISKLRVKPGDVAVHGE 1170

Query:  1203 SFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 1261
             + + + P+++SKS    + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGD
Sbjct:  1171 AVVCVTPRENSKSSMYYVLQSLKEELPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGD 1230

Query:  1262 NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 1321
             NLR VMAT+GVKG K SSNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML+
Sbjct:  1231 NLRAVMATHGVKGTKTSSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLL 1290

Query:  1322 ADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
             +DLMT KGEVLGITR GLAKMKESVL LASFE T+DHLFDAA++GQ D + GVSECIIMG
Sbjct:  1291 SDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTADHLFDAAYFGQKDSVCGVSECIIMG 1350

Query:  1382 LPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 1415
             +PMN+GTGL KLL +A   S P  R L+FDN EFH
Sbjct:  1351 IPMNIGTGLFKLLHKADKESTPPRRPLIFDNNEFH 1385

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032549 "ribonucleoside binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0032728 "positive regulation of interferon-beta production" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

UNIPROTKB|Q5ZL98 POLR3A "DNA-directed RNA polymerase III subunit RPC1" [Gallus gallus (taxid:9031)]

 Score = 854 (305.7 bits), Expect = 9.6e-261, Sum P(6) = 9.6e-261
 Identities = 173/275 (62%), Positives = 214/275 (77%)

Query:  1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGH 1202
             GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ +++RY  CI + R   G + V G 
Sbjct:  1111 GEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNAETVRYSICISKLRVKPGDVAVHGE 1170

Query:  1203 SFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 1261
             + + + P+++SKS    + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGD
Sbjct:  1171 AVVCVTPRENSKSSMYYVLQSLKEELPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGD 1230

Query:  1262 NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 1321
             NLR VMAT+GVKG K SSNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML+
Sbjct:  1231 NLRAVMATHGVKGTKTSSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLL 1290

Query:  1322 ADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
             +DLMT KGEVLGITR GLAKMKESVL LASFE T+DHLFDAA++GQ D + GVSECIIMG
Sbjct:  1291 SDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTADHLFDAAYFGQKDSVCGVSECIIMG 1350

Query:  1382 LPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 1415
             +PMN+GTGL KLL +A   S P  R L+FDN EFH
Sbjct:  1351 IPMNIGTGLFKLLHKADKESTPPRRPLIFDNNEFH 1385

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032549 "ribonucleoside binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|O14802 POLR3A "DNA-directed RNA polymerase III subunit RPC1" [Homo sapiens (taxid:9606)]

 Score = 836 (299.3 bits), Expect = 6.9e-257, Sum P(6) = 6.9e-257
 Identities = 168/275 (61%), Positives = 210/275 (76%)

Query:  1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGH 1202
             GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G 
Sbjct:  1111 GEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGE 1170

Query:  1203 SFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 1261
             + + + P+++SKS    + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGD
Sbjct:  1171 AVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGD 1230

Query:  1262 NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 1321
             NLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML+
Sbjct:  1231 NLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLL 1290

Query:  1322 ADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
             +DLMT KGEVLGITR GLAKMKESVL LASFE T+DHLFDAA++GQ D + GVSECIIMG
Sbjct:  1291 SDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTADHLFDAAYFGQKDSVCGVSECIIMG 1350

Query:  1382 LPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
             +PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct:  1351 IPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1385

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032549 "ribonucleoside binding" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=NAS

GO:0006351 "transcription, DNA-dependent" evidence=NAS

GO:0005666 "DNA-directed RNA polymerase III complex" evidence=NAS

GO:0045087 "innate immune response" evidence=IMP

GO:0032728 "positive regulation of interferon-beta production" evidence=IMP

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006383 "transcription from RNA polymerase III promoter" evidence=TAS

GO:0006385 "transcription elongation from RNA polymerase III promoter" evidence=TAS

GO:0006386 "termination of RNA polymerase III transcription" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|A4IF62 POLR3A "DNA-directed RNA polymerase III subunit RPC1" [Bos taurus (taxid:9913)]

 Score = 836 (299.3 bits), Expect = 6.9e-257, Sum P(6) = 6.9e-257
 Identities = 168/275 (61%), Positives = 211/275 (76%)

Query:  1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGH 1202
             GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G 
Sbjct:  1111 GEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDVAVHGE 1170

Query:  1203 SFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 1261
             + + + P+++SKS    + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGD
Sbjct:  1171 AVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGD 1230

Query:  1262 NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 1321
             NLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML+
Sbjct:  1231 NLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLL 1290

Query:  1322 ADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
             +DLMT KGEVLGITR GLAKMKESVL LASFE T+DHLFDAA++GQ D + GVSECIIMG
Sbjct:  1291 SDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTADHLFDAAYFGQKDSVCGVSECIIMG 1350

Query:  1382 LPMNVGTGLIKLLQAVPRSEPVPRT-LLFDNPEFH 1415
             +PMN+GTGL KLL    R    PR  L+FD  EFH
Sbjct:  1351 IPMNIGTGLFKLLHKANRDPSPPRRPLIFDTNEFH 1385

GO:0045087 "innate immune response" evidence=ISS

GO:0032728 "positive regulation of interferon-beta production" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

GO:0032549 "ribonucleoside binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1S2E6 POLR3A "DNA-directed RNA polymerase" [Sus scrofa (taxid:9823)]

 Score = 837 (299.7 bits), Expect = 1.1e-256, Sum P(6) = 1.1e-256
 Identities = 169/275 (61%), Positives = 211/275 (76%)

Query:  1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGH 1202
             GE+ EYIEEVF+PDD FILIKL ++RIRLL LEV+ +++RY  C+ + R   G + V G 
Sbjct:  1111 GEISEYIEEVFLPDDCFILIKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDVAVHGE 1170

Query:  1203 SFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 1261
             + + + P+++SKS    + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGD
Sbjct:  1171 AVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGD 1230

Query:  1262 NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 1321
             NLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML+
Sbjct:  1231 NLRAVMATHGVKGTQTTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLL 1290

Query:  1322 ADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
             +DLMT KGEVLGITR GLAKMKESVL LASFE T+DHLFDAA++GQ D + GVSECIIMG
Sbjct:  1291 SDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTADHLFDAAYFGQKDSVCGVSECIIMG 1350

Query:  1382 LPMNVGTGLIKLLQAVPRSEPVPRT-LLFDNPEFH 1415
             +PMN+GTGL KLL    R    PR  L+FD  EFH
Sbjct:  1351 IPMNIGTGLFKLLHKANRDPSPPRRPLIFDTDEFH 1385

GO:0045087 "innate immune response" evidence=IEA

GO:0032728 "positive regulation of interferon-beta production" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0032549 "ribonucleoside binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|J9P629 POLR3A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)]

 Score = 837 (299.7 bits), Expect = 2.2e-256, Sum P(6) = 2.2e-256
 Identities = 168/275 (61%), Positives = 211/275 (76%)

Query:  1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGH 1202
             GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G 
Sbjct:  1111 GEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDVAVHGE 1170

Query:  1203 SFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 1261
             + + + P+++SKS    + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGD
Sbjct:  1171 AVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGD 1230

Query:  1262 NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 1321
             NLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML+
Sbjct:  1231 NLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLL 1290

Query:  1322 ADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
             +DLMT KGEVLGITR GLAKMKESVL LASFE T+DHLFDAA++GQ D + GVSECIIMG
Sbjct:  1291 SDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTADHLFDAAYFGQKDSVCGVSECIIMG 1350

Query:  1382 LPMNVGTGLIKLLQAVPRSEPVPRT-LLFDNPEFH 1415
             +PMN+GTGL KLL    R    PR  L+FD  EFH
Sbjct:  1351 IPMNIGTGLFKLLHKADRDPSPPRRPLIFDTNEFH 1385

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0032549 "ribonucleoside binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

ZFIN|ZDB-GENE-050208-103 polr3a "polymerase (RNA) III (DNA directed) polypeptide A" [Danio rerio (taxid:7955)]

 Score = 846 (302.9 bits), Expect = 9.9e-255, Sum P(6) = 9.9e-255
 Identities = 169/275 (61%), Positives = 214/275 (77%)

Query:  1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGH 1202
             GE+ EYIEEVF+PDD+FIL+KL +DRIRLL LEV+ +++RY  C  + R   G + V G 
Sbjct:  1111 GEISEYIEEVFLPDDTFILVKLSLDRIRLLRLEVNAETVRYSICTSKLRVKPGDVQVHGE 1170

Query:  1203 SFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 1261
             + + + P+++SKS    + Q +KQ LP VV++G+  ++RAVIH ++  G  K+KLLVEGD
Sbjct:  1171 AVVCVSPRENSKSSMYYVLQSLKQDLPKVVVQGIPEVSRAVIHIDEQSGKQKFKLLVEGD 1230

Query:  1262 NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 1321
             N+R VMAT+GV G K +SNNTYEV KTLGIEAARSTI+ EI+  M NHGMSID RH ML+
Sbjct:  1231 NMRSVMATHGVNGSKTTSNNTYEVEKTLGIEAARSTIINEIQYTMVNHGMSIDRRHVMLL 1290

Query:  1322 ADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
             ADLM+ KGE+LGITR GLAKMKESVL LASFE T+DHLFDAA++GQ D + GVSECIIMG
Sbjct:  1291 ADLMSYKGEILGITRFGLAKMKESVLMLASFEKTADHLFDAAYFGQKDSVCGVSECIIMG 1350

Query:  1382 LPMNVGTGLIKLLQAVPR-SEPVPRTLLFDNPEFH 1415
             +PMN+GTGL KLL    R ++P  R LLFD+P+FH
Sbjct:  1351 IPMNIGTGLFKLLHRSNREADPPRRPLLFDSPDFH 1385

GO:0003677 "DNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0032549 "ribonucleoside binding" evidence=IEA

GO:0016779 "nucleotidyltransferase activity" evidence=IEA

GO:0016740 "transferase activity" evidence=IEA

UNIPROTKB|E2QXD8 POLR3A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)]

 Score = 837 (299.7 bits), Expect = 8.3e-246, Sum P(6) = 8.3e-246
 Identities = 168/275 (61%), Positives = 211/275 (76%)

Query:  1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGH 1202
             GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G 
Sbjct:  1097 GEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDVAVHGE 1156

Query:  1203 SFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 1261
             + + + P+++SKS    + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGD
Sbjct:  1157 AVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGD 1216

Query:  1262 NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 1321
             NLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML+
Sbjct:  1217 NLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLL 1276

Query:  1322 ADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
             +DLMT KGEVLGITR GLAKMKESVL LASFE T+DHLFDAA++GQ D + GVSECIIMG
Sbjct:  1277 SDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTADHLFDAAYFGQKDSVCGVSECIIMG 1336

Query:  1382 LPMNVGTGLIKLLQAVPRSEPVPRT-LLFDNPEFH 1415
             +PMN+GTGL KLL    R    PR  L+FD  EFH
Sbjct:  1337 IPMNIGTGLFKLLHKADRDPSPPRRPLIFDTNEFH 1371

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0032549 "ribonucleoside binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E9PTB6 Polr3a "DNA-directed RNA polymerase" [Rattus norvegicus (taxid:10116)]

 Score = 752 (269.8 bits), Expect = 5.2e-239, Sum P(6) = 5.2e-239
 Identities = 158/311 (50%), Positives = 204/311 (65%)

Query:    91 DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
             + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct:    26 EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query:   151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
             IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct:    86 IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKQQFLDFLKRPGLTYLQKRGLK 143

Query:   211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
             KKI +  +K S C +CG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct:   144 KKISDKCRKKSTCHYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query:   271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
             N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct:   204 NKEVEP--LLGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query:   330 IRPSVISDLKSD-NDVVLFNRQPSLHKLS--IMAHR---AKV-LPHRTFRFNECVCTPY- 381
             IRPSV+SDLKS  N+  L  +   +  L+  I  HR   AK  +    + F +  C  Y 
Sbjct:   262 IRPSVVSDLKSGTNEDDLTMKLTEIIFLNDVIKKHRISGAKTQMIMEDWDFLQLQCALYI 321

Query:   382 NADFDGDEMNV 392
             N++  G  +N+
Sbjct:   322 NSELSGIPLNM 332

GO:0003677 "DNA binding" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032549 "ribonucleoside binding" evidence=IEA

GO:0032728 "positive regulation of interferon-beta production" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

FB|FBgn0030687 CG17209 [Drosophila melanogaster (taxid:7227)]

 Score = 630 (226.8 bits), Expect = 4.2e-204, Sum P(5) = 4.2e-204
 Identities = 137/266 (51%), Positives = 184/266 (69%)

Query:  1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGISGHL-TVSGH 1202
             E+  Y+E V  P   ++ I +DM RI+LL L +D+D+I + I   R R     +  V+  
Sbjct:  1104 ELSSYVEVVCGPYSCYLAIGVDMARIKLLGLHIDLDTIVFSILKSRMRVKPTQVEVVASQ 1163

Query:  1203 SFLILKPKDSSKS-FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 1261
             S ++++ + +  S  N+++ ++   L +VV+ G+  INRAVI  +D      YKL +EG 
Sbjct:  1164 SRIVVRVEATRTSTINAELARLALSLQNVVVAGLPNINRAVIAVDDARQPPTYKLCIEGY 1223

Query:  1262 NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 1321
              LRDV+ATYGV G +  SNN  E+Y+TLGIEAAR+ IM+EI  VME HGMS+D+RH ML+
Sbjct:  1224 GLRDVIATYGVVGKRTRSNNICEIYQTLGIEAARTIIMSEITEVMEGHGMSVDWRHIMLL 1283

Query:  1322 ADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
             A  MT++GEVLGITRHGLAKM+ESV NLASFE T+DHLFDAA+YGQTD I+GVSE II+G
Sbjct:  1284 ASQMTARGEVLGITRHGLAKMRESVFNLASFEKTADHLFDAAYYGQTDAINGVSERIILG 1343

Query:  1382 LPMNVGTGLIKLLQA-----VPRSEP 1402
             +P  +GTG+ KLLQ      VP  EP
Sbjct:  1344 MPACIGTGIFKLLQQHEDKQVPPIEP 1369

GO:0006383 "transcription from RNA polymerase III promoter" evidence=ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS

GO:0005666 "DNA-directed RNA polymerase III complex" evidence=ISS

GO:0032549 "ribonucleoside binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	0.766
4th Layer	2.7.7.6	0.824

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	1423
cd02736	300	cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) o	1e-110
cd02736	300	cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) o	7e-88
PRK08566	882	PRK08566, PRK08566, DNA-directed RNA polymerase su	9e-74
PRK04309	383	PRK04309, PRK04309, DNA-directed RNA polymerase su	9e-74
cd06528	363	cd06528, RNAP_A'', A'' subunit of Archaeal RNA Pol	1e-71
TIGR02389	367	TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymer	2e-67
TIGR02390	867	TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer	8e-64
PRK14897	509	PRK14897, PRK14897, unknown domain/DNA-directed RN	7e-61
PRK14977	1321	PRK14977, PRK14977, bifunctional DNA-directed RNA	2e-55
pfam04997	330	pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, do	3e-54
pfam04998	447	pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, do	5e-53
smart00663	295	smart00663, RPOLA_N, RNA polymerase I subunit A N-	7e-51
cd02735	309	cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of	3e-50
COG0086	808	COG0086, RpoC, DNA-directed RNA polymerase, beta'	6e-50
PRK04309	383	PRK04309, PRK04309, DNA-directed RNA polymerase su	1e-45
cd06528	363	cd06528, RNAP_A'', A'' subunit of Archaeal RNA Pol	2e-45
pfam04998	447	pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, do	3e-45
PRK14898	858	PRK14898, PRK14898, DNA-directed RNA polymerase su	4e-44
cd00630	158	cd00630, RNAP_largest_subunit_C, Largest subunit o	4e-42
pfam04983	158	pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, do	1e-41
pfam00623	165	pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, do	2e-41
TIGR02389	367	TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymer	6e-41
cd02584	410	cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of	2e-38
PRK14897	509	PRK14897, PRK14897, unknown domain/DNA-directed RN	2e-37
PRK08566	882	PRK08566, PRK08566, DNA-directed RNA polymerase su	5e-36
PRK14898	858	PRK14898, PRK14898, DNA-directed RNA polymerase su	6e-35
TIGR02390	867	TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer	7e-35
cd02584	410	cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of	2e-33
COG0086	808	COG0086, RpoC, DNA-directed RNA polymerase, beta'	5e-29
cd02735	309	cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of	2e-28
PRK08566	882	PRK08566, PRK08566, DNA-directed RNA polymerase su	2e-27
pfam04998	447	pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, do	2e-27
COG0086	808	COG0086, RpoC, DNA-directed RNA polymerase, beta'	6e-25
PRK14977	1321	PRK14977, PRK14977, bifunctional DNA-directed RNA	9e-25
TIGR02390	867	TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer	3e-24
PRK14977	1321	PRK14977, PRK14977, bifunctional DNA-directed RNA	1e-23
COG0086	808	COG0086, RpoC, DNA-directed RNA polymerase, beta'	1e-21
TIGR02386	1140	TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase,	5e-20
PRK14977	1321	PRK14977, PRK14977, bifunctional DNA-directed RNA	5e-19
PRK14906	1460	PRK14906, PRK14906, DNA-directed RNA polymerase su	7e-19
PRK14977	1321	PRK14977, PRK14977, bifunctional DNA-directed RNA	2e-18
CHL00018	663	CHL00018, rpoC1, RNA polymerase beta' subunit	4e-18
PRK02625	627	PRK02625, rpoC1, DNA-directed RNA polymerase subun	7e-18
TIGR02387	619	TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase	7e-18
PRK00566	1156	PRK00566, PRK00566, DNA-directed RNA polymerase su	1e-17
PRK14844	2836	PRK14844, PRK14844, bifunctional DNA-directed RNA	9e-16
PRK09603	2890	PRK09603, PRK09603, bifunctional DNA-directed RNA	2e-15
cd00630	158	cd00630, RNAP_largest_subunit_C, Largest subunit o	2e-14
cd02584	410	cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of	8e-14
TIGR02386	1140	TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase,	1e-10
cd00630	158	cd00630, RNAP_largest_subunit_C, Largest subunit o	2e-10
PRK14977	1321	PRK14977, PRK14977, bifunctional DNA-directed RNA	3e-10
pfam04983	158	pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, do	3e-10
cd02736	300	cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) o	2e-09
CHL00117	1364	CHL00117, rpoC2, RNA polymerase beta'' subunit; Re	2e-09
COG0086	808	COG0086, RpoC, DNA-directed RNA polymerase, beta'	3e-09
cd02655	204	cd02655, RNAP_beta'_C, Largest subunit (beta') of	3e-09
PRK14906	1460	PRK14906, PRK14906, DNA-directed RNA polymerase su	4e-08
PRK00566	1156	PRK00566, PRK00566, DNA-directed RNA polymerase su	5e-08
PRK09603	2890	PRK09603, PRK09603, bifunctional DNA-directed RNA	5e-08
TIGR02388	1227	TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase	5e-08
cd02737	381	cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1)	5e-08
PRK08566	882	PRK08566, PRK08566, DNA-directed RNA polymerase su	6e-08
PRK00566	1156	PRK00566, PRK00566, DNA-directed RNA polymerase su	6e-08
PRK02597	1331	PRK02597, rpoC2, DNA-directed RNA polymerase subun	8e-08
TIGR02386	1140	TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase,	2e-07
PRK02597	1331	PRK02597, rpoC2, DNA-directed RNA polymerase subun	2e-07
cd02655	204	cd02655, RNAP_beta'_C, Largest subunit (beta') of	3e-07
PRK14906	1460	PRK14906, PRK14906, DNA-directed RNA polymerase su	8e-07
PRK14844	2836	PRK14844, PRK14844, bifunctional DNA-directed RNA	1e-06
CHL00117	1364	CHL00117, rpoC2, RNA polymerase beta'' subunit; Re	2e-06
COG0086	808	COG0086, RpoC, DNA-directed RNA polymerase, beta'	3e-06
TIGR02388	1227	TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase	3e-06
PRK14977	1321	PRK14977, PRK14977, bifunctional DNA-directed RNA	5e-06
cd00630	158	cd00630, RNAP_largest_subunit_C, Largest subunit o	9e-06
PRK14898	858	PRK14898, PRK14898, DNA-directed RNA polymerase su	2e-05
PRK14844	2836	PRK14844, PRK14844, bifunctional DNA-directed RNA	4e-05
PRK14844	2836	PRK14844, PRK14844, bifunctional DNA-directed RNA	5e-05
TIGR02390	867	TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer	7e-05
PRK09603	2890	PRK09603, PRK09603, bifunctional DNA-directed RNA	9e-05
PRK14906	1460	PRK14906, PRK14906, DNA-directed RNA polymerase su	1e-04
TIGR02386	1140	TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase,	3e-04
smart00663	295	smart00663, RPOLA_N, RNA polymerase I subunit A N-	0.001
cd02584	410	cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of	0.003
pfam00623	165	pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, do	0.004
TIGR02388	1227	TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase	0.004

>gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain

 Score =  350 bits (901), Expect = e-110
 Identities = 150/308 (48%), Positives = 193/308 (62%), Gaps = 33/308 (10%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE----- 1152
            KY+RA++EP TAVGA+AAQSIGEPGTQMTLKTFHFAG            + E I      
Sbjct: 1    KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNI 60

Query: 1153 -------EVFVPDD--SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHS 1203
                   ++    D  S  ++K  +++  L  +      I            ++ +    
Sbjct: 61   STPIITAKLENDRDEKSARIVKGRIEKTYLGEV---ASYIEEVYSPD---DCYILIKLDK 114

Query: 1204 FLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 1263
             +I K + S  +    +  +K+ LP VV+ G+  + RAVI+++  +G  KYKLLVEG  L
Sbjct: 115  KIIEKLQLSKSNLYFLLQSLKRKLPDVVVSGIPEVKRAVINKDKKKG--KYKLLVEGYGL 172

Query: 1264 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 1323
            R VM T GV G + +SN+  EV K LGIEAARSTI+ EI+  M++HGMSID RH ML+AD
Sbjct: 173  RAVMNTPGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLAD 232

Query: 1324 LMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP 1383
            LMT KGEVLGITR G+AKMKESVL LASFE T+DHLF+AA +G+ D I GVSECIIMG P
Sbjct: 233  LMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKP 292

Query: 1384 MNVGTGLI 1391
            M +GTGL 
Sbjct: 293  MPIGTGLF 300

Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. Length = 300

>gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain

 Score =  287 bits (737), Expect = 7e-88
 Identities = 129/273 (47%), Positives = 156/273 (57%), Gaps = 63/273 (23%)

Query: 725 FHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIIT 784
           FHF  V             AS+ +TL             GVPRIKEIINAS+NISTPIIT
Sbjct: 33  FHFAGV-------------ASMNITL-------------GVPRIKEIINASKNISTPIIT 66

Query: 785 AYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 844
           A L+ D D   ARIVKGR+E+T LGEV  YIEEV+ PDD +ILIKLD   I  L L    
Sbjct: 67  AKLENDRDEKSARIVKGRIEKTYLGEVASYIEEVYSPDDCYILIKLDKKIIEKLQL---- 122

Query: 845 DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINR 904
                                          S  +    +  +K+ LP VV+ G+  + R
Sbjct: 123 -------------------------------SKSNLYFLLQSLKRKLPDVVVSGIPEVKR 151

Query: 905 AVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMT 964
           AVI+++  +G  KYKLLVEG  LR VM T GV G + +SN+  EV K LGIEAARSTI+ 
Sbjct: 152 AVINKDKKKG--KYKLLVEGYGLRAVMNTPGVIGTRTTSNHIMEVEKVLGIEAARSTIIN 209

Query: 965 EIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
           EI+  M++HGMSID RH ML+ADLMT KGEVLG
Sbjct: 210 EIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLG 242

Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. Length = 300

>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated

 Score =  264 bits (678), Expect = 9e-74
 Identities = 102/270 (37%), Positives = 158/270 (58%), Gaps = 31/270 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR +VLP +TFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 414 DGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEA 473

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A++LM  + ++++PR G  +I   QD I+G YLLT+K+  F +
Sbjct: 474 RAE--------------ARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTK 519

Query: 461 AQTMRI-ASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            + + +  +  I +  +    I+       N   +      WTGKQIFSL L  + +   
Sbjct: 520 EEALDLLRAAGIDELPEPEPAIE-------NGKPY------WTGKQIFSLFLPKDLNLEF 566

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            A + +        +E C  D+YV+++N +LL G +DK  +G+  + ++   +++++G +
Sbjct: 567 KAKICSGCD--ECKKEDCEHDAYVVIKNGKLLEGVIDKKAIGA-EQGSILDRIVKEYGPE 623

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            A   +  ++R+   ++M RGF+ GI D  
Sbjct: 624 RARRFLDSVTRLAIRFIMLRGFTTGIDDED 653

Length = 882

>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A''; Validated

 Score =  250 bits (642), Expect = 9e-74
 Identities = 136/418 (32%), Positives = 213/418 (50%), Gaps = 96/418 (22%)

Query: 1031 LSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGH 1090
            +S ETL+ K  L+D S    + +K+ L E  ++  +T           E++    ++I  
Sbjct: 2    MSEETLEEK--LEDASLELPQKLKEELREKLEERKLT----------EEEV----EEI-- 43

Query: 1091 GRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----- 1145
                         E    +Y+R+ +EP  AVG +AAQSIGEPGTQMT++TFH+AG     
Sbjct: 44   ------------IEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEIN 91

Query: 1146 ---------------------------------------EVCEYIEEVFV---------- 1156
                                                   EV   IE   +          
Sbjct: 92   VTLGLPRLIEIVDARKEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISVD 151

Query: 1157 PDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF 1216
              +  I+I+LD +   L    + +D ++  IE+ +G  G + + G++ LI+ PK+ S   
Sbjct: 152  LANMTIIIELDEEM--LEDRGLTVDDVKEAIEKKKG--GEVEIEGNT-LIISPKEPSYR- 205

Query: 1217 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
              ++ ++ + + ++ IKG++GI R +I +E  E    Y +  EG NL++V+   GV   +
Sbjct: 206  --ELRKLAEKIRNIKIKGIKGIKRVIIRKEGDE----YVIYTEGSNLKEVLKVEGVDATR 259

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             ++NN +E+ + LGIEAAR+ I+ EIK  +E  G+ +D RH MLVAD+MT  GEV  I R
Sbjct: 260  TTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGR 319

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            HG++  K SVL  A+FE T  HL DAA  G+ D + GV+E II+G P+ +GTG ++L 
Sbjct: 320  HGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELT 377

Length = 383

>gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP)

 Score =  244 bits (624), Expect = 1e-71
 Identities = 118/346 (34%), Positives = 174/346 (50%), Gaps = 64/346 (18%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------- 1145
             +    +Y+R+ IEP  AVG +AAQSIGEPGTQMTL+TFH+AG                 
Sbjct: 25   IKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIV 84

Query: 1146 ---------------------------EVCEYIEEVFV----------PDDSFILIKLDM 1168
                                       EV   IEE  +            +  I I+LD 
Sbjct: 85   DARKEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISIDLFNMRITIELDE 144

Query: 1169 DRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLP 1228
            + +    + VD   +   IE+ +             ++   + S K    ++ ++ + + 
Sbjct: 145  EMLEDRGITVD--DVLKAIEKLKKGKVGEEGDVTLIVLKAEEPSIK----ELRKLAEKIL 198

Query: 1229 SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT 1288
            +  IKG++GI R ++ +E+ E    Y +  EG NL+ V+   GV   + ++NN +E+ + 
Sbjct: 199  NTKIKGIKGIKRVIVRKEEDE----YVIYTEGSNLKAVLKVEGVDPTRTTTNNIHEIEEV 254

Query: 1289 LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348
            LGIEAAR+ I+ EIK  +E  G+ +D RH MLVAD+MT  GEV  I RHG+A  K SVL 
Sbjct: 255  LGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLA 314

Query: 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             A+FE T  HL DAA  G+ D + GV E II+G P+ +GTG ++L 
Sbjct: 315  RAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELT 360

Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. Length = 363

>gnl|CDD|233842 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A''

 Score =  231 bits (592), Expect = 2e-67
 Identities = 123/347 (35%), Positives = 188/347 (54%), Gaps = 65/347 (18%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------- 1145
             +   E+Y+R+ I+P  AVG +AAQSIGEPGTQMT++TFH+AG                 
Sbjct: 29   IKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIV 88

Query: 1146 ---------------------------EVCEYIEEVFVPD----------DSFILIKLDM 1168
                                       EV + IE   + D          D  ++I+LD 
Sbjct: 89   DARKTPSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLADMTVIIELDE 148

Query: 1169 DRIRLLHLEVDIDSIRYCIERTR-GISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLL 1227
            ++++   + VD   +   I++ + G    + + G++  I  PK S K    ++ ++K+ +
Sbjct: 149  EQLKERGITVD--DVEKAIKKAKLGKVIEIDMDGNTITIKPPKPSLK----ELRKLKEKI 202

Query: 1228 PSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK 1287
             ++ IKG++GI R VI +E  E    Y +  EG NL++V+   GV   + ++N+ +E+ +
Sbjct: 203  KNLHIKGIKGIKRVVIRKEGDE----YVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAE 258

Query: 1288 TLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVL 1347
             LGIEAAR+ I+ EIK  +E  G+ +D RH MLVADLMT  GEV  I RHG++  K SVL
Sbjct: 259  VLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVL 318

Query: 1348 NLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
              A+FE T  HL DAA  G+ D ++GV E II+G P+ +GTG + L+
Sbjct: 319  ARAAFEVTVKHLLDAAIRGEVDELAGVIENIIVGQPIPLGTGDVDLV 365

This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein [Transcription, DNA-dependent RNA polymerase]. Length = 367

>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'

 Score =  234 bits (599), Expect = 8e-64
 Identities = 101/273 (36%), Positives = 150/273 (54%), Gaps = 37/273 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
            D D+VLFNRQPSLH++S+M H+ KVLP +TFR N  VC PYNADFDGDEMN+H+PQTEE
Sbjct: 409 IDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEE 468

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAE              A+ LM  + +++TPR G  +I    D+I+G YLLT K+  F 
Sbjct: 469 ARAE--------------ARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFT 514

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           + +   I              I+        P  +      WTGKQIFS  L      P 
Sbjct: 515 KEEVQTILGVAGYFGDPPEPAIE-------KPKEY------WTGKQIFSAFL------PE 555

Query: 520 NANLKTK---GRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
           + N + +     +    +E C  D+YV+++N +LL G +DK  +G+  K  + + ++R++
Sbjct: 556 DLNFEGRAKICSSDACKKEECPHDAYVVIKNGKLLKGVIDKKAIGA-EKGKILHRIVREY 614

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
           G + A   +  ++R+   ++  RGF+ GI D+ 
Sbjct: 615 GPEAARRFLDSVTRLFIRFITLRGFTTGIDDID 647

This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. Length = 867

>gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional

 Score =  217 bits (555), Expect = 7e-61
 Identities = 133/449 (29%), Positives = 206/449 (45%), Gaps = 94/449 (20%)

Query: 1003 ELKRLLDDIIAKNSSRSDPSLSAQEILALS--NETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            E KRL   I+ +N S S   L   E       N   D  + + D  +   R     +EE 
Sbjct: 90   EFKRLFGRILDENMSFSTGELLTAEEKEYYEENSNEDVLKVIDDVKKLGFRLPPSVIEEI 149

Query: 1061 SKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATA 1120
            +K        D   + +  +I                         RE+Y RA+++P  A
Sbjct: 150  AKAMKKKELSDDEYEEILRRI-------------------------REEYERARVDPYEA 184

Query: 1121 VGALAAQSIGEPGTQMTLKTFHFAG----------------------------------- 1145
            VG +AAQSIGEPGTQMT++TFH+AG                                   
Sbjct: 185  VGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARKKPSTPTMTIYLKKD 244

Query: 1146 ---------EVCEYIEEVFVPD---------DSFILIKLDMDRIRLLHLEVDIDSIRYCI 1187
                     EV + IE   + D         +  ++++LD ++++   +E D   I   I
Sbjct: 245  YREDEEKVREVAKKIENTTLIDVADIITDIAEMSVVVELDEEKMKERLIEYD--DILAAI 302

Query: 1188 ERTRGISGHLTVSGHSFLIL--KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHE 1245
             +        TV     +I     + S K    K+Y + + + S+ IKG++GI RA+  +
Sbjct: 303  SKLTFK----TVEIDDGIIRLKPQQPSFK----KLYLLAEKVKSLTIKGIKGIKRAIARK 354

Query: 1246 EDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 1305
            E+ E   ++ +  +G NL+DV+    V   +  +N+  E+   LGIEAAR+ I+ E K  
Sbjct: 355  ENDE--RRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRT 412

Query: 1306 MENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFY 1365
            ++  G+++D RH MLVAD+MT  G V  I RHG++  K SVL  A+FE T  HL  A   
Sbjct: 413  LQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEITGKHLLRAGIL 472

Query: 1366 GQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            G+ D ++GV+E II+G P+ +GTG + L+
Sbjct: 473  GEVDKLAGVAENIIVGQPITLGTGAVSLV 501

Length = 509

>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional

 Score =  211 bits (539), Expect = 2e-55
 Identities = 106/270 (39%), Positives = 154/270 (57%), Gaps = 29/270 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLHKLSI+AHR KVLP  TFR +  VC PYNADFDGDEMN+H+PQ E+A
Sbjct: 430 DGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDA 489

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A  LM  K NL++PR G  +I A QDFIT  YL+T+ +A F++
Sbjct: 490 RAE--------------AIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDK 535

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   IA         + GI          P +  +    WTGKQ+FSL L  + +    
Sbjct: 536 NEASNIAM--------LAGITDPLP----EPAIKTKDGPAWTGKQLFSLFLPKDFNFEGI 583

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSG--GKANVFYILLRDFGE 578
           A   + G+A  A +  C  D YV+++  EL++G +D + +G+      ++   + +D+GE
Sbjct: 584 AKW-SAGKAGEAKDPSCLGDGYVLIKEGELISGVIDDNIIGALVEEPESLIDRIAKDYGE 642

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            VA+  + ++  +    +++ GFS G GD+
Sbjct: 643 AVAIEFLNKILIIAKKEILHYGFSNGPGDL 672

Length = 1321

>gnl|CDD|218370 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain 1

 Score =  192 bits (490), Expect = 3e-54
 Identities = 89/258 (34%), Positives = 128/258 (49%), Gaps = 24/258 (9%)

Query: 89  KEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHF 148
             + +++ S  ++     Y     + P P GLLD RMGT +K++ C TCG  +++C GHF
Sbjct: 13  SPEEIRKWSVGEVTKPETYNYGSLK-PEPGGLLDERMGTIKKKSICETCGVEVTECPGHF 71

Query: 149 GYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKS 208
           G+I+L  PVFHIG+F+ +++IL+ +CK   C+ +LL E     F   + +P       K 
Sbjct: 72  GHIELAKPVFHIGFFKKILSILRCVCKL--CSSLLLNESVKYFFLKVVIDP--KGKNSKK 127

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKD---AIVEDLLAEYN 265
             KKI    KK S+C  CGE NG +K          K       KD   AI   L     
Sbjct: 128 RLKKINNLCKKKSICSKCGEDNGGLKAFEGCGKYQPKI-----SKDGAEAIKALLK---- 178

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
                  E++   +      LNP +VLQ+F+ I  ED  +L  N   ++P  +ILT L V
Sbjct: 179 --NIEIEELKEKLR-----KLNPEKVLQIFKKISKEDEEILGFNPSGNRPEWMILTVLPV 231

Query: 326 PPNCIRPSVISDLKSDND 343
           PP CIRPSV  D     +
Sbjct: 232 PPPCIRPSVQLDGGRFAE 249

RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand. Length = 330

>gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5

 Score =  192 bits (491), Expect = 5e-53
 Identities = 92/308 (29%), Positives = 127/308 (41%), Gaps = 61/308 (19%)

Query: 1101 CKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------- 1145
            C     R+KY R+ +EP  AVG +AAQSIGEPGTQMTL TFHFAG               
Sbjct: 138  CFLCYGRDKYRRSLVEPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKE 197

Query: 1146 --------------------------------EVCEYIEEVFVP-------DDSFILIKL 1166
                                            E    +    V        DD      +
Sbjct: 198  IINVAKNNKKPVITVLLIKNIVSDKARVKKQREEKTLLLLKKVTIIIVIYYDDDSESTVI 257

Query: 1167 DMDRIRLLHLEVDIDSI---RYCIERTRGISGHLTVSGHSFLILKPKDSSK--SFNSKMY 1221
              DRI +L   V  + +           G         ++  + K +   +         
Sbjct: 258  KKDRIWVLAYFVIPEEVAEEVALAIIIIGKRKSRKRKKNNLGVAKDEKGLEEEELLLLNK 317

Query: 1222 QMKQLLPSVVIKGVQGINRAVI-HEEDVEGVTKYKLLVEGDNLRDVMATYGV-KGVKCSS 1279
             +  +    V  GV   +  V  H    +   ++ L  EG+NL+ VM   GV    K  S
Sbjct: 318  ILLVIPGIKVKYGVILTDGRVDPHTILEKLGKEWLLKTEGNNLQAVMRLQGVIDNDKTYS 377

Query: 1280 NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
            N+  E+ K LGIEAAR +I+ EI+ V +  G+ ++ RH  L+ADLMT KGE+LGITR GL
Sbjct: 378  NDIREMLKKLGIEAARDSILLEIRNVFKFDGIYVNRRHLALLADLMTFKGELLGITRAGL 437

Query: 1340 AKMKESVL 1347
             + K S +
Sbjct: 438  NREKSSFI 445

RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound. Length = 447

>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus

 Score =  181 bits (462), Expect = 7e-51
 Identities = 56/109 (51%), Positives = 74/109 (67%), Gaps = 14/109 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQP+LH++SI AHR +VL  +T R N  VC+PYNADFDGDEMN+H+PQ+ EA
Sbjct: 201 DGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEA 260

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGY 449
           RAE              A+ LM   +N+++P+NG+ +I   QD + G Y
Sbjct: 261 RAE--------------ARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295

Length = 295

>gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain

 Score =  180 bits (458), Expect = 3e-50
 Identities = 104/318 (32%), Positives = 148/318 (46%), Gaps = 41/318 (12%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
            KY+R+ +EP  AVG LAAQSIGEP TQMTL TFHFAG                       
Sbjct: 1    KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKN 60

Query: 1146 ------EVCEYIEEVFVPDDSFILIKLDMDRIRLLHL--EVDIDSIRYCIERTRGISGHL 1197
                   +   ++     + +  L K  + R+ L  +  +V++  I   IER        
Sbjct: 61   IKTPSMTL--PLKNGKSAERAETLKK-RLSRVTLSDVVEKVEVTEILKTIERVFKKLLGK 117

Query: 1198 TVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLL 1257
                    I  P  S K     +  +++L    VI+ + GI R  + EED  G TKY ++
Sbjct: 118  WCE---VTIKLPLSSPK--LLLLSIVEKLARKAVIREIPGITRCFVVEEDKGGKTKYLVI 172

Query: 1258 VEGDNLRDVMATYGVKGV-KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 1316
             EG NL  +     +  V +  +N+ + +  T GIEAAR  I+ EI  V + +G+++D R
Sbjct: 173  TEGVNLAALWKFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPR 232

Query: 1317 HPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSE 1376
            H  L+AD MT +G      R G+     S L   SFE T   L  A   G  D +S  S 
Sbjct: 233  HLSLIADYMTFEGGYRPFNRIGMES-STSPLQKMSFETTLAFLKKATLNGDIDNLSSPSS 291

Query: 1377 CIIMGLPMNVGTGLIKLL 1394
             +++G P+N GTGL  LL
Sbjct: 292  RLVVGKPVNGGTGLFDLL 309

RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. Length = 309

>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]

 Score =  191 bits (487), Expect = 6e-50
 Identities = 80/274 (29%), Positives = 113/274 (41%), Gaps = 41/274 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPH-RTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           D D VL NR P+LH+LSIM     VLP  +  R +  VC  YNADFDGDEM VH+P + E
Sbjct: 360 DGDPVLLNRAPTLHRLSIMQAFEPVLPEGKAIRLHPLVCEAYNADFDGDEMAVHVPASGE 419

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A AE              A+ LM  + N++TP  G  ++A  QD + G YLLT  +A   
Sbjct: 420 AAAE--------------ARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLP 465

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                 I         D     +             +   + TGK I S I     +  +
Sbjct: 466 STPVGEIYL------KDEYADDREK------AEAIAKKIELTTGKVIVSTISPDLAELSI 513

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
                 +        E    D  V + N +L+ G +DK              + R++G +
Sbjct: 514 IVTTDGRRIFNRGLPEDK--DVLVKIVNGKLIKGVIDKKI----------VTIYREYGPE 561

Query: 580 VAVTA-MWRLSRMTSFYLMNRG-FSIGIGDVTPG 611
           VA  A +  L ++ +  +   G F IGIG     
Sbjct: 562 VASKALVKLLDKLKNLGIKGIGGFGIGIGRKDIE 595

Length = 808

>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A''; Validated

 Score =  169 bits (430), Expect = 1e-45
 Identities = 82/234 (35%), Positives = 139/234 (59%), Gaps = 16/234 (6%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP++T YL  +   D + A  V  ++E TTL  + + I      
Sbjct: 95  GLPRLIEIVDARKEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDIS--VDL 152

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            +  I+I+LD +   L    + +D ++  IE+ +G  G + + G++ LI+ PK+ S    
Sbjct: 153 ANMTIIIELDEEM--LEDRGLTVDDVKEAIEKKKG--GEVEIEGNT-LIISPKEPSYR-- 205

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
            ++ ++ + + ++ IKG++GI R +I +E  E    Y +  EG NL++V+   GV   + 
Sbjct: 206 -ELRKLAEKIRNIKIKGIKGIKRVIIRKEGDE----YVIYTEGSNLKEVLKVEGVDATRT 260

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           ++NN +E+ + LGIEAAR+ I+ EIK  +E  G+ +D RH MLVAD+MT  GEV
Sbjct: 261 TTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEV 314

Length = 383

>gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP)

 Score =  168 bits (427), Expect = 2e-45
 Identities = 76/234 (32%), Positives = 128/234 (54%), Gaps = 14/234 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP +T YL+++   D + A  V  ++E TTL  + E I      
Sbjct: 76  GLPRLIEIVDARKEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDIS--IDL 133

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            +  I I+LD + +    + VD   +   IE+ +             ++   + S K   
Sbjct: 134 FNMRITIELDEEMLEDRGITVD--DVLKAIEKLKKGKVGEEGDVTLIVLKAEEPSIK--- 188

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
            ++ ++ + + +  IKG++GI R ++ +E+ E    Y +  EG NL+ V+   GV   + 
Sbjct: 189 -ELRKLAEKILNTKIKGIKGIKRVIVRKEEDE----YVIYTEGSNLKAVLKVEGVDPTRT 243

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           ++NN +E+ + LGIEAAR+ I+ EIK  +E  G+ +D RH MLVAD+MT  GEV
Sbjct: 244 TTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEV 297

Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. Length = 363

>gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5

 Score =  169 bits (431), Expect = 3e-45
 Identities = 78/241 (32%), Positives = 113/241 (46%), Gaps = 7/241 (2%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPR+KEIIN ++N   P+IT  L K+   D AR+ K R E+T L      I  V   DD
Sbjct: 191 GVPRLKEIINVAKNNKKPVITVLLIKNIVSDKARVKKQREEKTLLLLKKVTIIIVIYYDD 250

Query: 824 SFILIKLDMDRIRLLHLEVDIDSI---RYCIERTRGISGHLTVSGHSFLILKPKDSSK-- 878
                 +  DRI +L   V  + +           G         ++  + K +   +  
Sbjct: 251 DSESTVIKKDRIWVLAYFVIPEEVAEEVALAIIIIGKRKSRKRKKNNLGVAKDEKGLEEE 310

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVI-HEEDVEGVTKYKLLVEGDNLRDVMATYGV- 936
                   +  +    V  GV   +  V  H    +   ++ L  EG+NL+ VM   GV 
Sbjct: 311 ELLLLNKILLVIPGIKVKYGVILTDGRVDPHTILEKLGKEWLLKTEGNNLQAVMRLQGVI 370

Query: 937 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
              K  SN+  E+ K LGIEAAR +I+ EI+ V +  G+ ++ RH  L+ADLMT KGE+L
Sbjct: 371 DNDKTYSNDIREMLKKLGIEAARDSILLEIRNVFKFDGIYVNRRHLALLADLMTFKGELL 430

Query: 997 G 997
           G
Sbjct: 431 G 431

RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound. Length = 447

>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A''; Provisional

 Score =  173 bits (441), Expect = 4e-44
 Identities = 90/233 (38%), Positives = 138/233 (59%), Gaps = 12/233 (5%)

Query: 1164 IKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQM 1223
            IK+++D   L    + I+S+   IE+  G+         + L LKPK  S         +
Sbjct: 623  IKVELDEETLADRGLTIESVEEAIEKKLGVK---IDRKGTVLYLKPKTPS------YKAL 673

Query: 1224 KQLLP---SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSN 1280
            ++ +P   ++V+KG+ GI R ++ +E+ E   +Y L  +G NLR+V    GV   + ++N
Sbjct: 674  RKRIPKIKNIVLKGIPGIERVLVKKEEHENDEEYVLYTQGSNLREVFKIEGVDTSRTTTN 733

Query: 1281 NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLA 1340
            N  E+ + LGIEAAR+ I+ E+   +E  G+ +D RH MLVAD+MT+ GEV  I RHG+A
Sbjct: 734  NIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGVA 793

Query: 1341 KMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
              K SVL  A+FE T  HL+DAA +G+ D + GV E +I+G P+ +GTG + L
Sbjct: 794  GEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDL 846

Length = 858

>gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase (RNAP), C-terminal domain

 Score =  151 bits (383), Expect = 4e-42
 Identities = 54/110 (49%), Positives = 73/110 (66%)

Query: 1281 NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLA 1340
            + +E+ + LGIEAAR TI+ EI+ V+ + G+S+D RH  L+AD+MT  G + G+TR G  
Sbjct: 49   SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFR 108

Query: 1341 KMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGL 1390
              K S L  ASFE T+ HL DAA  G+ D + GVSE II+G P  +GTG 
Sbjct: 109  ASKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158

RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria. Length = 158

>gnl|CDD|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3

 Score =  149 bits (379), Expect = 1e-41
 Identities = 57/182 (31%), Positives = 94/182 (51%), Gaps = 24/182 (13%)

Query: 427 NLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSW 486
           N+++P+NG+ +I  +QD + G YLLT+++ FF+R + M++    I               
Sbjct: 1   NILSPQNGKPIIGPSQDMVLGLYLLTRRDTFFDREEVMQLLMYGIVL------------- 47

Query: 487 RSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILR 546
              +P +      +WTGKQ FS +L          N   KG+  T  E  C  DSYV++ 
Sbjct: 48  --PHPAILKPIKPLWTGKQTFSRLLPN------EINP--KGKPKTNEETLCENDSYVLIN 97

Query: 547 NSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIG 606
           N EL++G +DK   G     ++ +I+ +++G +  V  + RL ++   YL   GFSIGI 
Sbjct: 98  NGELISGVIDKKLGG-KSLGSLIHIIYKEYGPEETVKFLDRLQKLGFRYLTKSGFSIGID 156

Query: 607 DV 608
           D+
Sbjct: 157 DI 158

RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking. Length = 158

>gnl|CDD|216030 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2

 Score =  149 bits (378), Expect = 2e-41
 Identities = 46/65 (70%), Positives = 55/65 (84%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVL NRQP+LH++SIMAHR +VL  +T R N  VC+PYNADFDGDEMN+H+PQ+EEA
Sbjct: 96  DGDVVLLNRQPTLHRMSIMAHRPRVLEGKTIRLNPSVCSPYNADFDGDEMNLHVPQSEEA 155

Query: 401 RAEAL 405
           RAEA 
Sbjct: 156 RAEAR 160

RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion. Length = 165

>gnl|CDD|233842 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A''

 Score =  155 bits (393), Expect = 6e-41
 Identities = 83/239 (34%), Positives = 139/239 (58%), Gaps = 15/239 (6%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP +T YL+ +   D + A  V  ++E T L +V + I      
Sbjct: 80  GLPRLIEIVDARKTPSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLA- 138

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTR-GISGHLTVSGHSFLILKPKDSSKSF 880
            D  ++I+LD ++++   + VD   +   I++ + G    + + G++  I  PK S K  
Sbjct: 139 -DMTVIIELDEEQLKERGITVD--DVEKAIKKAKLGKVIEIDMDGNTITIKPPKPSLK-- 193

Query: 881 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
             ++ ++K+ + ++ IKG++GI R VI +E  E    Y +  EG NL++V+   GV   +
Sbjct: 194 --ELRKLKEKIKNLHIKGIKGIKRVVIRKEGDE----YVIYTEGSNLKEVLKLEGVDKTR 247

Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
            ++N+ +E+ + LGIEAAR+ I+ EIK  +E  G+ +D RH MLVADLMT  GEV   G
Sbjct: 248 TTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIG 306

This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein [Transcription, DNA-dependent RNA polymerase]. Length = 367

>gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain

 Score =  148 bits (377), Expect = 2e-38
 Identities = 58/165 (35%), Positives = 96/165 (58%)

Query: 1230 VVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTL 1289
             V    +   +  I   + +   ++ L  +G NLR+V++  GV   + +SN+  E+++ L
Sbjct: 244  KVFIREENKKKVDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVL 303

Query: 1290 GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            GIEAAR  ++ E++ V+   G  +++RH  L+ D+MT +G ++ ITRHG+ +     L  
Sbjct: 304  GIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMR 363

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             SFE T D L +AA +G+TD + GVSE I++G    +GTG   LL
Sbjct: 364  CSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGCFDLL 408

RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures. Length = 410

>gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional

 Score =  148 bits (375), Expect = 2e-37
 Identities = 77/236 (32%), Positives = 131/236 (55%), Gaps = 19/236 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP +T YL KD   D +  R V  ++E TTL +V + I ++   
Sbjct: 218 GLPRLIEIVDARKKPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDVADIITDI--- 274

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL--KPKDSSKS 879
            +  ++++LD ++++   +E D   I   I +        TV     +I     + S K 
Sbjct: 275 AEMSVVVELDEEKMKERLIEYD--DILAAISKLTFK----TVEIDDGIIRLKPQQPSFK- 327

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
              K+Y + + + S+ IKG++GI RA+  +E+ E   ++ +  +G NL+DV+    V   
Sbjct: 328 ---KLYLLAEKVKSLTIKGIKGIKRAIARKENDE--RRWVIYTQGSNLKDVLEIDEVDPT 382

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           +  +N+  E+   LGIEAAR+ I+ E K  ++  G+++D RH MLVAD+MT  G V
Sbjct: 383 RTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSV 438

Length = 509

>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated

 Score =  148 bits (375), Expect = 5e-36
 Identities = 72/245 (29%), Positives = 114/245 (46%), Gaps = 38/245 (15%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + +++ S  +I++ + Y  D    PI  GL+D R+G       C TCG    +C GHFG+
Sbjct: 20  EEIRKMSVTKIITADTY--DDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGH 77

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  PV H+G+ + +  +L++ C+   C R+ L EE+   +  KL        +   L 
Sbjct: 78  IELARPVIHVGFAKLIYKLLRATCRE--CGRLKLTEEEIEEYLEKLERLKEWGSLADDLI 135

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           K++ +   K  VCPHCGE           KI  EK                  + E    
Sbjct: 136 KEVKKEAAKRMVCPHCGEK--------QYKIKFEKPTT---------------FYEER-- 170

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
             +    K       L P ++ +  E IP ED+ LL +N E+++P  ++LT L VPP  +
Sbjct: 171 --KEGLVK-------LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTV 221

Query: 331 RPSVI 335
           RPS+ 
Sbjct: 222 RPSIT 226

Length = 882

>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A''; Provisional

 Score =  144 bits (365), Expect = 6e-35
 Identities = 82/237 (34%), Positives = 131/237 (55%), Gaps = 18/237 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STPI+T +L  +  TD + A  V  ++E  TLG+V   I      
Sbjct: 561 GLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSIAIDLWT 620

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
                 IK+++D   L    + I+S+   IE+  G+         + L LKPK  S    
Sbjct: 621 QS----IKVELDEETLADRGLTIESVEEAIEKKLGVK---IDRKGTVLYLKPKTPS---- 669

Query: 882 SKMYQMKQLLP---SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
                +++ +P   ++V+KG+ GI R ++ +E+ E   +Y L  +G NLR+V    GV  
Sbjct: 670 --YKALRKRIPKIKNIVLKGIPGIERVLVKKEEHENDEEYVLYTQGSNLREVFKIEGVDT 727

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            + ++NN  E+ + LGIEAAR+ I+ E+   +E  G+ +D RH MLVAD+MT+ GEV
Sbjct: 728 SRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEV 784

Length = 858

>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'

 Score =  144 bits (365), Expect = 7e-35
 Identities = 77/269 (28%), Positives = 130/269 (48%), Gaps = 49/269 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + +++ S +++V+ + Y  D    PI  GL+D R+G  +    C TCG  + +C GHFG+
Sbjct: 15  EEIRKMSVVEVVTADTY--DDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGH 72

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN-PALSYLVRKSL 209
           I+L  PV H+G+ + +  IL++ C    C R+ L EE+   +  K+         +  +L
Sbjct: 73  IELARPVVHVGFAKEIYKILRATC--RKCGRITLTEEEIEQYLEKINKLKEEGGDLASTL 130

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
            +KI++   K   CPHCGE               E+ K + +K     E+          
Sbjct: 131 IEKIVKEAAKRMKCPHCGE---------------EQKKIKFEKPTYFYEE---------- 165

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
                    K G ++ L P E+ +  E IP ED  LL +N ++++P  ++LT L VPP  
Sbjct: 166 --------GKEGDVK-LTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVT 216

Query: 330 IRPSVI--SDLKSDNDVVLFNRQPSLHKL 356
           +RPS+   +  +S++D+         HKL
Sbjct: 217 VRPSITLETGERSEDDLT--------HKL 237

This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. Length = 867

>gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain

 Score =  134 bits (339), Expect = 2e-33
 Identities = 69/281 (24%), Positives = 122/281 (43%), Gaps = 51/281 (18%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           GVPR+KEIIN ++NI TP +T YL+     D + A+ ++ RLE TTL +V    E  + P
Sbjct: 63  GVPRLKEIINVAKNIKTPSLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDP 122

Query: 822 DD----------------------------SFILIKLDMDRIRLLHLEVDIDSIRYCIER 853
           D                             S  L+++++DR ++   ++ ++ I   I+ 
Sbjct: 123 DPQNTVIEEDKEFVESYFEFPDEDVEQDRLSPWLLRIELDRKKMTDKKLSMEQIAKKIKE 182

Query: 854 TRGISGHLTVS-----------------GHSFLILKPKDSSKSFNSKMYQMKQL----LP 892
                 ++  S                        +     K   S M     L      
Sbjct: 183 EFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEEDSEDDVFLKKIESNMLSDMTLKGIEGI 242

Query: 893 SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT 952
             V    +   +  I   + +   ++ L  +G NLR+V++  GV   + +SN+  E+++ 
Sbjct: 243 RKVFIREENKKKVDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEV 302

Query: 953 LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
           LGIEAAR  ++ E++ V+   G  +++RH  L+ D+MT +G
Sbjct: 303 LGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRG 343

RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures. Length = 410

>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]

 Score =  125 bits (316), Expect = 5e-29
 Identities = 63/226 (27%), Positives = 91/226 (40%), Gaps = 59/226 (26%)

Query: 114 TPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSI 173
            P   GL D R+    K+  CT CG+    C G FG+I+L  PV HI +F+ + ++L   
Sbjct: 35  KPERGGLFDERIFGPDKDYECT-CGKYKRICPGGFGHIELAAPVAHIWFFKSIPSLLDMT 93

Query: 174 CKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKV--SVCPHCGEING 231
           C++  C RVL        F A +       L     K ++L  T+ V  S C HCG    
Sbjct: 94  CRD--CERVLY-------FEAYV------VLGTDLEKIQLLNETEYVYDSFCAHCGAEAI 138

Query: 232 VVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEV 291
            +                         DL  E  E                  TL+P +V
Sbjct: 139 KILLEKP--------------------DLETEREEE-----------------TLSPTKV 161

Query: 292 LQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
            +L + + + D  LL      ++P  +ILT L VPP  +RPS+  D
Sbjct: 162 KKLLKRLKVVDAFLL----SGNRPEWMILTVLPVPPPDLRPSIQLD 203

Length = 808

>gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain

 Score =  117 bits (295), Expect = 2e-28
 Identities = 71/234 (30%), Positives = 106/234 (45%), Gaps = 34/234 (14%)

Query: 764 GVPRIKEII-NASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPD 822
           G+PR++EI+  AS+NI TP +T  L      + A  +K RL R TL +V E +E      
Sbjct: 46  GIPRLREILMTASKNIKTPSMTLPLKNGKSAERAETLKKRLSRVTLSDVVEKVE------ 99

Query: 823 DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS 882
                                +  I   IER                I  P  S K    
Sbjct: 100 ---------------------VTEILKTIERVFKKLLGKWCE---VTIKLPLSSPK--LL 133

Query: 883 KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV-KC 941
            +  +++L    VI+ + GI R  + EED  G TKY ++ EG NL  +     +  V + 
Sbjct: 134 LLSIVEKLARKAVIREIPGITRCFVVEEDKGGKTKYLVITEGVNLAALWKFSDILDVNRI 193

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +N+ + +  T GIEAAR  I+ EI  V + +G+++D RH  L+AD MT +G  
Sbjct: 194 YTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGY 247

RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. Length = 309

>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated

 Score =  120 bits (304), Expect = 2e-27
 Identities = 43/64 (67%), Positives = 56/64 (87%), Gaps = 1/64 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD+    +GFV++S+ SGLTPTEFFFH MGGREGLVDTAV+T+++GYMQRRL+ +L+DL 
Sbjct: 773 GDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLK 832

Query: 665 VQYD 668
           V+YD
Sbjct: 833 VEYD 836

Length = 882

>gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5

 Score =  117 bits (294), Expect = 2e-27
 Identities = 42/47 (89%), Positives = 45/47 (95%)

Query: 622 GLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           GLTP EFFFHTMGGREGL+DTAVKTAETGY+QRRLVK+LEDL VQYD
Sbjct: 1   GLTPQEFFFHTMGGREGLIDTAVKTAETGYLQRRLVKALEDLVVQYD 47

RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound. Length = 447

>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]

 Score =  112 bits (282), Expect = 6e-25
 Identities = 32/58 (55%), Positives = 41/58 (70%)

Query: 613 GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           G  ++SF  GLT  E+F H +GGR GLVDTA+KTA++GY+ RRLV   +DL VQ D  
Sbjct: 713 GPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADSGYLTRRLVDVAQDLIVQEDDC 770

Length = 808

>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional

 Score =  112 bits (281), Expect = 9e-25
 Identities = 59/172 (34%), Positives = 96/172 (55%), Gaps = 6/172 (3%)

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            +KGV  I RA +   + +G  ++ +   G NL  V+    +      +N+ +E+  TLGI
Sbjct: 1146 VKGVPDIERAWVELVEKDGRDEWIIQTSGSNLAAVLEMKCIDIANTITNDCFEIAGTLGI 1205

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI------TRHGLAKMKES 1345
            EAAR+ I  E+  ++E+ G+ +D R+ MLVAD+M S+G +  I       RHG A  K+S
Sbjct: 1206 EAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIGLQAAGVRHGFAGEKDS 1265

Query: 1346 VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 1397
             L  A+FE T+  +  AA  G+ + I G+ + +IMG  + +G+G + LL   
Sbjct: 1266 PLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDF 1317

Length = 1321

>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'

 Score =  110 bits (277), Expect = 3e-24
 Identities = 42/79 (53%), Positives = 57/79 (72%), Gaps = 7/79 (8%)

Query: 597 MNRGFS------IGIGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAET 649
           + RG+          GD+    +GFV++SF  GL PTE+FFH  GGREGLVDTAV+T+++
Sbjct: 752 IRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQS 811

Query: 650 GYMQRRLVKSLEDLCVQYD 668
           GYMQRRL+ +L+DL V+YD
Sbjct: 812 GYMQRRLINALQDLYVEYD 830

This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. Length = 867

>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional

 Score =  108 bits (272), Expect = 1e-23
 Identities = 78/277 (28%), Positives = 125/277 (45%), Gaps = 54/277 (19%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G+I G ++  D  ++    +I +   Y  D    P+  GLLD R+GT +    C TCG  
Sbjct: 11  GIIFGLISPAD-ARKIGFAEITAPEAY--DEDGLPVQGGLLDGRLGTIEPGQKCLTCGNL 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNP 199
            ++C GHFG+I+L  PV HI +   + ++L S C    CA++ L +E    F+  +  + 
Sbjct: 68  AANCPGHFGHIELAEPVIHIAFIDNIKDLLNSTCH--KCAKLKLPQEDLNVFKLIEEAHA 125

Query: 200 ALSYLVRKSLKKKILE--------TTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTK 251
           A   +  K +  +I+E          KK   CPHCG               HE       
Sbjct: 126 AARDIPEKRIDDEIIEEVRDQVKVYAKKAKECPHCG------------APQHE------- 166

Query: 252 KKDAIVEDLLAEYNEAVKF--NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN 309
                      E+ E   F    EIE H+       L P+E+  +FE I  +D+ L+  +
Sbjct: 167 ----------LEFEEPTIFIEKTEIEEHR-------LLPIEIRDIFEKIIDDDLELIGFD 209

Query: 310 AELSKPSDLILTRLLVPPNCIRPSVI--SDLKSDNDV 344
            + ++P   +L   LVPP   RPS+I  +  +S++D+
Sbjct: 210 PKKARPEWAVLQAFLVPPLTARPSIILETGERSEDDL 246

Length = 1321

>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]

 Score =  101 bits (254), Expect = 1e-21
 Identities = 88/408 (21%), Positives = 151/408 (37%), Gaps = 71/408 (17%)

Query: 1047 ENFVRDIKKFLEEFSKKESVTSHQDKVSQP--LREQILSHQDKIG-HGRESNPFPSACKA 1103
            E  + ++   L E    + V  ++     P   R  I+   + +   G+     P  C+A
Sbjct: 345  ERRLPEVWDVLREVIDGDPVLLNR----APTLHRLSIMQAFEPVLPEGKAIRLHPLVCEA 400

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV----------CEYIEE 1153
                            A G  AA++ G  GTQM + T H+ G +             +  
Sbjct: 401  YNADF-DGDEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTI 459

Query: 1154 V--FVPDDSFILIKLDMD-------------RIRLLHLEVDIDSIRYC------------ 1186
            V   +P      I L  +             +I L   +V + +I               
Sbjct: 460  VDAKLPSTPVGEIYLKDEYADDREKAEAIAKKIELTTGKVIVSTISPDLAELSIIVTTDG 519

Query: 1187 -----------------IERTRGISGHL-TVSGHSFLILKPKDSSKSFNSKMYQMKQLLP 1228
                             I   + I G +       +    P+ +SK+    + ++K L  
Sbjct: 520  RRIFNRGLPEDKDVLVKIVNGKLIKGVIDKKIVTIYREYGPEVASKALVKLLDKLKNL-- 577

Query: 1229 SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD--NLRDVMATYGVKGVKCSSNNTYEVY 1286
               IKG+ G    +  ++      K ++++E +   L+ ++        +   NN  E+ 
Sbjct: 578  --GIKGIGGFGIGIGRKDIEAEDEKDEIVIEAEGSVLKLILQYEEGDLTRTERNNIVEII 635

Query: 1287 KTLGIEAARSTIMTEIKLVMENHGMSI-DFRHPMLVADLMTSKGEVLGITRHGLAKMKES 1345
            + LGIEA R+ I+ EIK+ +E  G+   D RH  L    M     V  I + G+   K S
Sbjct: 636  EVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIVQLIGQQGVMGEKIS 695

Query: 1346 VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            VL  A+FE T  HL +A   G++  + G++E    G P+   TGL+  
Sbjct: 696  VLARAAFEVTVKHL-EAEGPGESSFLEGLTENEYFGHPIGGRTGLVDT 742

Length = 808

>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit, predominant form

 Score = 96.7 bits (241), Expect = 5e-20
 Identities = 41/109 (37%), Positives = 63/109 (57%), Gaps = 14/109 (12%)

Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
           VL NR P+LH+L I A    ++  +  R +  VCT +NADFDGD+M VH+P + EA+AE 
Sbjct: 403 VLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAE- 461

Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
                        A+ LM   +N++ P++G+ ++  +QD + G Y LT 
Sbjct: 462 -------------ARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTT 497

Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain [Transcription, DNA-dependent RNA polymerase]. Length = 1140

>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional

 Score = 93.6 bits (232), Expect = 5e-19
 Identities = 57/235 (24%), Positives = 109/235 (46%), Gaps = 10/235 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            G+ R  E+++A    STP +  YLD +   D++ A  +   L+     +V   I +  + 
Sbjct: 1014 GLERFIELVDARAKPSTPTMDIYLDDECKEDIEKAIEIARNLKEL---KVRALIADSAID 1070

Query: 822  DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERT-RGISGHLTVSGHSFLI--LKPKDSSK 878
            + + I +     R       + ++          +G    + +     ++  ++  D  K
Sbjct: 1071 NANEIKLIKPDKRALENGC-IPMERFAEIEAALAKGKKFEMELEDDLIILDLVEAADRDK 1129

Query: 879  SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
               + +    ++L   V KGV  I RA +   + +G  ++ +   G NL  V+    +  
Sbjct: 1130 PLATLIAIRNKILDKPV-KGVPDIERAWVELVEKDGRDEWIIQTSGSNLAAVLEMKCIDI 1188

Query: 939  VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
                +N+ +E+  TLGIEAAR+ I  E+  ++E+ G+ +D R+ MLVAD+M S+G
Sbjct: 1189 ANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRG 1243

Length = 1321

>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional

 Score = 93.4 bits (232), Expect = 7e-19
 Identities = 43/108 (39%), Positives = 62/108 (57%), Gaps = 14/108 (12%)

Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
           VL NR P+LH+L I A    ++  +  + +  VCT +NADFDGD+M VH+P + +A+AE 
Sbjct: 499 VLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAE- 557

Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLT 452
                        A+VLM + +N+ +P +G  L   TQD I G Y LT
Sbjct: 558 -------------ARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLT 592

Length = 1460

>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional

 Score = 91.6 bits (227), Expect = 2e-18
 Identities = 35/64 (54%), Positives = 46/64 (71%), Gaps = 1/64 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD  P   GFV+N++  GL   EFFFH MGGREGL+D A +T ++GY QRRL  +LED+ 
Sbjct: 809 GDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIR 868

Query: 665 VQYD 668
           ++YD
Sbjct: 869 LEYD 872

Length = 1321

>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit

 Score = 89.6 bits (223), Expect = 4e-18
 Identities = 42/111 (37%), Positives = 63/111 (56%), Gaps = 14/111 (12%)

Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
           VL NR P+LH+L I A +  ++  R    +  VC  +NADFDGD+M VH+P + EA+AE 
Sbjct: 450 VLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAE- 508

Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN 455
                        A++LM +  NL++P  G+ +   +QD + G Y+LT  N
Sbjct: 509 -------------ARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGN 546

Length = 663

>gnl|CDD|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma; Provisional

 Score = 89.0 bits (221), Expect = 7e-18
 Identities = 42/111 (37%), Positives = 64/111 (57%), Gaps = 14/111 (12%)

Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
           VL NR P+LH+L I A    ++  R  + +  VC  +NADFDGD+M VH+P + EA+AE 
Sbjct: 429 VLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAE- 487

Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN 455
                        A++LM   +N+++P  GE ++  +QD + G Y LT +N
Sbjct: 488 -------------ARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAEN 525

Length = 627

>gnl|CDD|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma subunit

 Score = 88.9 bits (220), Expect = 7e-18
 Identities = 40/111 (36%), Positives = 62/111 (55%), Gaps = 14/111 (12%)

Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
           V+ NR P+LH+L I A    ++  R  + +  VC  +NADFDGD+M VH+P + EA+ E 
Sbjct: 422 VMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTE- 480

Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN 455
                        A++LM   +N+++P  GE ++  +QD + G Y LT  N
Sbjct: 481 -------------ARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALN 518

The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''. Length = 619

>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional

 Score = 89.0 bits (222), Expect = 1e-17
 Identities = 43/109 (39%), Positives = 66/109 (60%), Gaps = 14/109 (12%)

Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
           VL NR P+LH+L I A    ++  +  + +  VCT +NADFDGD+M VH+P + EA+AE 
Sbjct: 411 VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAE- 469

Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
                        A+VLM + +N+++P NG+ +I  +QD + G Y LT+
Sbjct: 470 -------------ARVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTR 505

Length = 1156

>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional

 Score = 83.1 bits (205), Expect = 9e-16
 Identities = 41/108 (37%), Positives = 63/108 (58%), Gaps = 14/108 (12%)

Query: 345  VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
            VL NR P+LH+L I A    ++  +  + +  VCT +NADFDGD+M VH+P + EA+ E 
Sbjct: 1854 VLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLE- 1912

Query: 405  LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLT 452
                         A+VLM + +N+++P NG  +I  ++D + G Y LT
Sbjct: 1913 -------------ARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLT 1947

Length = 2836

>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed

 Score = 81.9 bits (202), Expect = 2e-15
 Identities = 41/108 (37%), Positives = 62/108 (57%), Gaps = 14/108 (12%)

Query: 345  VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
            VL NR P+LHK SI A   K++  +  + +  VC+ +NADFDGD+M VH+P ++EA AE 
Sbjct: 1810 VLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAE- 1868

Query: 405  LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLT 452
                          KVLM +  N++ P +G+ +   +QD + G Y L+
Sbjct: 1869 -------------CKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLS 1903

Length = 2890

>gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase (RNAP), C-terminal domain

 Score = 72.1 bits (177), Expect = 2e-14
 Identities = 25/53 (47%), Positives = 38/53 (71%)

Query: 945 NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
           + +E+ + LGIEAAR TI+ EI+ V+ + G+S+D RH  L+AD+MT  G + G
Sbjct: 49  SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRG 101

RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria. Length = 158

>gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain

 Score = 74.9 bits (185), Expect = 8e-14
 Identities = 23/37 (62%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++ R+ + P   VG +AAQSIGEP TQMTL TFHFAG
Sbjct: 18   RFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAG 54

RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures. Length = 410

>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit, predominant form

 Score = 66.2 bits (162), Expect = 1e-10
 Identities = 31/75 (41%), Positives = 42/75 (56%), Gaps = 13/75 (17%)

Query: 618 SFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYG 677
           SF  GLT  E+F  T G R+GL DTA+KTA++GY+ RRLV   +D+ V+ +         
Sbjct: 720 SFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREE--------- 770

Query: 678 QTDCISGVSECIIMG 692
             DC  G  E I + 
Sbjct: 771 --DC--GTEEGIEVE 781

Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain [Transcription, DNA-dependent RNA polymerase]. Length = 1140

>gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase (RNAP), C-terminal domain

 Score = 60.5 bits (147), Expect = 2e-10
 Identities = 24/26 (92%), Positives = 25/26 (96%)

Query: 1120 AVGALAAQSIGEPGTQMTLKTFHFAG 1145
            AVG LAAQSIGEPGTQMTL+TFHFAG
Sbjct: 3    AVGVLAAQSIGEPGTQMTLRTFHFAG 28

RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria. Length = 158

>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional

 Score = 64.7 bits (157), Expect = 3e-10
 Identities = 36/106 (33%), Positives = 52/106 (49%), Gaps = 12/106 (11%)

Query: 1048 NFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQI--------LSHQDKIGHGRESNPFPS 1099
            N  R I+K   E   K +    +D++ +  +E              D I           
Sbjct: 904  NLERIIEKQKIEDRGKGAS---KDEIEELAKEYTKTFNANLPKLLADAIHGAELKEDELE 960

Query: 1100 ACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A  AE  +E + +A++EP  A+G ++AQSI EPGTQMTL+TFH AG
Sbjct: 961  AICAEG-KEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAG 1005

Length = 1321

>gnl|CDD|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3

 Score = 59.9 bits (146), Expect = 3e-10
 Identities = 17/45 (37%), Positives = 32/45 (71%)

Query: 28 NLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
          N+++P+NG+ +I  +QD + G YLLT+++ FF+R + M++    I
Sbjct: 1  NILSPQNGKPIIGPSQDMVLGLYLLTRRDTFFDREEVMQLLMYGI 45

RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking. Length = 158

>gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain

 Score = 59.9 bits (146), Expect = 2e-09
 Identities = 21/32 (65%), Positives = 25/32 (78%)

Query: 671 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLI 702
           F+AA +G+ D I GVSECIIMG PM +GTGL 
Sbjct: 269 FNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300

Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. Length = 300

>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed

 Score = 62.3 bits (152), Expect = 2e-09
 Identities = 21/36 (58%), Positives = 25/36 (69%), Gaps = 4/36 (11%)

Query: 1120 AVGALAAQSIGEPGTQMTLKTFH----FAGEVCEYI 1151
            AVG +A QSIGEPGTQ+TL+TFH    F G   E +
Sbjct: 317  AVGIIAGQSIGEPGTQLTLRTFHTGGVFTGGTAEQV 352

Length = 1364

>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]

 Score = 61.1 bits (149), Expect = 3e-09
 Identities = 59/238 (24%), Positives = 103/238 (43%), Gaps = 16/238 (6%)

Query: 761 SQD--GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIE 816
            QD  G P +  I++A +  STP+   YL  +   D + A  +  ++E TT   +   I 
Sbjct: 447 IQDTVGGPYLLTIVDA-KLPSTPVGEIYLKDEYADDREKAEAIAKKIELTTGKVIVSTIS 505

Query: 817 EVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHL-TVSGHSFLILKPKD 875
                 +  I++  D  RI    L  D D +   I   + I G +       +    P+ 
Sbjct: 506 PD--LAELSIIVTTDGRRIFNRGLPEDKDVLVK-IVNGKLIKGVIDKKIVTIYREYGPEV 562

Query: 876 SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD--NLRDVMAT 933
           +SK+    + ++K L     IKG+ G    +  ++      K ++++E +   L+ ++  
Sbjct: 563 ASKALVKLLDKLKNL----GIKGIGGFGIGIGRKDIEAEDEKDEIVIEAEGSVLKLILQY 618

Query: 934 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI-DFRHPMLVADLMT 990
                 +   NN  E+ + LGIEA R+ I+ EIK+ +E  G+   D RH  L    M 
Sbjct: 619 EEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMN 676

Length = 808

>gnl|CDD|132721 cd02655, RNAP_beta'_C, Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain

 Score = 57.9 bits (141), Expect = 3e-09
 Identities = 20/31 (64%), Positives = 25/31 (80%)

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +E   AVG +AAQSIGEPGTQ+T++TFH  G
Sbjct: 3    VELGEAVGIIAAQSIGEPGTQLTMRTFHTGG 33

Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations. Length = 204

>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional

 Score = 58.0 bits (140), Expect = 4e-08
 Identities = 24/52 (46%), Positives = 38/52 (73%)

Query: 615 VQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
           ++ +F  GL+  E+F  T G R+GLVDTA++TA++GY+ RRLV   +D+ V+
Sbjct: 825 IKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQDVIVR 876

Length = 1460

>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional

 Score = 57.8 bits (141), Expect = 5e-08
 Identities = 23/40 (57%), Positives = 30/40 (75%)

Query: 618 SFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLV 657
           +F  GLT  E+F  T G R+GL DTA+KTA++GY+ RRLV
Sbjct: 729 NFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLV 768

Length = 1156

>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed

 Score = 57.6 bits (139), Expect = 5e-08
 Identities = 29/74 (39%), Positives = 37/74 (50%), Gaps = 9/74 (12%)

Query: 1098 PSACKAE--ACREKY-----VRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEY 1150
            P  CKA    C + Y           P  AVG +AAQSIGEPGTQ+TL+TFH  G     
Sbjct: 2250 PVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRS 2309

Query: 1151 IEE--VFVPDDSFI 1162
             +E  +    + F+
Sbjct: 2310 QDEREIVASKEGFV 2323

Length = 2890

>gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit

 Score = 57.6 bits (139), Expect = 5e-08
 Identities = 32/90 (35%), Positives = 49/90 (54%), Gaps = 14/90 (15%)

Query: 615 VQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA 674
           ++ +F  GLT TE+   + G R+GLVDTA++TA++GY+ RRLV   +D+ V+        
Sbjct: 158 IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVR-------- 209

Query: 675 FYGQTDCISGVSECIIMGLPMNVGTGLIKL 704
              + DC  G    I++   M  G   I L
Sbjct: 210 ---EEDC--GTERSIVVR-AMTEGDKKISL 233

The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria [Transcription, DNA-dependent RNA polymerase]. Length = 1227

>gnl|CDD|132724 cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain

 Score = 56.7 bits (137), Expect = 5e-08
 Identities = 34/115 (29%), Positives = 52/115 (45%), Gaps = 7/115 (6%)

Query: 1281 NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLA 1340
            +  ++   LGI+AA    +  ++  +   G S+   H +LVAD MT  GE +G+   G  
Sbjct: 261  SIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYK 320

Query: 1341 KMKESVLNL------ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
              + S L +      A F +       AA  G +D +SGV +    G    VGTG
Sbjct: 321  AQRRS-LKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTG 374

Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena. Length = 381

>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated

 Score = 57.2 bits (139), Expect = 6e-08
 Identities = 16/47 (34%), Positives = 30/47 (63%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           +LM  + ++++PR G  +I   QD I+G YLLT+K+  F + + + +
Sbjct: 479 ILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDL 525

Length = 882

>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional

 Score = 57.4 bits (140), Expect = 6e-08
 Identities = 18/28 (64%), Positives = 23/28 (82%)

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFH 1142
            +    AVG +AAQSIGEPGTQ+T++TFH
Sbjct: 876  VNIGEAVGVIAAQSIGEPGTQLTMRTFH 903

Length = 1156

>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta'; Provisional

 Score = 56.9 bits (138), Expect = 8e-08
 Identities = 23/40 (57%), Positives = 28/40 (70%), Gaps = 4/40 (10%)

Query: 1120 AVGALAAQSIGEPGTQMTLKTFH----FAGEVCEYIEEVF 1155
            AVG +AAQSIGEPGTQ+T++TFH    F GEV   +   F
Sbjct: 313  AVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSPF 352

Length = 1331

>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit, predominant form

 Score = 55.8 bits (135), Expect = 2e-07
 Identities = 20/31 (64%), Positives = 25/31 (80%)

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +E   AVG +AAQSIGEPGTQ+T++TFH  G
Sbjct: 868  VEIGEAVGVIAAQSIGEPGTQLTMRTFHTGG 898

Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain [Transcription, DNA-dependent RNA polymerase]. Length = 1140

>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta'; Provisional

 Score = 55.8 bits (135), Expect = 2e-07
 Identities = 24/47 (51%), Positives = 34/47 (72%)

Query: 619 FFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           F  GLT TE+   + G R+GLVDTA++TA++GY+ RRLV   +D+ V
Sbjct: 163 FREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIV 209

Length = 1331

>gnl|CDD|132721 cd02655, RNAP_beta'_C, Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain

 Score = 52.1 bits (126), Expect = 3e-07
 Identities = 41/145 (28%), Positives = 65/145 (44%), Gaps = 42/145 (28%)

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK-------------GE-- 1330
             K LG EA +  ++ EI+ V  + G++I+ +H  ++   MTSK             GE  
Sbjct: 62   IKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELV 121

Query: 1331 -------------------------VLGITRHGLAKMKESVLNLASFENTSDHLFDAAFY 1365
                                     +LGIT+  L    ES ++ ASF+ T+  L +AA  
Sbjct: 122  DLNEFEEENKRLLLLGKKPAKYEPVLLGITKASLNT--ESFISAASFQETTKVLTEAAIE 179

Query: 1366 GQTDCISGVSECIIMGLPMNVGTGL 1390
            G+ D + G+ E +I+G  +  GTGL
Sbjct: 180  GKIDWLRGLKENVILGRLIPAGTGL 204

Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations. Length = 204

>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional

 Score = 53.7 bits (129), Expect = 8e-07
 Identities = 26/52 (50%), Positives = 33/52 (63%), Gaps = 7/52 (13%)

Query: 1101 CKAE--ACREKY-----VRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C AE   C++ Y      R  +   TAVG +AAQSIGEPGTQ+T++TFH  G
Sbjct: 950  CHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGG 1001

Length = 1460

>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional

 Score = 53.5 bits (128), Expect = 1e-06
 Identities = 63/253 (24%), Positives = 109/253 (43%), Gaps = 66/253 (26%)

Query: 1189 RTRGISGHLTVSGHSFLILKPK--------DSSKSFNSKMYQMKQLLPSVVIKGVQGINR 1240
            +TR I+G L      F   +PK        D   +F+ K  + K+   S++IK V   + 
Sbjct: 2549 KTRDITGGLPRVIELFEARRPKEHAIVSEIDGYVAFSEKDRRGKR---SILIKPV---DE 2602

Query: 1241 AVIHEEDVEGVTKYKLLVEGDNLR--DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTI 1298
             +   E +   +K+ ++ EGD +R  D++             + +++ + LG+EA    +
Sbjct: 2603 QISPVEYLVSRSKHVIVNEGDFVRKGDLLMD--------GDPDLHDILRVLGLEALAHYM 2654

Query: 1299 MTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL-------------------------- 1332
            ++EI+ V    G+ ID +H  ++   M  K E+                           
Sbjct: 2655 ISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDRENDAMS 2714

Query: 1333 --------------GITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECI 1378
                          GITR  L     S ++ ASF+ T+  L +AAF G++D +SG+ E +
Sbjct: 2715 NSGKRPAHYLPILQGITRASLET--SSFISAASFQETTKVLTEAAFCGKSDPLSGLKENV 2772

Query: 1379 IMGLPMNVGTGLI 1391
            I+G  +  GTGLI
Sbjct: 2773 IVGRLIPAGTGLI 2785

Length = 2836

>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed

 Score = 52.2 bits (126), Expect = 2e-06
 Identities = 22/42 (52%), Positives = 31/42 (73%)

Query: 616 QNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLV 657
           Q++F  GL+ TE+     G R+G+VDTAV+TA+ GY+ RRLV
Sbjct: 166 QSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLV 207

Length = 1364

>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]

 Score = 51.9 bits (125), Expect = 3e-06
 Identities = 16/47 (34%), Positives = 23/47 (48%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
            LM  + N++TP  G  ++A  QD + G YLLT  +A         I
Sbjct: 426 GLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLPSTPVGEI 472

Length = 808

>gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit

 Score = 51.8 bits (124), Expect = 3e-06
 Identities = 28/61 (45%), Positives = 37/61 (60%), Gaps = 11/61 (18%)

Query: 1098 PSACKA--EACREKYVRA-----QIEPATAVGALAAQSIGEPGTQMTLKTFH----FAGE 1146
            P  C+A    CR+ Y  +      ++   AVG +AAQSIGEPGTQ+T++TFH    F GE
Sbjct: 282  PLTCEAARSVCRKCYGWSLAHAHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGE 341

Query: 1147 V 1147
            V
Sbjct: 342  V 342

The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria [Transcription, DNA-dependent RNA polymerase]. Length = 1227

>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional

 Score = 51.2 bits (122), Expect = 5e-06
 Identities = 22/48 (45%), Positives = 31/48 (64%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM  K NL++PR G  +I A QDFIT  YL+T+ +A F++ +   IA 
Sbjct: 496 LMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAM 543

Length = 1321

>gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase (RNAP), C-terminal domain

 Score = 47.0 bits (112), Expect = 9e-06
 Identities = 16/31 (51%), Positives = 20/31 (64%)

Query: 671 FDAAFYGQTDCISGVSECIIMGLPMNVGTGL 701
            DAA  G+ D + GVSE II+G P  +GTG 
Sbjct: 128 LDAAAAGEKDELEGVSENIILGRPAPLGTGS 158

RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria. Length = 158

>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A''; Provisional

 Score = 49.1 bits (117), Expect = 2e-05
 Identities = 23/60 (38%), Positives = 31/60 (51%), Gaps = 10/60 (16%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFI 1162
             +     Y+ A +EP  AVG +AAQSIGEPGTQM+L           Y E++ V +    
Sbjct: 42   IDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSLP----------YDEKIIVKEGGET 91

Length = 858

>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional

 Score = 48.1 bits (114), Expect = 4e-05
 Identities = 22/41 (53%), Positives = 29/41 (70%)

Query: 617  NSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLV 657
            ++F  GL   E+F  T G R+GL DTA+KTA +GY+ RRLV
Sbjct: 2182 SNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLV 2222

Length = 2836

>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional

 Score = 48.1 bits (114), Expect = 5e-05
 Identities = 22/55 (40%), Positives = 31/55 (56%)

Query: 1098 PSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIE 1152
            P  C     R+      +    AVG +AAQS+GEPGTQ+T++TFH  G +   +E
Sbjct: 2313 PGVCSLCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRGVE 2367

Length = 2836

>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'

 Score = 47.0 bits (112), Expect = 7e-05
 Identities = 17/46 (36%), Positives = 27/46 (58%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM  + +++TPR G  +I    D+I+G YLLT K+  F + +   I
Sbjct: 476 LMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTI 521

This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. Length = 867

>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed

 Score = 46.8 bits (111), Expect = 9e-05
 Identities = 20/41 (48%), Positives = 28/41 (68%)

Query: 617  NSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLV 657
            ++F  GL   E+F  T G R+GL DTA+KTA  GY+ R+L+
Sbjct: 2126 SNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLI 2166

Length = 2890

>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional

 Score = 46.4 bits (110), Expect = 1e-04
 Identities = 27/60 (45%), Positives = 40/60 (66%), Gaps = 2/60 (3%)

Query: 1331 VLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGL 1390
            +LGIT+  LA   +S L+ ASF+ T+  L DAA  G+ D ++G+ E +I+G P+  GTGL
Sbjct: 1179 LLGITKASLAT--DSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTGL 1236

Length = 1460

>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit, predominant form

 Score = 45.0 bits (107), Expect = 3e-04
 Identities = 38/148 (25%), Positives = 64/148 (43%), Gaps = 42/148 (28%)

Query: 1283 YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK-------------G 1329
            +++ +  GI+A +  ++ E++ V    G+ I+ +H  ++   M  K             G
Sbjct: 990  HDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPG 1049

Query: 1330 E---------------------------VLGITRHGLAKMKESVLNLASFENTSDHLFDA 1362
            E                           +LGIT+  L    ES L+ ASF+ T+  L DA
Sbjct: 1050 ELIDIHEFNEENRKLLEQGKKPASAIPQLLGITKASLNT--ESFLSAASFQETTKVLTDA 1107

Query: 1363 AFYGQTDCISGVSECIIMGLPMNVGTGL 1390
            A  G+ D + G+ E +I+G  +  GTGL
Sbjct: 1108 AIKGKVDYLLGLKENVIIGNLIPAGTGL 1135

Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain [Transcription, DNA-dependent RNA polymerase]. Length = 1140

>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus

 Score = 42.1 bits (100), Expect = 0.001
 Identities = 11/30 (36%), Positives = 19/30 (63%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGY 50
            LM   +N+++P+NG+ +I   QD + G Y
Sbjct: 266 ELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295

Length = 295

>gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain

 Score = 41.4 bits (98), Expect = 0.003
 Identities = 16/35 (45%), Positives = 23/35 (65%)

Query: 671 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 705
            +AA +G+TD + GVSE I++G    +GTG   LL
Sbjct: 374 LEAAAFGETDDLKGVSENIMLGQLAPIGTGCFDLL 408

RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures. Length = 410

>gnl|CDD|216030 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2

 Score = 39.5 bits (93), Expect = 0.004
 Identities = 11/16 (68%), Positives = 15/16 (93%)

Query: 406 PSLHKLSIMAHRAKVL 421
           P+LH++SIMAHR +VL
Sbjct: 106 PTLHRMSIMAHRPRVL 121

RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion. Length = 165

>gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit

 Score = 41.4 bits (97), Expect = 0.004
 Identities = 33/140 (23%), Positives = 61/140 (43%), Gaps = 42/140 (30%)

Query: 1290 GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK-------------GEV----- 1331
             ++  +  ++ E++ V ++ G+ I  +H  ++   MTSK             GE+     
Sbjct: 1084 SLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQ 1143

Query: 1332 ----------------------LGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTD 1369
                                  LGIT+  L    +S ++ ASF+ T+  L +AA  G++D
Sbjct: 1144 VEQVNEAMAITGGAPAQYTPVLLGITKASLNT--DSFISAASFQETTRVLTEAAIEGKSD 1201

Query: 1370 CISGVSECIIMGLPMNVGTG 1389
             + G+ E +I+G  +  GTG
Sbjct: 1202 WLRGLKENVIIGRLIPAGTG 1221

The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria [Transcription, DNA-dependent RNA polymerase]. Length = 1227

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	1423
KOG0261|consensus	1386		100.0
PRK14977	1321	bifunctional DNA-directed RNA polymerase A'/A'' su	100.0
KOG0262|consensus	1640		100.0
KOG0260|consensus	1605		100.0
TIGR02390	868	RNA_pol_rpoA1 DNA-directed RNA polymerase subunit	100.0
PRK08566	882	DNA-directed RNA polymerase subunit A'; Validated	100.0
TIGR02386	1140	rpoC_TIGR DNA-directed RNA polymerase, beta' subun	100.0
PRK00566	1156	DNA-directed RNA polymerase subunit beta'; Provisi	100.0
PRK14906	1460	DNA-directed RNA polymerase subunit beta'/alpha do	100.0
PRK14844	2836	bifunctional DNA-directed RNA polymerase subunit b	100.0
PRK09603	2890	bifunctional DNA-directed RNA polymerase subunit b	100.0
KOG0261|consensus	1386		100.0
COG0086	808	RpoC DNA-directed RNA polymerase, beta' subunit/16	100.0
KOG0260|consensus	1605		100.0
TIGR02389	367	RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit	100.0
cd02584	410	RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryoti	100.0
PRK14897	509	unknown domain/DNA-directed RNA polymerase subunit	100.0
cd06528	363	RNAP_A'' A'' subunit of Archaeal RNA Polymerase (R	100.0
PRK04309	383	DNA-directed RNA polymerase subunit A''; Validated	100.0
cd02736	300	RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryot	100.0
cd02735	309	RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic	100.0
KOG0262|consensus	1640		100.0
PRK14977	1321	bifunctional DNA-directed RNA polymerase A'/A'' su	100.0
cd02737	381	RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher	100.0
PRK14898	858	DNA-directed RNA polymerase subunit A''; Provision	100.0
TIGR02389	367	RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit	100.0
TIGR02388	1227	rpoC2_cyan DNA-directed RNA polymerase, beta'' sub	100.0
PF04998	277	RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; Int	100.0
PRK14897	509	unknown domain/DNA-directed RNA polymerase subunit	100.0
cd06528	363	RNAP_A'' A'' subunit of Archaeal RNA Polymerase (R	100.0
PRK04309	383	DNA-directed RNA polymerase subunit A''; Validated	100.0
PRK02597	1331	rpoC2 DNA-directed RNA polymerase subunit beta'; P	100.0
CHL00117	1364	rpoC2 RNA polymerase beta'' subunit; Reviewed	100.0
TIGR02386	1140	rpoC_TIGR DNA-directed RNA polymerase, beta' subun	100.0
PRK02625	627	rpoC1 DNA-directed RNA polymerase subunit gamma; P	100.0
TIGR02387	619	rpoC1_cyan DNA-directed RNA polymerase, gamma subu	100.0
PRK00566	1156	DNA-directed RNA polymerase subunit beta'; Provisi	100.0
CHL00018	663	rpoC1 RNA polymerase beta' subunit	100.0
PRK14906	1460	DNA-directed RNA polymerase subunit beta'/alpha do	100.0
cd00630	158	RNAP_largest_subunit_C Largest subunit of RNA poly	100.0
cd02655	204	RNAP_beta'_C Largest subunit (beta') of Bacterial	100.0
PF04997	337	RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; Int	100.0
PRK14844	2836	bifunctional DNA-directed RNA polymerase subunit b	100.0
PRK09603	2890	bifunctional DNA-directed RNA polymerase subunit b	100.0
cd02737	381	RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher	100.0
smart00663	295	RPOLA_N RNA polymerase I subunit A N-terminus.	100.0
TIGR02390	868	RNA_pol_rpoA1 DNA-directed RNA polymerase subunit	100.0
PF04998	277	RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; Int	100.0
PRK08566	882	DNA-directed RNA polymerase subunit A'; Validated	100.0
PF00623	166	RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; Int	99.91
cd02736	300	RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryot	99.9
cd02584	410	RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryoti	99.89
cd02655	204	RNAP_beta'_C Largest subunit (beta') of Bacterial	99.88
PF04983	158	RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; Int	99.86
cd02735	309	RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic	99.84
PRK14898	858	DNA-directed RNA polymerase subunit A''; Provision	99.83
cd00630	158	RNAP_largest_subunit_C Largest subunit of RNA poly	99.82
COG0086	808	RpoC DNA-directed RNA polymerase, beta' subunit/16	99.73
TIGR02388	1227	rpoC2_cyan DNA-directed RNA polymerase, beta'' sub	99.5
CHL00117	1364	rpoC2 RNA polymerase beta'' subunit; Reviewed	99.45
PF04983	158	RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; Int	99.06
PRK02597	1331	rpoC2 DNA-directed RNA polymerase subunit beta'; P	98.94
PRK02625	627	rpoC1 DNA-directed RNA polymerase subunit gamma; P	98.24
TIGR02387	619	rpoC1_cyan DNA-directed RNA polymerase, gamma subu	98.23
CHL00018	663	rpoC1 RNA polymerase beta' subunit	98.19
PF05000	108	RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; Int	91.13
PF04992	187	RNA_pol_Rpb1_6: RNA polymerase Rpb1, domain 6; Int	87.94

>KOG0261|consensus

Probab=100.00  E-value=3.2e-223  Score=1951.60  Aligned_cols=1001  Identities=53%  Similarity=0.880  Sum_probs=909.2

Q ss_pred             ccceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCC-CcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEcc
Q psy13846         76 KVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLP  154 (1423)
Q Consensus        76 ~~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~-P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~  154 (1423)
                      +.+|.. |+|++.||+||++.+++||.+..+|+ ...++ |.++|++|||||+++++..|+|||++..+|+|||||+.|+
T Consensus        10 ~kki~~-i~F~~~s~~ei~~~a~v~v~~~~LY~-~~~~~~P~~~G~LD~rMGvs~K~~~C~TCg~~la~C~GHfGy~~L~   87 (1386)
T KOG0261|consen   10 PKKIKH-IQFSILSPEEIRQQAEVEVSSKDLYD-ISTQRAPLPNGPLDPRMGVSNKKDKCATCGEGLADCIGHFGYLKLA   87 (1386)
T ss_pred             cceeee-EeeccCCHHHHHhcceEEeeccchhh-hhcccCCCcCCCcCcccCCCCCCCccchhccchhhcccccceEeec
Confidence            467889 99999999999999999999999994 22233 9999999999999999999999999999999999999999


Q ss_pred             CceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCcee
Q psy13846        155 LPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVK  234 (1423)
Q Consensus       155 ~PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~ir  234 (1423)
                      +||||+|||+.+.+||+|+|+.  |+.+|+++++++.|+.++++|..+++.++++.++|.+.|++..+|.|||+.||.|+
T Consensus        88 LPVFhiGyfk~ti~iLq~ICK~--Cs~ilL~~~~k~~fl~~lr~p~~~~l~k~~l~kri~~~CkK~~~C~hCg~~NG~VK  165 (1386)
T KOG0261|consen   88 LPVFHIGYFKATIQILQCICKN--CSSILLSEEDKRQFLKKLRNPGLDNLRKKALLKRIVAKCKKVNTCSHCGALNGTVK  165 (1386)
T ss_pred             ceeeeehhHHHHHHHHHHHHHh--hhhhhcCHHHHHHHHHHhhCCCCChHHHHHHHHHHHHHhhccccccccCCcCceee
Confidence            9999999999999999999999  99999999999999999999999999999999999999999999999999999999


Q ss_pred             ec-CcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCC
Q psy13846        235 KC-GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELS  313 (1423)
Q Consensus       235 k~-~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~a  313 (1423)
                      |. +.++|.|+.++...+ .++..+.+..+|+.+...+++++.++. ...+.|+|..|+++|++|.+.|+++|+|++..+
T Consensus       166 K~~~~lkIiHd~~~~~~k-~~~~~~~~~~~~~~~~~~n~e~~~~~~-~~~~~LnPl~vLnLFk~i~~~D~eLLg~~~~~~  243 (1386)
T KOG0261|consen  166 KAAALLKIIHDRFKLVKK-SDPLVTNERGEFKTAISHNKELEGHLS-SCCEELNPLVVLNLFKQIKEDDCELLGMDSEEG  243 (1386)
T ss_pred             ccccceeEeeehhhcccc-ccchhhhhHHHHHHHhhcCcchHhHHH-HHHhhcChHHHHHHHhhCCccccceeeeccCcC
Confidence            94 558999998754443 577777888999999999999998886 567889999999999999999999999999889


Q ss_pred             CCcceEEEEecCCCCCCCCcEEcCCCC-----------------------------------------------------
Q psy13846        314 KPSDLILTRLLVPPNCIRPSVISDLKS-----------------------------------------------------  340 (1423)
Q Consensus       314 rPe~liLt~lpVPP~~vRPsv~~g~~~-----------------------------------------------------  340 (1423)
                      ||+.++|++|||||.|+|||+++++..                                                     
T Consensus       244 ~P~~Li~t~~~vPP~cIRPSV~~~~k~gtnEDDlT~KltEIi~tn~vik~~~~~g~~~~~imE~Wd~lQl~~AlyINSEl  323 (1386)
T KOG0261|consen  244 RPENLIITRVPVPPVCIRPSVMSEDKAGTNEDDLTMKLTEIILTNDVIKKHLSKGTPINLIMEDWDFLQLQVALYINSEL  323 (1386)
T ss_pred             CchheEEEeccCCccccccceeecCCCCCCccchhhhhhhhhhHHHHHHHHhhcCCCchhhhhhhHHHHHHHHHhhcccC
Confidence            999999999999999999999998842                                                     


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        341 --------------------------------------------------------------------------------  340 (1423)
Q Consensus       341 --------------------------------------------------------------------------------  340 (1423)
                                                                                                      
T Consensus       324 ~g~~~~~~p~kp~RGf~QRLKGKqGRFRgNLSGKRVDFSGRTVISPDPNL~IdeVgVP~rvAkiLTfpE~Vt~~Ni~klr  403 (1386)
T KOG0261|consen  324 PGIPINMAPKKPTRGFVQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDEVGVPIRVAKILTFPERVTRANIRKLR  403 (1386)
T ss_pred             CCCCCCCCCCCchHHHHHHhcccCCceeccccCceeeccCceeeCCCCCcceeeccchHHHHHHhcchhhccHHHHHHHH
Confidence                                                                                            


Q ss_pred             --------------------------------------------------CCeEEEEecCccccccccceeeeEEecCCc
Q psy13846        341 --------------------------------------------------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRT  370 (1423)
Q Consensus       341 --------------------------------------------------~~d~Vl~nRqPsLHk~Simah~~~~~~~~t  370 (1423)
                                                                        +||+|||||||||||+|||+|++|+.||+|
T Consensus       404 ~lV~NGP~vhPGANyv~~r~~~~kr~L~yg~R~kiA~eLk~GdvVERHL~DgDvVLFNRQPSLHkmSIM~H~akV~p~RT  483 (1386)
T KOG0261|consen  404 QLVRNGPNVHPGANYVVQRGEGFKRFLKYGNRDKIADELKIGDVVERHLMDGDVVLFNRQPSLHKMSIMSHRAKVMPWRT  483 (1386)
T ss_pred             HHHhcCCCCCCCcchhhhcccchhhHhhcCcHHHHHHhhccchHHHhhcccCCEEEEcCCchHHHHHHHHHHhhcccCce
Confidence                                                              999999999999999999999999999999


Q ss_pred             eeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEe
Q psy13846        371 FRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYL  450 (1423)
Q Consensus       371 ir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~  450 (1423)
                      ||||+|+|+||||||||||||+||||+|||||||.              .||++.+|+++|++|+|+|+++|||++|+|+
T Consensus       484 fRFNEcvCtPYNADFDGDEMNlHvPQTEEAraEA~--------------~LMgvknNlvTPr~GEpiiAAtQDFiTg~YL  549 (1386)
T KOG0261|consen  484 FRFNECVCTPYNADFDGDEMNLHVPQTEEARAEAL--------------VLMGVKNNLVTPRNGEPIIAATQDFITGGYL  549 (1386)
T ss_pred             eeccccccCCcCCCCCcccccccCCchHHHHHHHH--------------HHhccccccccCCCCCceeehhhhhhhccee
Confidence            99999999999999999999999999999999999              9999999999999999999999999999999


Q ss_pred             ecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeeccccc
Q psy13846        451 LTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAY  530 (1423)
Q Consensus       451 ~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~  530 (1423)
                      +|.+|+|+++.++.+++.++.    +...+|      .+|||||+||..||||||+|+.+++|+...++..|+..+++.|
T Consensus       550 lt~KDtF~dRa~~~ql~s~~~----d~~~~i------~lppPaI~KP~~LwTGKQ~fsvlirpn~~s~v~~Nl~~k~k~~  619 (1386)
T KOG0261|consen  550 LTHKDTFLDRAEFSQLCSYMS----DAMTHI------DLPPPAILKPVELWTGKQLFSVLIRPNDDSPVRVNLDAKNKNF  619 (1386)
T ss_pred             eecccccccHHHHHHHHHHHh----cccccc------CCCChhhcCceeeeccCEEEEEEeccCCCCceEEeecccccee
Confidence            999999999999999999886    444556      8999999999999999999999999999999999999888887


Q ss_pred             cc----CcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecC
Q psy13846        531 TA----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIG  606 (1423)
Q Consensus       531 ~~----~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~  606 (1423)
                      +.    +.++|++|++|+|+|+++++|++||+.+|++++.++++.+.++||+.+|+..|+++.++..+||.++||||||+
T Consensus       620 ~~~~~k~~~mc~nDg~v~irns~l~sG~ldKs~lG~g~k~~lfy~llrDyg~~aAa~am~rlaklc~r~lgnrGFSIGi~  699 (1386)
T KOG0261|consen  620 SLVKGKSFEMCPNDGYVIIRNSELISGVLDKSTLGSGKKDSLFYILLRDYGSMAAADAMNRLAKLCARFLGNRGFSIGID  699 (1386)
T ss_pred             ecccCCCcccCCCCCeEEEecchhhhcccccccccCCCccceEeeehhhcchHHHHHHHHHHHHhhhhhccccccccccC
Confidence            43    56899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCc--------------------------------------------------------------------------
Q psy13846        607 DVTPGQ--------------------------------------------------------------------------  612 (1423)
Q Consensus       607 D~~~~~--------------------------------------------------------------------------  612 (1423)
                      |+.|.+                                                                          
T Consensus       700 DVqPg~~L~~~k~~lv~~gY~kc~~~I~e~~kG~L~~qpg~~~eetLEa~I~~~Ls~IRe~~G~~C~~eL~~~NsPliMa  779 (1386)
T KOG0261|consen  700 DVQPGEILSQEKEELVNRGYAKCDEKIEEYNKGKLQLQPGCNEEETLEAEILSELSTIREEAGKICIRELHPRNSPLIMA  779 (1386)
T ss_pred             CCCccHHHHHHHHHHHHhHHHHHHHHHHHHhccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccChHHHH
Confidence            999876                                                                          


Q ss_pred             --------------------------------------------------cccccccccCCCceeeeeecccccccchhc
Q psy13846        613 --------------------------------------------------GFVQNSFFSGLTPTEFFFHTMGGREGLVDT  642 (1423)
Q Consensus       613 --------------------------------------------------GfI~~sf~~GL~p~Efffh~maGReGLiDT  642 (1423)
                                                                        |||.|||++||+|.|||||+||||||||||
T Consensus       780 ~CGSKGS~INiSQMvACVGQQ~ISG~RvPdGf~dRsLPHF~r~Sk~P~aKGFV~NSFySGLTptEFfFHtm~GREGLVDT  859 (1386)
T KOG0261|consen  780 LCGSKGSKINISQMVACVGQQIISGHRVPDGFEDRSLPHFERHSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDT  859 (1386)
T ss_pred             HhcCCCCcccHHHHHHHhhhhhhcCCcCCCccccccCccccccCCCccccchhhhhcccCCCchhhheeecccccchhhh
Confidence                                                              999999999999999999999999999999


Q ss_pred             ccccCCCCcchHHHHHHHhhhhhcccceeeccccCCCccCCCcchheecCCCcccchhHHHHhhhcCCCCCCccccccCC
Q psy13846        643 AVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDN  722 (1423)
Q Consensus       643 AvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~  722 (1423)
                      |||||+||||||||||+|||+.++||+|||||.       +                                       
T Consensus       860 AVKTAETGYMqRRLmK~LEDL~~~YDgTVR~s~-------~---------------------------------------  893 (1386)
T KOG0261|consen  860 AVKTAETGYMQRRLMKSLEDLSVQYDGTVRNSN-------G---------------------------------------  893 (1386)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHHHhhcCceecCC-------C---------------------------------------
Confidence            999999999999999999999999999999761       0                                       


Q ss_pred             CCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeeecccCChHHHHHHHhhh
Q psy13846        723 PEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGR  802 (1423)
Q Consensus       723 ~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~~~e~a~~v~~r  802 (1423)
                                                                                                      
T Consensus       894 --------------------------------------------------------------------------------  893 (1386)
T KOG0261|consen  894 --------------------------------------------------------------------------------  893 (1386)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             hcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccccccccCCCCccccch
Q psy13846        803 LERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS  882 (1423)
Q Consensus       803 ie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~  882 (1423)
                             +++|+                                                                    
T Consensus       894 -------~vvqF--------------------------------------------------------------------  898 (1386)
T KOG0261|consen  894 -------DVVQF--------------------------------------------------------------------  898 (1386)
T ss_pred             -------cEEEE--------------------------------------------------------------------
Confidence                   11111                                                                    


Q ss_pred             hhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccccceeecccceeeccCchHHHHHHhchHHHHHHH
Q psy13846        883 KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTI  962 (1423)
Q Consensus       883 ~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~I  962 (1423)
                                                                        ++|.|+..    +.                
T Consensus       899 --------------------------------------------------~YG~DglD----Pa----------------  908 (1386)
T KOG0261|consen  899 --------------------------------------------------TYGGDGLD----PA----------------  908 (1386)
T ss_pred             --------------------------------------------------eecCCCCC----hh----------------
Confidence                                                              22223322    11                


Q ss_pred             HHHHHHHHHhcCccccCCchhhHhhhhccccccccCCcchhhHHHHHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhh
Q psy13846        963 MTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFL 1042 (1423)
Q Consensus       963 i~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~ 1042 (1423)
                            .||                         |...||+|.+.|+++++....+.++.++++++....++.|.. +|.
T Consensus       909 ------~mE-------------------------g~~~pv~f~r~~~~~~~~~~~~~~~~l~~~el~e~~~~~l~~-~f~  956 (1386)
T KOG0261|consen  909 ------MME-------------------------GKDQPVNFNRVFDHAKAIFPHRHDPPLSSEELDETLEEELLR-KFT  956 (1386)
T ss_pred             ------hhc-------------------------CCCCchhHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHH-Hhh
Confidence                  233                         455788999999999998888899999999999888887765 343


Q ss_pred             hhhhHHHHHHHHHHHHHhhhccccccccccC--CchhhhhhhccccccCcccCCCCCChhHHHHHHHHHhhhccCCCCcc
Q psy13846       1043 QDTSENFVRDIKKFLEEFSKKESVTSHQDKV--SQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATA 1120 (1423)
Q Consensus      1043 ~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~s~v~PGea 1120 (1423)
                       .+...|...+++|+..-.++..+.+...+.  ........+.+.+++|++++    +  .|++.|+.+|+++.+|||+|
T Consensus       957 -~~~~~F~~~~~~~i~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~t~kql----~--~f~~~~~~ky~~a~~EpGTa 1029 (1386)
T KOG0261|consen  957 -EKGDPFVHELREFIASLSKKIKKLQDKYGDECGPKFCPDLLYQISRLTEKQL----E--KFVERCLDKYMRAKVEPGTA 1029 (1386)
T ss_pred             -hhhhHHHHHHHHHHHHHHHHHHHHhhhcccccCCccCccceeeeeeccHHHH----H--HHHHHHHHHHHhhhcCCcch
Confidence             355678888888876544443322221111  11233457888899999988    7  99999999999999999999


Q ss_pred             hhhhhhcccCCcccccccccccccc------------------------------------------------------c
Q psy13846       1121 VGALAAQSIGEPGTQMTLKTFHFAG------------------------------------------------------E 1146 (1423)
Q Consensus      1121 VG~iAAQSIGEP~TQmTLnTFH~AG------------------------------------------------------~ 1146 (1423)
                      ||+|||||||||+|||||+||||||                                                      |
T Consensus      1030 vGAi~aQSIGEPGTQMTLKTFHFAGVASMNiTlGVPRIkEIINAsk~ISTPIItA~L~n~~d~~~Ar~VKgRiEKt~L~d 1109 (1386)
T KOG0261|consen 1030 VGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKTISTPIITAELENPHDERSARVVKGRIEKTTLGD 1109 (1386)
T ss_pred             hhhhhcccCCCCCceeeeeeeeecceeeeeeccCcchHHHHHhhhcccCccceeeeecCchhHHHHHHHhhhhhhhhHHH
Confidence            9999999999999999999999999                                                      6


Q ss_pred             ccceeEEEEccCCcEEEEEEchHHHHHhcccCCHHHHHHHHH---hccccCCceEEecCcEEEEEeCCCC-chhhhHHHH
Q psy13846       1147 VCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE---RTRGISGHLTVSGHSFLILKPKDSS-KSFNSKMYQ 1222 (1423)
Q Consensus      1147 i~~~i~~~~~~~~~~~~i~l~~~~~~~~~~~i~~~~i~~~i~---~~k~~~~~~~~~~~~~i~i~~~~~~-~~~~~~l~~ 1222 (1423)
                      |+++|+++|.|+.+++.|++|+++++++++++++++|..+|-   +.+.++.++.+.++..+++.+.... .+.++.|+.
T Consensus      1110 v~~yieeV~~p~~~fl~i~vd~~~I~~l~L~i~~~~I~~sI~~s~~~k~~~~~v~v~~~~~~~v~~~~~~~~S~~~~lq~ 1189 (1386)
T KOG0261|consen 1110 VCSYIEEVYGPDSCFLLIRVDLKRISLLQLEITIESIAYSILKSPKRKVKPNDVRVVGETTLRVTPVSDTKSSVYYNLQR 1189 (1386)
T ss_pred             HHHHHHHHhCCcceEEEEEecHhHHhhhhccccHHHHHHHHhcCCccccCCcceEEecceeEEEeecccccchhhhhHHH
Confidence            788999999999999999999999999999999999999994   4456788898888888888876533 345889999


Q ss_pred             HHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHHHHH
Q psy13846       1223 MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 1302 (1423)
Q Consensus      1223 l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei 1302 (1423)
                      ++..|++++|+|+|.|.|++|+.++.  .+.|.|.+||++|++||+.+||+..||+||++.||.++|||||||.+||+||
T Consensus      1190 lk~~L~~Vvv~gip~vnr~vi~~de~--~~~y~L~vEG~gLr~Vm~t~GV~g~~TtsNnv~Ev~~vLGIEAAR~~II~EI 1267 (1386)
T KOG0261|consen 1190 LKRSLPNVVVKGIPEVNRAVINIDEK--RGLYKLLVEGTGLRAVMNTDGVKGRRTTSNNVLEVEKVLGIEAARTTIISEI 1267 (1386)
T ss_pred             HHhhCCceEEecCcchhhhheeeccc--CCceEEEEeccchHHHhccCCccccccccCceEEeehhhchHHHHHHHHHHH
Confidence            99999999999999999999988653  2349999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeecc
Q psy13846       1303 KLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGL 1382 (1423)
Q Consensus      1303 ~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~ 1382 (1423)
                      ..+|++||++||+||++||||+|||+|+++||||+|+++|++|+|+.||||+|.+||++||.+|++|.+.|||||||+|.
T Consensus      1268 ~ytM~~HGmsiD~RHiMLLaDvMTyrGEVlGITRfGl~KM~~SVL~lASFEkT~DhLF~AA~~~k~D~I~GVSEcIIlG~ 1347 (1386)
T KOG0261|consen 1268 GYTMSNHGMSIDPRHIMLLADVMTYRGEVLGITRFGLAKMKDSVLMLASFEKTADHLFDAAAYGKKDAIEGVSECIILGI 1347 (1386)
T ss_pred             HHHHHhcCcccCHHHHHHHHHHhhhcceeeeeeehhhHHHHHHHHHHHhhhhhhHHHHHHHHhcCcccccchhhheeccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccceEEEeecCCCCC-CCCcccccCCCcccccc
Q psy13846       1383 PMNVGTGLIKLLQAVPRSE-PVPRTLLFDNPEFHTNT 1418 (1423)
Q Consensus      1383 ~~~~GTG~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~ 1418 (1423)
                      ++++|||.|+|++..+..+ +++++++|+....+++.
T Consensus      1348 pm~iGTG~fkl~~~~~~~~~~~~~~~if~~~~~~~~~ 1384 (1386)
T KOG0261|consen 1348 PMCIGTGIFKLLQRTDDKKVLKPKPPIFSSLNLHLSL 1384 (1386)
T ss_pred             ceeccccHHHHHHhcCCcccCCCCCCccccccccccc
Confidence            9999999999999887765 77789999999988765

>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional

Probab=100.00  E-value=1.3e-191  Score=1851.74  Aligned_cols=880  Identities=33%  Similarity=0.540  Sum_probs=742.9

Q ss_pred             cceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCc
Q psy13846         77 VFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP  156 (1423)
Q Consensus        77 ~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~P  156 (1423)
                      .+|.+ |+|++||||||+++||++|+++++|  |.+|+|++|||||||||+++++..|+|||++..+||||||||+|++|
T Consensus         7 ~~I~~-I~Fg~~S~eeIrk~Sv~~It~~~~~--d~~g~P~~gGl~DprlG~~d~~~~C~TCg~~~~~CpGHFGHIELa~P   83 (1321)
T PRK14977          7 KAIDG-IIFGLISPADARKIGFAEITAPEAY--DEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEP   83 (1321)
T ss_pred             ceece-EEEecCCHHHHHHhCeEEEeccccc--CCCCCcCCCCCCccccCCCCCCCCCCCCCCCCCcCCCeeEEEEccCC
Confidence            56888 9999999999999999999999999  77999999999999999999999999999999999999999999999


Q ss_pred             eeEEeeeccHHHHhhhccccccccccccChhhHHHHH--HHhcCCchhHHHH---HHHHHH----HHHHccCCccCCCCC
Q psy13846        157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFR--AKLRNPALSYLVR---KSLKKK----ILETTKKVSVCPHCG  227 (1423)
Q Consensus       157 V~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~--~kl~~~~~~~~~~---~~~~~~----i~~~~kk~k~C~~Cg  227 (1423)
                      |||||||+.++++|+|+|++  ||+|++++++...|.  .+..++......+   ..+..+    +...|++.++|||||
T Consensus        84 VfHpgf~k~i~~iLr~iC~~--C~rlll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~C~~C~  161 (1321)
T PRK14977         84 VIHIAFIDNIKDLLNSTCHK--CAKLKLPQEDLNVFKLIEEAHAAARDIPEKRIDDEIIEEVRDQVKVYAKKAKECPHCG  161 (1321)
T ss_pred             ceecccHHHHHHHHHHHHHH--hchhhcCcccHHHHHHHHHHhhhcccchhhhhhHHHHHHHHhhhhhhhccCCcCCCCC
Confidence            99999999999999999999  999999998877663  2222211111111   111122    223488899999999


Q ss_pred             CCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccc
Q psy13846        228 EINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLL  307 (1423)
Q Consensus       228 ~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~  307 (1423)
                      +.+|.+++.+......       .                    ++       .....|+|.+|+++|++||++|+++|+
T Consensus       162 ~~~~~i~~~~~~~~~~-------~--------------------~~-------~~~~~l~p~~v~~if~~i~~~d~~llg  207 (1321)
T PRK14977        162 APQHELEFEEPTIFIE-------K--------------------TE-------IEEHRLLPIEIRDIFEKIIDDDLELIG  207 (1321)
T ss_pred             CCCCeEEEeeceeeee-------c--------------------cc-------ccCcccCHHHHHHHHHhcCHHHHHHhC
Confidence            9999998764221100       0                    00       113578999999999999999999999


Q ss_pred             cccCCCCCcceEEEEecCCCCCCCCcEEcCCC--C---------------------------------------------
Q psy13846        308 MNAELSKPSDLILTRLLVPPNCIRPSVISDLK--S---------------------------------------------  340 (1423)
Q Consensus       308 m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~--~---------------------------------------------  340 (1423)
                      +++..+||+||||+++||||+|+||++.+++.  .                                             
T Consensus       208 ~~~~~~~p~~~il~~lpVpP~~~RP~v~~~~~~~~eddlt~~l~~Ii~~N~~l~~~~~~g~~~~~~~~~~~~LQ~~v~~~  287 (1321)
T PRK14977        208 FDPKKARPEWAVLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTF  287 (1321)
T ss_pred             CCCCCCCcceEEEeccccCCCCCcCcEEeCCCcccCCcHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHH
Confidence            99988999999999999999999999999753  1                                             


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        341 --------------------------------------------------------------------------------  340 (1423)
Q Consensus       341 --------------------------------------------------------------------------------  340 (1423)
                                                                                                      
T Consensus       288 ~dn~~~~~~~~~~~~~~rp~k~i~qrLkgKeGrfR~nlmGKRVdfSaRtVIspDP~L~i~EVGvP~~iA~~LT~Pe~Vt~  367 (1321)
T PRK14977        288 FDNATAGIPQAHHKGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNE  367 (1321)
T ss_pred             hcccccCCCccccccCCCchhHHHHHhccccccccccccccccccccceeEeCCCCcccccccCHHHHHHhCCCCEEEch
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------------CCeEEEEecCcccccccc
Q psy13846        341 --------------------------------------------------------------DNDVVLFNRQPSLHKLSI  358 (1423)
Q Consensus       341 --------------------------------------------------------------~~d~Vl~nRqPsLHk~Si  358 (1423)
                                                                                    +||+|||||||||||+||
T Consensus       368 ~Ni~~l~~lv~nG~~~~pGA~~i~~~~g~~~~l~~~~~~~~~~~~~~a~~L~~g~iV~Rhl~dGD~VL~NRQPSLHk~Si  447 (1321)
T PRK14977        368 NNIEKMKELVINGPDEFPGANAIRKGDGTKIRLDFLEDKGKDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSI  447 (1321)
T ss_pred             hhHHHHHHHHHcCCcccCCcceEEcCCCceeeehhhhhccchhHHHHHHhcccCcEEEEEeecCcEEEeccCCccccccc
Confidence                                                                          889999999999999999


Q ss_pred             ceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCcccc
Q psy13846        359 MAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLI  438 (1423)
Q Consensus       359 mah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~  438 (1423)
                      |||++|++|++||||||++|+||||||||||||+|+|||++|||||.              .||.+.+|++||++|+|++
T Consensus       448 mah~vkvl~~kT~Rln~~vC~pyNADFDGDEMNlHvPQS~eArAEa~--------------~Lm~v~~niisP~~G~Pi~  513 (1321)
T PRK14977        448 LAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAI--------------ELMGVKDNLISPRTGGPII  513 (1321)
T ss_pred             eEEEEEEecCceEEecccccCcccCCcccceeeeecCCCHHHHHHHH--------------HHHhhhhcEecCCCCCeeE
Confidence            99999999999999999999999999999999999999999999999              9999999999999999999


Q ss_pred             ccccceEEEEEeecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceee-cceeeeecceeeeecccCCCCc
Q psy13846        439 AATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFV-RTAVIWTGKQIFSLILKPNRDC  517 (1423)
Q Consensus       439 ~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~-kp~~~wtGKqi~s~il~~~~~~  517 (1423)
                      +++||+|+|+|+||.+|+|++++|+++++++...     .        ..+|+|||+ ||.++||||||||++||++   
T Consensus       514 gliQD~l~g~~lLT~~d~fl~~~e~~~l~~~~~~-----~--------~~lp~PaI~~kp~~lwTGKQi~s~iLp~~---  577 (1321)
T PRK14977        514 GALQDFITAAYLITKDDALFDKNEASNIAMLAGI-----T--------DPLPEPAIKTKDGPAWTGKQLFSLFLPKD---  577 (1321)
T ss_pred             EeehhhhhhhhhhccCcccCCHHHHHHHHHhCCC-----c--------cccCCCceecCCCCeeeHHHHHHHHcCCC---
Confidence            9999999999999999999999999999997531     1        158999999 9999999999999999875   


Q ss_pred             ccccceeeccccccc-----CcccccCCcEEEeccccccccccccCCcCC--CCCCchHHHHHHHhCHHHHHHHHHHhhh
Q psy13846        518 PVNANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGS--GGKANVFYILLRDFGEDVAVTAMWRLSR  590 (1423)
Q Consensus       518 ~~~~~~~~~~~~~~~-----~~~~~~~d~~v~i~~~ell~g~ldK~~~g~--~~~~~li~~i~~~~G~~~a~~~l~~l~~  590 (1423)
                         +|+..+.+.+..     ...+|++|++|+|+||||++|++||+++|+  +++++++|.+|++||+++|..||+++++
T Consensus       578 ---~n~~~~~~~~~~~~~~~~~~~~~~d~~v~I~~geLl~G~ldK~~~G~~~~~~~~Lih~i~~~yG~~~a~~fL~~l~~  654 (1321)
T PRK14977        578 ---FNFEGIAKWSAGKAGEAKDPSCLGDGYVLIKEGELISGVIDDNIIGALVEEPESLIDRIAKDYGEAVAIEFLNKILI  654 (1321)
T ss_pred             ---CCceecccccccccccccccCCCCcceEEeecCeEEeeecchHhhccccCCCCcHHHHHHHHhCHHHHHHHHHHHHH
Confidence               344433332221     223678899999999999999999999997  4679999999999999999999999999


Q ss_pred             hhhHHHhhcCcceecCCCCCCc----------------------------------------------------------
Q psy13846        591 MTSFYLMNRGFSIGIGDVTPGQ----------------------------------------------------------  612 (1423)
Q Consensus       591 l~~~~L~~~GfsiGi~D~~~~~----------------------------------------------------------  612 (1423)
                      ++++||+.+|||+|++|+++++                                                          
T Consensus       655 l~~~~L~~~GFSigi~D~~~~~~~~~~i~~~i~~~~~~v~~l~~~~~~~~~i~~~~~~~~~~~G~~~~~~~e~~i~~~l~  734 (1321)
T PRK14977        655 IAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLIDQRKITRKITIYKGKEELLRGMKEEEALEADIVNELD  734 (1321)
T ss_pred             HHHHHHHhCCEEEeeCcEecCHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccchhcCCCCcHHHHHHHHHHHHHH
Confidence            9999999999999999996332                                                          


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        613 --------------------------------------------------------------------------------  612 (1423)
Q Consensus       613 --------------------------------------------------------------------------------  612 (1423)
                                                                                                      
T Consensus       735 ~~r~~~~~~~~~~l~~~N~l~~Mv~SGAKGS~~Ni~Qi~~~lGQQ~ve~~~~~~~~G~Ri~~~~~~RtLPhF~~~d~~p~  814 (1321)
T PRK14977        735 KARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTGGRLHEGYKDRALSHFQEGDDNPD  814 (1321)
T ss_pred             HHHHHHHHHHHHhcCCCCcHHHHhhcccccCHHHHHHHHhccccccccccccccCCCCCCcCCCCCCcCCCCCCCCCCcc
Confidence                                                                                            


Q ss_pred             --cccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeecc-------ccCCCccCC
Q psy13846        613 --GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA-------FYGQTDCIS  683 (1423)
Q Consensus       613 --GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s-------~yG~~~~~~  683 (1423)
                        |||.|||++||+|+|||||||||||||||||||||+||||||||||+|||++|+||+||||+       .||+|+.+.
T Consensus       815 a~GfV~nsFl~GL~P~EfFFHaM~GREGLiDTAVKTA~SGYLQRrLvk~lEDl~v~YD~TVR~s~g~iiQF~YGeDG~d~  894 (1321)
T PRK14977        815 AHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDP  894 (1321)
T ss_pred             cccchhhhhcCCCCHHHHHHHhhcccccccccccccCcCchhHHHHHHHhcceEEecCCeEEeCCCCEEEEeecCCCcCH
Confidence              89999999999999999999999999999999999999999999999999999999999998       499987762


Q ss_pred             Ccc---------------------------------------------------------------------hheecCCC
Q psy13846        684 GVS---------------------------------------------------------------------ECIIMGLP  694 (1423)
Q Consensus       684 ~~~---------------------------------------------------------------------~~~~~~~~  694 (1423)
                      .-.                                                                     ...|.+++
T Consensus       895 ~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  974 (1321)
T PRK14977        895 QKLDHGEAFNLERIIEKQKIEDRGKGASKDEIEELAKEYTKTFNANLPKLLADAIHGAELKEDELEAICAEGKEGFEKAK  974 (1321)
T ss_pred             HHhccCCcccHHHHHHHhhhhccccCCCHHHHHHHHHHHHHhhhhhhHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcc
Confidence            110                                                                     01256678


Q ss_pred             cccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhh
Q psy13846        695 MNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINA  774 (1423)
Q Consensus       695 ~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIina  774 (1423)
                      ++|||+||.+||||||||+|||||    +|||+||+             +++|+|+             |||||+||+||
T Consensus       975 ~~pGe~VG~iaAQSiGEP~TQmTL----nTFH~AGv-------------~~~nvt~-------------GvpRl~Eii~a 1024 (1321)
T PRK14977        975 VEPGQAIGIISAQSIAEPGTQMTL----RTFHAAGI-------------KAMDVTH-------------GLERFIELVDA 1024 (1321)
T ss_pred             cCCcccchhhhhhhccCceeeecc----cccccccc-------------cccCccc-------------CccchHHhhhc
Confidence            999999999999999999999999    99999999             8999999             99999999999


Q ss_pred             hcCCCCceeeeecccC--ChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhh
Q psy13846        775 SRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE  852 (1423)
Q Consensus       775 Sk~ikTPiitv~L~~~--~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~  852 (1423)
                      ||+|+||+|+++|.++  .+.+.|+.++.+||+++++++++.++..|+++..  ++.+|..                   
T Consensus      1025 ~k~~~tp~m~~~l~~~~~~~~~~a~~v~~~ie~~~l~~~~~~~~i~~~~~~~--~i~~d~~------------------- 1083 (1321)
T PRK14977       1025 RAKPSTPTMDIYLDDECKEDIEKAIEIARNLKELKVRALIADSAIDNANEIK--LIKPDKR------------------- 1083 (1321)
T ss_pred             ccCCCCCeEEEEeCCcccchHHHHHHHHhheeeeEHHHhhhheEeeccCCce--EEecCHH-------------------
Confidence            9999999999999986  4678999999999999999999876544432200  0000000                   


Q ss_pred             hcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccccce
Q psy13846        853 RTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA  932 (1423)
Q Consensus       853 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~  932 (1423)
                                                                                                      
T Consensus      1084 -------------------------------------------------------------------------------- 1083 (1321)
T PRK14977       1084 -------------------------------------------------------------------------------- 1083 (1321)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             eecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCCcchhhHHHHHHHH
Q psy13846        933 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDII 1012 (1423)
Q Consensus       933 ~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~~~~~~~~~~~~~~ 1012 (1423)
                                                          .++.++                                      
T Consensus      1084 ------------------------------------~i~~~~-------------------------------------- 1089 (1321)
T PRK14977       1084 ------------------------------------ALENGC-------------------------------------- 1089 (1321)
T ss_pred             ------------------------------------HHHhcC--------------------------------------
Confidence                                                011000                                      


Q ss_pred             HhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHHHHHHHHhhhccccccccccCCchhhhhhhccccccCccc
Q psy13846       1013 AKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGR 1092 (1423)
Q Consensus      1013 ~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1092 (1423)
                                +....|.                     +.+....                          . .    ..
T Consensus      1090 ----------i~~~~i~---------------------~~i~~~~--------------------------~-~----~~ 1107 (1321)
T PRK14977       1090 ----------IPMERFA---------------------EIEAALA--------------------------K-G----KK 1107 (1321)
T ss_pred             ----------CCHHHHH---------------------HHHHHhh--------------------------c-C----Cc
Confidence                      0000000                     0000000                          0 0    00


Q ss_pred             CCCCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccccccceeEEEEccCCcEEEEEEchHHHH
Q psy13846       1093 ESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLDMDRIR 1172 (1423)
Q Consensus      1093 ~~~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG~i~~~i~~~~~~~~~~~~i~l~~~~~~ 1172 (1423)
                      +                                                                     .+..      
T Consensus      1108 ~---------------------------------------------------------------------~~~~------ 1112 (1321)
T PRK14977       1108 F---------------------------------------------------------------------EMEL------ 1112 (1321)
T ss_pred             e---------------------------------------------------------------------EEee------
Confidence            0                                                                     0000      


Q ss_pred             HhcccCCHHHHHHHHHhccccCCceEEecCcEEEEEeCC--CCchhhhHHHHHHhccCCcEEcccCCccEEEEecccccc
Q psy13846       1173 LLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD--SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEG 1250 (1423)
Q Consensus      1173 ~~~~~i~~~~i~~~i~~~k~~~~~~~~~~~~~i~i~~~~--~~~~~~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~ 1250 (1423)
                                                  +++.+.+.+.+  ..+...+.|+.++..+.+++|+|+|||+|++|...+..+
T Consensus      1113 ----------------------------~~~~i~~~~~~~~~~~~~~~~l~~l~~~l~~~~i~Gi~~I~r~~i~~~~~~~ 1164 (1321)
T PRK14977       1113 ----------------------------EDDLIILDLVEAADRDKPLATLIAIRNKILDKPVKGVPDIERAWVELVEKDG 1164 (1321)
T ss_pred             ----------------------------cCCEEEEecCcccccchHHHHHHHHHHhcCCcEEecCCCceEEEEEeeccCC
Confidence                                        00112222211  111235678889998999999999999999886432223


Q ss_pred             eeeEEEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeE
Q psy13846       1251 VTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 1330 (1423)
Q Consensus      1251 ~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~ 1330 (1423)
                      .++|+|.|||+||.++|.+++||+.||+||||+||+++|||||||++|++||++||+.||++||+|||+||||+||++|.
T Consensus      1165 ~~e~~l~teG~nl~~vl~~~~Vd~~rt~sN~i~ei~~~lGIEAaR~~ii~Ei~~v~~~~G~~V~~rHi~LlaD~MT~~G~ 1244 (1321)
T PRK14977       1165 RDEWIIQTSGSNLAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGT 1244 (1321)
T ss_pred             CeeEEEEecCcCHHHHhCCCCCcccccEECCHHHHHHhhhHHHHHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHccCce
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeee------cccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeeccccccccceEEEeecCC
Q psy13846       1331 VLGIT------RHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398 (1423)
Q Consensus      1331 ~~~i~------r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~~ 1398 (1423)
                      ++++|      ||||+++++|||++||||+|+++|++||++|+.|+++|||||||+|+++|+|||+|+|+++..
T Consensus      1245 ~~~i~~~~~~~R~Gi~~~~~s~l~~asFE~t~~~L~~AA~~g~~D~l~gvsenii~G~~~~~GTG~~~Ll~~~~ 1318 (1321)
T PRK14977       1245 IEAIGLQAAGVRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDFS 1318 (1321)
T ss_pred             EEeccccccccccccccCCCCHHHhcCHHHHHHHHHHHHHhcCcCccCChHHhhhcCCCccCccceEEEEeccc
Confidence            99999      999999899999999999999999999999999999999999999999999999999999854

>KOG0262|consensus

Probab=100.00  E-value=6.6e-189  Score=1696.77  Aligned_cols=986  Identities=32%  Similarity=0.487  Sum_probs=749.4

Q ss_pred             eeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCcee
Q psy13846         79 FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVF  158 (1423)
Q Consensus        79 i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~  158 (1423)
                      ... ++|++|+++||+++||++|++|.+|  |+.|||++|||||++|||-+....|.||++....||||||||+|+.|||
T Consensus        13 ~~~-v~Fg~yt~~ei~klSv~kIt~p~~~--D~lGhPi~GGLYDl~LGp~~~~~~C~TC~~~~~~CPGH~GHIeL~~pvy   89 (1640)
T KOG0262|consen   13 QPS-VSFGSYTDQEIRKLSVKKITNPITF--DNLGHPIPGGLYDLALGPLDNSDVCSTCNQDELNCPGHMGHIELPVPVY   89 (1640)
T ss_pred             ccc-eeeeccCHHHHhhcceeEecCceee--cccCCCCCCcccccccCCccchhhhhhhcchhhcCCCccCeeeeccccc
Confidence            445 9999999999999999999999999  8899999999999999999888899999999999999999999999999


Q ss_pred             EEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCc--------------------------------------
Q psy13846        159 HIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA--------------------------------------  200 (1423)
Q Consensus       159 h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~--------------------------------------  200 (1423)
                      ||.||+.++++|++.|.+  ||+|.+.+.+++.++++++...                                      
T Consensus        90 nPlfF~~ly~lLr~sCl~--Chhf~~k~~~v~~~~cqLrll~~G~i~ea~~Le~i~~~~~~d~~d~~~~~~k~~~~~~v~  167 (1640)
T KOG0262|consen   90 NPLFFDFLYNLLRGSCLF--CHHFRCKNVDVHILFCQLRLLEYGLIEEAEDLESITSETVEDNEDESLNEIKSCRAQYVT  167 (1640)
T ss_pred             CHHHHHHHHHHHHHHHHh--hhhcccCcHHHHHHHHHHHHHHhchHHHHHHHHHhhhhhhccCcchhHHHHHhhhhhhcc
Confidence            999999999999999999  9999999999988888877410                                      


Q ss_pred             ----------------hhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehhhhhcccccc----hhhHHHHH
Q psy13846        201 ----------------LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKK----KDAIVEDL  260 (1423)
Q Consensus       201 ----------------~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~~----~~~~~~~~  260 (1423)
                                      .....++.+..+|++.....++|++|+..+|.+||++..+++......+...    ......+.
T Consensus       168 ~~i~~~~~~~~~~~t~~~~~~~~~lv~~f~k~~l~~kkC~~C~~~~p~~rk~~~~kv~~~~~~~~~~~~~~~~~~i~~~~  247 (1640)
T KOG0262|consen  168 EAISEALLDKSEPNTKNSTELKKKLVTAFLKNALSRKKCPRCKHSNPKLRKDGFRKVFIDALSSKVGANVIRGAKIKKDV  247 (1640)
T ss_pred             HHHHHHhhcCCCccchhhHHHHHHHHHHHHHHhhccccCCcccCCCchhhccccceeeeehhcccccccchhheeeehhc
Confidence                            0012345667777777778899999999999999999988876543111000    00000000


Q ss_pred             H------HHh---hhh-------hccChhhhhhhccCccccCCHHHHHHHhhccCCCccccccc--c--c----CCCCCc
Q psy13846        261 L------AEY---NEA-------VKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLM--N--A----ELSKPS  316 (1423)
Q Consensus       261 ~------~~~---~~~-------~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m--~--~----~~arPe  316 (1423)
                      .      +++   .++       .....+.....+ ....+|.|.+|+++|+.+|.+|..+|..  .  .    ..+..+
T Consensus       248 ~~~~~~d~~~~G~~E~~~~g~d~~e~~~~~~~~~~-t~~~~l~~tevR~~l~~lf~ne~~~l~~lf~l~~~~~~k~~p~d  326 (1640)
T KOG0262|consen  248 GSKGFEDSGIDGSNEVEEDGKDLFEKSTEPAEFEK-TGKKYLLPTEVREHLRDLFKNEGELLSYLFPLWDSGSGKIDPSD  326 (1640)
T ss_pred             ccccccccccCCccccccccccccccccccccccc-cccccccHHHHHHHHHHHHhhhHHHHHHhhccccccccccCccc
Confidence            0      000   000       000001111111 2357899999999999999998766542  1  1    112235


Q ss_pred             ceEEEEecCCCCCCCCcEEcCCCC--------------------------------------------------------
Q psy13846        317 DLILTRLLVPPNCIRPSVISDLKS--------------------------------------------------------  340 (1423)
Q Consensus       317 ~liLt~lpVPP~~vRPsv~~g~~~--------------------------------------------------------  340 (1423)
                      +|||..++|||.++||.+++|+..                                                        
T Consensus       327 ~FFld~l~VpPtrfRP~s~~gd~~~en~Qt~~L~kVle~s~~i~~~~~~m~~kl~~~~k~~l~~~~g~~~kl~~aw~~LQ  406 (1640)
T KOG0262|consen  327 MFFLDNLLVPPTRFRPPSMLGDEVHENPQTLNLNKVLESSVLIRKLLKDMKGKLDEELKLILERLRGIFSKLINAWLQLQ  406 (1640)
T ss_pred             eeeeeccccCCcccCCchhcchhhhcChHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence            999999999999999999988863                                                        


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        341 --------------------------------------------------------------------------------  340 (1423)
Q Consensus       341 --------------------------------------------------------------------------------  340 (1423)
                                                                                                      
T Consensus       407 ~~vn~lfDs~~~~k~~r~~~pGikQiLEKKeGLFRkhMMGKRVN~AaRSVIsPDPnI~tnEIGIP~vFA~KLTyPepVt~  486 (1640)
T KOG0262|consen  407 ASVNVLFDSKMASKWSRDSPPGIKQILEKKEGLFRKHMMGKRVNYAARSVISPDPNIETNEIGIPPVFAKKLTYPEPVTP  486 (1640)
T ss_pred             HHHHHHhccccccccccCCCchHHHHHHHhhhhHHHHhhccccchhhccccCCCCCccccccCCchHHHhhccCCCcCCc
Confidence                                                                                            


Q ss_pred             ---------------------------------------------------------------------CCeEEEEecCc
Q psy13846        341 ---------------------------------------------------------------------DNDVVLFNRQP  351 (1423)
Q Consensus       341 ---------------------------------------------------------------------~~d~Vl~nRqP  351 (1423)
                                                                                           +||+||+||||
T Consensus       487 ~NV~elr~aViNGP~~hPGA~~iqd~dg~~t~l~~~~~~qR~alA~qLLtpst~~~~~~~~K~V~RHvknGDvvlmNRQP  566 (1640)
T KOG0262|consen  487 WNVNELRKAVINGPDVHPGATYIQDEDGTLTLLSPMTDEQREALANQLLTPSTGNPTEFGTKKVHRHVKNGDVVLMNRQP  566 (1640)
T ss_pred             ccHHHHHHHHhcCCCCCCCcceeecCCCceeecCCCCHHHHHHHHHHhhccccCCCcccCCceeeeeccCCcEEEEcCCC
Confidence                                                                                 99999999999


Q ss_pred             cccccccceeeeEEecC-CceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhcccccccc
Q psy13846        352 SLHKLSIMAHRAKVLPH-RTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVT  430 (1423)
Q Consensus       352 sLHk~Simah~~~~~~~-~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s  430 (1423)
                      ||||+|||||++||||+ ||+|+|+++|++|||||||||||+|+||++.|||||+              .|.++..|++.
T Consensus       567 TLHKPSimaHkaRVL~gEktlRlHYANCkaYNADFDGDEMN~HfPQse~araEa~--------------~ian~dsqYLv  632 (1640)
T KOG0262|consen  567 TLHKPSIMAHKARVLPGEKTLRLHYANCKAYNADFDGDEMNVHFPQSEIARAEAY--------------NIANTDSQYLV  632 (1640)
T ss_pred             ccccchhhhhhheecCCcceeeeeecccccccCCCCcchhcccCCchhhHHHHHH--------------HHhccCCceec
Confidence            99999999999999999 9999999999999999999999999999999999999              99999999999


Q ss_pred             CCCCccccccccceEEEEEeecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeec
Q psy13846        431 PRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLI  510 (1423)
Q Consensus       431 ~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~i  510 (1423)
                      |++|.||.+++|||+++...||.||+||++++|+++++....   +..++|      .++||+|+||.+|||||||+|.+
T Consensus       633 Pt~G~PlrGLIQDHiVsgv~LT~rd~Fftre~y~qLv~~~l~---~~~~rI------~~lpPtIlkP~~LWTGKQVIsTi  703 (1640)
T KOG0262|consen  633 PTDGTPLRGLIQDHIVSGVLLTMRDSFFTREDYQQLVFAGLS---DTFKRI------KLLPPTILKPAPLWTGKQVISTI  703 (1640)
T ss_pred             cCCCCchhhhhhhheeeeEEEEecccccCHHHHHHHHHHhhh---hhccce------eccCccccccccccccchHHHHH
Confidence            999999999999999999999999999999999999998764   344666      79999999999999999999998


Q ss_pred             ccCCC-Ccccccceeeccccccc-----CcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHH
Q psy13846        511 LKPNR-DCPVNANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTA  584 (1423)
Q Consensus       511 l~~~~-~~~~~~~~~~~~~~~~~-----~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~  584 (1423)
                      |.... .....+|+.++.+....     +.+-..+++.|+|++||||+|+|||.++|+ +.+||+|.+++.||+++++++
T Consensus       704 l~Ni~P~~~p~iNl~~kaKip~~~W~~~s~e~~l~Es~v~ir~GellcGVLDKa~~Ga-t~yGLvH~~~ElYG~~~s~~l  782 (1640)
T KOG0262|consen  704 LKNIIPEGHPPINLESKAKIPGKAWRVHSEEPKLNESQVLIREGELLCGVLDKAQFGA-TAYGLVHCCHELYGGETSGKL  782 (1640)
T ss_pred             HHhcCCCCCCcccchhcccCchhhcCCCCCcccCCcceEEEecCceEEEeechhhcCc-hhhhhhhhhhhhhCccchhhH
Confidence            64332 22345667666554332     111123457799999999999999999999 789999999999999999999


Q ss_pred             HHHhhhhhhHHHhhcCcceecCCCCCCc----------------------------------------------------
Q psy13846        585 MWRLSRMTSFYLMNRGFSIGIGDVTPGQ----------------------------------------------------  612 (1423)
Q Consensus       585 l~~l~~l~~~~L~~~GfsiGi~D~~~~~----------------------------------------------------  612 (1423)
                      |+.++|+++.||++||||+|++|+...+                                                    
T Consensus       783 Ls~~srlFT~ylq~~GFT~GvdDlll~~~~D~kR~~il~e~~~vG~qa~~~~~~l~~da~~del~~~le~~y~~d~~~~~  862 (1640)
T KOG0262|consen  783 LSVFSRLFTAYLQMHGFTLGVDDLLLDKDADKKRREILRESRNVGNQAAKEAFGLDVDAPPDELRSRLEAIYLKDADKLA  862 (1640)
T ss_pred             HHHHHHHHHHHHHHhccccccceeeechhhhHHHHHHHHhhhcccHHHHHHHhCCCCCCCHHHHHHHHHHHHhcchhHHH
Confidence            9999999999999999999999997655                                                    


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        613 --------------------------------------------------------------------------------  612 (1423)
Q Consensus       613 --------------------------------------------------------------------------------  612 (1423)
                                                                                                      
T Consensus       863 ~LD~~~k~~~n~~ts~I~~~cvP~GLlk~FP~N~mqlM~~SGAKGS~VN~~QISclLGQqeLEGkRvPlMvSGKtLPsF~  942 (1640)
T KOG0262|consen  863 MLDRVMKSELNGYTSEIVKKCVPDGLLKKFPENNMQLMIQSGAKGSNVNTSQISCLLGQQELEGKRVPLMVSGKTLPSFA  942 (1640)
T ss_pred             HHHHHHHHHHhhhhHHHHhhhccchhhhcCCcchHHHHHHhcCCcccccHHHHHHhhhhHhhcCCccceeecCCccCCcC
Confidence                                                                                            


Q ss_pred             ---------cccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeeccccCCCccCC
Q psy13846        613 ---------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCIS  683 (1423)
Q Consensus       613 ---------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~  683 (1423)
                               |||..||++|++|+|||||||||||||||||||||+||||||||+|+||+++|+||.|||++       ++
T Consensus       943 p~e~spraGGfI~~RFlTGi~PqeyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEgl~V~YD~TVRDs-------Dg 1015 (1640)
T KOG0262|consen  943 PYETSPRAGGFIDGRFLTGIKPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVHYDLTVRDS-------DG 1015 (1640)
T ss_pred             CCCCCCCCCCcccceeecCCCchHHhhhhhccccchhhhHHhcccchHHHHHHHHhhhhcEEeccceEEcC-------CC
Confidence                     99999999999999999999999999999999999999999999999999999999999965       23


Q ss_pred             CcchheecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCC
Q psy13846        684 GVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQD  763 (1423)
Q Consensus       684 ~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~  763 (1423)
                      .++|++|+                   |+                                                   
T Consensus      1016 svVQF~YG-------------------ED--------------------------------------------------- 1025 (1640)
T KOG0262|consen 1016 SVVQFMYG-------------------ED--------------------------------------------------- 1025 (1640)
T ss_pred             cEEEEeec-------------------Cc---------------------------------------------------
Confidence            33333321                   11                                                   


Q ss_pred             CchhhHHHHhhhcCCCCceeeeecccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccc
Q psy13846        764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVD  843 (1423)
Q Consensus       764 GvPRlkEIinaSk~ikTPiitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~  843 (1423)
                      |++-.|+              -+|+   ++++.   .     .-+..++..                             
T Consensus      1026 glDitKs--------------sfl~---~~~f~---~-----~Ny~avl~~----------------------------- 1051 (1640)
T KOG0262|consen 1026 GLDITKS--------------SFLN---KKEFP---T-----DNYEAVLLK----------------------------- 1051 (1640)
T ss_pred             cccccHH--------------hhcc---hhhhh---h-----hhHHHHHhh-----------------------------
Confidence            1110000              0000   00000   0     000000000                             


Q ss_pred             hhhhhHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeecc
Q psy13846        844 IDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE  923 (1423)
Q Consensus       844 ~~~I~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~e  923 (1423)
                                .                                                                     
T Consensus      1052 ----------~--------------------------------------------------------------------- 1052 (1640)
T KOG0262|consen 1052 ----------Y--------------------------------------------------------------------- 1052 (1640)
T ss_pred             ----------h---------------------------------------------------------------------
Confidence                      0                                                                     


Q ss_pred             CccccccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCCcchh
Q psy13846        924 GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVE 1003 (1423)
Q Consensus       924 G~nL~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~~~~~ 1003 (1423)
                                           ....|..-++++.|-..+- -+.++-.        +|                      
T Consensus      1053 ---------------------~~~~v~s~~d~~~a~~~~k-~i~kw~k--------k~---------------------- 1080 (1640)
T KOG0262|consen 1053 ---------------------KSESVLSAFDIKKASKYIK-KILKWKK--------KH---------------------- 1080 (1640)
T ss_pred             ---------------------ChHHHhhhhhhHHHHHHHH-HHHHHHh--------hh----------------------
Confidence                                 0111222233333322211 1111111        01                      


Q ss_pred             hHHHHHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHHHHHHHHhhhccccccccccCCchhhhhhhc
Q psy13846       1004 LKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILS 1083 (1423)
Q Consensus      1004 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1083 (1423)
                         .|....+.. ...+|.++          .+.++.++++.||+|.+.+..|..+++++.....               
T Consensus      1081 ---~w~~~~k~~-~cpdpv~~----------k~~p~~y~gsvsekf~~~i~~f~~~~~k~~~s~~--------------- 1131 (1640)
T KOG0262|consen 1081 ---MWFELDKKI-ACPDPVLA----------KYNPDKYLGSVSEKFRKKIDDFDDENAKKEKSEE--------------- 1131 (1640)
T ss_pred             ---ccchhhccc-CCCChhhh----------hcchhhhhccccHHHHHHHHHHHHHhhhhhcccc---------------
Confidence               111111111 12233332          4667889999999999999999977643322110               


Q ss_pred             cccccCcccCCCCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc------------------
Q psy13846       1084 HQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------ 1145 (1423)
Q Consensus      1084 ~~~~~~~~~~~~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG------------------ 1145 (1423)
                          -++       +  .|...++.||.+|+++|||+||+||||||||||||||||||||||                  
T Consensus      1132 ----~~~-------~--~lr~ll~~K~~~SLa~PGE~VGvlAAQSIGEPSTQMTLNTFHfAGrGemNVTLGIPRLREIlM 1198 (1640)
T KOG0262|consen 1132 ----PSE-------E--KLRRLLQLKYIRSLADPGEPVGVLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILM 1198 (1640)
T ss_pred             ----chH-------H--HHHHHHHHHHHHHhcCCCCcceeeeecccCCCcceeehhheeeccccceeeeecchHHHHHHH
Confidence                011       3  789999999999999999999999999999999999999999999                  


Q ss_pred             -------------------------------------cccceeE--EEEc--c-CC-cEEEEEEchHHHHHh--cccCCH
Q psy13846       1146 -------------------------------------EVCEYIE--EVFV--P-DD-SFILIKLDMDRIRLL--HLEVDI 1180 (1423)
Q Consensus      1146 -------------------------------------~i~~~i~--~~~~--~-~~-~~~~i~l~~~~~~~~--~~~i~~ 1180 (1423)
                                                           ++.+++.  +.+.  + .. ..+.+++++..-+.+  .+.+..
T Consensus      1199 tASanIkTP~mt~pi~~g~s~~ra~~i~~~l~rV~L~evlk~v~vte~~t~~~~~~~~~y~lr~~~~~~~~y~~e~~v~~ 1278 (1640)
T KOG0262|consen 1199 TASANIKTPSMTVPIKNGVSDERADDITKELRRVTLKEVLKKVGVTEKITMVENQSCKKYKLRFDLLPREEYQEEYDVRP 1278 (1640)
T ss_pred             HHhhccCCCceeeeccCCccHHHHHHHHHHHHHHHHHHHHhheeeeEEEEeeccccceEEEEEEeecCHHHhhhhcCCCH
Confidence                                                 1111111  1111  1 12 335666666554444  446677


Q ss_pred             HHHHHHHH------------h----cc---ccC-----Cce--------EEe---------------cC-----------
Q psy13846       1181 DSIRYCIE------------R----TR---GIS-----GHL--------TVS---------------GH----------- 1202 (1423)
Q Consensus      1181 ~~i~~~i~------------~----~k---~~~-----~~~--------~~~---------------~~----------- 1202 (1423)
                      ++|.+.++            +    .+   ...     .++        .+.               ++           
T Consensus      1279 e~i~~~m~~~Flk~L~~aI~k~~~k~~~~~~~~~dd~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ddddas~~k~~~k 1358 (1640)
T KOG0262|consen 1279 EDIEEVMENRFLKLLERAIKKKLKKAKYTRGMSNDDADPDDGNEVDNNDEVGGEDNEDSDDESEDDEDDDDASDAKLHKK 1358 (1640)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHhhccccccCCccccccCCccccccCCccccccccccccCcccchhHHHHhhh
Confidence            77665431            1    00   000     000        000               00           


Q ss_pred             -------------cEEEEEeC----------------------------------------------------------C
Q psy13846       1203 -------------SFLILKPK----------------------------------------------------------D 1211 (1423)
Q Consensus      1203 -------------~~i~i~~~----------------------------------------------------------~ 1211 (1423)
                                   ..+..+-.                                                          .
T Consensus      1359 ~~~~~dYe~~de~e~~~~~~~e~~~~~e~~e~d~e~g~dg~~~~~~~~~e~~~~~~~~er~~qs~~~~~~fi~~y~fd~~ 1438 (1640)
T KOG0262|consen 1359 TEEEADYESEDEDERVEEREDEGDEDEESDEDDEEVGLDGTPEPEEEDQEGQPEVNAVERREQSVKKRHDFISRYTFDKE 1438 (1640)
T ss_pred             hccccCcCCCchhhhhhhhhcccccccccccchhhcccCCCCCcccccccCCchhhHHHHHHHHHHHHHHHhhhhccccc
Confidence                         00000000                                                          0


Q ss_pred             CCc------------hhhhHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhccc-ccceecc
Q psy13846       1212 SSK------------SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG-VKGVKCS 1278 (1423)
Q Consensus      1212 ~~~------------~~~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~~~-vd~~~~~ 1278 (1423)
                      ..+            ....+.+.++..+++++|+.+|||+||++...+...++.-++.|+|+||.++|++.. +|.+++|
T Consensus      1439 ~~~wcev~~~lp~~~~k~~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~~~k~~~~l~TeGVnl~a~~~~~d~LDv~~ly 1518 (1640)
T KOG0262|consen 1439 SGKWCEVELKLPLDKEKLDMSSIVESIAPKSVIHQVPGIERCVVSEPQDDVKEKSVLLTEGVNLPALFDHADILDVNRLY 1518 (1640)
T ss_pred             cCcEEEEEEEecCCCcchHHHHHHHHHhcceeeeccCCceeeeccCCcccccccceehhcCccHHHHHHHHhhhhhhhhc
Confidence            000            012345667889999999999999999997653222223389999999999999765 5999999


Q ss_pred             cccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHH
Q psy13846       1279 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDH 1358 (1423)
Q Consensus      1279 sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~ 1358 (1423)
                      ||||++|+++|||||||++|++|+.+||..|||+||.|||+||||||||+|.+.|+||+||.. ++|||++||||+|.+|
T Consensus      1519 SNDI~ail~tyGVEAar~~Iv~Ev~~VF~vYGIsVd~RHLsLiADYMTf~G~y~pfnR~Gm~~-ssSP~qkMsFETt~~F 1597 (1640)
T KOG0262|consen 1519 SNDIHAILNTYGVEAARNAIVNEVNNVFKVYGISVDIRHLSLIADYMTFEGGYQPFNRMGMES-SSSPLQKMSFETTCQF 1597 (1640)
T ss_pred             cchHHHHHHHhhHHHHHHHHHHHHHHhhhheeeeecHHHHHHHHHHHhhcccccccccccccc-CCChhHhhhHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999965 8999999999999999


Q ss_pred             HHhhcccCCcccccccccceeeccccccccceEEEeecCCC
Q psy13846       1359 LFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 1399 (1423)
Q Consensus      1359 L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~~~ 1399 (1423)
                      |.+||.+|+.|.|++||++|++|+++..|||+|||+++.+.
T Consensus      1598 l~~Aa~~g~~D~L~sPSArLvvG~~~r~GTG~Fdll~~v~~ 1638 (1640)
T KOG0262|consen 1598 LKQAALFGEEDELSSPSARLVVGLPVRGGTGSFDLLQKVDF 1638 (1640)
T ss_pred             HHHHHhcCcccccCCCcceeEeccccCCCcceeeeeccCCC
Confidence            99999999999999999999999999999999999998765

>KOG0260|consensus

Probab=100.00  E-value=1.5e-179  Score=1608.07  Aligned_cols=996  Identities=33%  Similarity=0.522  Sum_probs=773.8

Q ss_pred             ccceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccC
Q psy13846         76 KVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL  155 (1423)
Q Consensus        76 ~~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~  155 (1423)
                      ...+.+ |+||++||+|||+|||.+|..|++++   .|+|..|||.|||||..++...|.|||.++.+||||||||+|+.
T Consensus        12 l~~v~~-vqFgi~spdeir~mSV~~i~~~e~~e---~~~pk~ggl~D~RlG~idr~~~CqTC~g~~~~CpGHFGhieLAk   87 (1605)
T KOG0260|consen   12 LRTVKS-VQFGILSPDEIRRMSVAEIEFPETME---GGRPKLGGLMDPRLGTIDRDSLCQTCGGNMFECPGHFGHIELAK   87 (1605)
T ss_pred             ceeeeE-EEeeccChhhhhcceeEEeecccccc---cCCCCcCCccccccCCCCccchhhhhccccccCCcccceeeecc
Confidence            356888 99999999999999999999999995   68999999999999999999999999999999999999999999


Q ss_pred             ceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCC-----------
Q psy13846        156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCP-----------  224 (1423)
Q Consensus       156 PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~-----------  224 (1423)
                      |||||||++++.++|+|+|++  |++++.++...........+.+     .+++...+++.|+++..|.           
T Consensus        88 PvfH~gFl~kv~kiL~cVC~~--C~ki~~~~~~~~~~~~~~~~~~-----~k~rl~~v~~vck~k~~ce~g~~~e~~g~s  160 (1605)
T KOG0260|consen   88 PVFHPGFLKKVKKILRCVCFY--CSKILKDKFNPKEDQILRKRYC-----SKGRLLMVLDVCKGKVVCEGGIDVESDGRS  160 (1605)
T ss_pred             ccccHHHHHHHHHHHHHhhhc--chheeecccCcchhhhhhhhcC-----CcchHHHHHHhhccceeeeccccccccccc
Confidence            999999999999999999999  9999987654322111111111     2467888999999999996           


Q ss_pred             CCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCccc
Q psy13846        225 HCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIP  304 (1423)
Q Consensus       225 ~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~  304 (1423)
                      +||..+|.+++.+ ++.+.. ++..    ++                 +..     ..+..+++++|.++|+.|.++|+.
T Consensus       161 gcg~kqP~i~r~g-l~l~a~-~k~~----~e-----------------~~~-----e~k~~ls~e~V~~i~k~Isded~~  212 (1605)
T KOG0260|consen  161 GCGLKQPSIRRLG-LDLWAF-WKQG----DE-----------------DSQ-----ESKRKLSAERVLEIFKRISDEDID  212 (1605)
T ss_pred             cccccCCceeccC-chhhhh-hhcc----Cc-----------------cCC-----cccccCcHHHHHHHHHhhchhhhh
Confidence            5999999999988 454432 1110    00                 000     235578999999999999999999


Q ss_pred             ccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCC--------------------------------------------
Q psy13846        305 LLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS--------------------------------------------  340 (1423)
Q Consensus       305 lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~--------------------------------------------  340 (1423)
                      .++|++..+||+||+||++||||+.+||++++++..                                            
T Consensus       213 ~lg~~~~~arpewmIlTvLPVPP~~vrP~iv~~~s~rg~DdlthkLadIiK~n~~l~r~e~~ga~~H~i~e~~~LlqfhV  292 (1605)
T KOG0260|consen  213 QLGFKPKIARPEWMILTVLPVPPPAVRPEIVMQGSARGEDDLTHKLADIIKKNIGLKRNEENGAPAHIIEEYEQLLQFHV  292 (1605)
T ss_pred             hhcCCCCcCCCceeEEEEecCCCCcccceeeecccccCcchhHHHHHHHHHHHHHHhhhhhcCCchhhHHHHHhHhhhhh
Confidence            999999999999999999999999999999987652                                            


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        341 --------------------------------------------------------------------------------  340 (1423)
Q Consensus       341 --------------------------------------------------------------------------------  340 (1423)
                                                                                                      
T Consensus       293 at~~Dn~~pgqp~a~qksGrplkSi~arlKgkegriRgnLmGKRvDFSaRTVItgDPnl~ldevGVP~sIAk~lTfpE~V  372 (1605)
T KOG0260|consen  293 ATYVDNDIPGQPQADQKSGRPLKSISARLKGKEGRIRGNLMGKRVDFSARTVITGDPNLSLDEVGVPRSIAKRLTFPEHV  372 (1605)
T ss_pred             hheecccccCCcccccccCCcccchhhhhccccchhhhcccccccCcceeeeecCCCCcchhcccCcHHHHhhccCccee
Confidence                                                                                            


Q ss_pred             ---------------------------------------------------------CCeEEEEecCccccccccceeee
Q psy13846        341 ---------------------------------------------------------DNDVVLFNRQPSLHKLSIMAHRA  363 (1423)
Q Consensus       341 ---------------------------------------------------------~~d~Vl~nRqPsLHk~Simah~~  363 (1423)
                                                                               |||+|||||||||||||||||++
T Consensus       373 tp~NidrLqeLV~~g~~~~pgakyiird~G~Ridlr~~~~~~d~~Lq~G~kVeRhl~DGD~VlfNRqPSlHKmSmmahrV  452 (1605)
T KOG0260|consen  373 TPFNIDRLQELVRRGLLEHPGAKYIIRDNGDRIDLRYHKRAGDIHLQPGYKVERHLMDGDVVLFNRQPSLHKMSMMAHRV  452 (1605)
T ss_pred             ccccHHHHHHHhhCCCCCCCCcceeeecCCcEEEEeecCCccccccccccEEEEeeccCCEEEEcCCCcHHHhhhhhcEE
Confidence                                                                     99999999999999999999999


Q ss_pred             EEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccc
Q psy13846        364 KVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQD  443 (1423)
Q Consensus       364 ~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD  443 (1423)
                      ||+|++|||+|+.+|+||||||||||||+|+|||++||||..              +|+.+.+|++||++|+|+++++||
T Consensus       453 rVlp~sTfrLNlsvtsPynADFDGDemnlhvPQS~etkAEl~--------------EL~~vpkQiispQsnkpvmgivQD  518 (1605)
T KOG0260|consen  453 RVLPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSLETKAELE--------------ELAMVPKQIISPQSNKPVMGIVQD  518 (1605)
T ss_pred             EEccCceEEeCeeecCCccCCCCCceeecccCcchhHHHHHH--------------HHhhhhhhhcCCcCCCcceeeehh
Confidence            999999999999999999999999999999999999999999              999999999999999999999999


Q ss_pred             eEEEEEeecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccC-CceeecceeeeecceeeeecccCCCCcccccc
Q psy13846        444 FITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWN-PVVFVRTAVIWTGKQIFSLILKPNRDCPVNAN  522 (1423)
Q Consensus       444 ~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~-~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~  522 (1423)
                      +|+|.+.+|.||.|+++.|++++++++.    +|.+        ..| +|+|+||.++|||||||++++|++.      |
T Consensus       519 TLta~R~~t~Rd~Fl~r~~vmnLlm~~p----~~d~--------~~Pa~pai~Kp~PlWTGkQifsliiP~~i------n  580 (1605)
T KOG0260|consen  519 TLTAVRKMTKRDVFLNRAQVMNLLMYVP----DWDG--------PPPAKPAILKPKPLWTGKQIFSLIIPGGI------N  580 (1605)
T ss_pred             hHHHHHHHhhHhhhhcHHHHHHHHhhcc----ccCC--------CCCCCcccCCCCcccchhhheeeecCCCc------c
Confidence            9999999999999999999999999984    4444        345 6899999999999999999999763      3


Q ss_pred             eeeccccccc--CcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcC
Q psy13846        523 LKTKGRAYTA--NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRG  600 (1423)
Q Consensus       523 ~~~~~~~~~~--~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~G  600 (1423)
                      +.........  ++...++|..++|.+|+++.|+++|+.+|+ +.++++|.+|.+.|++.|+.|.+.+|++.+.||..+|
T Consensus       581 ~~r~~s~h~d~~~~~~~p~dt~~lie~g~l~~g~l~Kkt~G~-s~g~lvh~i~~e~Gp~~~~~f~~~iQ~lin~wll~~g  659 (1605)
T KOG0260|consen  581 YIRDHSTHPDSEDELISPGDTRVLIEGGELLIGVLCKKTVGS-SAGGLVHVIFLEKGPKIARGFFDSIQTLINSWLLREG  659 (1605)
T ss_pred             eecccccCcCCCcccccCCCceEEEeCCceEEEEeecccccc-ccCceEEEeehhhCHHHHHHHHHHHHHHHHHHHHhcC
Confidence            3333222222  446688999999999999999999999998 7799999999999999999999999999999999999


Q ss_pred             cceecCCCCCCc--------------------------------------------------------------------
Q psy13846        601 FSIGIGDVTPGQ--------------------------------------------------------------------  612 (1423)
Q Consensus       601 fsiGi~D~~~~~--------------------------------------------------------------------  612 (1423)
                      ||+||+|++++.                                                                    
T Consensus       660 fsigIgDtiad~~t~~~iq~~I~~ak~dv~~vi~~a~~~~L~~~pg~tlretfe~~v~~vlndArd~~gssA~~sl~esN  739 (1605)
T KOG0260|consen  660 FSIGIGDTIADAATMCVIQNTIKEAKRDVLAVIREAQNNELEPTPGRTLRETFENKVNRVLNDARDKSGSSAQKSLSESN  739 (1605)
T ss_pred             ccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCcchhHHHHHHHHHHHHHHHHHHhhhhHHHhhhhhcc
Confidence            999999999877                                                                    


Q ss_pred             --------------------------------------------------------cccccccccCCCceeeeeeccccc
Q psy13846        613 --------------------------------------------------------GFVQNSFFSGLTPTEFFFHTMGGR  636 (1423)
Q Consensus       613 --------------------------------------------------------GfI~~sf~~GL~p~Efffh~maGR  636 (1423)
                                                                              |||.|||++||+|+|||||+||||
T Consensus       740 n~k~Mv~aGSKGs~inisQ~saCVGqQnVEgkrIpFGF~~Rtlphf~kDdysPesrGfVENSyL~GLtP~EfFfHamggR  819 (1605)
T KOG0260|consen  740 NFKTMVVAGSKGSFINISQVSACVGQQNVEGKRIPFGFPKRTLPHFSKDDYSPESRGFVENSYLTGLTPQEFFFHAMGGR  819 (1605)
T ss_pred             cHHHHHhhcCCCcceehhhhhhhhccccccccccccCCCcccccccccCCCCccccceeecccccCCCHHHHHHHHhccc
Confidence                                                                    999999999999999999999999


Q ss_pred             ccchhcccccCCCCcchHHHHHHHhhhhhcccceeeccc-------cCCCccCCCcchheecCCCcccchhHHHHhhhcC
Q psy13846        637 EGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAF-------YGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP  709 (1423)
Q Consensus       637 eGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~-------yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsi  709 (1423)
                      |||||||||||++|||||||||+|||++|+|||||||++       ||+|+.++-.+|..       -|++++...|...
T Consensus       820 EglidtavktaEtGyiqRRL~kameDimv~yDgTVRNs~gqviQf~YGeDG~d~~~vE~q-------~~~~l~~~~a~f~  892 (1605)
T KOG0260|consen  820 EGLIDTAVKTAETGYIQRRLMKAMEDIMVAYDGTVRNSLGQVIQFKYGEDGLDGHPVEFQ-------NGETLGSLNACFE  892 (1605)
T ss_pred             chhhhhhhcccccchHHHHHHHHHHHHHhhcCcceecccceeEEEEeccCccccceeecc-------ccccccchHHHHH
Confidence            999999999999999999999999999999999999993       99987655444432       2334443333321


Q ss_pred             CCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeeeccc
Q psy13846        710 RSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDK  789 (1423)
Q Consensus       710 ge~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~  789 (1423)
                                   ++|.+.-.              ..++.+            .-..-++|+-+.          ..+++
T Consensus       893 -------------~~~~~d~l--------------d~~~~~------------~~~~~~~e~~~~----------~~l~~  923 (1605)
T KOG0260|consen  893 -------------SEFAYDAL--------------DEPISL------------SSEEVVNEISEL----------LKLQN  923 (1605)
T ss_pred             -------------hhhhhhhh--------------cCcccc------------hhhhHhhhhhhh----------HHHHH
Confidence                         11110000              000111            000011111111          01222


Q ss_pred             CChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccccc
Q psy13846        790 DTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFL  869 (1423)
Q Consensus       790 ~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~~~  869 (1423)
                      ..+.|+.+.+++|-.   +       ..++...+..+++..+..++           |..+.++...             
T Consensus       924 lle~e~~~l~~dr~~---l-------~~i~~~g~~k~~lp~n~~r~-----------I~Na~~~f~~-------------  969 (1605)
T KOG0260|consen  924 LLECEYKKLVRDRRV---L-------LYIFEYGDAKWPLPENLQRI-----------IWNALKKFSI-------------  969 (1605)
T ss_pred             HHHHHHHhhhhhhhh---h-------hhhcccCCcccccchhHHHH-----------HHHHHhhccc-------------
Confidence            234455544444421   1       11223344455555555443           1111111100             


Q ss_pred             cccCCCCccccchhhhhhhhcCCceEEccccccc-eeeeecccccceeEEeeeccCccccccceeecccceeeccCchHH
Q psy13846        870 ILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGIN-RAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE  948 (1423)
Q Consensus       870 ~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~-r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~e  948 (1423)
                                   .......+.+.-+++|.+... ++++                         +.|.|.... .|.   
T Consensus       970 -------------~~r~~t~l~~~~v~~g~~~l~e~l~i-------------------------v~g~~~~sr-aqr--- 1007 (1605)
T KOG0260|consen  970 -------------DERKPTDLIPFKVVKGVKELAEKLVI-------------------------VRGEDYISR-AQR--- 1007 (1605)
T ss_pred             -------------ccccccccchhhhhhhhhhhhheeEE-------------------------eeCchhHHH-HHH---
Confidence                         000001111222222222210 1110                         001111000 000   


Q ss_pred             HHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCCcchhhHHHHHHHHHhccCCCCCCCCHHHH
Q psy13846        949 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEI 1028 (1423)
Q Consensus       949 V~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 1028 (1423)
                                                                                                    -+
T Consensus      1008 ------------------------------------------------------------------------------l~ 1009 (1605)
T KOG0260|consen 1008 ------------------------------------------------------------------------------LF 1009 (1605)
T ss_pred             ------------------------------------------------------------------------------HH
Confidence                                                                                          01


Q ss_pred             HHHhhhhcCcchhhhhhhHHHHHHHHHHHHHhhhccccccccccCCchhhhhhhccccccCcccCCCCCChhHHHHHHHH
Q psy13846       1029 LALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACRE 1108 (1423)
Q Consensus      1029 ~~~~~~~l~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1108 (1423)
                      ..++|+.|++                                         +.+..+++++.+++    +  |+.+++..
T Consensus      1010 ~~lLrs~l~~-----------------------------------------krv~~e~rls~eaf----~--w~~~~Ie~ 1042 (1605)
T KOG0260|consen 1010 NILLRSTLAT-----------------------------------------KRVLEEYRLSSEAF----E--WVLGEIEA 1042 (1605)
T ss_pred             HHHHHhhHHH-----------------------------------------HHHHHHhcccHHHH----H--HHhhhhhh
Confidence            1223333332                                         22335567888776    7  99999999


Q ss_pred             HhhhccCCCCcchhhhhhcccCCcccccccccccccc-------------------------------------------
Q psy13846       1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------------------------------- 1145 (1423)
Q Consensus      1109 ~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG------------------------------------------- 1145 (1423)
                      ++.++.+.|||+||++||||||||+|||||||||+||                                           
T Consensus      1043 ~f~qa~a~pgemvg~lAaqsvgePatqmTlntfh~aGVssknVt~gvprlkei~Nv~k~~ktpsLtV~l~g~~~k~~e~a 1122 (1605)
T KOG0260|consen 1043 RFLQAEASPGEMVGALAAQSVGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEIINVAKNAKTPSLTVYLTGEAAKDNEWA 1122 (1605)
T ss_pred             heeeeecCccchHhHHHHHHhCCchhhcccchhcccceeeeeeeccCcchhhhhhhhccCCCceEEEEecchhhcchHHH
Confidence            9999999999999999999999999999999999999                                           


Q ss_pred             -------------cccceeEEEEccCCcEEEE--------------------------EEchHHHHHhcccCCHHHHHHH
Q psy13846       1146 -------------EVCEYIEEVFVPDDSFILI--------------------------KLDMDRIRLLHLEVDIDSIRYC 1186 (1423)
Q Consensus      1146 -------------~i~~~i~~~~~~~~~~~~i--------------------------~l~~~~~~~~~~~i~~~~i~~~ 1186 (1423)
                                   +++...+++|+|+...+.|                          +|.+++..+.+..+++++|...
T Consensus      1123 k~v~~~le~ttl~~vt~~t~i~ydpdp~~tvI~ed~e~v~a~~e~pd~D~~~ispwlLrlelDr~~m~dk~ltm~~ia~~ 1202 (1605)
T KOG0260|consen 1123 KLVQCCLEHTTLKDVTRATEIYYDPDPQSTVIDEDREFVVAYYEMPDEDVGRISPWLLRLELDRASMTDKKLTMEQIAEK 1202 (1605)
T ss_pred             HHHhhhcccccHHhhhccCcceecCCCcceeeccchhhHHhhhcCcccchhhcChHHHHhhhhhhhcccccccHHHHHHH
Confidence                         2334445678887655444                          4455555555666778888777


Q ss_pred             HHhccccCCceEEecC----cEEEEEeCCCCchhhhHHHHH-HhccCCcEEcccCCccEEEEecccc---cceeeEEEEe
Q psy13846       1187 IERTRGISGHLTVSGH----SFLILKPKDSSKSFNSKMYQM-KQLLPSVVIKGVQGINRAVIHEEDV---EGVTKYKLLV 1258 (1423)
Q Consensus      1187 i~~~k~~~~~~~~~~~----~~i~i~~~~~~~~~~~~l~~l-~~~l~~~~v~Gi~~i~r~~i~~~~~---~~~~~~~l~t 1258 (1423)
                      |.+--..+-.....++    ..++++.-..+++ ...+..+ .+.|.++.++|++.|.++++...+.   +..++|.|+|
T Consensus      1203 i~~~f~~d~~~i~~ddna~klv~r~ri~~~~e~-D~~l~~Ie~~ml~~~~l~G~~~i~kV~m~~~~~G~f~~~~ew~LeT 1281 (1605)
T KOG0260|consen 1203 INRGFGSDLACIFSDDNAEKLVLRLRIAKEEED-DVFLKCIEANMLGDMTLRGIPDIFKVYMSPTEDGEFKPVDEWDLET 1281 (1605)
T ss_pred             HHhhccCCCceeecccCCcceEEEEEecCccch-hHHHHHHHHhhhhhcccCCccccceEEEeecCCCceeecceeEEec
Confidence            7431111111111111    2455555433222 2344555 4678899999999999999975432   2347999999


Q ss_pred             cCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeeccc
Q psy13846       1259 EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHG 1338 (1423)
Q Consensus      1259 eG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g 1338 (1423)
                      +|+||.+++..++||..||+|||+.+|+++|||||+|.++++|+..|....|.+||+||+.|++|.||++|.+++|+|||
T Consensus      1282 dg~~l~~v~s~~~vD~~rt~sn~l~ei~~vlgIea~r~a~~~e~~~vi~f~gsyVnyrhlaLl~dvmT~~g~lm~itRhg 1361 (1605)
T KOG0260|consen 1282 DGVNLRRVLSEPDVDPARTTSNDLVEIAEVLGIEAVRKALLRELLNVISFDGSYVNYRHLALLCDVMTARGHLMAITRHG 1361 (1605)
T ss_pred             CchhHHhhhccCCCCcccccccchhhhhhhhcHHHHHhhhhhhhhheEeecccchhHHHHHHHHHHHhcccceeeeeccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccchhhhccchhhHHHHHhhcccCCcccccccccceeeccccccccceEEEeecCCCCC
Q psy13846       1339 LAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 1401 (1423)
Q Consensus      1339 ~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~~~~~ 1401 (1423)
                      +++...++|+++|||||+++|.+||++++.|.++|++|+|++|++.|.|||+|+|+.+.+...
T Consensus      1362 ~nr~~tgaLmrcSfEetv~il~~aa~~~ekd~~rgvsEnImlgqlap~gTg~~d~~ld~e~l~ 1424 (1605)
T KOG0260|consen 1362 INRQDTGALMRCSFEETVDILMDAAAHAEKDPCRGVSENIMLGQLAPMGTGCFDLMLDAEKLK 1424 (1605)
T ss_pred             cchhhccccccccHHHHHHHHHHHHhhhccCCCccceeeeeecccccCCCcceeeeccHHhhh
Confidence            999899999999999999999999999999999999999999999999999999999977643

>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'

Probab=100.00  E-value=1.7e-128  Score=1238.18  Aligned_cols=533  Identities=39%  Similarity=0.689  Sum_probs=480.3

Q ss_pred             cceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCc
Q psy13846         77 VFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP  156 (1423)
Q Consensus        77 ~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~P  156 (1423)
                      .+|.+ |+|++||+|||+++||++|+++++|  |.+|+|++|||||||||+.++...|+|||++..+||||||||+|+.|
T Consensus         2 ~~I~~-I~F~~~S~eEI~k~Sv~~It~~~~~--d~~g~P~~gGL~D~RLG~~~~~~~C~TCg~~~~~CpGHFGhIeL~~P   78 (868)
T TIGR02390         2 KKIGS-IKFGLLSPEEIRKMSVVEVVTADTY--DDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARP   78 (868)
T ss_pred             ceeeE-EEEeCCCHHHHHHhCeeEEeccccc--CCCCCcCCCCccCcccCCCCCCCCCCCCCCCCCcCCCcceEEecccc
Confidence            35788 9999999999999999999999999  77999999999999999999999999999999999999999999999


Q ss_pred             eeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchh-HHHHHHHHHHHHHHccCCccCCCCCCCCCceee
Q psy13846        157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS-YLVRKSLKKKILETTKKVSVCPHCGEINGVVKK  235 (1423)
Q Consensus       157 V~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~-~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk  235 (1423)
                      |||||||+.++++|+|+|++  |++|++++++...|.+++++.... ...++.+.+++.+.|++.++|++||+.+|.+|+
T Consensus        79 Vfhpgf~~~i~kiL~~vC~~--C~rll~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~i~~~~~~~~~C~~Cg~~~p~ir~  156 (868)
T TIGR02390        79 VVHVGFAKEIYKILRATCRK--CGRITLTEEEIEQYLEKINKLKEEGGDLASTLIEKIVKEAAKRMKCPHCGEEQKKIKF  156 (868)
T ss_pred             ccchhHHHHHHHHHHHHhhh--cCceeeCccccHHHHHHHHhcccchhhhHHHHHHHHHHHhhcCCCCCCCCCcCceEEE
Confidence            99999999999999999999  999999988888888877654321 112257788899999988999999999999998


Q ss_pred             cCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCCCC
Q psy13846        236 CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP  315 (1423)
Q Consensus       236 ~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arP  315 (1423)
                      .+.... ..    ..                            + ...+.|+|.+|+++|++||++|+++|++++..++|
T Consensus       157 ~~~~~~-~~----~~----------------------------~-~~~~~L~p~~v~~ilk~I~~eD~~lLG~~p~~~~P  202 (868)
T TIGR02390       157 EKPTYF-YE----EG----------------------------K-EGDVKLTPSEIRERLEKIPDEDAELLGINPKVARP  202 (868)
T ss_pred             eeeeee-ee----cc----------------------------C-CCCeecCHHHHHHHHHhCCHHHHHHhCCCCCCCCc
Confidence            752211 00    00                            0 12356899999999999999999999999988999


Q ss_pred             cceEEEEecCCCCCCCCcEEcCCC-C------------------------------------------------------
Q psy13846        316 SDLILTRLLVPPNCIRPSVISDLK-S------------------------------------------------------  340 (1423)
Q Consensus       316 e~liLt~lpVPP~~vRPsv~~g~~-~------------------------------------------------------  340 (1423)
                      +||||++|||||+|+||++.+++. .                                                      
T Consensus       203 e~~ilt~LPVPP~~iRPsv~~~~g~~~EDDLT~~L~~II~~N~~Lk~~~~~g~~~~~~~~~~~~LQ~~v~~~~d~~~~~~  282 (868)
T TIGR02390       203 EWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGI  282 (868)
T ss_pred             ceeeEeccccCCCCCcCeEEeCCCcccCChHHHHHHHHHHHHHHHHHHHHcCCchhhhHHHHHHHHHHHHHHHcCCCCCC
Confidence            999999999999999999998753 1                                                      


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        341 --------------------------------------------------------------------------------  340 (1423)
Q Consensus       341 --------------------------------------------------------------------------------  340 (1423)
                                                                                                      
T Consensus       283 ~~~~~~~~~~~~~i~~~l~gK~G~~R~nl~GKRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~Vt~~N~~~l~~l  362 (868)
T TIGR02390       283 PPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREY  362 (868)
T ss_pred             CccccCCCCCchhhHhhhcccccccccccccccccccCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEehhhHHHHHHH
Confidence                                                                                            


Q ss_pred             -----------------------------------------------CCeEEEEecCccccccccceeeeEEecCCceee
Q psy13846        341 -----------------------------------------------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRF  373 (1423)
Q Consensus       341 -----------------------------------------------~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~  373 (1423)
                                                                     +||+|||||||||||+|||||++|++|++||||
T Consensus       363 v~ng~~~~pga~~i~~~~g~~~~l~~~~~~~~~~~l~~g~~v~rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~r~  442 (868)
T TIGR02390       363 VLNGPDSWPGANYVIRPDGRRIKIRDENKEELAERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRL  442 (868)
T ss_pred             HHcCCccCCCceEEEcCCCcEEechhhhHHHHHhhcccCCEEEEehhcCccceeccCCccccccceeEEEEEecCceEee
Confidence                                                           789999999999999999999999999999999


Q ss_pred             ccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecc
Q psy13846        374 NECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ  453 (1423)
Q Consensus       374 ~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~  453 (1423)
                      ||++|+||||||||||||+|+|||++|||||+              +||.+.+|++||++|+|+++++||+++|+|.||.
T Consensus       443 n~~~c~~~NADFDGDeMn~h~Pqs~~a~aEa~--------------~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~~LT~  508 (868)
T TIGR02390       443 NLAVCPPYNADFDGDEMNLHVPQTEEARAEAR--------------ELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTH  508 (868)
T ss_pred             ccccCCccccCcccceeeEecCCCHHHHHHHH--------------HHhhchhceecCCCCCeeEEeehhhhhheeeeee
Confidence            99999999999999999999999999999999              9999999999999999999999999999999999


Q ss_pred             cccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeeccccccc-
Q psy13846        454 KNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTA-  532 (1423)
Q Consensus       454 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~-  532 (1423)
                      +|+|+++++++++++...     +.  +      .+|+|+|++|.++||||||||++||+.      +|+..+.+.+.. 
T Consensus       509 ~d~f~~~~~~~~l~~~~~-----~~--~------~~~~p~i~kp~~lwTGKqi~s~~lp~~------~n~~~~~~~~~~~  569 (868)
T TIGR02390       509 KSTLFTKEEVQTILGVAG-----YF--G------DPPEPAIEKPKEYWTGKQIFSAFLPED------LNFEGRAKICSGS  569 (868)
T ss_pred             ccccCCHHHHHHHHhcCC-----cc--c------cCCCceecCCcccccHHHHHHHhcCCC------Ccceecccccccc
Confidence            999999999999987643     11  1      678999999999999999999999864      444444443321 


Q ss_pred             ---CcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCC
Q psy13846        533 ---NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVT  609 (1423)
Q Consensus       533 ---~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~  609 (1423)
                         ..+++++|+.|+|+|||+++|++||+++|+ ++++++|.+|++||++.|+.||+++++++++||+.+|||+|++|++
T Consensus       570 ~~~~~~~~~~d~~v~i~~g~ll~G~ldK~~lg~-~~~~li~~i~~~yG~~~a~~fl~~~~~l~~~~l~~~GfSigi~D~~  648 (868)
T TIGR02390       570 DACKKEECPHDAYVVIKNGKLLKGVIDKKAIGA-EKGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDID  648 (868)
T ss_pred             cccccccCCCcceEEEecCeEEeeeecHHHhcc-CcccHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhccEEeehhhee
Confidence               345688999999999999999999999998 5789999999999999999999999999999999999999999998


Q ss_pred             CCc-----------------------------------------------------------------------------
Q psy13846        610 PGQ-----------------------------------------------------------------------------  612 (1423)
Q Consensus       610 ~~~-----------------------------------------------------------------------------  612 (1423)
                      +++                                                                             
T Consensus       649 ~~~~~~~~~~~~i~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~~~~M~~sG  728 (868)
T TIGR02390       649 IPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTG  728 (868)
T ss_pred             eCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhhhcc
Confidence            654                                                                             


Q ss_pred             -----------------------------------------------cccccccccCCCceeeeeecccccccchhcccc
Q psy13846        613 -----------------------------------------------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVK  645 (1423)
Q Consensus       613 -----------------------------------------------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvK  645 (1423)
                                                                     |||.+||++||+|+|||||||||||||||||||
T Consensus       729 sKGS~~Ni~Qi~~~lGQQ~~~g~ri~~~~~~rtlp~f~~~d~~~~~~GfV~~sF~~GL~p~EfFfH~m~gReGLiDTAvK  808 (868)
T TIGR02390       729 ARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVR  808 (868)
T ss_pred             CCcccccHHHHHhccCccccCCCcCccccccCCCCCCCCCCCCcccCceecccccCCCCHHHHHHHHhhhcccccccccc
Confidence                                                           899999999999999999999999999999999


Q ss_pred             cCCCCcchHHHHHHHhhhhhcccceeecc-------ccCCCccC
Q psy13846        646 TAETGYMQRRLVKSLEDLCVQYDMSFDAA-------FYGQTDCI  682 (1423)
Q Consensus       646 Ta~sGYlqRrLvk~ledl~v~yD~tVR~s-------~yG~~~~~  682 (1423)
                      ||+||||||||||+|||++|+||+||||+       .||+|+.+
T Consensus       809 Ta~sGYLqRrLvk~lEdl~v~yD~tVR~~~g~iiQf~YG~dg~d  852 (868)
T TIGR02390       809 TSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVD  852 (868)
T ss_pred             ccccchhHHHHHHHHhheEEecCCeEEeCCCcEEEEeccCCCcC
Confidence            99999999999999999999999999987       37776443

This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.

>PRK08566 DNA-directed RNA polymerase subunit A'; Validated

Probab=100.00  E-value=3.6e-128  Score=1238.97  Aligned_cols=534  Identities=40%  Similarity=0.705  Sum_probs=483.9

Q ss_pred             ccceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccC
Q psy13846         76 KVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL  155 (1423)
Q Consensus        76 ~~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~  155 (1423)
                      ..+|.+ |+|++||++||+++||++|+++++|  |.+|+|++|||||||||++++...|+|||++..+||||||||+|+.
T Consensus         6 ~~~I~~-I~F~~~S~eEI~klSv~~It~~~~~--d~~g~P~~gGL~D~RLG~~~~~~~C~TCg~~~~~CPGHFGhIeL~~   82 (882)
T PRK08566          6 PKRIGS-IKFGLLSPEEIRKMSVTKIITADTY--DDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELAR   82 (882)
T ss_pred             ceeeee-EEEecCCHHHHHHhCeEEEeccccc--CCCCCcCCCCCCCcccCCCCCCCCCCCCCCCCCcCCCcceEEeccc
Confidence            356889 9999999999999999999999999  7799999999999999999999999999999999999999999999


Q ss_pred             ceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceee
Q psy13846        156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKK  235 (1423)
Q Consensus       156 PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk  235 (1423)
                      ||||||||+.+++||+|+|++  |++|++++++...|..+++.+...+...+.+.+++.+.|++.++|+|||+.+|.+++
T Consensus        83 PVfhpgf~~~v~~iL~~iC~~--C~rll~~~~~~~~~~~~l~~~~~~~~~~~~l~k~i~k~~k~~~~C~~Cg~~~~ki~~  160 (882)
T PRK08566         83 PVIHVGFAKLIYKLLRATCRE--CGRLKLTEEEIEEYLEKLERLKEWGSLADDLIKEVKKEAAKRMVCPHCGEKQYKIKF  160 (882)
T ss_pred             cccchhHHHHHHHHHHHhhhh--hCceeccccchHHHHHHHhchhhhhhhHHHHHHHHHHHhcCCCCCCCcCCCCceEEE
Confidence            999999999999999999999  999999998888899988876644445567888999999999999999999999987


Q ss_pred             cCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCCCC
Q psy13846        236 CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP  315 (1423)
Q Consensus       236 ~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arP  315 (1423)
                      ++.......     .                            + ...+.++|.+|+++|++||++|+++|++++..++|
T Consensus       161 ~~~~~~~~~-----~----------------------------~-~~~~~L~p~~V~~ilk~I~~eD~~lLg~~~~~~~P  206 (882)
T PRK08566        161 EKPTTFYEE-----R----------------------------K-EGLVKLTPSDIRERLEKIPDEDLELLGINPEVARP  206 (882)
T ss_pred             ecceeEEEe-----c----------------------------C-CCceeCCHHHHHHHHHhCCHHHHHHhCCCCCCCCc
Confidence            642111000     0                            0 12457899999999999999999999999999999


Q ss_pred             cceEEEEecCCCCCCCCcEEcCCC-C------------------------------------------------------
Q psy13846        316 SDLILTRLLVPPNCIRPSVISDLK-S------------------------------------------------------  340 (1423)
Q Consensus       316 e~liLt~lpVPP~~vRPsv~~g~~-~------------------------------------------------------  340 (1423)
                      +||||++|||||+|+||++.+++. .                                                      
T Consensus       207 e~~il~~lPVpP~~iRPsv~~~~g~~~eDDLT~~L~~II~~N~~Lk~~~~~g~~~~~~~~~~~~LQ~~v~~~~d~~~~~~  286 (882)
T PRK08566        207 EWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPGI  286 (882)
T ss_pred             ceeEEeeeecCCCCCcCcEEeCCCcccCchHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhcCCccCC
Confidence            999999999999999999998653 1                                                      


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        341 --------------------------------------------------------------------------------  340 (1423)
Q Consensus       341 --------------------------------------------------------------------------------  340 (1423)
                                                                                                      
T Consensus       287 ~~~~~~~~~~~~~i~~~l~gK~G~fR~nl~GKRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~v~~~N~~~l~~~  366 (882)
T PRK08566        287 PPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREY  366 (882)
T ss_pred             cccccCCCCCccchHHhcccCCCccccccccccccCcCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEchhhHHHHHHH
Confidence                                                                                            


Q ss_pred             -----------------------------------------------CCeEEEEecCccccccccceeeeEEecCCceee
Q psy13846        341 -----------------------------------------------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRF  373 (1423)
Q Consensus       341 -----------------------------------------------~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~  373 (1423)
                                                                     +||+|||||||||||+|||||++|++|++||||
T Consensus       367 v~ng~~~~pga~~i~~~~g~~~~l~~~~~~~~~~~l~~g~~v~Rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~r~  446 (882)
T PRK08566        367 VLNGPEKHPGANYVIRPDGRRIKLTDKNKEELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRL  446 (882)
T ss_pred             HHcCCCcCCCceEEEcCCCceeeehhhhHHHHHHhccccceehhhhhcCceeeecCCCcccccccceeEEEEecCceEee
Confidence                                                           789999999999999999999999999999999


Q ss_pred             ccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecc
Q psy13846        374 NECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ  453 (1423)
Q Consensus       374 ~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~  453 (1423)
                      ||++|+||||||||||||+|+|||++|||||+              .||.+.+|++||++|+|+++++||+++|+|+||.
T Consensus       447 n~~~c~~~NADFDGDeMn~h~Pqs~~a~aEa~--------------~Lm~~~~~~~sp~~g~pi~~~~QD~l~g~~~lt~  512 (882)
T PRK08566        447 NLAVCPPYNADFDGDEMNLHVPQTEEARAEAR--------------ILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTR  512 (882)
T ss_pred             ccccCCCccCCccCcEEEEecCCCHHHHHHHH--------------HHhcchhcEecCCCCCeeEEeehHHHHHHHHHHh
Confidence            99999999999999999999999999999999              9999999999999999999999999999999999


Q ss_pred             cccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeecccccc--
Q psy13846        454 KNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYT--  531 (1423)
Q Consensus       454 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~--  531 (1423)
                      +|+|++++|+++++++...      ..+      .+|+|+|++|.++||||||||++||++.      ++..+.+...  
T Consensus       513 ~d~f~~~~~~~~l~~~~~~------~~~------~~~~pai~~p~~lwTGKqi~s~~lp~~~------~~~~~~~~~~~~  574 (882)
T PRK08566        513 KSTLFTKEEALDLLRAAGI------DEL------PEPEPAIENGKPYWTGKQIFSLFLPKDL------NLEFKAKICSGC  574 (882)
T ss_pred             ccccCCHHHHHHHHHhCCc------ccc------ccCCcccCCCcccccHHHHHHHHcCCCC------Cceeeccccccc
Confidence            9999999999999998741      112      6889999999999999999999998753      3333222221  


Q ss_pred             --cCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCC
Q psy13846        532 --ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVT  609 (1423)
Q Consensus       532 --~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~  609 (1423)
                        ....++++|+.|+|+||||++|++||+.+|+ +.++++|.+|++||++.|+.||+++++++++||+.+|||||++|++
T Consensus       575 ~~~~~~~~~~d~~v~i~~gell~g~ldK~~lg~-~~~~li~~i~~~yG~~~a~~fl~~~~~l~~~~l~~~GfSigi~D~~  653 (882)
T PRK08566        575 DECKKEDCEHDAYVVIKNGKLLEGVIDKKAIGA-EQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDED  653 (882)
T ss_pred             cccccccCCCCceEEEecCEEEeccccHHHhhc-ccchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCEEeehhhcc
Confidence              1234678899999999999999999999998 4599999999999999999999999999999999999999999998


Q ss_pred             CCc-----------------------------------------------------------------------------
Q psy13846        610 PGQ-----------------------------------------------------------------------------  612 (1423)
Q Consensus       610 ~~~-----------------------------------------------------------------------------  612 (1423)
                      +++                                                                             
T Consensus       654 ~~~~~~~~~~~~i~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~~~~M~~SG  733 (882)
T PRK08566        654 IPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTG  733 (882)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcceeeeccc
Confidence            655                                                                             


Q ss_pred             -----------------------------------------------cccccccccCCCceeeeeecccccccchhcccc
Q psy13846        613 -----------------------------------------------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVK  645 (1423)
Q Consensus       613 -----------------------------------------------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvK  645 (1423)
                                                                     |||.+||++||+|+|||||||||||||||||||
T Consensus       734 sKGS~~N~~Qi~~~lGqQ~~~g~ri~~~~~~rtLP~f~~~d~~~~~~GfV~~sF~~GL~p~EfffH~m~GReGliDTAvk  813 (882)
T PRK08566        734 ARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVR  813 (882)
T ss_pred             cccCHHHHHHHHhccCceecCCCcCccCccCccCCCCCCCCCCcccCceeeccccCCCCHHHHHHHHhhhccccccccee
Confidence                                                           899999999999999999999999999999999


Q ss_pred             cCCCCcchHHHHHHHhhhhhcccceeecc-------ccCCCcc
Q psy13846        646 TAETGYMQRRLVKSLEDLCVQYDMSFDAA-------FYGQTDC  681 (1423)
Q Consensus       646 Ta~sGYlqRrLvk~ledl~v~yD~tVR~s-------~yG~~~~  681 (1423)
                      ||+||||||||||+|||++|+||+|||||       .||+|+.
T Consensus       814 Ta~sGYlqRrLvk~ledl~v~yD~tVR~s~g~iiQf~YG~dg~  856 (882)
T PRK08566        814 TSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGV  856 (882)
T ss_pred             eccCccchHHHHHHHhheEEeeCCceEcCCCcEEEEeccCCCc
Confidence            99999999999999999999999999987       3776643

>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form

Probab=100.00  E-value=2.5e-125  Score=1198.33  Aligned_cols=476  Identities=26%  Similarity=0.421  Sum_probs=370.1

Q ss_pred             EEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCC-CCC--------------CCCCccCCCCCCCcccC--
Q psy13846         83 IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRM-GTN--------------QKEANCTTCGQNLSDCV--  145 (1423)
Q Consensus        83 i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rL-G~~--------------~~~~~C~TCg~~~~eCp--  145 (1423)
                      +++++.|||+|+++|+.||++|++++ +.+.+|..+||+|+|+ ||.              ++...|.+||....+|+  
T Consensus         2 i~i~laSPe~I~~ws~geV~~petin-y~t~kPe~~GLfcerIFGp~k~~ec~Cgkyk~~~~~~~~C~~Cgve~t~~~vr   80 (1140)
T TIGR02386         2 IKISIASPDTIRNWSYGEVKKPETIN-YRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR   80 (1140)
T ss_pred             eEEEecCHHHHHhhhceEEeccceec-CCCCccCCCCcccchhcCCccCceeccccccccCcCCcCCCCCCCCcccchhh
Confidence            79999999999999999999999997 6799999999999998 997              46678999999999999  


Q ss_pred             -CccceEEccCceeEEeeecc-----------HHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHH
Q psy13846        146 -GHFGYIDLPLPVFHIGYFRC-----------VINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKI  213 (1423)
Q Consensus       146 -GHfGhIeL~~PV~h~gffd~-----------v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i  213 (1423)
                       +|||||+|+.||+|+|||+.           ..+.|+++|++  |+.+.+.+.........+...       .++. ++
T Consensus        81 r~rmGhI~La~Pv~Hiwy~k~~ps~~~~ll~~~~k~le~v~y~--~~~~v~~~~~~~~~~~~~~~~-------~~~~-~~  150 (1140)
T TIGR02386        81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYF--ENYVVLDPGDTKLDKKEVLDE-------TEYR-EV  150 (1140)
T ss_pred             hhcccceeecCCceeehhcCCCchHHHHHhCCCHHHhhheeec--cceEEeCCCCCchhhhhhhch-------hHHH-HH
Confidence             99999999999999999998           38999999999  999887663211101111000       0111 11


Q ss_pred             HHHccCCccCCCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHH
Q psy13846        214 LETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQ  293 (1423)
Q Consensus       214 ~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~e  293 (1423)
                      .+... ...=..||+........+ +.+            +.....+.+++..    ...    .. +..+.+...++.+
T Consensus       151 ~~~~~-~~~~~~~G~~ai~~~l~~-~dl------------~~~~~~~~~~~~~----~~~----~~-~~~~~~krl~~~~  207 (1140)
T TIGR02386       151 LKRYG-DGFRAGMGAEAIKELLEK-IDL------------DKEIEELKIQLRE----SKS----DQ-KRKKLLKRLEIVE  207 (1140)
T ss_pred             HHHhc-cCcccccchHHHHHHHhc-CCH------------HHHHHHHHHHHHh----ccc----hh-hHHhhhhHHHHHH
Confidence            11110 000112343221111000 000            0111111111111    000    00 1123455666666


Q ss_pred             HhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCC---------------------------------
Q psy13846        294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS---------------------------------  340 (1423)
Q Consensus       294 iLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~---------------------------------  340 (1423)
                      .|..             +++||+||+|++|||||+++||++.+++..                                 
T Consensus       208 ~f~~-------------s~~~Pewmil~~lPV~Pp~lRP~v~l~gg~~~~sDLn~lyr~II~~Nn~Lk~~~~~~ap~~ii  274 (1140)
T TIGR02386       208 AFKD-------------SGNRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIV  274 (1140)
T ss_pred             HHHh-------------cCCChHHhhhhcccCCCCccCCcEEeCCCccccCchHHHHHHHHHHHHHHHHHHHcCCcHHHH
Confidence            6665             357999999999999999999999997641                                 


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        341 --------------------------------------------------------------------------------  340 (1423)
Q Consensus       341 --------------------------------------------------------------------------------  340 (1423)
                                                                                                      
T Consensus       275 ~~~~~~LQ~aV~~liDn~~~g~~~~~~~~rplksls~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GlP~~m  354 (1140)
T TIGR02386       275 RNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKM  354 (1140)
T ss_pred             HHHHHHHHHHHHHHhcccccCCCccCcCCCchhhHHHhhcCCCCcccccccccccCCCCCCeEcCCCCcccccccChHHH
Confidence                                                                                            


Q ss_pred             --------------------------------------------CCeEEEEecCccccccccceeeeEEecCCceeeccC
Q psy13846        341 --------------------------------------------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNEC  376 (1423)
Q Consensus       341 --------------------------------------------~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~  376 (1423)
                                                                  ++|+|||||||||||+|||||++++++++|||+||+
T Consensus       355 A~~L~~Pf~i~~L~~~~~~~~i~~ak~~i~~~~~~v~~vl~~vi~~d~VLlNRqPTLHRlsIqAf~~~l~~gktirlhpl  434 (1140)
T TIGR02386       355 ALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPL  434 (1140)
T ss_pred             HHHcCchHHHHHHHHcCcccchHHHHHHHHhcCCccceEEEEccCCcEEEecCCCcccccccceeEEEEecCceEEEccc
Confidence                                                        789999999999999999999999999999999999


Q ss_pred             CCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccc-
Q psy13846        377 VCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN-  455 (1423)
Q Consensus       377 ~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~-  455 (1423)
                      +|+||||||||||||+|+|||++|||||+              .||.+.+|++||++|+|+++++||+++|+|.||.++ 
T Consensus       435 vC~~fNADFDGDeMnvHvPqS~eA~aEa~--------------~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~  500 (1140)
T TIGR02386       435 VCTAFNADFDGDQMAVHVPLSPEAQAEAR--------------ALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKP  500 (1140)
T ss_pred             ccCcccCCCCcceeEeecCCCHHHHHHHH--------------HHhCCcccEecCCCCCceEEeechhhheeeEeeeccc
Confidence            99999999999999999999999999999              999999999999999999999999999999999996 


Q ss_pred             -------cCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeee--ecceeeeecccCCCCcccccceeec
Q psy13846        456 -------AFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIW--TGKQIFSLILKPNRDCPVNANLKTK  526 (1423)
Q Consensus       456 -------~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~w--tGKqi~s~il~~~~~~~~~~~~~~~  526 (1423)
                             .|++++++......   +....+..++          ...++..+|  +|||+|+.++|++...      .  
T Consensus       501 ~~~~~~~~F~~~~e~~~~~~~---~~i~l~~~i~----------~~~~g~~~~tt~Gr~if~~ilP~~~~~------~--  559 (1140)
T TIGR02386       501 GAKGEGKIFSNVDEAIRAYDN---GKVHLHALIG----------VRTSGEILETTVGRVIFNEILPEGFPY------I--  559 (1140)
T ss_pred             cccCcCceeCCHHHHHHHHHc---CCccCCCceE----------EeccccEEEccchHHHHHHHcCCcccc------c--
Confidence                   68999998764321   1112222220          001234566  6999999999864210      0  


Q ss_pred             ccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecC
Q psy13846        527 GRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIG  606 (1423)
Q Consensus       527 ~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~  606 (1423)
                                  +       .    .+.++|+.+|     ++++.+|++||++.|+.||++++++..+|++.+|||+|++
T Consensus       560 ------------n-------~----~~~l~Kk~lg-----~LI~~i~~~~G~~~t~~~LD~lk~Lgf~~at~~GfSigi~  611 (1140)
T TIGR02386       560 ------------N-------D----NEPLSKKEIS-----SLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISAS  611 (1140)
T ss_pred             ------------c-------c----ccccchHHHH-----HHHHHHHHHhChHHHHHHHHHHHHHHHHHHHhcCeeeeec
Confidence                        0       0    0167888875     7999999999999999999999999999999999999999


Q ss_pred             CCCCCc--------------------------------------------------------------------------
Q psy13846        607 DVTPGQ--------------------------------------------------------------------------  612 (1423)
Q Consensus       607 D~~~~~--------------------------------------------------------------------------  612 (1423)
                      |+.+++                                                                          
T Consensus       612 Dl~ip~~K~~ii~~a~~~v~~i~~~y~~G~lt~~er~~kvi~iw~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~SGARGS  691 (1140)
T TIGR02386       612 DIVVPDEKYEILKEADKEVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLLKKDTYKFNPIFMMADSGARGN  691 (1140)
T ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCcHhhhhhcccccC
Confidence            996554                                                                          


Q ss_pred             -----------------------cccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhccc
Q psy13846        613 -----------------------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD  668 (1423)
Q Consensus       613 -----------------------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD  668 (1423)
                                             -||.+||++||+|+|||||||||||||+|||+|||+||||||||||++||++|.||
T Consensus       692 ~~ni~QL~GmrGlma~p~Grii~~PI~ssF~eGLtp~EyF~st~GaRkGLiDTAlKTAdSGYLtRRLVdv~qDviV~~d  770 (1140)
T TIGR02386       692 ISQFRQLAGMRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREE  770 (1140)
T ss_pred             HHHHHHHHhCCCcccCCCCCccccchhhccccCCCHHHHhhhccchhccccchheeecccceeeeehhhhhcceEEEeC
Confidence                                   47999999999999999999999999999999999999999999999999999995

Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.

>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional

Probab=100.00  E-value=2.5e-123  Score=1181.28  Aligned_cols=481  Identities=29%  Similarity=0.444  Sum_probs=368.5

Q ss_pred             ceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCC-CCCCCCCccCCCCCCC------cccC-----
Q psy13846         78 FFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRM-GTNQKEANCTTCGQNL------SDCV-----  145 (1423)
Q Consensus        78 ~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rL-G~~~~~~~C~TCg~~~------~eCp-----  145 (1423)
                      .+.. ++.++.|||+|+++|+-||++|++.+ +.+.+|..+||+|.|+ || .++..| .||+..      ..|+     
T Consensus         6 ~~~~-i~i~laspe~I~~ws~GeV~~petin-yrt~kPe~~GLfcerIFgp-~kd~eC-~Cgkyk~~~~~~~~C~~cgve   81 (1156)
T PRK00566          6 DFDA-IKIGLASPEKIRSWSYGEVKKPETIN-YRTLKPERDGLFCERIFGP-TKDYEC-LCGKYKRVRYKGIICERCGVE   81 (1156)
T ss_pred             Ccce-EEEEccCHHHHHHhhcceEccccccc-cCCCccCCCCcccchhcCc-ccCcEE-eCccccccCcCCcCCCCCCce
Confidence            4677 99999999999999999999999997 6799999999999997 66 467788 888532      4788     


Q ss_pred             --------CccceEEccCceeEEeeeccH-----------HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHH
Q psy13846        146 --------GHFGYIDLPLPVFHIGYFRCV-----------INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR  206 (1423)
Q Consensus       146 --------GHfGhIeL~~PV~h~gffd~v-----------~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~  206 (1423)
                              +|||||+|+.||.|+|||+..           .+.|+++|+.  |+.+...+... . +.+....  .....
T Consensus        82 ~~~~~vrr~rmGhI~La~Pv~Hiwy~k~~ps~i~~ll~~~~k~le~v~y~--~~~~v~~~~~~-~-~~~~~~~--~~~~~  155 (1156)
T PRK00566         82 VTRSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYF--ESYVVIDPGDT-P-LEKKQLL--TEEEY  155 (1156)
T ss_pred             eeechhhhhhcceeeecCceeeeeecCCCchHHHHHhCCCHHHhhheeec--ceEEEeCCCCC-c-hhhhccc--CHHHH
Confidence                    999999999999999999944           9999999999  99887766431 1 1100000  00011


Q ss_pred             HHHHHHHHHHccCCccCCCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccC
Q psy13846        207 KSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTL  286 (1423)
Q Consensus       207 ~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L  286 (1423)
                      +    ++.+... ...=..||+           +...+.+....  -+.....+.+++...   ...    .  +..+.+
T Consensus       156 ~----~~~~~~~-~~~~~~~Ga-----------~ai~~ll~~~d--l~~~~~~l~~~~~~~---~~~----~--~~~~~~  208 (1156)
T PRK00566        156 R----EALEEYG-DEFVAKMGA-----------EAIKELLKNID--LEAEAEELREELKET---GSE----Q--KRKKAL  208 (1156)
T ss_pred             H----HHHHHhc-ccccccccH-----------HHHHHHHHhCC--HHHHHHHHHHHHHhc---ccc----h--hHHHHH
Confidence            1    1111110 000001111           11111110000  011111111111110   000    0  112223


Q ss_pred             CHHHHHHHhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCC--------------------------
Q psy13846        287 NPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS--------------------------  340 (1423)
Q Consensus       287 ~p~~V~eiLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~--------------------------  340 (1423)
                      ...++.+.|..             +++||+||+|++|||||+|+||++.+++..                          
T Consensus       209 krl~~~~~f~~-------------s~~~Pewmil~~lPV~Pp~lRP~v~l~~g~~~~sDLn~lyr~II~rNnrLk~~~~~  275 (1156)
T PRK00566        209 KRLKVVEAFRK-------------SGNKPEWMILDVLPVIPPDLRPLVQLDGGRFATSDLNDLYRRVINRNNRLKRLLEL  275 (1156)
T ss_pred             HHHHHHHHHHc-------------CCCCccEeeEeecccCCCcccCceEeCCCcccCCchHHHHHHHHHHHHHHHHHHHc
Confidence            34444444443             357999999999999999999999998642                          


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        341 --------------------------------------------------------------------------------  340 (1423)
Q Consensus       341 --------------------------------------------------------------------------------  340 (1423)
                                                                                                      
T Consensus       276 ~ap~~ii~~~~~~LQ~aV~~lidn~~~g~~~~~~~~rplksls~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e  355 (1156)
T PRK00566        276 GAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQ  355 (1156)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHhccCccCCCcccccCCchhHHHHhhcCCCccccccccccccCCCCCceEeCCCCccccc
Confidence                                                                                            


Q ss_pred             ---------------------------------------------------CCeEEEEecCccccccccceeeeEEecCC
Q psy13846        341 ---------------------------------------------------DNDVVLFNRQPSLHKLSIMAHRAKVLPHR  369 (1423)
Q Consensus       341 ---------------------------------------------------~~d~Vl~nRqPsLHk~Simah~~~~~~~~  369 (1423)
                                                                         +||+|||||||||||+|||||++++++++
T Consensus       356 ~GvP~~mA~eL~~Pf~i~~L~~~g~~~~ik~ak~~~~~~~~~v~~vle~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gk  435 (1156)
T PRK00566        356 CGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGK  435 (1156)
T ss_pred             ccChHHHHHHhCcHHHHHHHHHcCCccchHhhhhhhhhhcCcceEEEEEecCCCEEEecCCCcccccccceeEEEEecCc
Confidence                                                               89999999999999999999999999999


Q ss_pred             ceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEE
Q psy13846        370 TFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGY  449 (1423)
Q Consensus       370 tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~  449 (1423)
                      ||||||++|+||||||||||||+|+|||++|||||+              .||.+.+|++||++|+|+++++||+++|+|
T Consensus       436 tirLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~--------------~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y  501 (1156)
T PRK00566        436 AIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEAR--------------VLMLSSNNILSPANGKPIIVPSQDMVLGLY  501 (1156)
T ss_pred             eEEECccccCccccccccceeEEecCCCHHHHHHHH--------------HHhCCcccEEecCCCCeeEEeehhhhhhhh
Confidence            999999999999999999999999999999999999              999999999999999999999999999999


Q ss_pred             eecccc--------cCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCccccc
Q psy13846        450 LLTQKN--------AFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNA  521 (1423)
Q Consensus       450 ~~t~~~--------~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~  521 (1423)
                      .||.++        .|++.+++.++.+..   ..+.+..+      .+++|. .+..+.|+|||+|+.++|++..     
T Consensus       502 ~LT~~~~~~~~~~~~F~~~~e~~~~~~~~---~i~l~~~i------~~~~~~-~~~i~tt~Gk~if~~ilP~~~~-----  566 (1156)
T PRK00566        502 YLTREREGAKGEGMVFSSPEEALRAYENG---EVDLHARI------KVRITS-KKLVETTVGRVIFNEILPEGLP-----  566 (1156)
T ss_pred             eeecccccccCCCceeCCHHHHHHHHHcC---CCCCCCeE------EecCCC-CceEEcCcHHHHHHhhccccce-----
Confidence            999998        789999998875432   12333333      122221 1234679999999999986410     


Q ss_pred             ceeecccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCc
Q psy13846        522 NLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGF  601 (1423)
Q Consensus       522 ~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~Gf  601 (1423)
                              |            +   +   ..|.+||+.+|     +++|.+|++||.+.|+.||++++++..+|++.+||
T Consensus       567 --------~------------~---n---~~g~ldKk~Lg-----~LI~~i~~~yG~~~t~~~LD~ik~Lgf~yat~~Gf  615 (1156)
T PRK00566        567 --------F------------I---N---VNKPLKKKEIS-----KIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGI  615 (1156)
T ss_pred             --------e------------e---c---ccceecHHHHH-----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCe
Confidence                    0            0   0   05789999986     59999999999999999999999999999999999


Q ss_pred             ceecCCCCCCc---------------------------------------------------------------------
Q psy13846        602 SIGIGDVTPGQ---------------------------------------------------------------------  612 (1423)
Q Consensus       602 siGi~D~~~~~---------------------------------------------------------------------  612 (1423)
                      |+|++|+++.+                                                                     
T Consensus       616 Sigi~Dl~ip~~K~~ii~~a~~~v~~i~~~y~~G~lt~~er~~kvi~~w~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~S  695 (1156)
T PRK00566        616 SIGIDDIVIPPEKKEIIEEAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMMKNLSKDQESFNPIYMMADS  695 (1156)
T ss_pred             EeehhhcCcChHHHHHHHHHHHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHHHHHHHHHHhCccccCCCCChheeeec
Confidence            99999997644                                                                     


Q ss_pred             ----------------------------cccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhh
Q psy13846        613 ----------------------------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC  664 (1423)
Q Consensus       613 ----------------------------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~  664 (1423)
                                                  .||.+||++||+|+|||||||||||||+|||||||+||||||||||++||++
T Consensus       696 GARGS~~ni~QL~GmrGlma~p~G~iie~pI~ssFreGLt~~EyFfst~GaRkGLiDTALKTAdSGYLtRRLVdvaqDvi  775 (1156)
T PRK00566        696 GARGSASQIRQLAGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVI  775 (1156)
T ss_pred             cCCcCHHHHHHHHhhcCccccCCCCEeehhhhhhhhcCCCHHHHhhcCcchhhcccchheeeccceeeehhHHHhhCceE
Confidence                                        4899999999999999999999999999999999999999999999999988


Q ss_pred             hccc
Q psy13846        665 VQYD  668 (1423)
Q Consensus       665 v~yD  668 (1423)
                      |.||
T Consensus       776 V~~~  779 (1156)
T PRK00566        776 VRED  779 (1156)
T ss_pred             EEEC
Confidence            8773

>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional

Probab=100.00  E-value=1.1e-112  Score=1079.08  Aligned_cols=272  Identities=31%  Similarity=0.488  Sum_probs=233.7

Q ss_pred             CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846        341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV  420 (1423)
Q Consensus       341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~  420 (1423)
                      ++|+|||||||||||+|||||++++++++||||||++|+||||||||||||+|+|||++|||||+              .
T Consensus       495 ~gd~VLlNRqPTLHRlsIqAf~~~L~~gktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~--------------~  560 (1460)
T PRK14906        495 QDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEAR--------------V  560 (1460)
T ss_pred             ccceeEeccCcccchhccceeeEEecCCceEEecccccCccccCCcCceeeeecCCCHHHHHHHH--------------H
Confidence            79999999999999999999999999999999999999999999999999999999999999999              9


Q ss_pred             hhccccccccCCCCccccccccceEEEEEeecc-cc-------cCCCHHHHHHHHHhhccCCccccceEe-eeecccc--
Q psy13846        421 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQ-KN-------AFFNRAQTMRIASTLIADTSDICGIIK-RFSWRSW--  489 (1423)
Q Consensus       421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~-~~-------~~~~~~~~~~l~~~~~~~~~~~~~~~~-~~~~~~l--  489 (1423)
                      ||.+.+|++||++|+|+++++||+++|.|.||. ++       .|.+..++..+.++..  ..+.+..+. ++.. .+  
T Consensus       561 Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~a~~~~~--~~~l~~~i~~~~~~-~~~~  637 (1460)
T PRK14906        561 LMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDARA--DLDLQAKIVVRLSR-DMTV  637 (1460)
T ss_pred             HhcchhcEecCCCCCeeEEeeeeeeeeeEEeeeccccccccCceeCCHHHHHHHHhcCC--CccccccEEEecCc-cccc
Confidence            999999999999999999999999999999997 43       6788888877766421  113343332 1100 00  


Q ss_pred             -------CCceeecceeeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEEEeccccccccccccCCcCC
Q psy13846        490 -------NPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGS  562 (1423)
Q Consensus       490 -------~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~  562 (1423)
                             ..+...++...|+||++|+.+||.+.                                 .++.+.++|+.+| 
T Consensus       638 ~~~~~~~~~~~~~~~~~tt~Gr~Ifn~ilP~d~---------------------------------~fvN~~l~KK~Lg-  683 (1460)
T PRK14906        638 RGSYGDLEETKAGERIETTVGRIIFNQVLPEDY---------------------------------PYLNYKMVKKDIG-  683 (1460)
T ss_pred             ccccccccCCCCCceEECCCCEEEEecccCCCc---------------------------------ccccceeeHHHHH-
Confidence                   00112235567999999999998531                                 1334578888886 


Q ss_pred             CCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCc------------------------------
Q psy13846        563 GGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ------------------------------  612 (1423)
Q Consensus       563 ~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~------------------------------  612 (1423)
                          ++++.+|++||...+..|+++++++..+|++.+|||+|++|++..+                              
T Consensus       684 ----~LI~~i~~~~G~~~t~~fLD~Ik~LGf~yaT~sG~SIgi~Di~ip~~K~~iI~~A~~~V~ei~~~y~~G~iT~~Er  759 (1460)
T PRK14906        684 ----RLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKPEILAEADEKVAAIDEDYEDGFLSERER  759 (1460)
T ss_pred             ----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCCEEEeecccccChHHHHHHHHHHHHHHHHHHHHHcCCCcHHHH
Confidence                5999999999999999999999999999999999999999984433                              


Q ss_pred             ---------------------------------------------------------------cccccccccCCCceeee
Q psy13846        613 ---------------------------------------------------------------GFVQNSFFSGLTPTEFF  629 (1423)
Q Consensus       613 ---------------------------------------------------------------GfI~~sf~~GL~p~Eff  629 (1423)
                                                                                     .||.+||.+||+|.|||
T Consensus       760 ~~kVi~iw~~a~d~v~~~~~~~l~~~N~i~mMa~SGARGS~~QI~QLaGmRGlma~p~G~iIe~PI~SnFrEGLt~~EyF  839 (1460)
T PRK14906        760 HKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKANFREGLSVLEYF  839 (1460)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccCCCeEeeeeccCcccHHHHHHHHhcccceecCCCCccccccccccccCCCHHHHH
Confidence                                                                           68999999999999999


Q ss_pred             eecccccccchhcccccCCCCcchHHHHHHHhhhhhcc
Q psy13846        630 FHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY  667 (1423)
Q Consensus       630 fh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~y  667 (1423)
                      ||||||||||+|||+|||+||||||||||++||++|..
T Consensus       840 iSt~GaRKGL~DTALKTAdSGYLTRRLVdVaQDViV~e  877 (1460)
T PRK14906        840 ISTHGARKGLVDTALRTADSGYLTRRLVDVAQDVIVRE  877 (1460)
T ss_pred             HHcccccchhhhhhhhccccchHHHHHHHhhhheEEEe
Confidence            99999999999999999999999999999999998765

>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional

Probab=100.00  E-value=2.8e-111  Score=1101.32  Aligned_cols=278  Identities=29%  Similarity=0.443  Sum_probs=231.8

Q ss_pred             CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846        341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV  420 (1423)
Q Consensus       341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~  420 (1423)
                      ++|+|||||||||||+|||||++++++++||||||++|+||||||||||||+|+|||++|||||+              .
T Consensus      1850 ~gd~VLlNRqPTLHR~sIqAf~~~l~~gktirlhp~vC~~fNADFDGDeMnvHvPqS~eA~aEa~--------------~ 1915 (2836)
T PRK14844       1850 KEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEAR--------------V 1915 (2836)
T ss_pred             cCCEEEecCCCccccccccceeeEeecCceEEecccCCCcccCCCCCceeeeecCCcHHHHHHHH--------------H
Confidence            79999999999999999999999999999999999999999999999999999999999999999              9


Q ss_pred             hhccccccccCCCCccccccccceEEEEEeecccccCC----CHHHHHHHHHhhccCCccccceEe-eeeccccCCceee
Q psy13846        421 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFF----NRAQTMRIASTLIADTSDICGIIK-RFSWRSWNPVVFV  495 (1423)
Q Consensus       421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~----~~~~~~~l~~~~~~~~~~~~~~~~-~~~~~~l~~p~i~  495 (1423)
                      ||.+.+|++||++|+|+++++||+++|+|.||.++.+.    ...++...+..+..+....+..++ ++.|-... ..-.
T Consensus      1916 Lm~~~~nilsP~~G~Pii~~~QD~ilG~y~LT~~~~~~~~~~~f~~~~~~~~a~~~~~~~i~~~i~~~~~~~~~~-~~~~ 1994 (2836)
T PRK14844       1916 LMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTLQEPKEDDLPSFGAFCEVEHSLSDGTLHIHSSIKYRMEYINSS-GETH 1994 (2836)
T ss_pred             HhCCcccEEecCCCceeEeehhhhhhhhhhhcccccccccccccCCHHHHHHHHHcCCcccCceEEeeeccccCC-CCcc
Confidence            99999999999999999999999999999999999754    335556666655433333444332 11110000 0000


Q ss_pred             cce-eeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHH
Q psy13846        496 RTA-VIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR  574 (1423)
Q Consensus       496 kp~-~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~  574 (1423)
                      .+. ....||++|+.+||....                             -+++++.|.++|+.+     .++|+.+|+
T Consensus      1995 ~~~~~tt~GR~if~~ilP~~~~-----------------------------~~~~~~n~~l~KK~l-----~~II~~~~~ 2040 (2836)
T PRK14844       1995 YKTICTTPGRLILWQIFPKHEN-----------------------------LGFDLINQVLTVKEI-----TSIVDLVYR 2040 (2836)
T ss_pred             cceEecccHHHHHHHHcCCccc-----------------------------cCcceEeeeechhHH-----HHHHHHHHH
Confidence            000 111599999999975311                             023566778888877     469999999


Q ss_pred             HhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCc------------------------------------------
Q psy13846        575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ------------------------------------------  612 (1423)
Q Consensus       575 ~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~------------------------------------------  612 (1423)
                      +||...++.||++++++..+|++.+|||+|++|+...+                                          
T Consensus      2041 ~yG~~~t~~fLD~lk~LGf~yaT~~G~SIgi~Di~iP~~K~~iI~~a~~~v~~i~~~y~~G~it~~Er~~kvi~iW~~~~ 2120 (2836)
T PRK14844       2041 NCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCT 2120 (2836)
T ss_pred             HhCHHHHHHHHHHHHHHHHHHHHhccEEeeHhHcccCHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999995443                                          


Q ss_pred             ---------------------------------------------------------cccccccccCCCceeeeeecccc
Q psy13846        613 ---------------------------------------------------------GFVQNSFFSGLTPTEFFFHTMGG  635 (1423)
Q Consensus       613 ---------------------------------------------------------GfI~~sf~~GL~p~Efffh~maG  635 (1423)
                                                                               .+|.+||.+||+|.|||||||||
T Consensus      2121 d~v~~~~~~~l~~~~~~~~~N~i~mMa~SGARGS~sQI~QLaGmRGLmakp~G~iIe~PI~SNFrEGLsv~EyFiSt~Ga 2200 (2836)
T PRK14844       2121 DMIANDMLKAISIYDGNSKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGA 2200 (2836)
T ss_pred             HHHHHHHHHhhhhccccCCCCceeeeecccCccCHHHHHHHHhcceeeecCCCCeeecchhhhhccCCCHHHhhhhcccc
Confidence                                                                     67999999999999999999999


Q ss_pred             cccchhcccccCCCCcchHHHHHHHhhhhhcc
Q psy13846        636 REGLVDTAVKTAETGYMQRRLVKSLEDLCVQY  667 (1423)
Q Consensus       636 ReGLiDTAvKTa~sGYlqRrLvk~ledl~v~y  667 (1423)
                      ||||+|||+|||+|||||||||+++||++|.-
T Consensus      2201 RKGL~DTALKTAdSGYLTRRLVDVaQDviI~e 2232 (2836)
T PRK14844       2201 RKGLADTALKTANSGYLTRRLVDVSQNCIVTK 2232 (2836)
T ss_pred             ccchhhhhhhcccccchhhhhhhhhceEEEEe
Confidence            99999999999999999999999999998653

>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed

Probab=100.00  E-value=1.8e-109  Score=1088.61  Aligned_cols=264  Identities=31%  Similarity=0.480  Sum_probs=232.2

Q ss_pred             CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846        341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV  420 (1423)
Q Consensus       341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~  420 (1423)
                      +||+|||||||||||+|||||++++++++||||||++|+||||||||||||+|+|||++|+|||+              .
T Consensus      1806 ~gd~VLlNRqPTLHR~sIqAf~~~l~~gktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~--------------~ 1871 (2890)
T PRK09603       1806 EGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECK--------------V 1871 (2890)
T ss_pred             cCCeEEecCCCccccccceeeeEEEecCceEEeccccCCcccCCCCCceeEEeecCCHHHHHHHH--------------H
Confidence            89999999999999999999999999999999999999999999999999999999999999999              9


Q ss_pred             hhccccccccCCCCccccccccceEEEEEeecccccCC--------CHHHHHHHHHhhccCCccccceEeeeeccccCCc
Q psy13846        421 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFF--------NRAQTMRIASTLIADTSDICGIIKRFSWRSWNPV  492 (1423)
Q Consensus       421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~--------~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p  492 (1423)
                      ||.+.+|++||++|+|+++++||+++|.|.||.+|.++        +..++..   ++..+....+.          +.|
T Consensus      1872 LM~s~~nilsP~~G~Pi~~p~QD~vlG~y~LT~~~~~~~~~~~~F~~~~e~~~---~~~~~~~~~~~----------~i~ 1938 (2890)
T PRK09603       1872 LMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIIT---AIDTKELDIHA----------KIR 1938 (2890)
T ss_pred             HhcccceEEEcCCCceeEEeecceeeeeEEeeccccCCCCccceeCCHHHHHH---HHHcCCCccCC----------cce
Confidence            99999999999999999999999999999999999643        4444432   22212112222          234


Q ss_pred             eeecceeeee--cceeeeecccCCCCcccccceeecccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHH
Q psy13846        493 VFVRTAVIWT--GKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFY  570 (1423)
Q Consensus       493 ~i~kp~~~wt--GKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~  570 (1423)
                      .+.+|..+||  |||+|+.+||....                               ..++.+.++|+.+|     ++++
T Consensus      1939 ~~~~p~~l~Tt~GK~ifs~ilP~~~~-------------------------------~~~~n~~ldKK~Lg-----~LI~ 1982 (2890)
T PRK09603       1939 VLDQGNIIATSAGRMIIKSILPDFIP-------------------------------TDLWNRPMKKKDIG-----VLVD 1982 (2890)
T ss_pred             eecCCcEEEcCccceeeeccCccccc-------------------------------cccEeeeechHHHH-----HHHH
Confidence            5557899999  99999999974310                               01223568899886     5999


Q ss_pred             HHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCc--------------------------------------
Q psy13846        571 ILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ--------------------------------------  612 (1423)
Q Consensus       571 ~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~--------------------------------------  612 (1423)
                      .+|++||...|+.||++++++..+|++.+|||+|++|+.+.+                                      
T Consensus      1983 ~i~~~yG~~~t~~fLD~lk~LGf~yat~~G~SIgI~Dl~ip~~K~~iI~~A~~eV~ei~~~y~~G~it~~Er~~kvid~w 2062 (2890)
T PRK09603       1983 YVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTW 2062 (2890)
T ss_pred             HHHHHHCHHHHHHHHHHHHHHHHHHHHhCCEeeeeccCcccHHHHHHHHHHHHHHHHHHHHHHcCCCCccHHHHHHHHHH
Confidence            999999999999999999999999999999999999996654                                      


Q ss_pred             -----------------------------------------------------------cccccccccCCCceeeeeecc
Q psy13846        613 -----------------------------------------------------------GFVQNSFFSGLTPTEFFFHTM  633 (1423)
Q Consensus       613 -----------------------------------------------------------GfI~~sf~~GL~p~Efffh~m  633 (1423)
                                                                                 .+|.+||++||+|+|||||||
T Consensus      2063 ~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~SGARGS~~NI~QLaGmrGqMakp~G~iie~PI~snFrEGLtp~EyFfst~ 2142 (2890)
T PRK09603       2063 TEVNDKMSKEMMTAIAKDKEGFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTH 2142 (2890)
T ss_pred             HHHHHHHHHHHHHHhhhcCCCCCcHHHHHhccccccHHHHHHHHHcCCcEECCCCCcccChhhcCcccCCCHHHHHHhcc
Confidence                                                                       578999999999999999999


Q ss_pred             cccccchhcccccCCCCcchHHHHHHHhhhhhcc
Q psy13846        634 GGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY  667 (1423)
Q Consensus       634 aGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~y  667 (1423)
                      ||||||+|||||||+||||||||||++||++|..
T Consensus      2143 GaRKGLiDTALKTAdSGYLTRRLVdvaQDviI~e 2176 (2890)
T PRK09603       2143 GARKGLADTALKTANAGYLTRKLIDVSQNVKVVS 2176 (2890)
T ss_pred             ccccchhhhhhhccccchhhhhHHHhhcceEEEe
Confidence            9999999999999999999999999999998876

>KOG0261|consensus

Probab=100.00  E-value=1e-110  Score=994.13  Aligned_cols=759  Identities=33%  Similarity=0.434  Sum_probs=598.8

Q ss_pred             hHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEecCCH
Q psy13846         11 LYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKE   90 (1423)
Q Consensus        11 ~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~~S~   90 (1423)
                      --|||||||.+||+|++|+||||+|+|+|+++||||||.||||+|||||+|+++++|+++++.+.       ..+.+..|
T Consensus       509 QTEEAraEA~~LMgvknNlvTPr~GEpiiAAtQDFiTg~YLlt~KDtF~dRa~~~ql~s~~~d~~-------~~i~lppP  581 (1386)
T KOG0261|consen  509 QTEEARAEALVLMGVKNNLVTPRNGEPIIAATQDFITGGYLLTHKDTFLDRAEFSQLCSYMSDAM-------THIDLPPP  581 (1386)
T ss_pred             chHHHHHHHHHHhccccccccCCCCCceeehhhhhhhcceeeecccccccHHHHHHHHHHHhccc-------cccCCCCh
Confidence            35999999999999999999999999999999999999999999999999999999999988761       33444444


Q ss_pred             HHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCC----CCCccCC---CCCCCcccCCccceEEccCceeEEeee
Q psy13846         91 DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQ----KEANCTT---CGQNLSDCVGHFGYIDLPLPVFHIGYF  163 (1423)
Q Consensus        91 eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~----~~~~C~T---Cg~~~~eCpGHfGhIeL~~PV~h~gff  163 (1423)
                      ..+        ...++|    |||++.+-|+-|--+..-    ....|.-   |+++. +.|..+||+-+.+.++-.|.+
T Consensus       582 aI~--------KP~~Lw----TGKQ~fsvlirpn~~s~v~~Nl~~k~k~~~~~~~k~~-~mc~nDg~v~irns~l~sG~l  648 (1386)
T KOG0261|consen  582 AIL--------KPVELW----TGKQLFSVLIRPNDDSPVRVNLDAKNKNFSLVKGKSF-EMCPNDGYVIIRNSELISGVL  648 (1386)
T ss_pred             hhc--------Cceeee----ccCEEEEEEeccCCCCceEEeeccccceeecccCCCc-ccCCCCCeEEEecchhhhccc
Confidence            433        455778    899999888877654321    1112322   77777 556689999999999999999


Q ss_pred             ccHHHHhhhccccccccccc--cChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCccee
Q psy13846        164 RCVINILQSICKNPTCARVL--LGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKI  241 (1423)
Q Consensus       164 d~v~~iL~~iC~~~~C~~ll--~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki  241 (1423)
                      |  +.+|...-+.++.+.+|  +++.++...++++.+.+..++-.++|+.+|.|..+..                .+.+.
T Consensus       649 d--Ks~lG~g~k~~lfy~llrDyg~~aAa~am~rlaklc~r~lgnrGFSIGi~DVqPg~----------------~L~~~  710 (1386)
T KOG0261|consen  649 D--KSTLGSGKKDSLFYILLRDYGSMAAADAMNRLAKLCARFLGNRGFSIGIDDVQPGE----------------ILSQE  710 (1386)
T ss_pred             c--cccccCCCccceEeeehhhcchHHHHHHHHHHHHhhhhhccccccccccCCCCccH----------------HHHHH
Confidence            9  88999999998999988  8899999999999999989999999999999885322                22222


Q ss_pred             hhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcc------------------
Q psy13846        242 SHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDI------------------  303 (1423)
Q Consensus       242 ~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~------------------  303 (1423)
                      ..+.....+.+|++.    +.+|+.              |.++..|++.-+++||.....++                  
T Consensus       711 k~~lv~~gY~kc~~~----I~e~~k--------------G~L~~qpg~~~eetLEa~I~~~Ls~IRe~~G~~C~~eL~~~  772 (1386)
T KOG0261|consen  711 KEELVNRGYAKCDEK----IEEYNK--------------GKLQLQPGCNEEETLEAEILSELSTIREEAGKICIRELHPR  772 (1386)
T ss_pred             HHHHHHhHHHHHHHH----HHHHhc--------------cccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcc
Confidence            222233334444433    333432              66777888888888887433222                  


Q ss_pred             -cccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCccc
Q psy13846        304 -PLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYN  382 (1423)
Q Consensus       304 -~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~n  382 (1423)
                       +-|.|+.+|++++.++++||.   +||+||+++|.|.+++|                 ..|.|||    |+.....|.+
T Consensus       773 NsPliMa~CGSKGS~INiSQMv---ACVGQQ~ISG~RvPdGf-----------------~dRsLPH----F~r~Sk~P~a  828 (1386)
T KOG0261|consen  773 NSPLIMALCGSKGSKINISQMV---ACVGQQIISGHRVPDGF-----------------EDRSLPH----FERHSKTPAA  828 (1386)
T ss_pred             cChHHHHHhcCCCCcccHHHHH---HHhhhhhhcCCcCCCcc-----------------ccccCcc----ccccCCCccc
Confidence             347788899999999999999   99999999999999999                 9999999    9999999999


Q ss_pred             CCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHH
Q psy13846        383 ADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ  462 (1423)
Q Consensus       383 adFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~  462 (1423)
                      .+|+-+++..+|.++|          ||||+|+||||+++++++|+.+|||+|+|+.+++| |++.|++|+|++.++..|
T Consensus       829 KGFV~NSFySGLTptE----------FfFHtm~GREGLVDTAVKTAETGYMqRRLmK~LED-L~~~YDgTVR~s~~~vvq  897 (1386)
T KOG0261|consen  829 KGFVANSFYSGLTPTE----------FFFHTMSGREGLVDTAVKTAETGYMQRRLMKSLED-LSVQYDGTVRNSNGDVVQ  897 (1386)
T ss_pred             cchhhhhcccCCCchh----------hheeecccccchhhhhhhhhhhhhHHHHHHHHHHH-HHHhhcCceecCCCcEEE
Confidence            9999999999999998          99999999999999999999999999999999999 999999999999999999


Q ss_pred             HHHHHHhhccCCccccceEeeeeccccCCceeecceeeeec-ceeeeecccCCCCcccccceeecccccccCcccccCCc
Q psy13846        463 TMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTG-KQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDS  541 (1423)
Q Consensus       463 ~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtG-Kqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~  541 (1423)
                      |.|+.++++  +..++++..        |..+.   ..|.- |.+    .|+....+                 +.+++ 
T Consensus       898 F~YG~DglD--Pa~mEg~~~--------pv~f~---r~~~~~~~~----~~~~~~~~-----------------l~~~e-  942 (1386)
T KOG0261|consen  898 FTYGGDGLD--PAMMEGKDQ--------PVNFN---RVFDHAKAI----FPHRHDPP-----------------LSSEE-  942 (1386)
T ss_pred             EeecCCCCC--hhhhcCCCC--------chhHH---HHHHHHHhc----CCCCCCCC-----------------CCHHH-
Confidence            999988874  446666531        22221   12211 111    11100000                 00000 


Q ss_pred             EEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCcccccccccc
Q psy13846        542 YVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFS  621 (1423)
Q Consensus       542 ~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~GfI~~sf~~  621 (1423)
                        +   .|-+...+.+.....  ....++.         -.+|+..+.+-....-..+|--++-. ..++          
T Consensus       943 --l---~e~~~~~l~~~f~~~--~~~F~~~---------~~~~i~~~~~~~~~~~~~~~d~~~~~-~~~~----------  995 (1386)
T KOG0261|consen  943 --L---DETLEEELLRKFTEK--GDPFVHE---------LREFIASLSKKIKKLQDKYGDECGPK-FCPD----------  995 (1386)
T ss_pred             --H---HHHHHHHHHHHhhhh--hhHHHHH---------HHHHHHHHHHHHHHHhhhcccccCCc-cCcc----------
Confidence              0   000111122222111  0111211         23344444333221111222211100 0000          


Q ss_pred             CCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeeccccCCCccCCCcchheecCCCcccchhH
Q psy13846        622 GLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGL  701 (1423)
Q Consensus       622 GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~~~~~~~~~~~~~~~g~~v  701 (1423)
                                            +.+-.++-....|-++++.+.-+|                       +++.+|||+||
T Consensus       996 ----------------------~~~~~~~~t~kql~~f~~~~~~ky-----------------------~~a~~EpGTav 1030 (1386)
T KOG0261|consen  996 ----------------------LLYQISRLTEKQLEKFVERCLDKY-----------------------MRAKVEPGTAV 1030 (1386)
T ss_pred             ----------------------ceeeeeeccHHHHHHHHHHHHHHH-----------------------HhhhcCCcchh
Confidence                                  111122223345777777777666                       67889999999


Q ss_pred             HHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCc
Q psy13846        702 IKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTP  781 (1423)
Q Consensus       702 g~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTP  781 (1423)
                      |+++|||||||+|||||    +|||||||             |||||||             |||||||||||+|+||||
T Consensus      1031 GAi~aQSIGEPGTQMTL----KTFHFAGV-------------ASMNiTl-------------GVPRIkEIINAsk~ISTP 1080 (1386)
T KOG0261|consen 1031 GAIAAQSIGEPGTQMTL----KTFHFAGV-------------ASMNITL-------------GVPRIKEIINASKTISTP 1080 (1386)
T ss_pred             hhhhcccCCCCCceeee----eeeeecce-------------eeeeecc-------------CcchHHHHHhhhcccCcc
Confidence            99999999999999999    99999999             9999999             999999999999999999


Q ss_pred             eeeeecccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhc---cccc
Q psy13846        782 IITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERT---RGIS  858 (1423)
Q Consensus       782 iitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~---~~~~  858 (1423)
                      +|++.|.++.|...||.++.|||+|+|+|+++||+++|.|+++|+.|++|++++++++|++++++|.++|.+.   +..+
T Consensus      1081 IItA~L~n~~d~~~Ar~VKgRiEKt~L~dv~~yieeV~~p~~~fl~i~vd~~~I~~l~L~i~~~~I~~sI~~s~~~k~~~ 1160 (1386)
T KOG0261|consen 1081 IITAELENPHDERSARVVKGRIEKTTLGDVCSYIEEVYGPDSCFLLIRVDLKRISLLQLEITIESIAYSILKSPKRKVKP 1160 (1386)
T ss_pred             ceeeeecCchhHHHHHHHhhhhhhhhHHHHHHHHHHHhCCcceEEEEEecHhHHhhhhccccHHHHHHHHhcCCccccCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999543   3456


Q ss_pred             CcccccccccccccCC-CCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccccceeeccc
Q psy13846        859 GHLTVSGHSFLILKPK-DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK  937 (1423)
Q Consensus       859 ~~i~~~~~~~~~~~~~-~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gvD  937 (1423)
                      .+|.+.++..+.+.|. +++.+.++.++.++..+|+|+|+|+|.|+|++|+.+++.+.  |.|++||.+|+++|+++||+
T Consensus      1161 ~~v~v~~~~~~~v~~~~~~~~S~~~~lq~lk~~L~~Vvv~gip~vnr~vi~~de~~~~--y~L~vEG~gLr~Vm~t~GV~ 1238 (1386)
T KOG0261|consen 1161 NDVRVVGETTLRVTPVSDTKSSVYYNLQRLKRSLPNVVVKGIPEVNRAVINIDEKRGL--YKLLVEGTGLRAVMNTDGVK 1238 (1386)
T ss_pred             cceEEecceeEEEeecccccchhhhhHHHHHhhCCceEEecCcchhhhheeecccCCc--eEEEEeccchHHHhccCCcc
Confidence            7888888766666664 34445577899999999999999999999999998765433  99999999999999999999


Q ss_pred             ceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       938 ~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      +.+|+||+++||+++|||||||.+||+||.++|.+||++||+||||||||+||++|+|+|+.
T Consensus      1239 g~~TtsNnv~Ev~~vLGIEAAR~~II~EI~ytM~~HGmsiD~RHiMLLaDvMTyrGEVlGIT 1300 (1386)
T KOG0261|consen 1239 GRRTTSNNVLEVEKVLGIEAARTTIISEIGYTMSNHGMSIDPRHIMLLADVMTYRGEVLGIT 1300 (1386)
T ss_pred             ccccccCceEEeehhhchHHHHHHHHHHHHHHHHhcCcccCHHHHHHHHHHhhhcceeeeee
Confidence            99999999999999999999999999999999999999999999999999999999999984

>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]

Probab=100.00  E-value=8.8e-84  Score=812.15  Aligned_cols=497  Identities=33%  Similarity=0.489  Sum_probs=415.9

Q ss_pred             eeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCcee
Q psy13846         79 FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVF  158 (1423)
Q Consensus        79 i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~  158 (1423)
                      +.+ ++|+++||++||+ |+.+|+.|++|  |..++|..+||+|+|||..+++..| |||+....||||||||||+.||+
T Consensus         4 ~~~-i~~gl~sp~~ir~-~s~ev~~pet~--~~~~~P~~~Gl~d~ri~~~~~~~~C-~Cg~~~~~~~~~~GhIeLa~Pv~   78 (808)
T COG0086           4 IFD-IKFGLASPEEIRS-WSGEVKKPETI--NYRTKPERGGLFDERIFGPDKDYEC-TCGKYKRICPGGFGHIELAAPVA   78 (808)
T ss_pred             cce-eEEecCCHHHHHh-cceEEcCcccc--CCCCcccCCCccchhhcCCCCCcee-cCCCCcCcCCCCceeEEeecceE
Confidence            456 9999999999999 77999999999  5556999999999999999999999 99999999999999999999999


Q ss_pred             EEeeeccHHHHhhhccccccccccccChhhHHHHH-HHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecC
Q psy13846        159 HIGYFRCVINILQSICKNPTCARVLLGEEKAAGFR-AKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG  237 (1423)
Q Consensus       159 h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~-~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~  237 (1423)
                      |+|||+.+.++|++.|..  |+++++.  ++..++ ..+.....  +....+        -....|+|||+.++.+++.+
T Consensus        79 hi~f~k~~~~~L~~~~~~--~~~v~~~--~~~~~~~~~l~~~~~--~~~~~~--------~~~~~~~~~Ga~~~~~~~~~  144 (808)
T COG0086          79 HIWFFKSIPSLLDMTCRD--CERVLYF--EAYVVLGTDLEKIQL--LNETEY--------VYDSFCAHCGAEAIKILLEK  144 (808)
T ss_pred             EechhhccHHHHhhhHHh--hhhhhhH--hHHHHhccchhhhcc--cchhee--------eccccCCCCCchhHHHHHhC
Confidence            999999999999999999  9999988  333333 11111110  000011        22378999999998777665


Q ss_pred             cceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCCCCcc
Q psy13846        238 LLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD  317 (1423)
Q Consensus       238 ~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe~  317 (1423)
                      ...+...                                  + .  +.++|.++.++|++|...|+.+++    ++||+|
T Consensus       145 ~~~~~~~----------------------------------~-~--~~~~~~~~~~~~~~l~~~d~~~~~----~~~pew  183 (808)
T COG0086         145 PDLETER----------------------------------E-E--ETLSPTKVKKLLKRLKVVDAFLLS----GNRPEW  183 (808)
T ss_pred             cchhhhh----------------------------------h-h--cccCHHHHHHHHhhccHHHHHHhc----CCCcce
Confidence            3222110                                  0 1  356899999999999999988888    589999


Q ss_pred             eEEEEecCCCCCCCCcEEcCCCC---------------------------------------------------------
Q psy13846        318 LILTRLLVPPNCIRPSVISDLKS---------------------------------------------------------  340 (1423)
Q Consensus       318 liLt~lpVPP~~vRPsv~~g~~~---------------------------------------------------------  340 (1423)
                      |+|+++||||+++||++.+++..                                                         
T Consensus       184 mil~vlpV~Pp~~RP~i~ld~g~~a~~dl~~~~~~ii~~n~rlk~~~~~~~~~iv~~~~~~lQ~~v~~~~Dn~~~~~~~~  263 (808)
T COG0086         184 MILTVLPVPPPDLRPSIQLDGGRFAESDLNDLYRRVINRNNRLKRLLELAAPIIVRNEKRMLQEAVDALFDNRRPRAVTG  263 (808)
T ss_pred             eEEEeeccCCCCCCcceecCCCccchhHHHHHHHHHHHHHHHhHHhhhhcchHHHHHHHHHHHHHHHHHhhcCCCCCccC
Confidence            99999999999999999988742                                                         


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        341 --------------------------------------------------------------------------------  340 (1423)
Q Consensus       341 --------------------------------------------------------------------------------  340 (1423)
                                                                                                      
T Consensus       264 ~rPlksl~~~LkgK~GrFR~nL~GKRVd~SgRsVI~~~P~l~~~e~GvP~~~A~~L~~p~~v~~~~~~~~~~~a~~~~~~  343 (808)
T COG0086         264 GRPLKSLSQRLKGKQGRFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELFKPFVVTELNIEGLRTGAKYAKRM  343 (808)
T ss_pred             CCccccHHHHhcCCCceeeccccccccCCCCceeecCCCCccccccCCHHHHHHHhccCEEEEehhhhhhhcCCceEEec
Confidence                                                                                            


Q ss_pred             ----------------CCeEEEEecCccccccccceeeeEEec-CCceeeccCCCCcccCCCcccccccccCCCHHHHhc
Q psy13846        341 ----------------DNDVVLFNRQPSLHKLSIMAHRAKVLP-HRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE  403 (1423)
Q Consensus       341 ----------------~~d~Vl~nRqPsLHk~Simah~~~~~~-~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE  403 (1423)
                                      ++|.|||||||||||+|||+|..++++ ++|||+|+++|.||||||||||||+|+||+++|+||
T Consensus       344 ~~~~~~~~w~Vl~evi~gd~Vl~NR~PtLHrlsImq~~e~vl~~gkt~rLh~lVc~~yNADFDGDeM~~Hvp~s~ea~AE  423 (808)
T COG0086         344 VERRLPEVWDVLREVIDGDPVLLNRAPTLHRLSIMQAFEPVLPEGKAIRLHPLVCEAYNADFDGDEMAVHVPASGEAAAE  423 (808)
T ss_pred             ccccccccchHHHHHhcCCccccccCChHHHHHHHhhceeeccccceeecchhhccccccccCchhhhccccchHHHHHH
Confidence                            899999999999999999999999999 799999999999999999999999999999999999


Q ss_pred             ccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHHHHHHhhccCCccccceEee
Q psy13846        404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKR  483 (1423)
Q Consensus       404 ~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  483 (1423)
                      |+              .+|.+.+|+.||..|+|+++.+||++.|.|+||..|+++...+.++++..-.    .  ..+  
T Consensus       424 a~--------------~lm~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~d~~~~~~~~~ei~l~~~----~--~~~--  481 (808)
T COG0086         424 AR--------------GLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLPSTPVGEIYLKDE----Y--ADD--  481 (808)
T ss_pred             HH--------------HhhccccccccCCCCCceEeecceEEeccEEEEEecccCCCCcceEEEeccc----c--ccc--
Confidence            99              9999999999999999999999999999999999999988888777654310    0  111  


Q ss_pred             eeccccCCceeecceeeeecceeeeecccCCCCcccccceeecccccccCcccccC-CcEEEeccccccccccccCCcCC
Q psy13846        484 FSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHR-DSYVILRNSELLAGSMDKSTLGS  562 (1423)
Q Consensus       484 ~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~-d~~v~i~~~ell~g~ldK~~~g~  562 (1423)
                          ..+++++.++..+|+||++++.+++......+..+........   .....+ |..+.+.|++++.|.++|...  
T Consensus       482 ----~e~~~ai~~~~~~~~~k~i~~~i~~~~~~~~i~~t~~~~~~~~---~~~~~~~d~~~~i~~~~l~~~~i~k~~~--  552 (808)
T COG0086         482 ----REKAEAIAKKIELTTGKVIVSTISPDLAELSIIVTTDGRRIFN---RGLPEDKDVLVKIVNGKLIKGVIDKKIV--  552 (808)
T ss_pred             ----hhhhHHHhcccceeeeeEEEEEeeccCCcceEEEecchhhhhh---ccCCcccceeeEEeccccceeeehhhHH--
Confidence                3457899999999999999998776543222222221111111   111122 577899999999999988764  


Q ss_pred             CCCCchHHHHHHHhCHHHHH-HHHHHhhhhhhHHHhhcC-cceecCCCC---CCc-------------------------
Q psy13846        563 GGKANVFYILLRDFGEDVAV-TAMWRLSRMTSFYLMNRG-FSIGIGDVT---PGQ-------------------------  612 (1423)
Q Consensus       563 ~~~~~li~~i~~~~G~~~a~-~~l~~l~~l~~~~L~~~G-fsiGi~D~~---~~~-------------------------  612 (1423)
                              .++++||+.++. .+++.+.++.+.+++..| |+++++|.-   +..                         
T Consensus       553 --------~i~~~~g~~~~~~~~~~~~dkl~~~~~~~~~~~~~~i~~~d~~~~~~~~e~v~~ae~~v~~~i~~~~~g~lt  624 (808)
T COG0086         553 --------TIYREYGPEVASKALVKLLDKLKNLGIKGIGGFGIGIGRKDIEAEDEKDEIVIEAEGSVLKLILQYEEGDLT  624 (808)
T ss_pred             --------HHHHHhCchhhHHHHHHHHHHHHHhheeeeccceEEeecccccchHHHHHHHHHHHHHHHHHHHHhhcCCcc
Confidence                    678999998888 999999999999999988 988888763   211                         


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        613 --------------------------------------------------------------------------------  612 (1423)
Q Consensus       613 --------------------------------------------------------------------------------  612 (1423)
                                                                                                      
T Consensus       625 ~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~~~~i~~m~~~Gs~~n~sq~~~~iG~~gv~g~r~~~~~~~~Fe~  704 (808)
T COG0086         625 RTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIVQLIGQQGVMGEKISVLARAAFEV  704 (808)
T ss_pred             ccCCCCeEEEeehHHHHHHHHHHHHHHhhhHHhcCCcchhHHHHhhhhhccCHHHHHHHhhhheeeccCCCccccccccc
Confidence                                                                                            


Q ss_pred             --------cccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeecc
Q psy13846        613 --------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA  674 (1423)
Q Consensus       613 --------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s  674 (1423)
                              |||.++|++||+|.|||||+||||+||+|||+|||+|||||||||+++|||+|.||++||++
T Consensus       705 ~~~~~~a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~KTa~sGYl~RrLv~~~qdl~v~~d~~~~~g  774 (808)
T COG0086         705 TVKHLEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADSGYLTRRLVDVAQDLIVQEDDCVTDG  774 (808)
T ss_pred             ccccceeeeeeecccCCCCCcceEEeecCccccchHHHhhhhcccCcceEEeechhcceEEEecCeEeec
Confidence                    88999999999999999999999999999999999999999999999999999999999975

>KOG0260|consensus

Probab=100.00  E-value=8.1e-75  Score=701.10  Aligned_cols=796  Identities=20%  Similarity=0.258  Sum_probs=533.1

Q ss_pred             HHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEecCCHH
Q psy13846         12 YYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKED   91 (1423)
Q Consensus        12 ~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~~S~e   91 (1423)
                      -+|||||+.||++||+||||||+|+|+||++||+|||+|++|.||+||+|+++|||+||+- .        |+....-  
T Consensus       486 S~etkAEl~EL~~vpkQiispQsnkpvmgivQDTLta~R~~t~Rd~Fl~r~~vmnLlm~~p-~--------~d~~~Pa--  554 (1605)
T KOG0260|consen  486 SLETKAELEELAMVPKQIISPQSNKPVMGIVQDTLTAVRKMTKRDVFLNRAQVMNLLMYVP-D--------WDGPPPA--  554 (1605)
T ss_pred             chhHHHHHHHHhhhhhhhcCCcCCCcceeeehhhHHHHHHHhhHhhhhcHHHHHHHHhhcc-c--------cCCCCCC--
Confidence            4799999999999999999999999999999999999999999999999999999999961 1        1111110  


Q ss_pred             HHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCceeEEeeeccH--HHH
Q psy13846         92 RVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCV--INI  169 (1423)
Q Consensus        92 eIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~gffd~v--~~i  169 (1423)
                           --.......+|    +|+++.+-++++.+........-.--+ ...--||--+ +-+....++.|.+.+.  .+.
T Consensus       555 -----~pai~Kp~PlW----TGkQifsliiP~~in~~r~~s~h~d~~-~~~~~p~dt~-~lie~g~l~~g~l~Kkt~G~s  623 (1605)
T KOG0260|consen  555 -----KPAILKPKPLW----TGKQIFSLIIPGGINYIRDHSTHPDSE-DELISPGDTR-VLIEGGELLIGVLCKKTVGSS  623 (1605)
T ss_pred             -----CcccCCCCccc----chhhheeeecCCCcceecccccCcCCC-cccccCCCce-EEEeCCceEEEEeeccccccc
Confidence                 00023566788    999999999998876543211111011 1133455444 3445566667766532  334


Q ss_pred             hhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehhhhhccc
Q psy13846        170 LQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNR  249 (1423)
Q Consensus       170 L~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~  249 (1423)
                      +..+.+-  |.. ..+++..+.|...++..-...+.+.+|+.+|.+.....                ..++.+++.+.+.
T Consensus       624 ~g~lvh~--i~~-e~Gp~~~~~f~~~iQ~lin~wll~~gfsigIgDtiad~----------------~t~~~iq~~I~~a  684 (1605)
T KOG0260|consen  624 AGGLVHV--IFL-EKGPKIARGFFDSIQTLINSWLLREGFSIGIGDTIADA----------------ATMCVIQNTIKEA  684 (1605)
T ss_pred             cCceEEE--eeh-hhCHHHHHHHHHHHHHHHHHHHHhcCccccccccccCH----------------HHHHHHHHHHHHH
Confidence            4444333  322 25677777888777665555566778888887764322                1122222222111


Q ss_pred             ccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhcc-------------------CCCccccccccc
Q psy13846        250 TKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAI-------------------PLEDIPLLLMNA  310 (1423)
Q Consensus       250 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I-------------------~~~d~~lL~m~~  310 (1423)
                      +    ..+-+.+++..             . ..++..++.+.+++|++.                   -.+-+.++.|..
T Consensus       685 k----~dv~~vi~~a~-------------~-~~L~~~pg~tlretfe~~v~~vlndArd~~gssA~~sl~esNn~k~Mv~  746 (1605)
T KOG0260|consen  685 K----RDVLAVIREAQ-------------N-NELEPTPGRTLRETFENKVNRVLNDARDKSGSSAQKSLSESNNFKTMVV  746 (1605)
T ss_pred             H----HHHHHHHHHHh-------------h-ccccCCcchhHHHHHHHHHHHHHHHHHHhhhhHHHhhhhhcccHHHHHh
Confidence            1    01111111110             1 346677888888888872                   122246677777


Q ss_pred             CCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCccccc
Q psy13846        311 ELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEM  390 (1423)
Q Consensus       311 ~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m  390 (1423)
                      .|++++.++|+|+.   +||+||.+.|.+++.+|                 .-|++||    |-..+-+|...+|+.+++
T Consensus       747 aGSKGs~inisQ~s---aCVGqQnVEgkrIpFGF-----------------~~Rtlph----f~kDdysPesrGfVENSy  802 (1605)
T KOG0260|consen  747 AGSKGSFINISQVS---ACVGQQNVEGKRIPFGF-----------------PKRTLPH----FSKDDYSPESRGFVENSY  802 (1605)
T ss_pred             hcCCCcceehhhhh---hhhccccccccccccCC-----------------Ccccccc----cccCCCCccccceeeccc
Confidence            88999999999999   99999999999999999                 9999999    999999999999999999


Q ss_pred             ccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHHHHHHhh
Q psy13846        391 NVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL  470 (1423)
Q Consensus       391 ~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~  470 (1423)
                      -.+|.|.|          |||||||||||++++++++..+||-+|+|+.+++| +++.||.|+|+++++..||.|+.+++
T Consensus       803 L~GLtP~E----------fFfHamggREglidtavktaEtGyiqRRL~kameD-imv~yDgTVRNs~gqviQf~YGeDG~  871 (1605)
T KOG0260|consen  803 LTGLTPQE----------FFFHAMGGREGLIDTAVKTAETGYIQRRLMKAMED-IMVAYDGTVRNSLGQVIQFKYGEDGL  871 (1605)
T ss_pred             ccCCCHHH----------HHHHHhcccchhhhhhhcccccchHHHHHHHHHHH-HHhhcCcceecccceeEEEEeccCcc
Confidence            99999665          99999999999999999999999999999999999 99999999999999999999999987


Q ss_pred             ccCCccccceEeeeeccccCCceeecc-eeeeecceeeeecccCCCCc--cc----c--cceeec-ccccccCcccccCC
Q psy13846        471 IADTSDICGIIKRFSWRSWNPVVFVRT-AVIWTGKQIFSLILKPNRDC--PV----N--ANLKTK-GRAYTANEEFCHRD  540 (1423)
Q Consensus       471 ~~~~~~~~~~~~~~~~~~l~~p~i~kp-~~~wtGKqi~s~il~~~~~~--~~----~--~~~~~~-~~~~~~~~~~~~~d  540 (1423)
                      ++..+...         .++.   +++ ...+-.+.-++.+..+....  .+    .  .++... ...|..    ...|
T Consensus       872 d~~~vE~q---------~~~~---l~~~~a~f~~~~~~d~ld~~~~~~~~~~~~e~~~~~~l~~lle~e~~~----l~~d  935 (1605)
T KOG0260|consen  872 DGHPVEFQ---------NGET---LGSLNACFESEFAYDALDEPISLSSEEVVNEISELLKLQNLLECEYKK----LVRD  935 (1605)
T ss_pred             ccceeecc---------cccc---ccchHHHHHhhhhhhhhcCcccchhhhHhhhhhhhHHHHHHHHHHHHh----hhhh
Confidence            64321111         1111   010 00011111111111000000  00    0  000000 000000    0000


Q ss_pred             cEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCccccccccc
Q psy13846        541 SYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFF  620 (1423)
Q Consensus       541 ~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~GfI~~sf~  620 (1423)
                      ..+.    -.+....++++.+                +......+.+.++.+....      .-..|+++          
T Consensus       936 r~~l----~~i~~~g~~k~~l----------------p~n~~r~I~Na~~~f~~~~------r~~t~l~~----------  979 (1605)
T KOG0260|consen  936 RRVL----LYIFEYGDAKWPL----------------PENLQRIIWNALKKFSIDE------RKPTDLIP----------  979 (1605)
T ss_pred             hhhh----hhhcccCCccccc----------------chhHHHHHHHHHhhccccc------ccccccch----------
Confidence            0000    0001111222221                1222222222222211100      01112222          


Q ss_pred             cCCCceeeeeecccccccchhcccccCCCCcchH--HHHHHHhhhhhcccceeecc-----ccCCC-ccCCCcchheecC
Q psy13846        621 SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQR--RLVKSLEDLCVQYDMSFDAA-----FYGQT-DCISGVSECIIMG  692 (1423)
Q Consensus       621 ~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqR--rLvk~ledl~v~yD~tVR~s-----~yG~~-~~~~~~~~~~~~~  692 (1423)
                               |++.-|-..+.-.-+--.-.-|+.|  ||..    +-++-+..+++.     +-.++ +|..|.++..+.+
T Consensus       980 ---------~~v~~g~~~l~e~l~iv~g~~~~sraqrl~~----~lLrs~l~~krv~~e~rls~eaf~w~~~~Ie~~f~q 1046 (1605)
T KOG0260|consen  980 ---------FKVVKGVKELAEKLVIVRGEDYISRAQRLFN----ILLRSTLATKRVLEEYRLSSEAFEWVLGEIEARFLQ 1046 (1605)
T ss_pred             ---------hhhhhhhhhhhheeEEeeCchhHHHHHHHHH----HHHHhhHHHHHHHHHhcccHHHHHHHhhhhhhheee
Confidence                     1233333333333332233335555  2111    111111111111     11111 3445666667788


Q ss_pred             CCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHH
Q psy13846        693 LPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEII  772 (1423)
Q Consensus       693 ~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIi  772 (1423)
                      +...||+-||.+||||+|||.|||||    +|||+|||             ++.|+|+             ||||+|||+
T Consensus      1047 a~a~pgemvg~lAaqsvgePatqmTl----ntfh~aGV-------------ssknVt~-------------gvprlkei~ 1096 (1605)
T KOG0260|consen 1047 AEASPGEMVGALAAQSVGEPATQMTL----NTFHYAGV-------------SSKNVTL-------------GVPRLKEII 1096 (1605)
T ss_pred             eecCccchHhHHHHHHhCCchhhccc----chhcccce-------------eeeeeec-------------cCcchhhhh
Confidence            99999999999999999999999999    99999999             7889999             999999999


Q ss_pred             hhhcCCCCceeeeecccC--ChHHHHHHHhhhhcccchhhhhhhheeeecCCC--------------------------c
Q psy13846        773 NASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD--------------------------S  824 (1423)
Q Consensus       773 naSk~ikTPiitv~L~~~--~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~--------------------------~  824 (1423)
                      |.+|++|||.+++||..+  .+.|+|+.+..+||++++.++...-+++|+|+.                          .
T Consensus      1097 Nv~k~~ktpsLtV~l~g~~~k~~e~ak~v~~~le~ttl~~vt~~t~i~ydpdp~~tvI~ed~e~v~a~~e~pd~D~~~is 1176 (1605)
T KOG0260|consen 1097 NVAKNAKTPSLTVYLTGEAAKDNEWAKLVQCCLEHTTLKDVTRATEIYYDPDPQSTVIDEDREFVVAYYEMPDEDVGRIS 1176 (1605)
T ss_pred             hhhccCCCceEEEEecchhhcchHHHHHHhhhcccccHHhhhccCcceecCCCcceeeccchhhHHhhhcCcccchhhcC
Confidence            999999999999999887  578999999999999999999988788887752                          2


Q ss_pred             ceeeehhhhHHHhhccccchhhhhHHhhhcccccCccccccc----ccccccCCCC--ccccchhhhhh-hhcCCceEEc
Q psy13846        825 FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGH----SFLILKPKDS--SKSFNSKMYQM-KQLLPSVVIK  897 (1423)
Q Consensus       825 ~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~----~~~~~~~~~~--~~~~~~~l~~l-~~~l~~v~Ik  897 (1423)
                      .|+++|.+||.++.+..+.+..|.+.|.+.++.+.....+.+    ..+.++..+.  ++.|   +..+ ...+.++...
T Consensus      1177 pwlLrlelDr~~m~dk~ltm~~ia~~i~~~f~~d~~~i~~ddna~klv~r~ri~~~~e~D~~---l~~Ie~~ml~~~~l~ 1253 (1605)
T KOG0260|consen 1177 PWLLRLELDRASMTDKKLTMEQIAEKINRGFGSDLACIFSDDNAEKLVLRLRIAKEEEDDVF---LKCIEANMLGDMTLR 1253 (1605)
T ss_pred             hHHHHhhhhhhhcccccccHHHHHHHHHhhccCCCceeecccCCcceEEEEEecCccchhHH---HHHHHHhhhhhcccC
Confidence            245677777777777788888888888776654333222221    1222332211  1122   2233 3457788899


Q ss_pred             cccccceeeeeccccc---ceeEEeeeccCccccccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcC
Q psy13846        898 GVQGINRAVIHEEDVE---GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHG  974 (1423)
Q Consensus       898 Gi~~I~r~~i~~~~~~---~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~G  974 (1423)
                      |+++|.+++|+.+...   ...+|.|.++|.+|+.++..+++|..+|+||++.|++.+|||||+|..++.|+..+....|
T Consensus      1254 G~~~i~kV~m~~~~~G~f~~~~ew~LeTdg~~l~~v~s~~~vD~~rt~sn~l~ei~~vlgIea~r~a~~~e~~~vi~f~g 1333 (1605)
T KOG0260|consen 1254 GIPDIFKVYMSPTEDGEFKPVDEWDLETDGVNLRRVLSEPDVDPARTTSNDLVEIAEVLGIEAVRKALLRELLNVISFDG 1333 (1605)
T ss_pred             CccccceEEEeecCCCceeecceeEEecCchhHHhhhccCCCCcccccccchhhhhhhhcHHHHHhhhhhhhhheEeecc
Confidence            9999999999865432   3478999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCchhhHhhhhccccccccCC
Q psy13846        975 MSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       975 i~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      .+||+||+.||+|+||++|.++++.
T Consensus      1334 syVnyrhlaLl~dvmT~~g~lm~it 1358 (1605)
T KOG0260|consen 1334 SYVNYRHLALLCDVMTARGHLMAIT 1358 (1605)
T ss_pred             cchhHHHHHHHHHHHhcccceeeee
Confidence            9999999999999999999999864

>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''

Probab=100.00  E-value=2.6e-72  Score=651.56  Aligned_cols=294  Identities=39%  Similarity=0.608  Sum_probs=253.2

Q ss_pred             cccCcc-cCCCCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc--------------c----
Q psy13846       1086 DKIGHG-RESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------E---- 1146 (1423)
Q Consensus      1086 ~~~~~~-~~~~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG--------------~---- 1146 (1423)
                      ++++++ ++    +  ||+++|+.+|.+++++||||||+|||||||||+||||||||||||              |    
T Consensus        17 ~~~~~~~~~----~--~~l~~i~~ky~~alv~PGeaVG~IAAQSIGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEIINa   90 (367)
T TIGR02389        17 REISDKEEL----D--EIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDA   90 (367)
T ss_pred             cCCCHHHHH----H--HHHHHHHHHHHHhcCCCccccchhhhhhcCCccccccccccccccccccCccccchhHHHHhhc
Confidence            346666 66    7  999999999999999999999999999999999999999999999              1    


Q ss_pred             --------------------------------------ccceeEEEEccCCcEEEEEEchHHHHHhcccCCHHHHHHHHH
Q psy13846       1147 --------------------------------------VCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE 1188 (1423)
Q Consensus      1147 --------------------------------------i~~~i~~~~~~~~~~~~i~l~~~~~~~~~~~i~~~~i~~~i~ 1188 (1423)
                                                            |+.+++..+.  ...+.++||.+.++..  .+++++|..+|.
T Consensus        91 ~k~i~TP~~ti~L~~~~~~~~~~a~~v~~~iE~t~l~dv~~~~~~~~~--~~~l~i~ld~~~l~~~--~i~~~~i~~~i~  166 (367)
T TIGR02389        91 RKTPSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLA--DMTVIIELDEEQLKER--GITVDDVEKAIK  166 (367)
T ss_pred             ccCCCCCeEEEEecCcchhhHHHHHHHHHHhhheeHHHHHhhhheecc--CcEEEEEECHHHHHhc--CCCHHHHHHHHH
Confidence                                                  1222222222  3356778888877665  689999999986


Q ss_pred             hccccCCceEEecCcEEEEEeCCCCchhhhHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhh
Q psy13846       1189 RTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA 1268 (1423)
Q Consensus      1189 ~~k~~~~~~~~~~~~~i~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~ 1268 (1423)
                      +.+.........++..+++++..   +....|+.+++.+.+++|+|+|||+||++.++    +++|+|.|||+||.++|+
T Consensus       167 ~~~~~~~~~~~~~~~~i~i~~~~---~~~~~l~~l~~~l~~~~v~Gi~gI~r~~i~~~----~~~~~l~teG~nl~~v~~  239 (367)
T TIGR02389       167 KAKLGKVIEIDMDGNTITIKPPK---PSLKELRKLKEKIKNLHIKGIKGIKRVVIRKE----GDEYVIYTEGSNLKEVLK  239 (367)
T ss_pred             HhcccccceeecCCCEEEEEecC---chHHHHHHHHHHhhhceEeCCCCceEEEEECC----CCeEEEEEeccCHHHHHc
Confidence            54321111111233567777642   23456888999999999999999999999843    358999999999999999


Q ss_pred             cccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhh
Q psy13846       1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348 (1423)
Q Consensus      1269 ~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~ 1348 (1423)
                      +++||++|++||||++|+++|||||||++|++|+++||+.||++||+|||+||||+||++|.+.|+||+|+++++.|||+
T Consensus       240 ~~~VD~~rt~sNdI~ei~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~  319 (367)
T TIGR02389       240 LEGVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLA  319 (367)
T ss_pred             CCCCccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhcCCceEEeccccccccCCCCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999888999999


Q ss_pred             hccchhhHHHHHhhcccCCcccccccccceeeccccccccceEEEeec
Q psy13846       1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396 (1423)
Q Consensus      1349 ~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~ 1396 (1423)
                      +||||+|+++|++||.+|+.|+|+|||||||+|+++|+|||+|+|+++
T Consensus       320 ~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~~  367 (367)
T TIGR02389       320 RAAFEVTVKHLLDAAIRGEVDELAGVIENIIVGQPIPLGTGDVDLVMD  367 (367)
T ss_pred             hcChHhHHHHHHHHhhcCCCCcCCChHHHhhcCCCcCCcCCeEEEeeC
Confidence            999999999999999999999999999999999999999999999874

This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.

>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain

Probab=100.00  E-value=9.9e-71  Score=647.67  Aligned_cols=369  Identities=31%  Similarity=0.476  Sum_probs=300.3

Q ss_pred             ecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhH
Q psy13846        690 IMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIK  769 (1423)
Q Consensus       690 ~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlk  769 (1423)
                      |.++.++||++||.+||||||||+|||||    +|||||||             ||+|+||             ||||||
T Consensus        19 ~~~~~~~~ge~vg~~aaQSiGEP~TQmTL----nTFH~AGV-------------as~NVTl-------------GVPRLk   68 (410)
T cd02584          19 FNRSLVHPGEMVGTIAAQSIGEPATQMTL----NTFHFAGV-------------SAKNVTL-------------GVPRLK   68 (410)
T ss_pred             HHHhhcCCCCCcchhhhhhcCCchhcccc----cccccccc-------------ccccccc-------------CccchH
Confidence            36678999999999999999999999999    99999999             9999999             999999


Q ss_pred             HHHhhhcCCCCceeeeecccC--ChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhh
Q psy13846        770 EIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI  847 (1423)
Q Consensus       770 EIinaSk~ikTPiitv~L~~~--~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I  847 (1423)
                      |||||+|+||||+|++||.++  .|.+.|+.++.+||+++|+|++.+++++|+|+.++..++.|.+.++.+         
T Consensus        69 EIInasK~ikTP~~tv~L~~~~~~d~~~A~~v~~~IE~t~l~dv~~~~~i~ydp~~~~~~i~~d~~~i~~~---------  139 (410)
T cd02584          69 EIINVAKNIKTPSLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESY---------  139 (410)
T ss_pred             HHhhcccCCCCCeEEEEecCcccchHHHHHHHHhheeEeEHHHhhhheEEEecCcccceeecccHHHHHHh---------
Confidence            999999999999999999998  679999999999999999999999999999988776665555443110         


Q ss_pred             hHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccc
Q psy13846        848 RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL  927 (1423)
Q Consensus       848 ~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL  927 (1423)
                                                                                                      
T Consensus       140 --------------------------------------------------------------------------------  139 (410)
T cd02584         140 --------------------------------------------------------------------------------  139 (410)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             cccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCCcchhhHHH
Q psy13846        928 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRL 1007 (1423)
Q Consensus       928 ~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~~~~~~~~~ 1007 (1423)
                                                                ++                          ..+       
T Consensus       140 ------------------------------------------~~--------------------------~~d-------  144 (410)
T cd02584         140 ------------------------------------------FE--------------------------FPD-------  144 (410)
T ss_pred             ------------------------------------------hc--------------------------cCc-------
Confidence                                                      00                          000       


Q ss_pred             HHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHHHHHHHHhhhccccccccccCCchhhhhhhccccc
Q psy13846       1008 LDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDK 1087 (1423)
Q Consensus      1008 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1087 (1423)
                                   ...                                                                
T Consensus       145 -------------~~~----------------------------------------------------------------  147 (410)
T cd02584         145 -------------EDV----------------------------------------------------------------  147 (410)
T ss_pred             -------------ccc----------------------------------------------------------------
Confidence                         000                                                                


Q ss_pred             cCcccCCCCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccccccceeEEEEccCCcEEEEEEc
Q psy13846       1088 IGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLD 1167 (1423)
Q Consensus      1088 ~~~~~~~~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG~i~~~i~~~~~~~~~~~~i~l~ 1167 (1423)
                       ..+.                                                                  ...+.+++.
T Consensus       148 -~~~~------------------------------------------------------------------~~~~~lrl~  160 (410)
T cd02584         148 -EQDR------------------------------------------------------------------LSPWLLRIE  160 (410)
T ss_pred             -cccc------------------------------------------------------------------cCCeeEEEE
Confidence             0000                                                                  001133344


Q ss_pred             hHHHHHhcccCCHHHHHHHHHhccccCCceEEecCc----EEEEEeCCCC-------chhhhHHHHHHhccCCcEEcccC
Q psy13846       1168 MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHS----FLILKPKDSS-------KSFNSKMYQMKQLLPSVVIKGVQ 1236 (1423)
Q Consensus      1168 ~~~~~~~~~~i~~~~i~~~i~~~k~~~~~~~~~~~~----~i~i~~~~~~-------~~~~~~l~~l~~~l~~~~v~Gi~ 1236 (1423)
                      ++..+.....+++++|..+|++.......+..++++    .+++++....       +...+..+.++..+++++|+|+|
T Consensus       161 ld~~~~~~~~i~~~~i~~~i~~~~~~~~~v~~~~~~~~~~~iri~~~~~~~~~~~~~~~~~~l~~~~~~~l~~i~l~Gi~  240 (410)
T cd02584         161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEEDSEDDVFLKKIESNMLSDMTLKGIE  240 (410)
T ss_pred             ECHHHHHHcCCCHHHHHHHHHHhcCCCeEEEEcCCCcceeEEEEEecCccccccccchhHHHHHHHHHhhCCCcEEeCCC
Confidence            444444455778888888776432111122222222    4555543211       11233445557889999999999


Q ss_pred             CccEEEEecccc----------cceeeEEEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHh
Q psy13846       1237 GINRAVIHEEDV----------EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVM 1306 (1423)
Q Consensus      1237 ~i~r~~i~~~~~----------~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~ 1306 (1423)
                      ||+|+++..++.          ++.++|+|+|||+||+++|++++||++|++||||++|+++|||||||++|++||++||
T Consensus       241 ~I~r~~i~~~~~~~~~~~~g~~~~~~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~  320 (410)
T cd02584         241 GIRKVFIREENKKKVDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAARKALLKELRNVI  320 (410)
T ss_pred             CceEEEEEcCCceEecCCCCcccCCcceEEEecCcCHHHHhCCCCCccccCEeCCHHHHHHhcCHHHHHHHHHHHHHHHH
Confidence            999999975321          1245799999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeecccccc
Q psy13846       1307 ENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV 1386 (1423)
Q Consensus      1307 ~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~ 1386 (1423)
                      +.||++||+|||+||||+||++|.++||||+||++++.|||++||||+|+++|++||++|+.|+|+|||||||+|+++|+
T Consensus       321 ~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~  400 (410)
T cd02584         321 SFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPI  400 (410)
T ss_pred             HhcCCccCHHHHHHHHHHHhhceEEeeEeeeeeeccCCChhhhccchhHHHHHHHHHhcCCCCcCCCchHheeecCcccc
Confidence            99999999999999999999999999999999998889999999999999999999999999999999999999999999


Q ss_pred             ccceEEEeec
Q psy13846       1387 GTGLIKLLQA 1396 (1423)
Q Consensus      1387 GTG~~~l~~~ 1396 (1423)
                      |||+|+|++|
T Consensus       401 GTG~f~l~~d  410 (410)
T cd02584         401 GTGCFDLLLD  410 (410)
T ss_pred             ccceEEEEeC
Confidence            9999999975

RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.

>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional

Probab=100.00  E-value=1e-70  Score=648.33  Aligned_cols=300  Identities=35%  Similarity=0.589  Sum_probs=254.8

Q ss_pred             cccccCcccCCCCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc--------------cccc
Q psy13846       1084 HQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149 (1423)
Q Consensus      1084 ~~~~~~~~~~~~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG--------------~i~~ 1149 (1423)
                      ..++++.+++    +  +|+++|..+|.+++|+||||||+|||||||||+||||||||||||              ||.+
T Consensus       154 ~~~~l~~~~~----~--~i~~ei~~~y~~~~v~pGE~VG~IAAQSIGEP~TQMTLnTFH~AGVas~NVTlGVPRLkEIIN  227 (509)
T PRK14897        154 KKKELSDDEY----E--EILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVD  227 (509)
T ss_pred             HHcCCCHHHH----H--HHHHHHHHHHHHhccCCCCCcchhhhhhhCCccccccccccccccccccccccCcchhHHHhh
Confidence            3456777776    7  999999999999999999999999999999999999999999999              2211


Q ss_pred             e--------eEEEEcc-------------------------------CCcEEEEEEchHHHHHhcccCCHHHHHHHHHhc
Q psy13846       1150 Y--------IEEVFVP-------------------------------DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERT 1190 (1423)
Q Consensus      1150 ~--------i~~~~~~-------------------------------~~~~~~i~l~~~~~~~~~~~i~~~~i~~~i~~~ 1190 (1423)
                      .        +..+..+                               ....+.++||.+.+...  .+++++|..+|.+.
T Consensus       228 a~K~isTP~mtiyL~~~~~~d~e~A~~V~~~IE~ttL~dv~~~~~d~~~~~i~i~Ld~~~l~~~--~l~~~~I~~~I~~~  305 (509)
T PRK14897        228 ARKKPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDVADIITDIAEMSVVVELDEEKMKER--LIEYDDILAAISKL  305 (509)
T ss_pred             cccCCCCceEEEEecCcccccHHHHHHHHhhheeeEHHHHHHHHHHhccceEEEEECHHHHHHc--CCCHHHHHHHHHhc
Confidence            1        1111111                               12335666777666654  67889999998763


Q ss_pred             cccCCceEEecCcEEEEEeCCCCchhhhHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhcc
Q psy13846       1191 RGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 1270 (1423)
Q Consensus      1191 k~~~~~~~~~~~~~i~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~~ 1270 (1423)
                      +.  ..+ ..+++.+++.+..   +.+..|..+++.+++++|+|+|||+||+++.++  ++++|+|.|||+||+++|+++
T Consensus       306 ~~--~~~-~~~~~~I~i~~~~---~~~~~L~~l~~~l~~i~I~GipgI~r~~i~~~~--~~~~~~L~TeG~NL~~vl~~~  377 (509)
T PRK14897        306 TF--KTV-EIDDGIIRLKPQQ---PSFKKLYLLAEKVKSLTIKGIKGIKRAIARKEN--DERRWVIYTQGSNLKDVLEID  377 (509)
T ss_pred             cc--eEE-ecCCCEEEEEeCc---hHHHHHHHHHHHhhccEEeCCCCccEEEEecCC--CCceeEEEeeccCHHHHhcCC
Confidence            21  111 1233556666642   224578888899999999999999999998653  235799999999999999999


Q ss_pred             cccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhc
Q psy13846       1271 GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLA 1350 (1423)
Q Consensus      1271 ~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~a 1350 (1423)
                      +||++||+||||++|+++|||||||++|++|++.||+.||++||+|||+||||+||++|.+.|+|||||+.++.|||++|
T Consensus       378 ~VD~~rt~SNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHL~LIAD~MT~~G~v~~i~R~Gi~~~~~SpL~rA  457 (509)
T PRK14897        378 EVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARA  457 (509)
T ss_pred             CcccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhCcCCcccccccccccccCCCHHHhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999988899999999


Q ss_pred             cchhhHHHHHhhcccCCcccccccccceeeccccccccceEEEeecCCC
Q psy13846       1351 SFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 1399 (1423)
Q Consensus      1351 SFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~~~ 1399 (1423)
                      |||+|+++|++||++|+.|+|+|||||||+|+++|+|||+|+|+++...
T Consensus       458 SFE~T~~~L~~AA~~Ge~D~L~GvsenII~G~~ipvGTG~fdL~~~~~~  506 (509)
T PRK14897        458 AFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLVYKGRK  506 (509)
T ss_pred             chHhHHHHHHHHhhcCCCCcCCChHHhhhcCCccCCcCceEEEEecCCC
Confidence            9999999999999999999999999999999999999999999998554

>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP)

Probab=100.00  E-value=7.8e-70  Score=632.14  Aligned_cols=296  Identities=39%  Similarity=0.591  Sum_probs=255.8

Q ss_pred             ccccccCcccCCCCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc-----------------
Q psy13846       1083 SHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------- 1145 (1423)
Q Consensus      1083 ~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG----------------- 1145 (1423)
                      ...++++++++    +  ||+++++.+|.+++++||||||++||||||||+||||||||||||                 
T Consensus        11 ~~~~~l~~~~~----~--~~~~~~~~~~~~~~~~~Ge~vG~iaAQSiGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEII   84 (363)
T cd06528          11 LKEHGLTLSEA----E--EIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIV   84 (363)
T ss_pred             HHHcCCCHHHH----H--HHHHHHHHHHHHHhhccCccccceeeeecCccceecccccccccccccccCccccccHHHHh
Confidence            35567888877    7  999999999999999999999999999999999999999999999                 


Q ss_pred             ---------------------------------------cccceeEEEEccCCcEEEEEEchHHHHHhcccCCHHHHHHH
Q psy13846       1146 ---------------------------------------EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYC 1186 (1423)
Q Consensus      1146 ---------------------------------------~i~~~i~~~~~~~~~~~~i~l~~~~~~~~~~~i~~~~i~~~ 1186 (1423)
                                                             +|+.++++  +++.+.+.++||.+.++..  .+++++|..+
T Consensus        85 na~K~i~TP~mti~L~~~~~~~~~~a~~v~~~iE~t~l~di~~~~~i--~~~~~~l~i~ld~~~l~~~--~l~~~~i~~~  160 (363)
T cd06528          85 DARKEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISI--DLFNMRITIELDEEMLEDR--GITVDDVLKA  160 (363)
T ss_pred             hcccCCCCceEEEEecCcchhhHHHHHHHHHhhceeEHHHhhhheEE--eccCcEEEEEECHHHHHHc--CCCHHHHHHH
Confidence                                                   12222222  2445667778888887775  5799999999


Q ss_pred             HHhccccCCceEEecCcEEEEEeCCCCchhhhHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHH
Q psy13846       1187 IERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 1266 (1423)
Q Consensus      1187 i~~~k~~~~~~~~~~~~~i~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~ 1266 (1423)
                      |.+...  ..+...++..+++...  ++.....|+.+++.+.+++|+|+|||+||++.+++    ++|+|.|||+||+++
T Consensus       161 i~~~~~--~~~~~~~~~~~~~~~~--~~~~~~~l~~l~~~l~~~~v~Gi~gI~r~~i~~~~----~~~~l~teG~nl~~v  232 (363)
T cd06528         161 IEKLKK--GKVGEEGDVTLIVLKA--EEPSIKELRKLAEKILNTKIKGIKGIKRVIVRKEE----DEYVIYTEGSNLKAV  232 (363)
T ss_pred             HHHhcC--CcccccCCccEEEEcC--CcchHHHHHHHHHhhcccEEeCCCCceEEEEecCC----ceEEEEecCcCHHHH
Confidence            865321  1122222222333332  22335688999999999999999999999998653    489999999999999


Q ss_pred             hhcccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccch
Q psy13846       1267 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346 (1423)
Q Consensus      1267 ~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~ 1346 (1423)
                      |.+++||++|++||||++|+++|||||||++|++||++||+.||++||+|||+||||+||++|++.|+||+|+++++.||
T Consensus       233 ~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~R~gi~~~~~S~  312 (363)
T cd06528         233 LKVEGVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSV  312 (363)
T ss_pred             hcCCCCcccccccCCHHHHHHhCCHHHHHHHHHHHHHHHHHhcCCeecHHHHHHHHHHhccCCceecccchhhcCCCCCh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999998888999


Q ss_pred             hhhccchhhHHHHHhhcccCCcccccccccceeeccccccccceEEEeec
Q psy13846       1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396 (1423)
Q Consensus      1347 l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~ 1396 (1423)
                      |++||||+|+++|++||.+|+.|+|+|||||||+|+++|+|||+|+|+++
T Consensus       313 L~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~d  362 (363)
T cd06528         313 LARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELTMD  362 (363)
T ss_pred             hhhCchhhHHHHHHHHHhcCCCCcCCCcHHHeeeCCCCCCcCCeeEEEec
Confidence            99999999999999999999999999999999999999999999999986

Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.

>PRK04309 DNA-directed RNA polymerase subunit A''; Validated

Probab=100.00  E-value=2e-69  Score=632.76  Aligned_cols=294  Identities=40%  Similarity=0.653  Sum_probs=256.7

Q ss_pred             cccCcccCCCCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc--------------cc----
Q psy13846       1086 DKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EV---- 1147 (1423)
Q Consensus      1086 ~~~~~~~~~~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG--------------~i---- 1147 (1423)
                      ++++++++    +  +|++.|..+|.+++++||||||++||||||||+||||||||||||              ||    
T Consensus        33 ~~l~~~~~----~--~~~~~i~~~y~~~~v~pGe~VG~iaAQsIGEP~TQMTL~TFH~AGva~~nVTlGvPRlkEIina~  106 (383)
T PRK04309         33 RKLTEEEV----E--EIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDAR  106 (383)
T ss_pred             cCCCHHHH----H--HHHHHHHHHHHHhhcCCCCccchhhhhhccchhhhcccccccccCccccCcccCchhHHHHHhcc
Confidence            45788776    7  999999999999999999999999999999999999999999999              11    


Q ss_pred             --------------------------------------cceeEEEEccCCcEEEEEEchHHHHHhcccCCHHHHHHHHHh
Q psy13846       1148 --------------------------------------CEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIER 1189 (1423)
Q Consensus      1148 --------------------------------------~~~i~~~~~~~~~~~~i~l~~~~~~~~~~~i~~~~i~~~i~~ 1189 (1423)
                                                            +.+++.  +++...+.++||...++.+  .+++++|..+|.+
T Consensus       107 K~~~TP~~tv~L~~~~~~d~~~a~~v~~~iE~t~L~~v~~~i~~--~~~~~~l~i~ld~~~i~~~--~l~~~~I~~~i~~  182 (383)
T PRK04309        107 KEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV--DLANMTIIIELDEEMLEDR--GLTVDDVKEAIEK  182 (383)
T ss_pred             cCCCCCeEEEEecCcccccHHHHHHHHhheeeeEHhhhhhheEe--ccCCcEEEEEECHHHHHHc--CCCHHHHHHHHHH
Confidence                                                  111111  2334556778888777765  6799999999865


Q ss_pred             ccccCCceEEecCcEEEEEeCCCCchhhhHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhc
Q psy13846       1190 TRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMAT 1269 (1423)
Q Consensus      1190 ~k~~~~~~~~~~~~~i~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~ 1269 (1423)
                      ...  ..+.+. .+.+.+++..   +....|+.++..+++++|+|+|||+||++.++    +++|+|.|||+||.++|++
T Consensus       183 ~~~--~~~~~~-~~~i~i~~~~---~~~~~l~~l~~~l~~~~vkGi~gI~r~~i~~~----~~~~~l~teG~nl~~v~~~  252 (383)
T PRK04309        183 KKG--GEVEIE-GNTLIISPKE---PSYRELRKLAEKIRNIKIKGIKGIKRVIIRKE----GDEYVIYTEGSNLKEVLKV  252 (383)
T ss_pred             hcC--cceecc-CCeEEEEecC---chHHHHHHHHHHhcccEEECCCCceEEEEecC----CCeEEEEEcccCHHHHhcC
Confidence            321  223333 3556666652   23467888999999999999999999999864    3589999999999999999


Q ss_pred             ccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhh
Q psy13846       1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349 (1423)
Q Consensus      1270 ~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~ 1349 (1423)
                      ++||++|++||||++|+++|||||||++|++|++.||+.||++||+|||+||||+||++|++.|+||+|+++++.|||++
T Consensus       253 ~~VD~~rt~sNdI~ei~~vlGIEAAR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~  332 (383)
T PRK04309        253 EGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLAR  332 (383)
T ss_pred             CCEeeccccCCCHHHHHHHcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhccCceEEeeechhhcCCCCCHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998889999999


Q ss_pred             ccchhhHHHHHhhcccCCcccccccccceeeccccccccceEEEeecCCC
Q psy13846       1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 1399 (1423)
Q Consensus      1350 aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~~~ 1399 (1423)
                      ||||+|+++|++||++|+.|+++|||||||+|+++|+|||+|+|+++.+.
T Consensus       333 aSFE~T~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~~~~~  382 (383)
T PRK04309        333 AAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDPPL  382 (383)
T ss_pred             CchhhHHHHHHHHHhcCCCCCCCCcHHHhhcCCCcCCCCceEEEEcCCCC
Confidence            99999999999999999999999999999999999999999999998764

>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain

Probab=100.00  E-value=3.4e-68  Score=604.08  Aligned_cols=170  Identities=63%  Similarity=0.922  Sum_probs=161.5

Q ss_pred             HHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHH
Q psy13846       1220 MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIM 1299 (1423)
Q Consensus      1220 l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii 1299 (1423)
                      ++.+++.|++++|+|+|||+||++.+++.  .++|.|.|||+||.++|++++||++|++||||++|+++|||||||++|+
T Consensus       131 ~~~l~~~l~~~~v~Gi~gI~r~~i~~~~~--~~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii  208 (300)
T cd02736         131 LQSLKRKLPDVVVSGIPEVKRAVINKDKK--KGKYKLLVEGYGLRAVMNTPGVIGTRTTSNHIMEVEKVLGIEAARSTII  208 (300)
T ss_pred             HHHHHHHhccceEeCCCCceEEEEecCCC--CCcEEEEEecccHHHHhcCCcEeccCCccCCHHHHHHhcCHHHHHHHHH
Confidence            34456678899999999999999986532  3589999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCccccccccccee
Q psy13846       1300 TEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECII 1379 (1423)
Q Consensus      1300 ~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii 1379 (1423)
                      +||++||+.||++||+|||+||||+||++|.++||||+|++++++|||++||||+|.++|++||.+|+.|+|+|||||||
T Consensus       209 ~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~itR~gi~~~~~S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~ii  288 (300)
T cd02736         209 NEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECII  288 (300)
T ss_pred             HHHHHHHHhcCCccCHHHHHHHHHHHhccCceeeeecccccccCCCHHHhcchHhHHHHHHHHhhcCCCCcCCCcHHHee
Confidence            99999999999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             eccccccccceE
Q psy13846       1380 MGLPMNVGTGLI 1391 (1423)
Q Consensus      1380 ~G~~~~~GTG~~ 1391 (1423)
                      +|+++|+|||+|
T Consensus       289 ~G~~~~~GTG~f  300 (300)
T cd02736         289 MGKPMPIGTGLF  300 (300)
T ss_pred             eCCCcCCCCCCC
Confidence            999999999987

Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.

>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain

Probab=100.00  E-value=4e-66  Score=591.95  Aligned_cols=177  Identities=35%  Similarity=0.463  Sum_probs=166.8

Q ss_pred             hhHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhc-ccccceecccccHHHHHHHhCHHHHH
Q psy13846       1217 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMAT-YGVKGVKCSSNNTYEVYKTLGIEAAR 1295 (1423)
Q Consensus      1217 ~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~-~~vd~~~~~sN~i~~i~~~lGIEAar 1295 (1423)
                      .+.++.+++.+.+++|+|+|||+||++.+++..+..+|.+.|||+||.++|.+ ++||++|++||||++|+++|||||||
T Consensus       132 ~~~~~~~~~~l~~~~i~gi~gI~r~~i~~~~~~~~~~~~l~teG~nl~~v~~~~~~vd~~r~~sNdi~ei~~~lGIEAar  211 (309)
T cd02735         132 LLLLSIVEKLARKAVIREIPGITRCFVVEEDKGGKTKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAMLNTYGIEAAR  211 (309)
T ss_pred             HHHHHHHHHHhcccEEeCCCCccEEEEecCcCCCceEEEEEeccccHHHHHhccCccccccceeCCHHHHHHhhCHHHHH
Confidence            35667788899999999999999999987643334579999999999999998 78999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccc
Q psy13846       1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375 (1423)
Q Consensus      1296 ~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s 1375 (1423)
                      ++|++|+++||+.||++||+|||+||||+||++|.+.|+||+|| +.+.|||++||||+|.++|++||.+|+.|+|+|||
T Consensus       212 ~~ii~Ei~~v~~~~Gi~V~~rHl~LiaD~MT~~G~~~~~nr~gi-~~~~S~l~~asFE~t~~~L~~Aa~~g~~D~l~g~s  290 (309)
T cd02735         212 RAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGM-ESSTSPLQKMSFETTLAFLKKATLNGDIDNLSSPS  290 (309)
T ss_pred             HHHHHHHHHHHHhcCCeeCHHHHHHHHHHHHhCCcEeecchhhe-ccCCCHHHhhhhhhHHHHHHHHhhcCCCCCCCChH
Confidence            99999999999999999999999999999999999999999999 56899999999999999999999999999999999


Q ss_pred             cceeeccccccccceEEEe
Q psy13846       1376 ECIIMGLPMNVGTGLIKLL 1394 (1423)
Q Consensus      1376 ~~ii~G~~~~~GTG~~~l~ 1394 (1423)
                      |||++|+++|+|||+|||+
T Consensus       291 ~~ii~G~~~~~GTG~fdll  309 (309)
T cd02735         291 SRLVVGKPVNGGTGLFDLL  309 (309)
T ss_pred             HheeeCCccCccceeEEeC
Confidence            9999999999999999985

RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.

>KOG0262|consensus

Probab=100.00  E-value=3.9e-63  Score=602.67  Aligned_cols=782  Identities=20%  Similarity=0.236  Sum_probs=478.4

Q ss_pred             hhhhHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEec
Q psy13846          8 TLTLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTV   87 (1423)
Q Consensus         8 ~~~~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~   87 (1423)
                      -|---|.|||||..|..+-.|.+.|.+|.|+-|.||||+...-+||.||+||+||+.|+|+..   +-.....       
T Consensus       609 HfPQse~araEa~~ian~dsqYLvPt~G~PlrGLIQDHiVsgv~LT~rd~Fftre~y~qLv~~---~l~~~~~-------  678 (1640)
T KOG0262|consen  609 HFPQSEIARAEAYNIANTDSQYLVPTDGTPLRGLIQDHIVSGVLLTMRDSFFTREDYQQLVFA---GLSDTFK-------  678 (1640)
T ss_pred             cCCchhhHHHHHHHHhccCCceeccCCCCchhhhhhhheeeeEEEEecccccCHHHHHHHHHH---hhhhhcc-------
Confidence            455568999999999999999999999999999999999999999999999999999999983   3221111       


Q ss_pred             CCHHHHhhcceeeeecCcccccCCCCCCcCCccc----cCCCCCCCCCCccCCCCCCCcccCCcc-----ceEEccCcee
Q psy13846         88 TKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLL----DRRMGTNQKEANCTTCGQNLSDCVGHF-----GYIDLPLPVF  158 (1423)
Q Consensus        88 ~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLl----D~rLG~~~~~~~C~TCg~~~~eCpGHf-----GhIeL~~PV~  158 (1423)
                          +|.-+.-.=.....+|    +||++.+.++    ++..-+.+-...-.+-| ..+.|++--     .|+.+..+.+
T Consensus       679 ----rI~~lpPtIlkP~~LW----TGKQVIsTil~Ni~P~~~p~iNl~~kaKip~-~~W~~~s~e~~l~Es~v~ir~Gel  749 (1640)
T KOG0262|consen  679 ----RIKLLPPTILKPAPLW----TGKQVISTILKNIIPEGHPPINLESKAKIPG-KAWRVHSEEPKLNESQVLIREGEL  749 (1640)
T ss_pred             ----ceeccCcccccccccc----ccchHHHHHHHhcCCCCCCcccchhcccCch-hhcCCCCCcccCCcceEEEecCce
Confidence                1111111122455677    8988876544    22222221111111111 123333333     6799999999


Q ss_pred             EEeeeccH------HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccC----------Ccc
Q psy13846        159 HIGYFRCV------INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKK----------VSV  222 (1423)
Q Consensus       159 h~gffd~v------~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk----------~k~  222 (1423)
                      .+|.+|+-      +-|.+       |-+=+++.+.....+--+.+....|++.++|.-++.|..-.          ..-
T Consensus       750 lcGVLDKa~~Gat~yGLvH-------~~~ElYG~~~s~~lLs~~srlFT~ylq~~GFT~GvdDlll~~~~D~kR~~il~e  822 (1640)
T KOG0262|consen  750 LCGVLDKAQFGATAYGLVH-------CCHELYGGETSGKLLSVFSRLFTAYLQMHGFTLGVDDLLLDKDADKKRREILRE  822 (1640)
T ss_pred             EEEeechhhcCchhhhhhh-------hhhhhhCccchhhHHHHHHHHHHHHHHHhccccccceeeechhhhHHHHHHHHh
Confidence            99999976      33333       33335787777666666666666777777777776664210          123


Q ss_pred             CCCCCCCCCceeec-CcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHH--------HHH
Q psy13846        223 CPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLE--------VLQ  293 (1423)
Q Consensus       223 C~~Cg~~~~~irk~-~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~--------V~e  293 (1423)
                      |.+||...  ++.. ++....         ..++....+.+.|.    ...+....++.+....+++.+        -.-
T Consensus       823 ~~~vG~qa--~~~~~~l~~da---------~~del~~~le~~y~----~d~~~~~~LD~~~k~~~n~~ts~I~~~cvP~G  887 (1640)
T KOG0262|consen  823 SRNVGNQA--AKEAFGLDVDA---------PPDELRSRLEAIYL----KDADKLAMLDRVMKSELNGYTSEIVKKCVPDG  887 (1640)
T ss_pred             hhcccHHH--HHHHhCCCCCC---------CHHHHHHHHHHHHh----cchhHHHHHHHHHHHHHhhhhHHHHhhhccch
Confidence            45554321  0000 000000         00111111111111    000000000000001111111        112


Q ss_pred             HhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceee
Q psy13846        294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRF  373 (1423)
Q Consensus       294 iLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~  373 (1423)
                      +++..+.+.+.  .|..+|++++..|..||.   .+.+|+...|.|.+-=+                 ..|.||-    |
T Consensus       888 Llk~FP~N~mq--lM~~SGAKGS~VN~~QIS---clLGQqeLEGkRvPlMv-----------------SGKtLPs----F  941 (1640)
T KOG0262|consen  888 LLKKFPENNMQ--LMIQSGAKGSNVNTSQIS---CLLGQQELEGKRVPLMV-----------------SGKTLPS----F  941 (1640)
T ss_pred             hhhcCCcchHH--HHHHhcCCcccccHHHHH---HhhhhHhhcCCccceee-----------------cCCccCC----c
Confidence            33333433222  344578999999999998   88999998887765555                 7889998    9


Q ss_pred             ccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecc
Q psy13846        374 NECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ  453 (1423)
Q Consensus       374 ~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~  453 (1423)
                      .|-..+|-..+|.-+.+-.++-|          ++||||.|+||||+++|+++|.-|||-||.||.-++- +.+.|++|+
T Consensus       942 ~p~e~spraGGfI~~RFlTGi~P----------qeyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEg-l~V~YD~TV 1010 (1640)
T KOG0262|consen  942 APYETSPRAGGFIDGRFLTGIKP----------QEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEG-LKVHYDLTV 1010 (1640)
T ss_pred             CCCCCCCCCCCcccceeecCCCc----------hHHhhhhhccccchhhhHHhcccchHHHHHHHHhhhh-cEEeccceE
Confidence            99999999999999999999984          4599999999999999999999999999999999999 999999999


Q ss_pred             cccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeecccccccC
Q psy13846        454 KNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTAN  533 (1423)
Q Consensus       454 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~  533 (1423)
                      ||+.++..||+|+.++++...                 -.++.+      |+-.            ..|++.--..+   
T Consensus      1011 RDsDgsvVQF~YGEDglDitK-----------------ssfl~~------~~f~------------~~Ny~avl~~~--- 1052 (1640)
T KOG0262|consen 1011 RDSDGSVVQFMYGEDGLDITK-----------------SSFLNK------KEFP------------TDNYEAVLLKY--- 1052 (1640)
T ss_pred             EcCCCcEEEEeecCccccccH-----------------Hhhcch------hhhh------------hhhHHHHHhhh---
Confidence            999999999999998875211                 111111      1100            00100000000   


Q ss_pred             cccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCcc
Q psy13846        534 EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQG  613 (1423)
Q Consensus       534 ~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~G  613 (1423)
                                   +.   .+++                  ...+.+.|......+-+--..- |..-++.++.  .+++ 
T Consensus      1053 -------------~~---~~v~------------------s~~d~~~a~~~~k~i~kw~kk~-~w~~~~k~~~--cpdp- 1094 (1640)
T KOG0262|consen 1053 -------------KS---ESVL------------------SAFDIKKASKYIKKILKWKKKH-MWFELDKKIA--CPDP- 1094 (1640)
T ss_pred             -------------Ch---HHHh------------------hhhhhHHHHHHHHHHHHHHhhh-ccchhhcccC--CCCh-
Confidence                         00   0111                  1112222222221111100000 2222223332  2221 


Q ss_pred             ccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeeccccCCCccCCCcchheecCC
Q psy13846        614 FVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGL  693 (1423)
Q Consensus       614 fI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~~~~~~~~~~~  693 (1423)
                       |...|     +.+-|+-+++-+       ..+.-++|.+|+ .|- +   -.|+.+ -       +-..-+.+.-|.+.
T Consensus      1095 -v~~k~-----~p~~y~gsvsek-------f~~~i~~f~~~~-~k~-~---~s~~~~-~-------~~lr~ll~~K~~~S 1148 (1640)
T KOG0262|consen 1095 -VLAKY-----NPDKYLGSVSEK-------FRKKIDDFDDEN-AKK-E---KSEEPS-E-------EKLRRLLQLKYIRS 1148 (1640)
T ss_pred             -hhhhc-----chhhhhccccHH-------HHHHHHHHHHHh-hhh-h---ccccch-H-------HHHHHHHHHHHHHH
Confidence             00000     011111111111       112334566665 211 0   011111 0       00000112234677


Q ss_pred             CcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHH-
Q psy13846        694 PMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEII-  772 (1423)
Q Consensus       694 ~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIi-  772 (1423)
                      +.+|||+||.|||||||||.|||||    +||||||.             +.||+||             |+|||+||+ 
T Consensus      1149 La~PGE~VGvlAAQSIGEPSTQMTL----NTFHfAGr-------------GemNVTL-------------GIPRLREIlM 1198 (1640)
T KOG0262|consen 1149 LADPGEPVGVLAAQSIGEPSTQMTL----NTFHFAGR-------------GEMNVTL-------------GIPRLREILM 1198 (1640)
T ss_pred             hcCCCCcceeeeecccCCCcceeeh----hheeeccc-------------cceeeee-------------cchHHHHHHH
Confidence            8999999999999999999999999    99999998             8899999             999999999 


Q ss_pred             hhhcCCCCceeeeecccCChHHHHHHHhhhhcccchhhhhhhhee--eec--CCCc-c-eeeehhhh-HHHh-hccccch
Q psy13846        773 NASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEE--VFV--PDDS-F-ILIKLDMD-RIRL-LHLEVDI  844 (1423)
Q Consensus       773 naSk~ikTPiitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~--~~~--~~~~-~-~~i~ld~~-r~~~-~~l~i~~  844 (1423)
                      .||++|+||+|++.+.+..+.+-|..+..++.+++|+++++++..  .+.  ++.. . ..|++++- +... .++.+..
T Consensus      1199 tASanIkTP~mt~pi~~g~s~~ra~~i~~~l~rV~L~evlk~v~vte~~t~~~~~~~~~y~lr~~~~~~~~y~~e~~v~~ 1278 (1640)
T KOG0262|consen 1199 TASANIKTPSMTVPIKNGVSDERADDITKELRRVTLKEVLKKVGVTEKITMVENQSCKKYKLRFDLLPREEYQEEYDVRP 1278 (1640)
T ss_pred             HHhhccCCCceeeeccCCccHHHHHHHHHHHHHHHHHHHHhheeeeEEEEeeccccceEEEEEEeecCHHHhhhhcCCCH
Confidence            999999999999999999888999999999999999999998642  222  2222 1 23444431 1111 1111111


Q ss_pred             hh------------hhHHhhh----cc---cc-----c----------Ccc-----------------------------
Q psy13846        845 DS------------IRYCIER----TR---GI-----S----------GHL-----------------------------  861 (1423)
Q Consensus       845 ~~------------I~~~i~~----~~---~~-----~----------~~i-----------------------------  861 (1423)
                      +.            +..+|++    .+   ..     +          .++                             
T Consensus      1279 e~i~~~m~~~Flk~L~~aI~k~~~k~~~~~~~~~dd~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ddddas~~k~~~k 1358 (1640)
T KOG0262|consen 1279 EDIEEVMENRFLKLLERAIKKKLKKAKYTRGMSNDDADPDDGNEVDNNDEVGGEDNEDSDDESEDDEDDDDASDAKLHKK 1358 (1640)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHhhccccccCCccccccCCccccccCCccccccccccccCcccchhHHHHhhh
Confidence            11            2222211    10   00     0          000                             


Q ss_pred             -----cccccc---ccccc----C--CCC-------c---------------c----------------------ccch-
Q psy13846        862 -----TVSGHS---FLILK----P--KDS-------S---------------K----------------------SFNS-  882 (1423)
Q Consensus       862 -----~~~~~~---~~~~~----~--~~~-------~---------------~----------------------~~~~-  882 (1423)
                           +..+..   ....+    +  .++       .               +                      .|.+ 
T Consensus      1359 ~~~~~dYe~~de~e~~~~~~~e~~~~~e~~e~d~e~g~dg~~~~~~~~~e~~~~~~~~er~~qs~~~~~~fi~~y~fd~~ 1438 (1640)
T KOG0262|consen 1359 TEEEADYESEDEDERVEEREDEGDEDEESDEDDEEVGLDGTPEPEEEDQEGQPEVNAVERREQSVKKRHDFISRYTFDKE 1438 (1640)
T ss_pred             hccccCcCCCchhhhhhhhhcccccccccccchhhcccCCCCCcccccccCCchhhHHHHHHHHHHHHHHHhhhhccccc
Confidence                 000000   00000    0  000       0               0                      0000 


Q ss_pred             ------------------hh-hhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccccceeecc-cceeec
Q psy13846        883 ------------------KM-YQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV-KGVKCS  942 (1423)
Q Consensus       883 ------------------~l-~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gv-D~~~t~  942 (1423)
                                        .+ ..+.+..+..+|..++||.|+++....+.++..-.+.|+|.||..+..+..+ |..+.+
T Consensus      1439 ~~~wcev~~~lp~~~~k~~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~~~k~~~~l~TeGVnl~a~~~~~d~LDv~~ly 1518 (1640)
T KOG0262|consen 1439 SGKWCEVELKLPLDKEKLDMSSIVESIAPKSVIHQVPGIERCVVSEPQDDVKEKSVLLTEGVNLPALFDHADILDVNRLY 1518 (1640)
T ss_pred             cCcEEEEEEEecCCCcchHHHHHHHHHhcceeeeccCCceeeeccCCcccccccceehhcCccHHHHHHHHhhhhhhhhc
Confidence                              01 1134467889999999999999987654444445899999999998888765 899999


Q ss_pred             cCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        943 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       943 SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      ||||+.|++++||||||++|++|+..||..+||+||.||+.|+|||||+.|.+...+
T Consensus      1519 SNDI~ail~tyGVEAar~~Iv~Ev~~VF~vYGIsVd~RHLsLiADYMTf~G~y~pfn 1575 (1640)
T KOG0262|consen 1519 SNDIHAILNTYGVEAARNAIVNEVNNVFKVYGISVDIRHLSLIADYMTFEGGYQPFN 1575 (1640)
T ss_pred             cchHHHHHHHhhHHHHHHHHHHHHHHhhhheeeeecHHHHHHHHHHHhhcccccccc
Confidence            999999999999999999999999999999999999999999999999999987653

>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional

Probab=100.00  E-value=3.1e-60  Score=620.30  Aligned_cols=370  Identities=18%  Similarity=0.162  Sum_probs=273.5

Q ss_pred             HHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEecCCHH
Q psy13846         12 YYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKED   91 (1423)
Q Consensus        12 ~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~~S~e   91 (1423)
                      -+||||||++||+|++||+||++|+|+||++||+|+|+|+||.||+||+|+++++|++|.  +....+        ..|.
T Consensus       486 S~eArAEa~~Lm~v~~niisP~~G~Pi~gliQD~l~g~~lLT~~d~fl~~~e~~~l~~~~--~~~~~l--------p~Pa  555 (1321)
T PRK14977        486 IEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLA--GITDPL--------PEPA  555 (1321)
T ss_pred             CHHHHHHHHHHHhhhhcEecCCCCCeeEEeehhhhhhhhhhccCcccCCHHHHHHHHHhC--CCcccc--------CCCc
Confidence            479999999999999999999999999999999999999999999999999999999972  211111        1111


Q ss_pred             HHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccC-CCCCCCcccCCccceEEccCceeEEeeeccHH---
Q psy13846         92 RVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCT-TCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVI---  167 (1423)
Q Consensus        92 eIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~-TCg~~~~eCpGHfGhIeL~~PV~h~gffd~v~---  167 (1423)
                      .+       .....+|    |||++.+.++++.+....+...+. .|+.+....|...|++.+...++..|.+|+-.   
T Consensus       556 I~-------~kp~~lw----TGKQi~s~iLp~~~n~~~~~~~~~~~~~~~~~~~~~~d~~v~I~~geLl~G~ldK~~~G~  624 (1321)
T PRK14977        556 IK-------TKDGPAW----TGKQLFSLFLPKDFNFEGIAKWSAGKAGEAKDPSCLGDGYVLIKEGELISGVIDDNIIGA  624 (1321)
T ss_pred             ee-------cCCCCee----eHHHHHHHHcCCCCCceecccccccccccccccCCCCcceEEeecCeEEeeecchHhhcc
Confidence            11       0234688    999999999988775543332222 23333333455799999999999999999531   


Q ss_pred             ------HHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCccee
Q psy13846        168 ------NILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKI  241 (1423)
Q Consensus       168 ------~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki  241 (1423)
                            .+++.+...       ++++....|++++.+....++...+|+.++.|.....                    .
T Consensus       625 ~~~~~~~Lih~i~~~-------yG~~~a~~fL~~l~~l~~~~L~~~GFSigi~D~~~~~--------------------~  677 (1321)
T PRK14977        625 LVEEPESLIDRIAKD-------YGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPD--------------------E  677 (1321)
T ss_pred             ccCCCCcHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHHHhCCEEEeeCcEecCH--------------------H
Confidence                  244444444       8889999999999988888888888888887764211                    0


Q ss_pred             hhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhh--------------------ccCCC
Q psy13846        242 SHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFE--------------------AIPLE  301 (1423)
Q Consensus       242 ~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe--------------------~I~~~  301 (1423)
                      ..++..+..++......++.+.|...    +.+... + +..+.+++...++.|+                    .++ .
T Consensus       678 ~~~~i~~~i~~~~~~v~~l~~~~~~~----~~i~~~-~-~~~~~~~G~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~-~  750 (1321)
T PRK14977        678 AKQEIEDDIQGMKDEVSDLIDQRKIT----RKITIY-K-GKEELLRGMKEEEALEADIVNELDKARDKAGSSANDCID-A  750 (1321)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhh----cccccc-c-cchhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-C
Confidence            00001000000111122222222200    000000 0 1112222222222221                    132 3


Q ss_pred             cccccccccCCCCCcceEEEEecCCCCCCCCcEEc--------CCCCCCeEEEEecCccccccccceeeeEEecCCceee
Q psy13846        302 DIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS--------DLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRF  373 (1423)
Q Consensus       302 d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~--------g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~  373 (1423)
                      +++++.|..+|||+++++++||.   +|++||...        |.++..++                 ..|+|||    |
T Consensus       751 ~N~l~~Mv~SGAKGS~~Ni~Qi~---~~lGQQ~ve~~~~~~~~G~Ri~~~~-----------------~~RtLPh----F  806 (1321)
T PRK14977        751 DNAGKIMAKTGARGSMANLAQIA---GALGQQKRKTRIGFVLTGGRLHEGY-----------------KDRALSH----F  806 (1321)
T ss_pred             CCcHHHHhhcccccCHHHHHHHH---hccccccccccccccCCCCCCcCCC-----------------CCCcCCC----C
Confidence            57888899999999999999999   999999998        77777777                 9999999    9


Q ss_pred             ccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecc
Q psy13846        374 NECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ  453 (1423)
Q Consensus       374 ~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~  453 (1423)
                      .+.+.+|...+|+-+++..+|.+.|          ||||+||||||++++|++|+.|||.+|+|+.++|| +.+.||.|+
T Consensus       807 ~~~d~~p~a~GfV~nsFl~GL~P~E----------fFFHaM~GREGLiDTAVKTA~SGYLQRrLvk~lED-l~v~YD~TV  875 (1321)
T PRK14977        807 QEGDDNPDAHGFVKNNYREGLNAAE----------FFFHAMGGREGLIDKARRTEDSGYFQRRLANALED-IRLEYDETV  875 (1321)
T ss_pred             CCCCCCcccccchhhhhcCCCCHHH----------HHHHhhcccccccccccccCcCchhHHHHHHHhcc-eEEecCCeE
Confidence            9999999999999999999999766          99999999999999999999999999999999999 999999999


Q ss_pred             cccCCCHHHHHHHHHhhc
Q psy13846        454 KNAFFNRAQTMRIASTLI  471 (1423)
Q Consensus       454 ~~~~~~~~~~~~l~~~~~  471 (1423)
                      ||+.+++.||.|+.++++
T Consensus       876 R~s~g~iiQF~YGeDG~d  893 (1321)
T PRK14977        876 RDPHGHIIQFKFGEDGID  893 (1321)
T ss_pred             EeCCCCEEEEeecCCCcC
Confidence            999999999999988875

>cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain

Probab=100.00  E-value=1.2e-57  Score=531.44  Aligned_cols=177  Identities=25%  Similarity=0.319  Sum_probs=164.2

Q ss_pred             HHHHHHhccCCcEEcccCCccEEEEe--ccc---------ccceeeEEEEec---------CccHHHHhh-----ccccc
Q psy13846       1219 KMYQMKQLLPSVVIKGVQGINRAVIH--EED---------VEGVTKYKLLVE---------GDNLRDVMA-----TYGVK 1273 (1423)
Q Consensus      1219 ~l~~l~~~l~~~~v~Gi~~i~r~~i~--~~~---------~~~~~~~~l~te---------G~nl~~~~~-----~~~vd 1273 (1423)
                      +++.+...|.+++|||+|+|++|.|.  +..         .+.+++|+|.|+         |.+|..+|+     +++||
T Consensus       174 ~~~~i~~~lL~~~lkG~~~I~kv~i~~~~~~~~~~~~~~~~~~~~E~vLe~~~~~~~~~t~G~~~~~vl~~c~~~~~~ID  253 (381)
T cd02737         174 LRDRIIPFLLETVIKGDERIKSVNILWEDSPSTSWVKSVGKSSRGELVLEVTVEESCKKTRGNAWNVVMDACIPVMDLID  253 (381)
T ss_pred             HHHHHHHHHhheeecccCCeeEEEEEecCCCcccccccccccccceEEEEEEeccccccccchhHHHHHHhhhcccccCc
Confidence            56667776778999999999999997  221         124579999988         999999995     89999


Q ss_pred             ceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeeccccccccc-----chhh
Q psy13846       1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKE-----SVLN 1348 (1423)
Q Consensus      1274 ~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~-----S~l~ 1348 (1423)
                      ++|++||||++|+++|||||||++|++||+.||+.||++||+|||+||||+||++|.++||||+||+++..     |||+
T Consensus       254 ~~rt~sNdI~ev~~~lGIEAAR~~ii~El~~v~~~~G~~Vd~rHL~LlAD~MT~~G~~~~~nR~Gi~~~~~s~~~~spl~  333 (381)
T cd02737         254 WERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRSLKISAPFT  333 (381)
T ss_pred             CCCcEECCHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhccCCceEEecchhhhhcccccccCCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999997654     8999


Q ss_pred             hccchhhHHHHHhhcccCCcccccccccceeeccccccccce-EEEee
Q psy13846       1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGL-IKLLQ 1395 (1423)
Q Consensus      1349 ~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~-~~l~~ 1395 (1423)
                      +||||+|+++|++||.+|+.|+|+|||++|+||+++|+|||+ |||++
T Consensus       334 ~asFE~t~~~l~~AA~~g~~D~l~gvs~~ii~G~~~~vGTG~~fdll~  381 (381)
T cd02737         334 EACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSKFEILW  381 (381)
T ss_pred             HhhHHHHHHHHHHHHhccCCCCCCChHHheeeCCcCCCcCCcceeeeC
Confidence            999999999999999999999999999999999999999997 99985

Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.

>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional

Probab=100.00  E-value=1.6e-54  Score=555.80  Aligned_cols=182  Identities=41%  Similarity=0.648  Sum_probs=170.7

Q ss_pred             hHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHH
Q psy13846       1218 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297 (1423)
Q Consensus      1218 ~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ 1297 (1423)
                      ..+..+...|.+++|+|+|||+||++.+++..+.++|+|.|||+||+++|++++||++||+||||++|+++|||||||++
T Consensus       671 ~~~~~~~~~l~~~~i~gi~gI~~~~i~~~~~~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~  750 (858)
T PRK14898        671 KALRKRIPKIKNIVLKGIPGIERVLVKKEEHENDEEYVLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNA  750 (858)
T ss_pred             HHHHHHHHHhcCcEEECCCCccEEEEecCCCCCCceEEEEecCcCHHHHhcCCCCcccccccCCHHHHHHhhCHHHHHHH
Confidence            34555556799999999999999999865432336899999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccc
Q psy13846       1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSEC 1377 (1423)
Q Consensus      1298 ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ 1377 (1423)
                      |++||++||+.||++||+|||+||||+||++|.++|+||+||+.++.|||++||||+|+++|++||++|++|+|+|||||
T Consensus       751 ii~Ei~~v~~~~gi~V~~rHl~liad~MT~~G~~~~~~r~gi~~~~~s~l~~asFe~t~~~l~~Aa~~g~~D~l~g~s~~  830 (858)
T PRK14898        751 IINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIEN  830 (858)
T ss_pred             HHHHHHHHHHhcCCccCHHHHHHHHHHHccCCcEEEeccCCccCCCCCHHHhcChHhHHHHHHHHhhcCCCCcCCCchHH
Confidence            99999999999999999999999999999999999999999988889999999999999999999999999999999999


Q ss_pred             eeeccccccccceEEEeecCCC
Q psy13846       1378 IIMGLPMNVGTGLIKLLQAVPR 1399 (1423)
Q Consensus      1378 ii~G~~~~~GTG~~~l~~~~~~ 1399 (1423)
                      ||+|+++|+|||+|+|+++...
T Consensus       831 ii~G~~~~~GTG~~~l~~~~~~  852 (858)
T PRK14898        831 VIVGKPIKLGTGCVDLRIDREY  852 (858)
T ss_pred             eeeCCccCCcCceEEEEecCcc
Confidence            9999999999999999998654

>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''

Probab=100.00  E-value=1.3e-52  Score=487.18  Aligned_cols=269  Identities=32%  Similarity=0.500  Sum_probs=230.9

Q ss_pred             ecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhH
Q psy13846        690 IMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIK  769 (1423)
Q Consensus       690 ~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlk  769 (1423)
                      |.+++++|||+||++||||||||+|||||    +|||||||             ||||+||             |||||+
T Consensus        36 y~~alv~PGeaVG~IAAQSIGEP~TQMTL----nTFH~AGV-------------as~nVTl-------------GVPRlk   85 (367)
T TIGR02389        36 YLRSLIDPGEAVGIVAAQSIGEPGTQMTM----RTFHYAGV-------------AELNVTL-------------GLPRLI   85 (367)
T ss_pred             HHHhcCCCccccchhhhhhcCCccccccc----cccccccc-------------cccCccc-------------cchhHH
Confidence            57789999999999999999999999999    99999999             9999999             999999


Q ss_pred             HHHhhhcCCCCceeeeecccCC--hHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhh
Q psy13846        770 EIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI  847 (1423)
Q Consensus       770 EIinaSk~ikTPiitv~L~~~~--~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I  847 (1423)
                      |||||+|+||||+|++||.++.  +.++|+.++.+||+++|+|++.+++++|.  ++.+.+++|.+++.  .+.++++.|
T Consensus        86 EIINa~k~i~TP~~ti~L~~~~~~~~~~a~~v~~~iE~t~l~dv~~~~~~~~~--~~~l~i~ld~~~l~--~~~i~~~~i  161 (367)
T TIGR02389        86 EIVDARKTPSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLA--DMTVIIELDEEQLK--ERGITVDDV  161 (367)
T ss_pred             HHhhcccCCCCCeEEEEecCcchhhHHHHHHHHHHhhheeHHHHHhhhheecc--CcEEEEEECHHHHH--hcCCCHHHH
Confidence            9999999999999999999764  67899999999999999999999987764  44566677777664  446788899


Q ss_pred             hHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccc
Q psy13846        848 RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL  927 (1423)
Q Consensus       848 ~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL  927 (1423)
                      +.++.+.+.........+...+.+++..  .. ...++.+++.+++++|+|+|||+|+++.++    .++|.+.|+|+||
T Consensus       162 ~~~i~~~~~~~~~~~~~~~~~i~i~~~~--~~-~~~l~~l~~~l~~~~v~Gi~gI~r~~i~~~----~~~~~l~teG~nl  234 (367)
T TIGR02389       162 EKAIKKAKLGKVIEIDMDGNTITIKPPK--PS-LKELRKLKEKIKNLHIKGIKGIKRVVIRKE----GDEYVIYTEGSNL  234 (367)
T ss_pred             HHHHHHhcccccceeecCCCEEEEEecC--ch-HHHHHHHHHHhhhceEeCCCCceEEEEECC----CCeEEEEEeccCH
Confidence            9988765432221111122333333321  11 235888889999999999999999999743    2479999999999


Q ss_pred             cccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        928 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       928 ~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      ++++.+++||+.+|+||||++|+++|||||||++|++|++.+|+.||++||+|||+||||+||++|++.+.+
T Consensus       235 ~~v~~~~~VD~~rt~sNdI~ei~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~  306 (367)
T TIGR02389       235 KEVLKLEGVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIG  306 (367)
T ss_pred             HHHHcCCCCccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhcCCceEEecc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999864

This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.

>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit

Probab=100.00  E-value=1e-52  Score=534.29  Aligned_cols=111  Identities=31%  Similarity=0.521  Sum_probs=104.6

Q ss_pred             cccHHHHHHH----------------hCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccce-------------e
Q psy13846       1279 SNNTYEVYKT----------------LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK-------------G 1329 (1423)
Q Consensus      1279 sN~i~~i~~~----------------lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~-------------G 1329 (1423)
                      +.|.|+++.+                +|+||+|..|++|+++||+.||+.|++|||++|+|+||.+             |
T Consensus      1057 ~~~ph~iL~~~~~~~~~~~g~~~aa~~s~~~~q~~lv~eiq~vy~~QGv~I~~kHieiIvrqMtskV~i~~~G~t~~lpG 1136 (1227)
T TIGR02388      1057 PINPHDILDVFFSYYKDQDGLYEAAQESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPG 1136 (1227)
T ss_pred             CCCHHHHHhhhhhhhcccchhHHHHHHHHHHHHHHHHHHHHHHHHhcceEeehhhHHHHHHHHhceEEEeeCCCcccCCc
Confidence            5678888887                4999999999999999999999999999999999999987             5


Q ss_pred             E---------------------------EEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeecc
Q psy13846       1330 E---------------------------VLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGL 1382 (1423)
Q Consensus      1330 ~---------------------------~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~ 1382 (1423)
                      +                           ++||||++++  ..|+|++||||+|+++|++||++|+.|+|+|++||||+|+
T Consensus      1137 eli~~~~~~~~n~~l~~~~~~~~~y~pvLlGITkasL~--t~Sfis~ASFqeTtrvL~~Aai~g~~D~l~glkENvI~G~ 1214 (1227)
T TIGR02388      1137 ELVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASLN--TDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGR 1214 (1227)
T ss_pred             ceeeHHHHHHHHHHHHhcCCCccccceeEeeeeecccc--ccchhhhccHHHHHHHHHHHHHcCCcccccCchhheeecC
Confidence            4                           7999999997  5899999999999999999999999999999999999999


Q ss_pred             ccccccceE
Q psy13846       1383 PMNVGTGLI 1391 (1423)
Q Consensus      1383 ~~~~GTG~~ 1391 (1423)
                      ++|+|||..
T Consensus      1215 liP~GTG~~ 1223 (1227)
T TIGR02388      1215 LIPAGTGFS 1223 (1227)
T ss_pred             ccccCCCcc
Confidence            999999974

The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.

>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA

Probab=100.00  E-value=1.6e-53  Score=489.14  Aligned_cols=252  Identities=43%  Similarity=0.628  Sum_probs=199.0

Q ss_pred             CCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeecc-------ccCCCccCCCcchheecCCC
Q psy13846        622 GLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA-------FYGQTDCISGVSECIIMGLP  694 (1423)
Q Consensus       622 GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s-------~yG~~~~~~~~~~~~~~~~~  694 (1423)
                      ||+|.|||||||||||||||||||||+||||||||||++||++|+||+|||++       .||+|+             +
T Consensus         1 Gl~~~e~f~~~~~~R~gl~dta~kTa~sGyl~R~lv~~~~~~~v~~~~~~~~~~~~i~~~~~~~~~-------------~   67 (277)
T PF04998_consen    1 GLTPTEYFFHCMGGREGLIDTAVKTADSGYLQRRLVKVLEDLIVRYDDCVRNSGGSIIQFIYGEDG-------------L   67 (277)
T ss_dssp             C-THHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHTTHEEETTSEEESTTSEEEESSCTTTS-------------B
T ss_pred             CcCHHHHHHHHhcccccccccceeeeccccchhhhhhccceEEEEEcCccccccceeeeccccccc-------------c
Confidence            89999999999999999999999999999999999999999999999999987       366552             7


Q ss_pred             cccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhh
Q psy13846        695 MNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINA  774 (1423)
Q Consensus       695 ~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIina  774 (1423)
                      ++|||+||.|||||||||+|||||    +|||+||+             +++++|+             |+||++||+++
T Consensus        68 v~~Ge~VGiiaAQSIGEP~TQ~TL----~TFH~aG~-------------~~~~vt~-------------giprl~eii~~  117 (277)
T PF04998_consen   68 VEPGEAVGIIAAQSIGEPGTQMTL----RTFHTAGV-------------ASKNVTQ-------------GIPRLKEIINA  117 (277)
T ss_dssp             --TTSBHHHHHHHHHHCHGCCSHH----SCTSSSCS-------------STSSCSS-------------SHHHHHHHHTT
T ss_pred             cCccccchhhhhchhcchhHHhhh----cccccCce-------------eeecccc-------------cceeecccccc
Confidence            899999999999999999999999    99999999             7778888             99999999999


Q ss_pred             hcCCCCceeeeecccCCh--HHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhh
Q psy13846        775 SRNISTPIITAYLDKDTD--LDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE  852 (1423)
Q Consensus       775 Sk~ikTPiitv~L~~~~~--~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~  852 (1423)
                      ++++++|+++.+......  .+....+............                                         
T Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------------------------------  156 (277)
T PF04998_consen  118 SKKIKTPIITVYGKKKIISEKKKIKIIRKKIKIIKNGKK-----------------------------------------  156 (277)
T ss_dssp             CSSSSSEEEEECSCSSECSSSHHHHHHHHTCSSSCSTTC-----------------------------------------
T ss_pred             ccccccceEEeecccceecccccceEEEEeeeeeecccc-----------------------------------------
Confidence            999999999988865432  1222122111111000000                                         


Q ss_pred             hcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeee-cccccceeEEeeeccCccccccc
Q psy13846        853 RTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIH-EEDVEGVTKYKLLVEGDNLRDVM  931 (1423)
Q Consensus       853 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~-~~~~~~~~~~~l~~eG~nL~~vl  931 (1423)
                                                                +..+.......... ........+|.+.++|+++..++
T Consensus       157 ------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~l~~v~  194 (277)
T PF04998_consen  157 ------------------------------------------VKNGDKIKKGSIISKDILEKKSKEYVLQTEGSNLQEVY  194 (277)
T ss_dssp             ------------------------------------------EHTTCESSSSCSEHHHHCEECCCCCEEECCSHHHHHHT
T ss_pred             ------------------------------------------eecceeeecceeeeeccccchhHHHHHHHHhhhchhhe
Confidence                                                      00000000000000 00011235789999999999999


Q ss_pred             eeec-ccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        932 ATYG-VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       932 ~~~g-vD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      ..+| +|+.++.+|+|++|++++||||||++|++|++.+++.+|++||+||++|+||.||++|.++|+.
T Consensus       195 ~~qgvid~~k~~sn~I~qm~~~~GIeaar~~i~~e~~~v~~~~g~~vn~rhl~llad~mt~~g~~~git  263 (277)
T PF04998_consen  195 SSQGVIDNDKHISNDIRQMLSKLGIEAARNSIIKELKNVFESYGIEVNKRHLSLLADYMTYKGVLLGIT  263 (277)
T ss_dssp             CSTT-EETCHHECSHHHHHHHHHEHHHHHHHHHHHHHCHHHHCTSCCCHHHHHHHHHHHCCCSS---CC
T ss_pred             ecccccCCCEEEeceeEeeeeeEEEEECCCceeecCcEeeHHHHHHHHHHHHHhCCCcCeeeeEEEEEE
Confidence            9999 8999999999999999999999999999999999999999999999999999999999999975

Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....

>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional

Probab=100.00  E-value=8.2e-51  Score=479.85  Aligned_cols=300  Identities=29%  Similarity=0.447  Sum_probs=241.6

Q ss_pred             chHHHHHHHhhhhhcccceeeccccCCCccCCCcchheecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccc
Q psy13846        652 MQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVY  731 (1423)
Q Consensus       652 lqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~  731 (1423)
                      |-.++.+-|..+...|..|-..-     +..-+.....|.+++++||++||.+||||||||+|||||    +||||||| 
T Consensus       141 lp~~~~~el~~~~~~~~l~~~~~-----~~i~~ei~~~y~~~~v~pGE~VG~IAAQSIGEP~TQMTL----nTFH~AGV-  210 (509)
T PRK14897        141 LPPSVIEEIAKAMKKKELSDDEY-----EEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTM----RTFHYAGV-  210 (509)
T ss_pred             CCHHHHHHHHHHHHHcCCCHHHH-----HHHHHHHHHHHHHhccCCCCCcchhhhhhhCCccccccc----cccccccc-
Confidence            66667776666666664332210     000011122367889999999999999999999999999    99999999 


Q ss_pred             cccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeeecccCC--hHHHHHHHhhhhcccchh
Q psy13846        732 YERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLG  809 (1423)
Q Consensus       732 ~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~--~~e~a~~v~~rie~~~l~  809 (1423)
                                  |++|+||             |||||+|||||+|+||||+|++||.++.  |.++|+.++.+||+++|+
T Consensus       211 ------------as~NVTl-------------GVPRLkEIINa~K~isTP~mtiyL~~~~~~d~e~A~~V~~~IE~ttL~  265 (509)
T PRK14897        211 ------------AEMNVTL-------------GLPRLIEIVDARKKPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLI  265 (509)
T ss_pred             ------------ccccccc-------------CcchhHHHhhcccCCCCceEEEEecCcccccHHHHHHHHhhheeeEHH
Confidence                        9999999             9999999999999999999999999774  788999999999999999


Q ss_pred             hhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccccccccCCCCccccchhhhhhhh
Q psy13846        810 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQ  889 (1423)
Q Consensus       810 dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~  889 (1423)
                      |+++++..+   .++.+.+++|.+++  ..+.++++.|..+|.+...  ..+.. +++.+.+.+..  .. ...++++.+
T Consensus       266 dv~~~~~d~---~~~~i~i~Ld~~~l--~~~~l~~~~I~~~I~~~~~--~~~~~-~~~~I~i~~~~--~~-~~~L~~l~~  334 (509)
T PRK14897        266 DVADIITDI---AEMSVVVELDEEKM--KERLIEYDDILAAISKLTF--KTVEI-DDGIIRLKPQQ--PS-FKKLYLLAE  334 (509)
T ss_pred             HHHHHHHHh---ccceEEEEECHHHH--HHcCCCHHHHHHHHHhccc--eEEec-CCCEEEEEeCc--hH-HHHHHHHHH
Confidence            999876544   34445556666555  5566777889988876321  11221 22233343321  12 236778888


Q ss_pred             cCCceEEccccccceeeeecccccceeEEeeeccCccccccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHH
Q psy13846        890 LLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV  969 (1423)
Q Consensus       890 ~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v  969 (1423)
                      .+++++|+|+|||+|+++..+++  ...|.|.|+|+||++++.++|||+.+|+||||+||+++|||||||++|++|++.+
T Consensus       335 ~l~~i~I~GipgI~r~~i~~~~~--~~~~~L~TeG~NL~~vl~~~~VD~~rt~SNdI~eI~~vlGIEAAR~~Ii~Ei~~V  412 (509)
T PRK14897        335 KVKSLTIKGIKGIKRAIARKEND--ERRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRT  412 (509)
T ss_pred             HhhccEEeCCCCccEEEEecCCC--CceeEEEeeccCHHHHhcCCCcccccCccCCHHHHHHhcCHHHHHHHHHHHHHHH
Confidence            99999999999999999986543  3469999999999999999999999999999999999999999999999999999


Q ss_pred             HHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        970 MENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       970 ~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      |+.||++||+|||+||||+||++|++.+.+
T Consensus       413 ~~~~Gi~Vd~RHL~LIAD~MT~~G~v~~i~  442 (509)
T PRK14897        413 LQEQGLNVDIRHIMLVADMMTFDGSVKAIG  442 (509)
T ss_pred             HHhcCCcccHHHHHHHHHHhCcCCcccccc
Confidence            999999999999999999999999998875

>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP)

Probab=100.00  E-value=2.5e-50  Score=469.13  Aligned_cols=268  Identities=32%  Similarity=0.482  Sum_probs=229.3

Q ss_pred             ecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhH
Q psy13846        690 IMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIK  769 (1423)
Q Consensus       690 ~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlk  769 (1423)
                      |.++.++||++||.+||||+|||+|||||    +|||||||             ||||+||             |||||+
T Consensus        32 ~~~~~~~~Ge~vG~iaAQSiGEP~TQMTL----nTFH~AGV-------------as~nVTl-------------GVPRlk   81 (363)
T cd06528          32 YLRSLIEPGEAVGIVAAQSIGEPGTQMTL----RTFHYAGV-------------AEINVTL-------------GLPRLI   81 (363)
T ss_pred             HHHHhhccCccccceeeeecCccceeccc----cccccccc-------------ccccCcc-------------ccccHH
Confidence            46778999999999999999999999999    99999999             9999999             999999


Q ss_pred             HHHhhhcCCCCceeeeecccC--ChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhh
Q psy13846        770 EIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI  847 (1423)
Q Consensus       770 EIinaSk~ikTPiitv~L~~~--~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I  847 (1423)
                      |||||+|+||||+|++||.++  .+.+.|+.++.+||+++|+|++.++++.  ++++.+.+++|.+++..  +.++++.|
T Consensus        82 EIIna~K~i~TP~mti~L~~~~~~~~~~a~~v~~~iE~t~l~di~~~~~i~--~~~~~l~i~ld~~~l~~--~~l~~~~i  157 (363)
T cd06528          82 EIVDARKEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISID--LFNMRITIELDEEMLED--RGITVDDV  157 (363)
T ss_pred             HHhhcccCCCCceEEEEecCcchhhHHHHHHHHHhhceeEHHHhhhheEEe--ccCcEEEEEECHHHHHH--cCCCHHHH
Confidence            999999999999999999977  4678999999999999999999998875  34566677777776654  45788899


Q ss_pred             hHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccc
Q psy13846        848 RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL  927 (1423)
Q Consensus       848 ~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL  927 (1423)
                      ..++.+.......  ..++..+.+....  +.....++.+++.+++++|+|+|||+|+.++.++    ++|.+.|+|+||
T Consensus       158 ~~~i~~~~~~~~~--~~~~~~~~~~~~~--~~~~~~l~~l~~~l~~~~v~Gi~gI~r~~i~~~~----~~~~l~teG~nl  229 (363)
T cd06528         158 LKAIEKLKKGKVG--EEGDVTLIVLKAE--EPSIKELRKLAEKILNTKIKGIKGIKRVIVRKEE----DEYVIYTEGSNL  229 (363)
T ss_pred             HHHHHHhcCCccc--ccCCccEEEEcCC--cchHHHHHHHHHhhcccEEeCCCCceEEEEecCC----ceEEEEecCcCH
Confidence            9998765432221  1121111111111  1222467888899999999999999999998654    379999999999


Q ss_pred             cccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        928 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       928 ~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      ++++.+++||+.+|+|||++||+++|||||||++|++|++.+|+.||++||+|||+||||+||++|++.+.+
T Consensus       230 ~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~  301 (363)
T cd06528         230 KAVLKVEGVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIG  301 (363)
T ss_pred             HHHhcCCCCcccccccCCHHHHHHhCCHHHHHHHHHHHHHHHHHhcCCeecHHHHHHHHHHhccCCceeccc
Confidence            999999999999999999999999999999999999999999999999999999999999999999998865

Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.

>PRK04309 DNA-directed RNA polymerase subunit A''; Validated

Probab=100.00  E-value=7.1e-50  Score=468.24  Aligned_cols=266  Identities=33%  Similarity=0.538  Sum_probs=230.1

Q ss_pred             ecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhH
Q psy13846        690 IMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIK  769 (1423)
Q Consensus       690 ~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlk  769 (1423)
                      |.++.++|||+||.+||||||||+|||||    +||||||+             +++|+||             |||||+
T Consensus        51 y~~~~v~pGe~VG~iaAQsIGEP~TQMTL----~TFH~AGv-------------a~~nVTl-------------GvPRlk  100 (383)
T PRK04309         51 YLRSLVEPGEAVGVVAAQSIGEPGTQMTM----RTFHYAGV-------------AEINVTL-------------GLPRLI  100 (383)
T ss_pred             HHHhhcCCCCccchhhhhhccchhhhccc----ccccccCc-------------cccCccc-------------CchhHH
Confidence            56788999999999999999999999999    99999999             8999999             999999


Q ss_pred             HHHhhhcCCCCceeeeecccCC--hHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhh
Q psy13846        770 EIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI  847 (1423)
Q Consensus       770 EIinaSk~ikTPiitv~L~~~~--~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I  847 (1423)
                      |||||+|+||||+|++||.++.  |.++|+.++.+||+++|+++++++++.  ++++.+.+++|.+++.  .++++++.|
T Consensus       101 EIina~K~~~TP~~tv~L~~~~~~d~~~a~~v~~~iE~t~L~~v~~~i~~~--~~~~~l~i~ld~~~i~--~~~l~~~~I  176 (383)
T PRK04309        101 EIVDARKEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISVD--LANMTIIIELDEEMLE--DRGLTVDDV  176 (383)
T ss_pred             HHHhcccCCCCCeEEEEecCcccccHHHHHHHHhheeeeEHhhhhhheEec--cCCcEEEEEECHHHHH--HcCCCHHHH
Confidence            9999999999999999999874  789999999999999999999998864  3456667777777765  456688899


Q ss_pred             hHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccc
Q psy13846        848 RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL  927 (1423)
Q Consensus       848 ~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL  927 (1423)
                      +..|.+.+.....  +. ...+.+++..   .....++.+...+++++|+|++||+|+++.+++    ++|.+.|+|+||
T Consensus       177 ~~~i~~~~~~~~~--~~-~~~i~i~~~~---~~~~~l~~l~~~l~~~~vkGi~gI~r~~i~~~~----~~~~l~teG~nl  246 (383)
T PRK04309        177 KEAIEKKKGGEVE--IE-GNTLIISPKE---PSYRELRKLAEKIRNIKIKGIKGIKRVIIRKEG----DEYVIYTEGSNL  246 (383)
T ss_pred             HHHHHHhcCccee--cc-CCeEEEEecC---chHHHHHHHHHHhcccEEECCCCceEEEEecCC----CeEEEEEcccCH
Confidence            9998766543221  11 1222333321   112467788899999999999999999997542    479999999999


Q ss_pred             cccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        928 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       928 ~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      ++++.+++||+.+|+||||++|+++|||||||++|++|++.+|+.||++||+|||+||||+||++|++.+.+
T Consensus       247 ~~v~~~~~VD~~rt~sNdI~ei~~vlGIEAAR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~  318 (383)
T PRK04309        247 KEVLKVEGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIG  318 (383)
T ss_pred             HHHhcCCCEeeccccCCCHHHHHHHcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhccCceEEeee
Confidence            999999999999999999999999999999999999999999999999999999999999999999999864

>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional

Probab=100.00  E-value=1.4e-49  Score=509.72  Aligned_cols=113  Identities=29%  Similarity=0.472  Sum_probs=105.7

Q ss_pred             cccHHHHHHH----------------hCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeE------------
Q psy13846       1279 SNNTYEVYKT----------------LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE------------ 1330 (1423)
Q Consensus      1279 sN~i~~i~~~----------------lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~------------ 1330 (1423)
                      +.|.|+++.+                +|+||+|..+++|+++||+.||++||+|||++|+|+||.++.            
T Consensus      1058 ~~~ph~iL~~~f~~~~~~~g~~~aa~~~~~~~~~~lv~evq~Vy~~QGv~I~dkHieiIvrqMt~kV~i~d~Gdt~~lpG 1137 (1331)
T PRK02597       1058 PINPHELLEIFFEDLRDRKGLYEAALEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPG 1137 (1331)
T ss_pred             CCCHHHHHhhhhhhhcccchhhHHHHHhHHHHHHHHHHHHHHHHHhcCeEechhhHHhHHHHHhCcEEEeeCCCcccCCc
Confidence            5788999998                899999999999999999999999999999999999998843            


Q ss_pred             ----------------------------EEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeecc
Q psy13846       1331 ----------------------------VLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGL 1382 (1423)
Q Consensus      1331 ----------------------------~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~ 1382 (1423)
                                                  ++||||..++  ..|+|++||||+|+++|++||++|+.|+|+|++||||+|+
T Consensus      1138 eli~~~~~~~~N~~~~~~~~~~a~y~pvLlGItkasl~--T~sfis~aSFqeT~rvL~~AAi~g~~D~l~GlkENVI~G~ 1215 (1331)
T PRK02597       1138 ELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLN--TDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGR 1215 (1331)
T ss_pred             ceeeHHHHHHHHHHHHhcCCCcceeeeeeeeeeeeccc--cCChhhhccHHHHHHHHHHHHHcCCCcccCCchhheeecC
Confidence                                        3888998887  5899999999999999999999999999999999999999


Q ss_pred             ccccccceEEE
Q psy13846       1383 PMNVGTGLIKL 1393 (1423)
Q Consensus      1383 ~~~~GTG~~~l 1393 (1423)
                      ++|+|||++.+
T Consensus      1216 liP~GTG~~~~ 1226 (1331)
T PRK02597       1216 LIPAGTGFSGF 1226 (1331)
T ss_pred             ccccCcCchhh
Confidence            99999999744

>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed

Probab=100.00  E-value=2.4e-48  Score=504.08  Aligned_cols=108  Identities=33%  Similarity=0.536  Sum_probs=100.6

Q ss_pred             HhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccce--------------eE-----------------------
Q psy13846       1288 TLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK--------------GE----------------------- 1330 (1423)
Q Consensus      1288 ~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~--------------G~----------------------- 1330 (1423)
                      -+.|||+|..|++|+++||+.||+.|++|||++|+|+||.+              |+                       
T Consensus      1180 ~lS~~~~~~~lv~eiq~vy~~qGv~i~~kHieiivrqmt~kv~i~~~g~~~v~~pge~i~~~~~~~~~~~~~~~~~~~~~ 1259 (1364)
T CHL00117       1180 ELSIAQSQISLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEDGMSNVFLPGELIGLLRAERINRALEEAICYRPI 1259 (1364)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCcEeehhhhhhhHHHhhCeEEEeecCccCccCCcceeeHHHHHHHhHHhhcCcceeee
Confidence            44599999999999999999999999999999999999985              44                       


Q ss_pred             EEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeeccccccccceEEEeecC
Q psy13846       1331 VLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 1397 (1423)
Q Consensus      1331 ~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~ 1397 (1423)
                      ++||||++++  .+|+|++||||+|+++|++||++|++|+|+|++||||+|+++|+|||..++....
T Consensus      1260 llGitkasl~--t~Sfis~aSFqeT~rvL~~aai~g~~D~l~glkenvi~g~~ip~GTG~~~~~~~~ 1324 (1364)
T CHL00117       1260 LLGITKASLN--TQSFISEASFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKGLVHRS 1324 (1364)
T ss_pred             eeeeeehhcc--ccchhhhcchHHHHHHHHHHHHcCCcccccCchhheeecCcccCCCCchhhhhhh
Confidence            6799999998  5899999999999999999999999999999999999999999999998776543

>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form

Probab=100.00  E-value=1.6e-48  Score=497.30  Aligned_cols=627  Identities=16%  Similarity=0.185  Sum_probs=379.7

Q ss_pred             hhHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCC--------cccCHHHHHHHHHHhhcccccceee
Q psy13846         10 TLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN--------AFFNRAQTMRIASTLIAGRKVFFRG   81 (1423)
Q Consensus        10 ~~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~--------~~~~~~~~~~~~~~~~~~~~~~i~~   81 (1423)
                      -.-+||||||++||++++||+||++|+|++|.+||+++|+|+||.+|        +|++++++++.+.   . +...+..
T Consensus       453 PqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~---~-~~i~l~~  528 (1140)
T TIGR02386       453 PLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYD---N-GKVHLHA  528 (1140)
T ss_pred             CCCHHHHHHHHHHhCCcccEecCCCCCceEEeechhhheeeEeeeccccccCcCceeCCHHHHHHHHH---c-CCccCCC
Confidence            34579999999999999999999999999999999999999999996        7999999987542   2 2222333


Q ss_pred             eEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCceeEEe
Q psy13846         82 LIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIG  161 (1423)
Q Consensus        82 ~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~g  161 (1423)
                      .+...              .....+|  ..+|+.+.+-++++.++..+...                             
T Consensus       529 ~i~~~--------------~~g~~~~--tt~Gr~if~~ilP~~~~~~n~~~-----------------------------  563 (1140)
T TIGR02386       529 LIGVR--------------TSGEILE--TTVGRVIFNEILPEGFPYINDNE-----------------------------  563 (1140)
T ss_pred             ceEEe--------------ccccEEE--ccchHHHHHHHcCCccccccccc-----------------------------
Confidence            11111              0111223  12688888878776665443210                             


Q ss_pred             eec--cHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcc
Q psy13846        162 YFR--CVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLL  239 (1423)
Q Consensus       162 ffd--~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~  239 (1423)
                      .++  .+.+++..+...       ++.+....|++++++....+..+.+++.++.|......             |   .
T Consensus       564 ~l~Kk~lg~LI~~i~~~-------~G~~~t~~~LD~lk~Lgf~~at~~GfSigi~Dl~ip~~-------------K---~  620 (1140)
T TIGR02386       564 PLSKKEISSLIDLLYEV-------HGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDE-------------K---Y  620 (1140)
T ss_pred             ccchHHHHHHHHHHHHH-------hChHHHHHHHHHHHHHHHHHHHhcCeeeeeccCCCCHH-------------H---H
Confidence            222  123555555555       77888899999999988888888888888887632110             0   0


Q ss_pred             eehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhcc--CccccCCHHHHHHHhhccCCCcccccccccCCCCCcc
Q psy13846        240 KISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKF--GLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD  317 (1423)
Q Consensus       240 ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe~  317 (1423)
                      +++.        +.+..+.+..+.|..-.....+.......  ......-...+.+.|..-.+..++++.|..+|||++.
T Consensus       621 ~ii~--------~a~~~v~~i~~~y~~G~lt~~er~~kvi~iw~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~SGARGS~  692 (1140)
T TIGR02386       621 EILK--------EADKEVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLLKKDTYKFNPIFMMADSGARGNI  692 (1140)
T ss_pred             HHHH--------HHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCcHhhhhhcccccCH
Confidence            1111        11111222222222110000000000000  0000001222223332110124789999999999999


Q ss_pred             eEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCC
Q psy13846        318 LILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQT  397 (1423)
Q Consensus       318 liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~  397 (1423)
                      .++.||.   .|.++++...+                         +++|.                |.-+++..+|.+.
T Consensus       693 ~ni~QL~---GmrGlma~p~G-------------------------rii~~----------------PI~ssF~eGLtp~  728 (1140)
T TIGR02386       693 SQFRQLA---GMRGLMAKPSG-------------------------DIIEL----------------PIKSSFREGLTVL  728 (1140)
T ss_pred             HHHHHHH---hCCCcccCCCC-------------------------Ccccc----------------chhhccccCCCHH
Confidence            9999999   88887643221                         22222                4677788899866


Q ss_pred             HHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHHHHHHhhccCCccc
Q psy13846        398 EEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDI  477 (1423)
Q Consensus       398 ~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~  477 (1423)
                      |          ||||+||||+|+++++.+|+.|||.+|+|+...|| +...|+=+..+..+....       +.    +.
T Consensus       729 E----------yF~st~GaRkGLiDTAlKTAdSGYLtRRLVdv~qD-viV~~dDCgT~~gi~v~~-------~~----~~  786 (1140)
T TIGR02386       729 E----------YFISTHGARKGLADTALKTADSGYLTRRLVDVAQD-VVVREEDCGTEEGIEVEA-------IV----EG  786 (1140)
T ss_pred             H----------Hhhhccchhccccchheeecccceeeeehhhhhcc-eEEEeCCCCCCCCEEEEE-------ee----cC
Confidence            6          99999999999999999999999999999999999 666654332111000000       00    00


Q ss_pred             cceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEEEecccccccccccc
Q psy13846        478 CGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDK  557 (1423)
Q Consensus       478 ~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK  557 (1423)
                      .+++            +....+-..|+.+...+.                         .+..+.++...++++...+  
T Consensus       787 ~~~~------------i~~l~~ri~GR~~~~di~-------------------------~~~~~~~i~~~~~~i~~~~--  827 (1140)
T TIGR02386       787 KDEI------------IESLKDRIVGRYSAEDVY-------------------------DPDTGKLIAEANTLITEEI--  827 (1140)
T ss_pred             CceE------------EeehhheeEEEEEhhheE-------------------------eCCCCcEEEeCCCCcCHHH--
Confidence            0000            000011112332211111                         1222334444444432211  


Q ss_pred             CCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCccccccccccCCCceeeeeecccccc
Q psy13846        558 STLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGRE  637 (1423)
Q Consensus       558 ~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~GfI~~sf~~GL~p~Efffh~maGRe  637 (1423)
                                 ...+..                        .|    +.-+...+     -           + +|-++.
T Consensus       828 -----------~~~i~~------------------------~~----i~~v~iRS-----~-----------l-tC~s~~  851 (1140)
T TIGR02386       828 -----------AEKIEN------------------------SG----IEKVKVRS-----V-----------L-TCESEH  851 (1140)
T ss_pred             -----------HHHHHH------------------------cC----CCEEEecC-----C-----------e-eeCCCC
Confidence                       111111                        01    11111000     0           0 000011


Q ss_pred             cchhcccccCCCCcchHHHHHHHhhhhhcccceeeccccCCCccCCCcchheecCCCcccchhHHHHhhhcCCCCCCccc
Q psy13846        638 GLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRT  717 (1423)
Q Consensus       638 GLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~t  717 (1423)
                                              +        |=..|||.|         ++++.+++.|+|||++||||||||+||+|
T Consensus       852 ------------------------g--------vC~~CYG~~---------La~~~~V~~GeaVGiiAAQSIGEPGTQLT  890 (1140)
T TIGR02386       852 ------------------------G--------VCQKCYGRD---------LATGKLVEIGEAVGVIAAQSIGEPGTQLT  890 (1140)
T ss_pred             ------------------------C--------CccccCCCc---------ccCCcEecccccceeEeeeecCCCcchhe
Confidence                                    1        112268887         56788999999999999999999999999


Q ss_pred             cccCCCCcccCcccccccccccccccccc--ceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeeecccCChHHH
Q psy13846        718 LLFDNPEFHFPQVYYERRRDYSVKVTASV--KVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDY  795 (1423)
Q Consensus       718 L~~~~~tFh~agv~~~~~~~~~~~~~as~--~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~~~e~  795 (1423)
                      |    +|||.+|+             |+.  +||+             |+||+.|+++|++ +|.+.+-......     
T Consensus       891 m----RTFHtGGv-------------~~~~~DIT~-------------GlpRv~elfear~-p~~~a~iae~~G~-----  934 (1140)
T TIGR02386       891 M----RTFHTGGV-------------AGASGDITQ-------------GLPRVKELFEART-PKDKAVIAEVDGT-----  934 (1140)
T ss_pred             h----hheeeccc-------------ccccccccc-------------Cchhhhhhhhccc-CCCceEEEecCCE-----
Confidence            9    99999999             554  8998             9999999999953 4444433322210     


Q ss_pred             HHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccccccccCCC
Q psy13846        796 ARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD  875 (1423)
Q Consensus       796 a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~~~~~~~~~  875 (1423)
                                      +++++   ..                                                      
T Consensus       935 ----------------v~~~~---~~------------------------------------------------------  941 (1140)
T TIGR02386       935 ----------------VEIIE---DI------------------------------------------------------  941 (1140)
T ss_pred             ----------------EEEee---cc------------------------------------------------------
Confidence                            00000   00                                                      


Q ss_pred             CccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCc--cccccceeecccceeeccCchHHHHHHh
Q psy13846        876 SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD--NLRDVMATYGVKGVKCSSNNTYEVYKTL  953 (1423)
Q Consensus       876 ~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~--nL~~vl~~~gvD~~~t~SN~i~eV~~~L  953 (1423)
                                             .+|-.+++|..+++ ...+|.+-. |.  ...+...+...|...-.+-|++||++++
T Consensus       942 -----------------------~~~~~~i~i~~~~~-~~~~y~ip~-~~~l~v~~gd~V~~G~~l~~g~~~~~~il~v~  996 (1140)
T TIGR02386       942 -----------------------VKNKRVVVIKDEND-EEKKYTIPF-GAQLRVKDGDSVSAGDKLTEGSIDPHDLLRIK  996 (1140)
T ss_pred             -----------------------cCCcEEEEEECCCC-ceeEEeccC-CceEEecCCCEEccCCcccCCCCCHHHHHHhc
Confidence                                   00000111111100 000111100 00  0011111223344445567999999999


Q ss_pred             chHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------cchhhHHHHHHHHHhccCCCCCCCCHH
Q psy13846        954 GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-------TPVELKRLLDDIIAKNSSRSDPSLSAQ 1026 (1423)
Q Consensus       954 GIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-------~~~~~~~~~~~~~~~~~~~~~~~l~~~ 1026 (1423)
                      ||||+|+.|++|+++++..||++||++||++++++||++++|...|       ..|+...+.+.++....++..|+...+
T Consensus       997 G~~a~~~~lv~evq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt~~l~g~~v~~~~~~~~n~~~~~~g~~~~~~~~ 1076 (1140)
T TIGR02386       997 GIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAIP 1076 (1140)
T ss_pred             CHHHHHHHHHHHHHHHHHhCCccccchhHhHHHHHHhCcEEEEeCCCcCCCCCCeeeHHHHHHHHHHHHhCCCCCcccee
Confidence            9999999999999999999999999999999999999999999655       567778888888887788888998888


Q ss_pred             HHHHHhhhhcCcchhhhhhhHHHHHHHH
Q psy13846       1027 EILALSNETLDSKEFLQDTSENFVRDIK 1054 (1423)
Q Consensus      1027 ~~~~~~~~~l~~~~~~~~~~~~f~~~~~ 1054 (1423)
                      .+++++++.|++++|+++||  |++-.+
T Consensus      1077 ~llGitkasl~t~SflsaAS--FqeTtk 1102 (1140)
T TIGR02386      1077 QLLGITKASLNTESFLSAAS--FQETTK 1102 (1140)
T ss_pred             eeeeeeehhccCCCcccccc--hhhHHH
Confidence            99999999999999998776  655433

Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.

>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional

Probab=100.00  E-value=1.3e-47  Score=459.80  Aligned_cols=103  Identities=41%  Similarity=0.720  Sum_probs=101.0

Q ss_pred             CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846        341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV  420 (1423)
Q Consensus       341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~  420 (1423)
                      +||+|||||||||||+|||||++++++++||||||++|+||||||||||||+|+|||++|||||+              .
T Consensus       425 ~gd~VLlNRqPTLHR~sIqAf~~~l~~~ktirlhplvC~~fNADFDGDeMnvHvPqS~~A~aEa~--------------~  490 (627)
T PRK02625        425 EGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEAR--------------L  490 (627)
T ss_pred             cCcEEEecCCCccccccceeEeeEEcCCCeEEeccccCCcccCCcCCCeEEEecCCCHHHHHHHH--------------H
Confidence            79999999999999999999999999999999999999999999999999999999999999999              9


Q ss_pred             hhccccccccCCCCccccccccceEEEEEeecccccC
Q psy13846        421 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAF  457 (1423)
Q Consensus       421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~  457 (1423)
                      ||.+.+|++||++|+|+++++||+++|+|.||.+|..
T Consensus       491 Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~LT~~~~~  527 (627)
T PRK02625        491 LMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPG  527 (627)
T ss_pred             HhcCccceEEcCCCceeEeechhhhhheeeeeccCcc
Confidence            9999999999999999999999999999999999843

>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit

Probab=100.00  E-value=7.9e-48  Score=461.00  Aligned_cols=102  Identities=39%  Similarity=0.711  Sum_probs=100.4

Q ss_pred             CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846        341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV  420 (1423)
Q Consensus       341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~  420 (1423)
                      +||+|||||||||||+|||||++++++++||||||++|+||||||||||||+|+|||++|||||+              +
T Consensus       418 ~gd~VLlNRqPTLHR~sIqAf~~~l~~~ktirlhplvC~~fNADFDGDeMnvHvPqS~eA~aEa~--------------~  483 (619)
T TIGR02387       418 TGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTEAR--------------L  483 (619)
T ss_pred             cCCEEEecCCCccchhcceeeeeEEecCCeEEECcccCCcccCCCCCceeeeecCCCHHHHHHHH--------------H
Confidence            69999999999999999999999999999999999999999999999999999999999999999              9


Q ss_pred             hhccccccccCCCCccccccccceEEEEEeeccccc
Q psy13846        421 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNA  456 (1423)
Q Consensus       421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~  456 (1423)
                      ||.+.+|++||++|+|+++++||+++|+|.||.++.
T Consensus       484 Lm~~~~nilsP~~G~Pi~~~~QD~llg~y~LT~~~~  519 (619)
T TIGR02387       484 LMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNP  519 (619)
T ss_pred             HhhchhcEEecCCCceeEeechhhhhhhheeecccc
Confidence            999999999999999999999999999999999884

The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.

>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional

Probab=100.00  E-value=6.6e-47  Score=483.06  Aligned_cols=620  Identities=17%  Similarity=0.199  Sum_probs=372.8

Q ss_pred             hhHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCC--------cccCHHHHHHHHHHhhcccccceee
Q psy13846         10 TLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN--------AFFNRAQTMRIASTLIAGRKVFFRG   81 (1423)
Q Consensus        10 ~~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~--------~~~~~~~~~~~~~~~~~~~~~~i~~   81 (1423)
                      -.-+||||||+.||++++||+||++|+|++|.+||+++|+|+||.+|        +|++++++++++.+   + ...+..
T Consensus       461 PqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~---~-~i~l~~  536 (1156)
T PRK00566        461 PLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYEN---G-EVDLHA  536 (1156)
T ss_pred             CCCHHHHHHHHHHhCCcccEEecCCCCeeEEeehhhhhhhheeecccccccCCCceeCCHHHHHHHHHc---C-CCCCCC
Confidence            34579999999999999999999999999999999999999999999        89999999988652   2 222222


Q ss_pred             eEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCceeEEe
Q psy13846         82 LIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIG  161 (1423)
Q Consensus        82 ~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~g  161 (1423)
                      .+....  +       ..++  -++|    +|+.+.+-++++.++..+.                             .+
T Consensus       537 ~i~~~~--~-------~~~~--i~tt----~Gk~if~~ilP~~~~~~n~-----------------------------~g  572 (1156)
T PRK00566        537 RIKVRI--T-------SKKL--VETT----VGRVIFNEILPEGLPFINV-----------------------------NK  572 (1156)
T ss_pred             eEEecC--C-------CCce--EEcC----cHHHHHHhhccccceeecc-----------------------------cc
Confidence            122211  0       0011  1234    7888888887665432211                             13


Q ss_pred             eecc--HHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcc
Q psy13846        162 YFRC--VINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLL  239 (1423)
Q Consensus       162 ffd~--v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~  239 (1423)
                      .+++  +.+++..++..       ++.+....|++++++....+..+.+++.++.|......             |.   
T Consensus       573 ~ldKk~Lg~LI~~i~~~-------yG~~~t~~~LD~ik~Lgf~yat~~GfSigi~Dl~ip~~-------------K~---  629 (1156)
T PRK00566        573 PLKKKEISKIINEVYRR-------YGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPE-------------KK---  629 (1156)
T ss_pred             eecHHHHHHHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHHHhcCeEeehhhcCcChH-------------HH---
Confidence            4442  13444444444       78888999999999988888888899998888732110             00   


Q ss_pred             eehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhcc---CccccCCHHHHHHHhhccCCCcccccccccCCCCCc
Q psy13846        240 KISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKF---GLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS  316 (1423)
Q Consensus       240 ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe  316 (1423)
                      +++.        +.+..+++..+.|+.-.-...+.......   ...+ .-...+.+.|..-...+++++.|..+|||++
T Consensus       630 ~ii~--------~a~~~v~~i~~~y~~G~lt~~er~~kvi~~w~~~~d-~v~~~~~~~l~~~~~~~N~i~mMa~SGARGS  700 (1156)
T PRK00566        630 EIIE--------EAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATD-EVAKAMMKNLSKDQESFNPIYMMADSGARGS  700 (1156)
T ss_pred             HHHH--------HHHHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHH-HHHHHHHHhCccccCCCCChheeeeccCCcC
Confidence            1111        01111222222222211000000000000   0000 0122222333211123688999999999999


Q ss_pred             ceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCC
Q psy13846        317 DLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQ  396 (1423)
Q Consensus       317 ~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~  396 (1423)
                      ..++.||.   .+.++++..    +|..                     ++                .|.-+.+..+|.+
T Consensus       701 ~~ni~QL~---GmrGlma~p----~G~i---------------------ie----------------~pI~ssFreGLt~  736 (1156)
T PRK00566        701 ASQIRQLA---GMRGLMAKP----SGEI---------------------IE----------------TPIKSNFREGLTV  736 (1156)
T ss_pred             HHHHHHHH---hhcCccccC----CCCE---------------------ee----------------hhhhhhhhcCCCH
Confidence            99999999   888775422    1221                     11                1566778889986


Q ss_pred             CHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHHHHHHhhccCCcc
Q psy13846        397 TEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSD  476 (1423)
Q Consensus       397 ~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~  476 (1423)
                      .|          ||||+||||+|+++++.+|+.|||.+|+|+...|| +...++=.     ++..       ++......
T Consensus       737 ~E----------yFfst~GaRkGLiDTALKTAdSGYLtRRLVdvaqD-viV~~~DC-----gT~~-------gi~~~~~~  793 (1156)
T PRK00566        737 LE----------YFISTHGARKGLADTALKTADSGYLTRRLVDVAQD-VIVREDDC-----GTDR-------GIEVTAII  793 (1156)
T ss_pred             HH----------HhhcCcchhhcccchheeeccceeeehhHHHhhCc-eEEEECCC-----CCcC-------CEEEEEec
Confidence            66          99999999999999999999999999999999999 44443211     1100       00000000


Q ss_pred             ccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEEEeccccccccccc
Q psy13846        477 ICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMD  556 (1423)
Q Consensus       477 ~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ld  556 (1423)
                      ..+++            +..-.+...|+-+...+.                         .+..+.++...++++...  
T Consensus       794 ~~~~~------------i~~l~~~~~GR~~~~di~-------------------------~~~t~~~i~~~~~~i~~~--  834 (1156)
T PRK00566        794 EGGEV------------IEPLEERILGRVLAEDVV-------------------------DPETGEVIVPAGTLIDEE--  834 (1156)
T ss_pred             cCCEE------------EeEhhheeEeEEEhhhee-------------------------cCCCCcEEEcCCCccCHH--
Confidence            00000            000011112222211111                         122233444444432211  


Q ss_pred             cCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCccccccccccCCCceeeeeeccccc
Q psy13846        557 KSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGR  636 (1423)
Q Consensus       557 K~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~GfI~~sf~~GL~p~Efffh~maGR  636 (1423)
                                 +...+..                        .    |+..+...+                        
T Consensus       835 -----------~~~~i~~------------------------~----~i~~v~iRS------------------------  851 (1156)
T PRK00566        835 -----------IADKIEE------------------------A----GIEEVKIRS------------------------  851 (1156)
T ss_pred             -----------HHHHHHH------------------------c----CCCEEEEcC------------------------
Confidence                       1111100                        0    111111000                        


Q ss_pred             ccchhcccccCCCCcchHHHHHHHhhhhhcccceeeccccCCCccCCCcchheecCCCcccchhHHHHhhhcCCCCCCcc
Q psy13846        637 EGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPR  716 (1423)
Q Consensus       637 eGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~  716 (1423)
                             +-|                |  .-...|=..|||.|         ++++.+++.|||||+|||||||||+||+
T Consensus       852 -------~lt----------------C--~s~~gvC~~CYG~~---------La~~~~v~iGeaVGiIAAQSIGEPGTQL  897 (1156)
T PRK00566        852 -------VLT----------------C--ETRHGVCAKCYGRD---------LATGKLVNIGEAVGVIAAQSIGEPGTQL  897 (1156)
T ss_pred             -------Cee----------------e--cCCCcccHhhhCcc---------ccCCCCcccCcceeEEeeeecCCCccce
Confidence                   000                0  00001111268887         5678899999999999999999999999


Q ss_pred             ccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeeecccCChHHHH
Q psy13846        717 TLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYA  796 (1423)
Q Consensus       717 tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~~~e~a  796 (1423)
                      ||    +|||.+|+                +||+             |+||+.|++.| +++|.+.+-......      
T Consensus       898 Tm----RTFHtGGv----------------dIT~-------------Glprv~elfea-r~pk~~a~ise~~G~------  937 (1156)
T PRK00566        898 TM----RTFHTGGV----------------DITG-------------GLPRVAELFEA-RKPKGPAIIAEIDGT------  937 (1156)
T ss_pred             ee----eeeeecce----------------eccC-------------Cccchhhheee-ccCCCceEEEecCCE------
Confidence            99    99999997                5777             99999999999 455555433322210      


Q ss_pred             HHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccccccccCCCC
Q psy13846        797 RIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDS  876 (1423)
Q Consensus       797 ~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~~~~~~~~~~  876 (1423)
                                     +++++.                                                           
T Consensus       938 ---------------v~~~~~-----------------------------------------------------------  943 (1156)
T PRK00566        938 ---------------VSFGKE-----------------------------------------------------------  943 (1156)
T ss_pred             ---------------EEeccc-----------------------------------------------------------
Confidence                           000000                                                           


Q ss_pred             ccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCc--cccccceeecccceeeccCchHHHHHHhc
Q psy13846        877 SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD--NLRDVMATYGVKGVKCSSNNTYEVYKTLG  954 (1423)
Q Consensus       877 ~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~--nL~~vl~~~gvD~~~t~SN~i~eV~~~LG  954 (1423)
                                            .+|-.+++|..++. ...+|.+ -.+.  ...+...+...|...-.+-|++||++++|
T Consensus       944 ----------------------~~~~~~i~i~~~~~-~~~~y~v-p~~~~~~v~~gd~v~~G~~l~~g~~~~~~il~v~G  999 (1156)
T PRK00566        944 ----------------------TKGKRRIVITPDDG-EEREYLI-PKGKHLLVQEGDHVEAGDKLTDGSIDPHDILRVLG  999 (1156)
T ss_pred             ----------------------cCCceEEEEeCCCC-ceEEEEc-cCCCeeeecCCCEEccCCcccCCCCCHHHHHHhcC
Confidence                                  00000011110000 0011110 0000  00111112223444445668999999999


Q ss_pred             hHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------cchhhHHHHHHHHHhccCCCCCCCCHHH
Q psy13846        955 IEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-------TPVELKRLLDDIIAKNSSRSDPSLSAQE 1027 (1423)
Q Consensus       955 IEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-------~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 1027 (1423)
                      +||+|..|++|+++++..||++||++||++++++||.+++|...|       ..|+..++.+.+++...++..|+.....
T Consensus      1000 ~~~~~~~lv~eiq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt~~~~g~~v~~~~~~~~n~~~~~~g~~~~~~~~~ 1079 (1156)
T PRK00566       1000 VEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGKEPATGRPV 1079 (1156)
T ss_pred             HHHHHHHHHHHHHHHHHhCCcccccceeehHHHHHhCCeEEecCCCcCCCCCceeeHHHHHHHHHHHHHCCCCCCcccce
Confidence            999999999999999999999999999999999999999998655       5677888888888877888888888889


Q ss_pred             HHHHhhhhcCcchhhhhhhHHHHHH
Q psy13846       1028 ILALSNETLDSKEFLQDTSENFVRD 1052 (1423)
Q Consensus      1028 ~~~~~~~~l~~~~~~~~~~~~f~~~ 1052 (1423)
                      +++++++.|++++|+++||  |++-
T Consensus      1080 llGItka~l~t~SflsaAS--FQeT 1102 (1156)
T PRK00566       1080 LLGITKASLATESFLSAAS--FQET 1102 (1156)
T ss_pred             eeeeeecccccCccccccc--ccch
Confidence            9999999999999998776  5443

>CHL00018 rpoC1 RNA polymerase beta' subunit

Probab=100.00  E-value=2.4e-46  Score=453.14  Aligned_cols=103  Identities=41%  Similarity=0.655  Sum_probs=101.3

Q ss_pred             CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846        341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV  420 (1423)
Q Consensus       341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~  420 (1423)
                      +||+|||||||||||+|||||++++.+++||||||++|+||||||||||||+|+|||++|||||+              .
T Consensus       446 ~gd~VLlNRqPTLHR~sIqAf~~~L~~gktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~--------------~  511 (663)
T CHL00018        446 QGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEAR--------------L  511 (663)
T ss_pred             cCceeeecCCCcccccccceeeEEecCCCeEEeCcccCCcccCCccCcEEEEecCCCHHHHHHHH--------------H
Confidence            89999999999999999999999999999999999999999999999999999999999999999              9


Q ss_pred             hhccccccccCCCCccccccccceEEEEEeecccccC
Q psy13846        421 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAF  457 (1423)
Q Consensus       421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~  457 (1423)
                      ||.+.+|++||++|+|+++++||+++|+|.||.+|..
T Consensus       512 Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~  548 (663)
T CHL00018        512 LMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNRR  548 (663)
T ss_pred             HhcCccceeEcCCCceeEeechhhhhhhheecccCCC
Confidence            9999999999999999999999999999999999863

>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional

Probab=100.00  E-value=1.2e-43  Score=451.65  Aligned_cols=617  Identities=16%  Similarity=0.175  Sum_probs=362.4

Q ss_pred             hHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeeccc-CC-------cccCHHHHHHHHHHhhcccccceeee
Q psy13846         11 LYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ-KN-------AFFNRAQTMRIASTLIAGRKVFFRGL   82 (1423)
Q Consensus        11 ~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~-~~-------~~~~~~~~~~~~~~~~~~~~~~i~~~   82 (1423)
                      .-+||||||+.||++++||+||++|+|++|.+||+++|+|+||. +|       .|.+.+++++++.|.   ....+...
T Consensus       550 qS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~a~~~~---~~~~l~~~  626 (1460)
T PRK14906        550 LSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDAR---ADLDLQAK  626 (1460)
T ss_pred             CCHHHHHHHHHHhcchhcEecCCCCCeeEEeeeeeeeeeEEeeeccccccccCceeCCHHHHHHHHhcC---CCcccccc
Confidence            45799999999999999999999999999999999999999996 55       799999999888742   11112210


Q ss_pred             EEEecCCHHHHhh-cceeeeec---CcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCcee
Q psy13846         83 IEGTVTKEDRVQQ-QSHIQIVS---KNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVF  158 (1423)
Q Consensus        83 i~F~~~S~eeIrk-lSv~eIt~---~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~  158 (1423)
                      |...+  +.++.- .+......   ...+. ...|+.+.+.+                       ||-.++++.      
T Consensus       627 i~~~~--~~~~~~~~~~~~~~~~~~~~~~~-tt~Gr~Ifn~i-----------------------lP~d~~fvN------  674 (1460)
T PRK14906        627 IVVRL--SRDMTVRGSYGDLEETKAGERIE-TTVGRIIFNQV-----------------------LPEDYPYLN------  674 (1460)
T ss_pred             EEEec--CcccccccccccccCCCCCceEE-CCCCEEEEecc-----------------------cCCCccccc------
Confidence            11110  000000 00000000   00000 00222222222                       333333221      


Q ss_pred             EEeeecc--HHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeec
Q psy13846        159 HIGYFRC--VINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC  236 (1423)
Q Consensus       159 h~gffd~--v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~  236 (1423)
                        +.+++  +..|++.+...       ++......|+++++.....+..+.+++.++.|.....            - |.
T Consensus       675 --~~l~KK~Lg~LI~~i~~~-------~G~~~t~~fLD~Ik~LGf~yaT~sG~SIgi~Di~ip~------------~-K~  732 (1460)
T PRK14906        675 --YKMVKKDIGRLVNDCCNR-------YSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPD------------D-KP  732 (1460)
T ss_pred             --ceeeHHHHHHHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHHHhCCEEEeecccccCh------------H-HH
Confidence              12331  13344444444       6778888999999988777777778887777752100            0 00


Q ss_pred             CcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCCCCc
Q psy13846        237 GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS  316 (1423)
Q Consensus       237 ~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe  316 (1423)
                         +++.        +.+..+.+..+.|+.-.-...+....+. ..+....-.-...+.+.+. ..++++.|+.+|||++
T Consensus       733 ---~iI~--------~A~~~V~ei~~~y~~G~iT~~Er~~kVi-~iw~~a~d~v~~~~~~~l~-~~N~i~mMa~SGARGS  799 (1460)
T PRK14906        733 ---EILA--------EADEKVAAIDEDYEDGFLSERERHKQVV-DIWTEATEEVGEAMLAGFD-EDNPIYMMADSGARGN  799 (1460)
T ss_pred             ---HHHH--------HHHHHHHHHHHHHHcCCCcHHHHHHHHH-HHHHHHHHHHHHHHHHhcc-cCCCeEeeeeccCccc
Confidence               1111        1111222222222211000000000000 0000000011122233332 3688999999999999


Q ss_pred             ceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCC
Q psy13846        317 DLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQ  396 (1423)
Q Consensus       317 ~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~  396 (1423)
                      +.++.||.   .+.++++...+    .+                          +..           |.-.++..+|.+
T Consensus       800 ~~QI~QLa---GmRGlma~p~G----~i--------------------------Ie~-----------PI~SnFrEGLt~  835 (1460)
T PRK14906        800 IKQIRQLA---GMRGLMADMKG----EI--------------------------IDL-----------PIKANFREGLSV  835 (1460)
T ss_pred             HHHHHHHH---hcccceecCCC----Cc--------------------------ccc-----------ccccccccCCCH
Confidence            99999999   88888653222    11                          000           244567788886


Q ss_pred             CHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEee-cccccCCCHHHHHHHHHhhccCCc
Q psy13846        397 TEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLL-TQKNAFFNRAQTMRIASTLIADTS  475 (1423)
Q Consensus       397 ~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~-t~~~~~~~~~~~~~l~~~~~~~~~  475 (1423)
                      .|          ||||+||||+|+++|+.+|+.|||..|+|+...||.++...+- |.+...                  
T Consensus       836 ~E----------yFiSt~GaRKGL~DTALKTAdSGYLTRRLVdVaQDViV~e~DCgT~~Gi~------------------  887 (1460)
T PRK14906        836 LE----------YFISTHGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREEDCGTDEGVT------------------  887 (1460)
T ss_pred             HH----------HHHHcccccchhhhhhhhccccchHHHHHHHhhhheEEEeccCCCCCCEE------------------
Confidence            66          9999999999999999999999999999999999955443221 111000                  


Q ss_pred             cccceEeeeeccccCCceeec--c-eeeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEEEeccccccc
Q psy13846        476 DICGIIKRFSWRSWNPVVFVR--T-AVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLA  552 (1423)
Q Consensus       476 ~~~~~~~~~~~~~l~~p~i~k--p-~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~  552 (1423)
                           +          .++..  + .+-.-|+-+...+.                         .+. +.+++..++++.
T Consensus       888 -----v----------~~~~~~~~l~~ri~GR~~~~di~-------------------------~~~-g~~i~~~~~~I~  926 (1460)
T PRK14906        888 -----Y----------PLVKPKGDVDTNLIGRCLLEDVC-------------------------DPN-GEVLLSAGDYIE  926 (1460)
T ss_pred             -----E----------EEeecccchhheeeeEEEHhhhc-------------------------CCC-CCEEEeCCCeeC
Confidence                 0          00000  0 00011221111111                         121 334444444432


Q ss_pred             cccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCccccccccccCCCceeeeeec
Q psy13846        553 GSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHT  632 (1423)
Q Consensus       553 g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~GfI~~sf~~GL~p~Efffh~  632 (1423)
                      ...            +...+.                        ..|    +.                          
T Consensus       927 ~~~------------~~~~i~------------------------~~g----i~--------------------------  940 (1460)
T PRK14906        927 SMD------------DLKRLV------------------------EAG----VT--------------------------  940 (1460)
T ss_pred             cHH------------HHHHHH------------------------HCC----CC--------------------------
Confidence            110            000000                        000    00                          


Q ss_pred             ccccccchhcccccCCCCcchHHHHHHHhhhhhcccceee------ccccCCCccCCCcchheecCCCcccchhHHHHhh
Q psy13846        633 MGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFD------AAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ  706 (1423)
Q Consensus       633 maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR------~s~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~a  706 (1423)
                                                   .|.|..=.|..      ..|||.|         ++++.+++.|+|||+|||
T Consensus       941 -----------------------------~v~iRS~ltC~s~~gvC~kCYG~d---------Latg~~V~iGeaVGiIAA  982 (1460)
T PRK14906        941 -----------------------------KVQIRTLMTCHAEYGVCQKCYGWD---------LATRRPVNIGTAVGIIAA  982 (1460)
T ss_pred             -----------------------------EEEEeCCeeECCCCCChhhCcCCc---------ccCCcEeccccceeeeee
Confidence                                         11111111111      1268987         668889999999999999


Q ss_pred             hcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeee
Q psy13846        707 AVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAY  786 (1423)
Q Consensus       707 qsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~  786 (1423)
                      ||||||+||+||    +|||.+|+             ++.+||+             |+||+.|++.|++ ||.+-+-..
T Consensus       983 QSIGEPGTQLTM----RTFHtGGv-------------~~~dit~-------------GLpRv~eLfEar~-pk~~a~i~e 1031 (1460)
T PRK14906        983 QSIGEPGTQLTM----RTFHSGGV-------------AGDDITQ-------------GLPRVAELFEARK-PKGEAVLAE 1031 (1460)
T ss_pred             eecCCCcceeee----eeeecccc-------------ccccccc-------------Ccchhhhheeecc-CCCceeeec
Confidence            999999999999    99999998             5578888             9999999999964 233321111


Q ss_pred             cccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCccccccc
Q psy13846        787 LDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGH  866 (1423)
Q Consensus       787 L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~  866 (1423)
                      ..                                   ..                                         
T Consensus      1032 ~~-----------------------------------G~----------------------------------------- 1035 (1460)
T PRK14906       1032 IS-----------------------------------GT----------------------------------------- 1035 (1460)
T ss_pred             cC-----------------------------------CE-----------------------------------------
Confidence            10                                   00                                         


Q ss_pred             ccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCcccc----ccceeecccceeec
Q psy13846        867 SFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR----DVMATYGVKGVKCS  942 (1423)
Q Consensus       867 ~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~----~vl~~~gvD~~~t~  942 (1423)
                                                 |.|..-+|-.+++|..++.+ ..+|. .-.+..|.    +.-.+...|...-.
T Consensus      1036 ---------------------------v~i~~~~~~~~i~i~~~~~~-~~~y~-v~~~~~~~~~v~~gd~v~~G~~l~~G 1086 (1460)
T PRK14906       1036 ---------------------------LQITGDKTEKTLTIHDQDGN-SREYV-VSARVQFMPGVEDGVEVRVGQQITRG 1086 (1460)
T ss_pred             ---------------------------EEeccCCCceEEEEECCCCc-eeEEE-ccCCcccccccCCCCEEccCCCccCC
Confidence                                       00100011112222222110 01221 11121111    11223334555566


Q ss_pred             cCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------cchhhHHHHHHHHHhc
Q psy13846        943 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-------TPVELKRLLDDIIAKN 1015 (1423)
Q Consensus       943 SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-------~~~~~~~~~~~~~~~~ 1015 (1423)
                      +-|.++++++.|+||++.+|++|+++|+..||+.||.+||++++.+|+.+-+|...|       ..|+...+.+.+.+..
T Consensus      1087 ~~~p~~il~~~g~~~~~~ylv~eVQ~VYr~QGV~InDKHiEvIvRQMl~kV~I~d~Gdt~fl~Ge~vd~~~~~~~n~~~~ 1166 (1460)
T PRK14906       1087 SVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTANNLI 1166 (1460)
T ss_pred             CCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCceeccccHHHHHHHHhceEEEecCCCcCCCCCCeeeHHHHHHHHHHHH
Confidence            779999999999999999999999999999999999999999999999999998765       5577788888887777


Q ss_pred             cCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHH
Q psy13846       1016 SSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRD 1052 (1423)
Q Consensus      1016 ~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~ 1052 (1423)
                      .++..|+...+.+++++++.|++++|+++||  |++.
T Consensus      1167 ~~g~~pa~~~p~llGITKasL~t~SflSaAS--FQeT 1201 (1460)
T PRK14906       1167 LEGKQPPVGQPLLLGITKASLATDSWLSAAS--FQET 1201 (1460)
T ss_pred             HcCCCCceeeeEEeeeeeccccccccccccc--ccch
Confidence            8888888888889999999999999998876  5543

>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain

Probab=100.00  E-value=7.4e-44  Score=369.38  Aligned_cols=110  Identities=49%  Similarity=0.703  Sum_probs=108.2

Q ss_pred             cHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHH
Q psy13846       1281 NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLF 1360 (1423)
Q Consensus      1281 ~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~ 1360 (1423)
                      ||++|+++|||||||++|++||++||+.||++||+|||+||||+||++|.++|+||+||++.+.|||++||||+|.++|+
T Consensus        49 dI~~i~~~lGIEAaR~~iv~El~~v~~~~Gi~V~~rHl~LIAD~MT~~G~~~ginr~g~~~~~~Spl~~aSFE~t~~~L~  128 (158)
T cd00630          49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLL  128 (158)
T ss_pred             cHHHHHHHhCHHHHHHHHHHHHHHHHHhcCceecHHHHHHHHHHHhcCCcccccccccccccCCCHHHHcCHHHHHHHHH
Confidence            89999999999999999999999999999999999999999999999999999999999877899999999999999999


Q ss_pred             hhcccCCcccccccccceeeccccccccce
Q psy13846       1361 DAAFYGQTDCISGVSECIIMGLPMNVGTGL 1390 (1423)
Q Consensus      1361 ~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~ 1390 (1423)
                      +||.+|+.|+|+|+|+||+||+++|+|||+
T Consensus       129 ~AA~~g~~D~l~g~s~~ii~Gk~~~~GTG~  158 (158)
T cd00630         129 DAAAAGEKDELEGVSENIILGRPAPLGTGS  158 (158)
T ss_pred             HHhhcCCCCCCCCcHHhhhccCCCCCCCCC
Confidence            999999999999999999999999999995

RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe

>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain

Probab=100.00  E-value=1.4e-42  Score=372.38  Aligned_cols=109  Identities=35%  Similarity=0.534  Sum_probs=105.0

Q ss_pred             ccHHHHHHHh--CHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeE---------------------------
Q psy13846       1280 NNTYEVYKTL--GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE--------------------------- 1330 (1423)
Q Consensus      1280 N~i~~i~~~l--GIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~--------------------------- 1330 (1423)
                      ||++++++++  ||||||++|++|+++||+.||++||+||++||||+||+++.                           
T Consensus        54 ~~~~~il~~~~~Giea~r~~iv~EIq~Vy~~qGV~I~dKHielIv~qMT~kv~i~~~g~s~~l~Ge~v~~~~~~~~N~~~  133 (204)
T cd02655          54 INPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRL  133 (204)
T ss_pred             CCHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcCeeecHHHHHHHHHHHhcCeEEecCCCcccCCCceeeHHHHHHHHHHH
Confidence            8999999999  99999999999999999999999999999999999999955                           


Q ss_pred             -------------EEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeeccccccccce
Q psy13846       1331 -------------VLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGL 1390 (1423)
Q Consensus      1331 -------------~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~ 1390 (1423)
                                   ++||||++++  ++|||++||||+|+++|++||++|++|+|+|++||||+|+++|+|||+
T Consensus       134 ~~~~~~~~~y~p~llGItk~~l~--~~Sfls~ASFqeT~kvL~~AAi~gk~D~L~GlkeNVI~G~liPaGTG~  204 (204)
T cd02655         134 LLLGKKPAKYEPVLLGITKASLN--TESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL  204 (204)
T ss_pred             HhCCCCcccccceeeeeeecccc--CCCccccCChHHHHHHHHHHHhcCCCCCCCCchhheEECCccCCCCCC
Confidence                         4599999997  589999999999999999999999999999999999999999999995

Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.

>PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 RNA polymerases catalyse the DNA-dependent polymerisation of RNA

Probab=100.00  E-value=2.4e-41  Score=397.24  Aligned_cols=249  Identities=33%  Similarity=0.511  Sum_probs=178.5

Q ss_pred             cceeeeEEEecCCHHHHhhcceeeeecCcccccCCC-CCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccC
Q psy13846         77 VFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQ-RTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL  155 (1423)
Q Consensus        77 ~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~-g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~  155 (1423)
                      .+|.+ |+|++|||+||+++||++|+++.+|  |.. |+|+.|||||||||+.++...|+|||+...+||||||||+|+.
T Consensus         2 ~~i~~-i~f~~~s~~eI~~~Sv~~i~~~~~~--~~~~~~p~~~Gl~d~rlG~~~~~~~C~tC~~~~~~CpGHfGhI~L~~   78 (337)
T PF04997_consen    2 KKIKS-IQFGIYSPEEIRKLSVKEITNPETF--DNLTGKPIKGGLYDPRLGPIDKKQICSTCGLNYTECPGHFGHIELAL   78 (337)
T ss_dssp             EEEEE-EEEEE--HHHHHHHEEEB--SSTSB--CTSSSSCBSSSSSSSSSS-SSSSSTSSSSSSSSSSCCCSEEEEEEEE
T ss_pred             CeeeE-EEEEeCCHHHHHHhCcEEEechhhc--cCCCCCCccccccChhhcCCCcccccccccccccccCCceeEEEeCH
Confidence            46888 9999999999999999999999999  555 9999999999999999999999999999999999999999999


Q ss_pred             ceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceee
Q psy13846        156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKK  235 (1423)
Q Consensus       156 PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk  235 (1423)
                      ||||||||+.++++|+++|+.  |+++++.+++...+...+....  ...+......+.+.|++...|++|+..++.+++
T Consensus        79 PV~h~~f~~~i~~iL~~~C~~--C~~l~~~~~~~~~~~~~~~~~~--~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~  154 (337)
T PF04997_consen   79 PVYHPGFFKEIPKILRCICKK--CSRLLLSEKEKYFYLKILLKLK--KKKKKERLKIISKECKKKSICSHCKAINGKIKK  154 (337)
T ss_dssp             EEETCCCHHHHHHHHTTSCTT--TSCTSTCCCCHTSCHHHCHCSH--SSSHHHHHHHHHHHHHHTCSSTSTCC-SSS---
T ss_pred             HHHhhcccccceeeecccccc--cccccccccccccccccccccc--cccchhHHHHHHHhhhhhhhhcccccccccccc
Confidence            999999999999999999999  9999999887644443333321  223345667778888888999999988877653


Q ss_pred             cCcceehhhhhccccc-chhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCCC
Q psy13846        236 CGLLKISHEKYKNRTK-KKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK  314 (1423)
Q Consensus       236 ~~~~ki~~e~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~ar  314 (1423)
                      ....+... ....... ........    +...+... +.....+ ...+.++|.+++++|+++++++..++++.+..++
T Consensus       155 ~~~~~~~~-~~~~~~~~~~~~~~~~----i~~~i~~~-~~~~~~~-~~~~~l~~~~v~~ilk~l~~~~~~~l~~~~~~~~  227 (337)
T PF04997_consen  155 VEKSKKCE-GCGKKNPKIRKEGAEK----IQEEIKKK-ESNKEIK-EELRILTPEEVRQILKKLSKEDKELLGFDPSGSR  227 (337)
T ss_dssp             SSSEETSS-SSSSBSCEEEEESHCC----CCCHHHSC-CHHHHHH-CHCECESHHHHHHHHHHSHHHHHHHHHHHTTTBS
T ss_pred             cccchhcc-cccccCcccccchhhh----cccccccc-cccccch-hhhhhhhhhhhhhcchhhhhhheeeeeccccccc
Confidence            10000000 0000000 00000000    00000000 0001111 2234689999999999999999999999988899


Q ss_pred             CcceEEEEecCCCCCCCCcEEcCCC
Q psy13846        315 PSDLILTRLLVPPNCIRPSVISDLK  339 (1423)
Q Consensus       315 Pe~liLt~lpVPP~~vRPsv~~g~~  339 (1423)
                      |+||||++|||||+++||++.+|+.
T Consensus       228 P~~~~l~~lpVpP~~~RP~v~~~~~  252 (337)
T PF04997_consen  228 PEWFFLTVLPVPPPRFRPSVQLGGG  252 (337)
T ss_dssp             GGGSEEEEEEE-TGGGS-EEEESSS
T ss_pred             cceeEEeeeecCCceeeeeeeeecc
Confidence            9999999999999999999999875

Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which is a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_W 3QQC_A 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2AUJ_D 1ZYR_D 1SMY_D ....

>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional

Probab=100.00  E-value=2e-40  Score=437.08  Aligned_cols=114  Identities=18%  Similarity=0.264  Sum_probs=100.9

Q ss_pred             eecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------cchhhH
Q psy13846        933 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-------TPVELK 1005 (1423)
Q Consensus       933 ~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-------~~~~~~ 1005 (1423)
                      +...|...-.+.+++|+++++|+||+|++|++|+++++..||++||.+||++++++||++-+|...|       ..|+..
T Consensus      2625 V~~G~~l~~G~~~p~dil~v~G~ea~~~ylv~Evq~VYr~QGV~IndKHiEvIvrQMl~kV~I~d~Gdt~~l~Ge~v~~~ 2704 (2836)
T PRK14844       2625 VRKGDLLMDGDPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKL 2704 (2836)
T ss_pred             EcCCCCccCCCCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCeeecccEeeeehhhhhceeEEecCCCcccCCCceecHH
Confidence            4445666777889999999999999999999999999999999999999999999999998888765       456777


Q ss_pred             HHHHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhh
Q psy13846       1006 RLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTS 1046 (1423)
Q Consensus      1006 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~ 1046 (1423)
                      .+.+.+.....++..|+...+.+++++++.|++++|+++||
T Consensus      2705 ~~~~~n~~~~~~g~~pa~~~pvllGITkasL~t~SflSaAS 2745 (2836)
T PRK14844       2705 EVDRENDAMSNSGKRPAHYLPILQGITRASLETSSFISAAS 2745 (2836)
T ss_pred             HHHHHHHHHHhcCCCCceeeeeeeceeeccccCCChhhcCC
Confidence            78777777777788899888889999999999999998877

>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed

Probab=100.00  E-value=9.9e-40  Score=432.17  Aligned_cols=111  Identities=15%  Similarity=0.274  Sum_probs=99.6

Q ss_pred             ccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------cchhhHHHH
Q psy13846        936 VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-------TPVELKRLL 1008 (1423)
Q Consensus       936 vD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-------~~~~~~~~~ 1008 (1423)
                      .|...-.+-+.+|+++++|++|...+|++|+++|+..||+.||.+||++++.+|+.+-+|...|       ..|+...+.
T Consensus      2717 G~~l~~G~~~p~dil~~~g~~~~~~ylv~EVQ~VYr~QGV~InDKHIEvIvrQMl~kV~I~d~GDt~fl~Ge~vd~~~~~ 2796 (2890)
T PRK09603       2717 GEAMTDGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFK 2796 (2890)
T ss_pred             CCCcCCCCCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCEEeccceehhhHhhhheeEEEEcCCCcccCCCceeeHHHHH
Confidence            3455555668999999999999999999999999999999999999999999999999998766       556777888


Q ss_pred             HHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhh
Q psy13846       1009 DDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTS 1046 (1423)
Q Consensus      1009 ~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~ 1046 (1423)
                      +.+.+....+..|+...+.+++++++.|.+++|+++||
T Consensus      2797 ~~n~~~~~~g~~pa~~~p~LlGITKAsL~t~SfiSAAS 2834 (2890)
T PRK09603       2797 EENARVIALKGEPAIAEPVLLGITRAAIGSDSIISAAS 2834 (2890)
T ss_pred             HHHHHHHHcCCCCceeeeeeeeeehhhhcccchhhccc
Confidence            88888888888899988889999999999999998887

>cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain

Probab=100.00  E-value=2.8e-37  Score=360.92  Aligned_cols=265  Identities=19%  Similarity=0.155  Sum_probs=197.0

Q ss_pred             chhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhh--h
Q psy13846        698 GTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINA--S  775 (1423)
Q Consensus       698 g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIina--S  775 (1423)
                      |+.||.|||||||||.|||||    ++||++|+.                                +|||||||||.  +
T Consensus         1 GE~VG~LAAqSIgEPAtQmtL----ntfh~agvs--------------------------------~vprLKEiLn~~~~   44 (381)
T cd02737           1 GEPVGSLAATAISEPAYKALL----DPPQSLESS--------------------------------PLELLKEVLECRSK   44 (381)
T ss_pred             CCcchhHHHhhhcchHHHhhh----ccchhcCCc--------------------------------cHHHHHHHhccccc
Confidence            688999999999999999999    999999972                                79999999999  7


Q ss_pred             cCCCCceeeeeccc-------CCh-HHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhcc-------
Q psy13846        776 RNISTPIITAYLDK-------DTD-LDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHL-------  840 (1423)
Q Consensus       776 k~ikTPiitv~L~~-------~~~-~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l-------  840 (1423)
                      +++|||.++++|..       +.. .+.|+.++++||+++|+++++..+++|+|+....++..|.+.++...+       
T Consensus        45 ~~~ktps~~v~L~~~~~~~~~~~~~~~~a~~Vq~~Le~~tL~~v~~~~~I~Ydp~~~~t~i~~d~~~~~~~~~~~~~~~~  124 (381)
T cd02737          45 SKSKENDRRVILSLHLCKCDHGFEYERAALEVKNHLERVTLEDLATTSMIKYSPQATEAIVGEIGDQLNTKKKGKKKAIF  124 (381)
T ss_pred             CCCCCCCEEEEEeccccccccchHHHHHHHHHHHHhhhccHHHhhheEEEEECCCcccccccccHHHHHhhhhhhhhccc
Confidence            88999999999975       221 457999999999999999999999999999777777776665432110       


Q ss_pred             ccchhh--hhHHhhhcccccCcccccccc-cccccCC-CCccc----cchhhhhhhhcCCceEEccccccceeeeecccc
Q psy13846        841 EVDIDS--IRYCIERTRGISGHLTVSGHS-FLILKPK-DSSKS----FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDV  912 (1423)
Q Consensus       841 ~i~~~~--I~~~i~~~~~~~~~i~~~~~~-~~~~~~~-~~~~~----~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~  912 (1423)
                      ..+.+.  .-..+.+... +.......+. .+.+... ..+..    ....+..+...+.+++|||+++|+++.|...+.
T Consensus       125 ~~~~~~~~~spw~~r~~l-~~~~~~~~~~~ci~~~~~~~~~~~~~~~~~~~~~~i~~~lL~~~lkG~~~I~kv~i~~~~~  203 (381)
T cd02737         125 STSLKITKFSPWVCHFHL-DKECQKLSDGPCLTFSVSKEVSKSSEELLDVLRDRIIPFLLETVIKGDERIKSVNILWEDS  203 (381)
T ss_pred             ccccccccCCcceEEEEE-ehhHhcCCCCceEEeecCcccccchhHHHHHHHHHHHHHHhheeecccCCeeEEEEEecCC
Confidence            001100  0000000000 0000000000 0000010 11111    111233444445579999999999999973221


Q ss_pred             -----------cceeEEeeecc---------Cccccccc-----eeecccceeeccCchHHHHHHhchHHHHHHHHHHHH
Q psy13846        913 -----------EGVTKYKLLVE---------GDNLRDVM-----ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK  967 (1423)
Q Consensus       913 -----------~~~~~~~l~~e---------G~nL~~vl-----~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~  967 (1423)
                                 ....+|+|.|+         |.+++.+|     .+++||+.+++||||++|+++|||||||++|++|++
T Consensus       204 ~~~~~~~~~~~~~~~E~vLe~~~~~~~~~t~G~~~~~vl~~c~~~~~~ID~~rt~sNdI~ev~~~lGIEAAR~~ii~El~  283 (381)
T cd02737         204 PSTSWVKSVGKSSRGELVLEVTVEESCKKTRGNAWNVVMDACIPVMDLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLE  283 (381)
T ss_pred             CcccccccccccccceEEEEEEeccccccccchhHHHHHHhhhcccccCcCCCcEECCHHHHHHHHhHHHHHHHHHHHHH
Confidence                       23468999987         99999999     589999999999999999999999999999999999


Q ss_pred             HHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        968 LVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       968 ~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      .+++.||++||+|||+||||+||++|++.+.+
T Consensus       284 ~v~~~~G~~Vd~rHL~LlAD~MT~~G~~~~~n  315 (381)
T cd02737         284 SAVSMTGKSVLREHLLLVADSMTYSGEFVGLN  315 (381)
T ss_pred             HHHHhcCCcccHHHHHHHHHHhccCCceEEec
Confidence            99999999999999999999999999999975

Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.

>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus

Probab=100.00  E-value=2.1e-36  Score=343.76  Aligned_cols=95  Identities=59%  Similarity=0.974  Sum_probs=93.5

Q ss_pred             CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846        341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV  420 (1423)
Q Consensus       341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~  420 (1423)
                      +||+|||||||||||+|||||++++++++||||||++|+||||||||||||+|+|||++|||||.              .
T Consensus       201 dgd~Vl~NRqPsLHr~si~a~~v~v~~~~tir~n~~~c~~fNADFDGDeMnih~pqs~~a~aEa~--------------~  266 (295)
T smart00663      201 DGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEAR--------------E  266 (295)
T ss_pred             cCCEEEEecCCccccccceeEEEEEecCceEEecCccCCcccCCcCCCEEEEecCCCHHHHHHHH--------------H
Confidence            67899999999999999999999999999999999999999999999999999999999999999              9


Q ss_pred             hhccccccccCCCCccccccccceEEEEE
Q psy13846        421 LMANKSNLVTPRNGELLIAATQDFITGGY  449 (1423)
Q Consensus       421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~  449 (1423)
                      ||.+.+|++||++|+|+++++||+++|+|
T Consensus       267 Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~  295 (295)
T smart00663      267 LMLVPNNILSPKNGKPIIGPIQDMLLGLY  295 (295)
T ss_pred             HhhhhhccccCCCCCeeEeeecceeeecC
Confidence            99999999999999999999999999986

>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'

Probab=100.00  E-value=9.6e-37  Score=392.50  Aligned_cols=361  Identities=19%  Similarity=0.219  Sum_probs=274.7

Q ss_pred             HHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEecCCHH
Q psy13846         12 YYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKED   91 (1423)
Q Consensus        12 ~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~~S~e   91 (1423)
                      -+||||||++||+|++||+||++|+|++|++||+|+|+|+||.||+||+++++++++++-.          ++..+..|.
T Consensus       466 s~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~~LT~~d~f~~~~~~~~l~~~~~----------~~~~~~~p~  535 (868)
T TIGR02390       466 TEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAG----------YFGDPPEPA  535 (868)
T ss_pred             CHHHHHHHHHHhhchhceecCCCCCeeEEeehhhhhheeeeeeccccCCHHHHHHHHhcCC----------ccccCCCce
Confidence            4799999999999999999999999999999999999999999999999999999998521          111111121


Q ss_pred             HHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCC-CCCCcccCCccceEEccCceeEEeeeccH----
Q psy13846         92 RVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTC-GQNLSDCVGHFGYIDLPLPVFHIGYFRCV----  166 (1423)
Q Consensus        92 eIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TC-g~~~~eCpGHfGhIeL~~PV~h~gffd~v----  166 (1423)
                       |       +....+|    ||+++.+.++++.+....+...+..+ +.....|+ ..++|.+.+.++..|.+|+-    
T Consensus       536 -i-------~kp~~lw----TGKqi~s~~lp~~~n~~~~~~~~~~~~~~~~~~~~-~d~~v~i~~g~ll~G~ldK~~lg~  602 (868)
T TIGR02390       536 -I-------EKPKEYW----TGKQIFSAFLPEDLNFEGRAKICSGSDACKKEECP-HDAYVVIKNGKLLKGVIDKKAIGA  602 (868)
T ss_pred             -e-------cCCcccc----cHHHHHHHhcCCCCcceecccccccccccccccCC-CcceEEEecCeEEeeeecHHHhcc
Confidence             1       2356788    99999999998766654433333322 11223454 58899999999999999843    


Q ss_pred             --HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehhh
Q psy13846        167 --INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHE  244 (1423)
Q Consensus       167 --~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e  244 (1423)
                        ..|++.+...       ++++....|++++.+....++...+|+.++.|......                    ..+
T Consensus       603 ~~~~li~~i~~~-------yG~~~a~~fl~~~~~l~~~~l~~~GfSigi~D~~~~~~--------------------~~~  655 (868)
T TIGR02390       603 EKGKILHRIVRE-------YGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKE--------------------AKE  655 (868)
T ss_pred             CcccHHHHHHHH-------HCHHHHHHHHHHHHHHHHHHHHhccEEeehhheeeCHH--------------------HHH
Confidence              1344444444       78889999999999988888888999999888753210                    111


Q ss_pred             hhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHH-------------------HHhhccCCCcccc
Q psy13846        245 KYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL-------------------QLFEAIPLEDIPL  305 (1423)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~-------------------eiLe~I~~~d~~l  305 (1423)
                      ...+..++..+...++.+.|..              +..+.+++.+++                   +...+.-+.++.+
T Consensus       656 ~~~~~i~~~~~~~~~~~~~~~~--------------g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~~  721 (868)
T TIGR02390       656 EIEELIEKAEKRVDNLIERYRN--------------GELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHA  721 (868)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHc--------------CCCccCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcch
Confidence            1111111111222233333322              111112221111                   1222222235788


Q ss_pred             cccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCC
Q psy13846        306 LLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADF  385 (1423)
Q Consensus       306 L~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadF  385 (1423)
                      +.|..+||+++.++++||.   +|++||...|.|++.++                 ..|+|||    |.+.+..|...+|
T Consensus       722 ~~M~~sGsKGS~~Ni~Qi~---~~lGQQ~~~g~ri~~~~-----------------~~rtlp~----f~~~d~~~~~~Gf  777 (868)
T TIGR02390       722 VIMARTGARGSLLNITQMA---AMVGQQSVRGGRIRRGY-----------------RNRTLPH----FKKGDIGAKARGF  777 (868)
T ss_pred             hhhhhccCCcccccHHHHH---hccCccccCCCcCcccc-----------------ccCCCCC----CCCCCCCcccCce
Confidence            8999999999999999999   99999999999998888                 8999999    8899999999999


Q ss_pred             cccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHHH
Q psy13846        386 DGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMR  465 (1423)
Q Consensus       386 dgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~  465 (1423)
                      +-+++..+|.+.|          ||||+||||||+++++++|+.|||.+|+|+.++|| +.+.||.|+||+.+++.||.|
T Consensus       778 V~~sF~~GL~p~E----------fFfH~m~gReGLiDTAvKTa~sGYLqRrLvk~lEd-l~v~yD~tVR~~~g~iiQf~Y  846 (868)
T TIGR02390       778 VRSSFKKGLDPTE----------YFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQD-LYVEYDGTVRDTRGNLIQFKY  846 (868)
T ss_pred             ecccccCCCCHHH----------HHHHHhhhccccccccccccccchhHHHHHHHHhh-eEEecCCeEEeCCCcEEEEec
Confidence            9999999999776          99999999999999999999999999999999999 999999999999999999999


Q ss_pred             HHHhhc
Q psy13846        466 IASTLI  471 (1423)
Q Consensus       466 l~~~~~  471 (1423)
                      +.++++
T Consensus       847 G~dg~d  852 (868)
T TIGR02390       847 GEDGVD  852 (868)
T ss_pred             cCCCcC
Confidence            988875

This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.

>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA

Probab=100.00  E-value=1.3e-36  Score=349.18  Aligned_cols=99  Identities=44%  Similarity=0.656  Sum_probs=90.5

Q ss_pred             ceeeEEEEecCccHHHHhhccc-ccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccce
Q psy13846       1250 GVTKYKLLVEGDNLRDVMATYG-VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328 (1423)
Q Consensus      1250 ~~~~~~l~teG~nl~~~~~~~~-vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~ 1328 (1423)
                      ...+|.+.++|.||+.+|..++ +|++++++|||++|+++|||||||++|++|+..|+..||++||+|||+|+||+||++
T Consensus       177 ~~~~~~l~~~g~~l~~v~~~qgvid~~k~~sn~I~qm~~~~GIeaar~~i~~e~~~v~~~~g~~vn~rhl~llad~mt~~  256 (277)
T PF04998_consen  177 KSKEYVLQTEGSNLQEVYSSQGVIDNDKHISNDIRQMLSKLGIEAARNSIIKELKNVFESYGIEVNKRHLSLLADYMTYK  256 (277)
T ss_dssp             CCCCCEEECCSHHHHHHTCSTT-EETCHHECSHHHHHHHHHEHHHHHHHHHHHHHCHHHHCTSCCCHHHHHHHHHHHCCC
T ss_pred             hhHHHHHHHHhhhchhheecccccCCCEEEeceeEeeeeeEEEEECCCceeecCcEeeHHHHHHHHHHHHHhCCCcCeee
Confidence            3468899999999999999999 799999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEeeecccccccccchhh
Q psy13846       1329 GEVLGITRHGLAKMKESVLN 1348 (1423)
Q Consensus      1329 G~~~~i~r~g~~~~~~S~l~ 1348 (1423)
                      |.++||||+||+++++|+++
T Consensus       257 g~~~gitR~gl~~~~~S~~~  276 (277)
T PF04998_consen  257 GVLLGITRHGLNSNKSSFLS  276 (277)
T ss_dssp             SS---CCTTTTSSSSSSHHH
T ss_pred             eEEEEEEHHHhccCCCCccC
Confidence            99999999999986566554

Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....

>PRK08566 DNA-directed RNA polymerase subunit A'; Validated

Probab=100.00  E-value=2.5e-36  Score=389.83  Aligned_cols=363  Identities=21%  Similarity=0.252  Sum_probs=277.7

Q ss_pred             hHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEecCCH
Q psy13846         11 LYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKE   90 (1423)
Q Consensus        11 ~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~~S~   90 (1423)
                      .-+||||||++||+|++||+||++|+|++|.+||+|+|+|+||.||+||+|++++++++|..   ...+      .+..|
T Consensus       469 qs~~a~aEa~~Lm~~~~~~~sp~~g~pi~~~~QD~l~g~~~lt~~d~f~~~~~~~~l~~~~~---~~~~------~~~~p  539 (882)
T PRK08566        469 QTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAG---IDEL------PEPEP  539 (882)
T ss_pred             CCHHHHHHHHHHhcchhcEecCCCCCeeEEeehHHHHHHHHHHhccccCCHHHHHHHHHhCC---cccc------ccCCc
Confidence            35799999999999999999999999999999999999999999999999999999999741   1100      01111


Q ss_pred             HHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCC-CcccCCccceEEccCceeEEeeeccH---
Q psy13846         91 DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN-LSDCVGHFGYIDLPLPVFHIGYFRCV---  166 (1423)
Q Consensus        91 eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~-~~eCpGHfGhIeL~~PV~h~gffd~v---  166 (1423)
                      .        -.....+|    |||++.+.++.+.+....+...+..+... ...|+ ..|++.+...++..|.+++-   
T Consensus       540 a--------i~~p~~lw----TGKqi~s~~lp~~~~~~~~~~~~~~~~~~~~~~~~-~d~~v~i~~gell~g~ldK~~lg  606 (882)
T PRK08566        540 A--------IENGKPYW----TGKQIFSLFLPKDLNLEFKAKICSGCDECKKEDCE-HDAYVVIKNGKLLEGVIDKKAIG  606 (882)
T ss_pred             c--------cCCCcccc----cHHHHHHHHcCCCCCceeeccccccccccccccCC-CCceEEEecCEEEeccccHHHhh
Confidence            0        11334788    99999999998766554444444444332 23455 48999999999999999954   


Q ss_pred             ---HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehh
Q psy13846        167 ---INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISH  243 (1423)
Q Consensus       167 ---~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~  243 (1423)
                         ..|++.++..       ++++....|++++.+....++...+|+.++.|.+....                    ..
T Consensus       607 ~~~~~li~~i~~~-------yG~~~a~~fl~~~~~l~~~~l~~~GfSigi~D~~~~~~--------------------~~  659 (882)
T PRK08566        607 AEQGSILDRIVKE-------YGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEE--------------------AK  659 (882)
T ss_pred             cccchHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHHHhcCEEeehhhcccCHH--------------------HH
Confidence               3466666666       88889999999999988889999999999988753220                    00


Q ss_pred             hhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHH-------------------HHHHHhhccCCCccc
Q psy13846        244 EKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPL-------------------EVLQLFEAIPLEDIP  304 (1423)
Q Consensus       244 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~-------------------~V~eiLe~I~~~d~~  304 (1423)
                      ++..+..++......++.++|..              +..+.+++.                   .+.+...+--+.+++
T Consensus       660 ~~~~~~i~~~~~~~~~~~~~~~~--------------g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~  725 (882)
T PRK08566        660 EEIDEIIEEAEKRVEELIEAYEN--------------GELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNP  725 (882)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHc--------------CCCccccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCc
Confidence            00111111111122233333322              111111111                   111122221233578


Q ss_pred             ccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCC
Q psy13846        305 LLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNAD  384 (1423)
Q Consensus       305 lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nad  384 (1423)
                      ++.|..+||+++..+++||.   +|++||...|.+++.++                 ..|+|||    |.+.+.+|...+
T Consensus       726 ~~~M~~SGsKGS~~N~~Qi~---~~lGqQ~~~g~ri~~~~-----------------~~rtLP~----f~~~d~~~~~~G  781 (882)
T PRK08566        726 AVIMARTGARGSMLNLTQMA---ACVGQQSVRGERIRRGY-----------------RDRTLPH----FKPGDLGAEARG  781 (882)
T ss_pred             ceeeeccccccCHHHHHHHH---hccCceecCCCcCccCc-----------------cCccCCC----CCCCCCCcccCc
Confidence            89999999999999999999   99999999999888888                 8899999    889999999999


Q ss_pred             CcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHH
Q psy13846        385 FDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM  464 (1423)
Q Consensus       385 Fdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~  464 (1423)
                      |+-+++-.+|.+.|          ||||+||||||++++|++|+.|||.+|+|+..+|| +.+.||.|+||+.+++.||.
T Consensus       782 fV~~sF~~GL~p~E----------fffH~m~GReGliDTAvkTa~sGYlqRrLvk~led-l~v~yD~tVR~s~g~iiQf~  850 (882)
T PRK08566        782 FVRSSYKSGLTPTE----------FFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQD-LKVEYDGTVRDTRGNIVQFK  850 (882)
T ss_pred             eeeccccCCCCHHH----------HHHHHhhhcccccccceeeccCccchHHHHHHHhh-eEEeeCCceEcCCCcEEEEe
Confidence            99999999999776          99999999999999999999999999999999999 99999999999999999999


Q ss_pred             HHHHhhc
Q psy13846        465 RIASTLI  471 (1423)
Q Consensus       465 ~l~~~~~  471 (1423)
                      |+.++++
T Consensus       851 YG~dg~d  857 (882)
T PRK08566        851 YGEDGVD  857 (882)
T ss_pred             ccCCCcC
Confidence            9988875

>PF00623 RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; InterPro: IPR000722 RNA polymerases catalyse the DNA dependent polymerisation of RNA from DNA, using the four ribonucleoside triphosphates as substrates

Probab=99.91  E-value=7.3e-26  Score=238.56  Aligned_cols=66  Identities=67%  Similarity=1.129  Sum_probs=58.2

Q ss_pred             CCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhccc
Q psy13846        340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEAL  405 (1423)
Q Consensus       340 ~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~  405 (1423)
                      .+||+|||||||||||+|||||++++++++|||+||++|+||||||||||||+|+||+++|++|+.
T Consensus        96 ~~gd~vl~nRqPtLh~~s~~a~~~~~~~~~t~~~~~~~c~~~NADFDGDem~i~~p~~~~a~~E~~  161 (166)
T PF00623_consen   96 CDGDIVLLNRQPTLHRMSIMAHKVRVLPGKTIRINPLVCSPFNADFDGDEMNIHLPQSYEARAEAK  161 (166)
T ss_dssp             TTT-EEEEEESS-SSGGGEEEEEEEEESSSSEEEEGGGHHHHT--TSS-EEEEE--SSHHHHHHHH
T ss_pred             hcCceeEEeccchhccceeeeeeeeeecccEEEeeccchhhhhccCCcceEEEEecCCHHHHHHHH
Confidence            499999999999999999999999999999999999999999999999999999999999999999

Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Eukaryotic RNA polymerase I is essentially used to transcribe ribosomal RNA units, polymerase II is used for mRNA precursors, and III is used to transcribe 5S and tRNA genes. Each class of RNA polymerase is assembled from nine to fourteen different polypeptides. Members of the family include the largest subunit from eukaryotes; the gamma subunit from Cyanobacteria; the beta' subunit from bacteria; the A' subunit from archaea; and the B'' subunit from chloroplast RNA polymerases.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 2PMZ_Q 3HKZ_I 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N ....

>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain

Probab=99.90  E-value=4.1e-24  Score=244.08  Aligned_cols=243  Identities=54%  Similarity=0.751  Sum_probs=223.1

Q ss_pred             ecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhH
Q psy13846        690 IMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIK  769 (1423)
Q Consensus       690 ~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlk  769 (1423)
                      |.+++++||++||.+||||||||+|||||    +|||+||+             +++|+||             |||||+
T Consensus         2 y~~~~v~pGe~vG~iaaQsiGEp~TQmTL----~TFH~aGv-------------~~~nvtl-------------GvPRlk   51 (300)
T cd02736           2 YMRAKVEPGTAVGAIAAQSIGEPGTQMTL----KTFHFAGV-------------ASMNITL-------------GVPRIK   51 (300)
T ss_pred             chhhccCCCccchhhhhhhcCCccccccc----cccccccc-------------ccccccc-------------CchHHH
Confidence            35678999999999999999999999999    99999999             8999999             999999


Q ss_pred             HHHhhhcCCCCceeeeecccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhH
Q psy13846        770 EIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY  849 (1423)
Q Consensus       770 EIinaSk~ikTPiitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~  849 (1423)
                      |||||||+||||+|++||.++.+.+.|+.++.+||+++|+|++.+++++|+|+.+++.+++|.+.+..+++.  .     
T Consensus        52 EIinasK~~~TP~~ti~l~~~~~~~~a~~v~~~ie~t~l~di~~~~~~~~~p~~~~~~i~~d~~~i~~~~l~--~-----  124 (300)
T cd02736          52 EIINASKNISTPIITAKLENDRDEKSARIVKGRIEKTYLGEVASYIEEVYSPDDCYILIKLDKKIIEKLQLS--K-----  124 (300)
T ss_pred             HHHhcccCCCCCeEEEEecCcccHHHHHHHHHHHhhccHHHhhhheEEEEcCCCceEEEEecHHHHHHhcCC--c-----
Confidence            999999999999999999998899999999999999999999999999999999999999999887544330  0     


Q ss_pred             HhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccc
Q psy13846        850 CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRD  929 (1423)
Q Consensus       850 ~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~  929 (1423)
                                                  +.....++.+++.+++++|+|+|||+|+.+.+++.  .++|.|.|+|+||++
T Consensus       125 ----------------------------~~~~~~~~~l~~~l~~~~v~Gi~gI~r~~i~~~~~--~~~~~l~teG~nl~~  174 (300)
T cd02736         125 ----------------------------SNLYFLLQSLKRKLPDVVVSGIPEVKRAVINKDKK--KGKYKLLVEGYGLRA  174 (300)
T ss_pred             ----------------------------ccHHHHHHHHHHHhccceEeCCCCceEEEEecCCC--CCcEEEEEecccHHH
Confidence                                        01223466788899999999999999999986543  247999999999999


Q ss_pred             cceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        930 VMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       930 vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      ++.+++||+.+|+||||++|+++|||||||++|++|++++|+.||++||+|||+||||+||++|.+.|..
T Consensus       175 v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~it  244 (300)
T cd02736         175 VMNTPGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGIT  244 (300)
T ss_pred             HhcCCcEeccCCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHhccCceeeee
Confidence            9999999999999999999999999999999999999999999999999999999999999999999874

Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.

>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain

Probab=99.89  E-value=1.4e-23  Score=248.55  Aligned_cols=176  Identities=24%  Similarity=0.431  Sum_probs=138.4

Q ss_pred             cceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccc----cccccCCCCc-------cccchhhhhhhhcCC
Q psy13846        824 SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHS----FLILKPKDSS-------KSFNSKMYQMKQLLP  892 (1423)
Q Consensus       824 ~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~----~~~~~~~~~~-------~~~~~~l~~l~~~l~  892 (1423)
                      +.|.+++.+++.++....++++.|...|++.++....+..+.++    .+.+++....       .......+.++..++
T Consensus       153 ~~~~lrl~ld~~~~~~~~i~~~~i~~~i~~~~~~~~~v~~~~~~~~~~~iri~~~~~~~~~~~~~~~~~~l~~~~~~~l~  232 (410)
T cd02584         153 SPWLLRIELDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEEDSEDDVFLKKIESNMLS  232 (410)
T ss_pred             CCeeEEEEECHHHHHHcCCCHHHHHHHHHHhcCCCeEEEEcCCCcceeEEEEEecCccccccccchhHHHHHHHHHhhCC
Confidence            56788888888888888899988888887654433333222222    2233322111       011122344568899


Q ss_pred             ceEEccccccceeeeecccc------c----ceeEEeeeccCccccccceeecccceeeccCchHHHHHHhchHHHHHHH
Q psy13846        893 SVVIKGVQGINRAVIHEEDV------E----GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTI  962 (1423)
Q Consensus       893 ~v~IkGi~~I~r~~i~~~~~------~----~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~I  962 (1423)
                      +++|+|++||+|+++..++.      .    ...+|.+.|+|+||++++.++|||+.+|+||||+||+++|||||||++|
T Consensus       233 ~i~l~Gi~~I~r~~i~~~~~~~~~~~~g~~~~~~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~i  312 (410)
T cd02584         233 DMTLKGIEGIRKVFIREENKKKVDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAARKAL  312 (410)
T ss_pred             CcEEeCCCCceEEEEEcCCceEecCCCCcccCCcceEEEecCcCHHHHhCCCCCccccCEeCCHHHHHHhcCHHHHHHHH
Confidence            99999999999999975421      1    2357999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        963 MTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       963 i~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      ++|++.+|+.||++||+|||+||||+||++|++.+++
T Consensus       313 i~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~  349 (410)
T cd02584         313 LKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAIT  349 (410)
T ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHHhhceEEeeEe
Confidence            9999999999999999999999999999999999875

RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.

>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain

Probab=99.88  E-value=1.9e-23  Score=225.03  Aligned_cols=109  Identities=22%  Similarity=0.356  Sum_probs=93.4

Q ss_pred             CchHHHHHHh--chHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------cchhhHHHHHHHHHh
Q psy13846        944 NNTYEVYKTL--GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-------TPVELKRLLDDIIAK 1014 (1423)
Q Consensus       944 N~i~eV~~~L--GIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-------~~~~~~~~~~~~~~~ 1014 (1423)
                      ||++++.+++  ||||||..|++|++++++.||++||+|||+|+||+||+++++...+       ..+++.++...++..
T Consensus        54 ~~~~~il~~~~~Giea~r~~iv~EIq~Vy~~qGV~I~dKHielIv~qMT~kv~i~~~g~s~~l~Ge~v~~~~~~~~N~~~  133 (204)
T cd02655          54 INPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRL  133 (204)
T ss_pred             CCHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcCeeecHHHHHHHHHHHhcCeEEecCCCcccCCCceeeHHHHHHHHHHH
Confidence            4778888888  9999999999999999999999999999999999999999998654       667777777777776


Q ss_pred             ccCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHHH
Q psy13846       1015 NSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIK 1054 (1423)
Q Consensus      1015 ~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~ 1054 (1423)
                      ...+..+....+.+++++++.|.+++|+++||  |.+..+
T Consensus       134 ~~~~~~~~~y~p~llGItk~~l~~~Sfls~AS--FqeT~k  171 (204)
T cd02655         134 LLLGKKPAKYEPVLLGITKASLNTESFISAAS--FQETTK  171 (204)
T ss_pred             HhCCCCcccccceeeeeeeccccCCCccccCC--hHHHHH
Confidence            66677777777778999999999999998776  655444

Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.

>PF04983 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; InterPro: IPR007066 RNA polymerases catalyse the DNA dependent polymerisation of RNA

Probab=99.86  E-value=2.3e-23  Score=220.28  Aligned_cols=158  Identities=32%  Similarity=0.529  Sum_probs=131.5

Q ss_pred             ccccCCCCccccccccceEEEEEeecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeeccee
Q psy13846        427 NLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQI  506 (1423)
Q Consensus       427 ~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi  506 (1423)
                      |++||++|+|+++++||+++|+|.||.++.|++++|+.++++.....    ..      +...+.|+|.+|.++|||||+
T Consensus         1 NilSP~~G~Pii~~~QD~vlG~y~LT~~~~f~~~~e~~~~~~~~~~~----~~------~~~~~~~~I~~~~~~~tgk~~   70 (158)
T PF04983_consen    1 NILSPANGKPIIGPTQDMVLGAYYLTSEDTFLSRDEAQQALMNGLID----DK------KIVLLHPAILKPKELWTGKQT   70 (158)
T ss_dssp             GSEETTTTEESSS--SHHHHHHHHHSSTTTEESHHHHHHHHHCSST--------------CHCSSSSBSSSSSCEECHHH
T ss_pred             CccCCCCCCceEEeccceEeEEEEEEecccccchHHHHHHHHccccc----cc------ceeccchhhhccccceeeccH
Confidence            68999999999999999999999999999999999999999987421    00      115678999999999999999


Q ss_pred             eeecccCCCCcccccceeecccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHH
Q psy13846        507 FSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMW  586 (1423)
Q Consensus       507 ~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~  586 (1423)
                      ++.+||.+      ++.....        -+++++.++|++|+++.|.+||+++|.++.+++++.+|++||++.+..||+
T Consensus        71 ~s~il~~~------i~~~~~~--------~~~~~~~~~i~~g~~l~g~l~k~~lgk~~~~~li~~i~~~yG~~~~~~~ld  136 (158)
T PF04983_consen   71 FSRILPNE------INPEGFS--------NDPDDGYVVINNGELLSGVLDKKTLGKKSLGSLIHQIYREYGPEATVQFLD  136 (158)
T ss_dssp             HHTTSHTT------HHEEEST--------SCHSSHSEEECTSSEEEC--SHHHHSCSHTTCHHHHHHHHSHHHHHHHHHH
T ss_pred             HHHhcccc------ccccccc--------ccccccceeecCCccchhheehheecccchhhHHHHHHHHHCHHHHHHHHH
Confidence            99999853      3333221        012367899999999999999999995578899999999999999999999


Q ss_pred             HhhhhhhHHHhhcCcceecCCC
Q psy13846        587 RLSRMTSFYLMNRGFSIGIGDV  608 (1423)
Q Consensus       587 ~l~~l~~~~L~~~GfsiGi~D~  608 (1423)
                      +++++..+|++.+|||+|++|+
T Consensus       137 ~i~~lg~~~~t~~GfSvgi~D~  158 (158)
T PF04983_consen  137 AIKRLGFRYLTRSGFSVGIDDM  158 (158)
T ss_dssp             HHHHHHHHHHHHHTBB-SGGGC
T ss_pred             HHHHHHHHHHHHcCeeEecccC
Confidence            9999999999999999999996

Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....

>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain

Probab=99.84  E-value=1e-21  Score=226.13  Aligned_cols=247  Identities=33%  Similarity=0.424  Sum_probs=206.8

Q ss_pred             ecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhH
Q psy13846        690 IMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIK  769 (1423)
Q Consensus       690 ~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlk  769 (1423)
                      |.+++++|||+||.+||||||||+|||||    +||||||+             +++|+||             |||||+
T Consensus         2 y~~slv~PGE~VG~iaAQSIGEPsTQMTL----nTFH~AGv-------------~~~nVTl-------------GvPRL~   51 (309)
T cd02735           2 YMRSLVEPGEAVGLLAAQSIGEPSTQMTL----NTFHFAGR-------------GEMNVTL-------------GIPRLR   51 (309)
T ss_pred             chhccCCCCcccchhhhhccCCccccccc----ccccccCc-------------ccccccc-------------ccccHH
Confidence            45678999999999999999999999999    99999999             8999999             999999


Q ss_pred             HHH-hhhcCCCCceeeeecccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhh
Q psy13846        770 EII-NASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIR  848 (1423)
Q Consensus       770 EIi-naSk~ikTPiitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~  848 (1423)
                      ||| +|||+||||+|+++|.++.+.+.|+.++++|++++|+|+++++++.|      +...++......+          
T Consensus        52 EIi~~Ask~i~TP~m~v~l~~~~~~~~a~~~~~~ie~~~l~dv~~~~~v~~------i~~~~~~~~~~~~----------  115 (309)
T cd02735          52 EILMTASKNIKTPSMTLPLKNGKSAERAETLKKRLSRVTLSDVVEKVEVTE------ILKTIERVFKKLL----------  115 (309)
T ss_pred             HHHhhhccCCCCCeEEEEecCchhHHHHHHHHhheeEeEHHHhhhhhehhH------HHHHHHHHhhhhh----------
Confidence            998 89999999999999999988899999999999999999999987654      1111111111000          


Q ss_pred             HHhhhcccccCccccccccccccc-CCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccc
Q psy13846        849 YCIERTRGISGHLTVSGHSFLILK-PKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL  927 (1423)
Q Consensus       849 ~~i~~~~~~~~~i~~~~~~~~~~~-~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL  927 (1423)
                             .        ....+.+. +.+..+  ...++.+++.+++++|+|+|||+|+.+.++++.+..+|.+.++|.||
T Consensus       116 -------~--------~~~~~~i~~~~~~~~--~~~~~~~~~~l~~~~i~gi~gI~r~~i~~~~~~~~~~~~l~teG~nl  178 (309)
T cd02735         116 -------G--------KWCEVTIKLPLSSPK--LLLLSIVEKLARKAVIREIPGITRCFVVEEDKGGKTKYLVITEGVNL  178 (309)
T ss_pred             -------C--------CEEEEEEEecCCchh--HHHHHHHHHHhcccEEeCCCCccEEEEecCcCCCceEEEEEeccccH
Confidence                   0        00001111 111111  12345678889999999999999999987765555679999999999


Q ss_pred             ccccee-ecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        928 RDVMAT-YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       928 ~~vl~~-~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      ++++.+ +++|+.+++|||+++|+++|||||||+.|++|++.+++.||++||+|||+||||+||++|++.+.+
T Consensus       179 ~~v~~~~~~vd~~r~~sNdi~ei~~~lGIEAar~~ii~Ei~~v~~~~Gi~V~~rHl~LiaD~MT~~G~~~~~n  251 (309)
T cd02735         179 AALWKFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFN  251 (309)
T ss_pred             HHHHhccCccccccceeCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCCeeCHHHHHHHHHHHHhCCcEeecc
Confidence            999999 699999999999999999999999999999999999999999999999999999999999998864

RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.

>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional

Probab=99.83  E-value=5.9e-21  Score=246.70  Aligned_cols=246  Identities=36%  Similarity=0.564  Sum_probs=203.7

Q ss_pred             CccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeeecccCC--
Q psy13846        714 VPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDT--  791 (1423)
Q Consensus       714 tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~--  791 (1423)
                      ||+||    +||||||+             ++||+||             |||||+|||||||+||||+|+++|.++.  
T Consensus       541 ~~~~L----nTFH~AGv-------------~~~nVTl-------------GvPRL~EIinask~i~TP~m~i~l~~~~~~  590 (858)
T PRK14898        541 THNTM----RTFHYAGV-------------AEINVTL-------------GLPRMIEIVDARKEPSTPIMTVHLKGEYAT  590 (858)
T ss_pred             ecccc----ceeeccCc-------------ccccccc-------------CCchHHHHhcccCCCCCceEEEEECCCccc
Confidence            78999    99999999             8999999             9999999999999999999999999875  


Q ss_pred             hHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccccccc
Q psy13846        792 DLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL  871 (1423)
Q Consensus       792 ~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~~~~~  871 (1423)
                      +.+.|+.++++|++++|+|++++++....  ...+.+.|  ++..+..+.++++.|...|++.+...  +.. ....+.+
T Consensus       591 ~~~~a~~v~~~ie~~~L~dv~~~~~~~~~--~~~~~i~l--~~~~~~~~~l~~~~i~~~i~~~~~~~--~~~-~~~~~~~  663 (858)
T PRK14898        591 DREKAEEVAKKIESLTLGDVATSIAIDLW--TQSIKVEL--DEETLADRGLTIESVEEAIEKKLGVK--IDR-KGTVLYL  663 (858)
T ss_pred             hHHHHHHHHhheeeEEHHHHHHHhhhhcc--ccEEEEEE--CHHHHHHcCCCHHHHHHHHHHhcccc--ccC-CCCEEEE
Confidence            56899999999999999999998773211  11244444  44445566778889999887654321  111 2233333


Q ss_pred             cCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccccceeecccceeeccCchHHHHH
Q psy13846        872 KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK  951 (1423)
Q Consensus       872 ~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~eV~~  951 (1423)
                      .+...   ....++.+...+++++|+|+|||+|+.+.+++..+..+|.+.|+|+||++++.+++||+.+|+||||++|++
T Consensus       664 ~~~~~---~~~~~~~~~~~l~~~~i~gi~gI~~~~i~~~~~~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~  740 (858)
T PRK14898        664 KPKTP---SYKALRKRIPKIKNIVLKGIPGIERVLVKKEEHENDEEYVLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQE  740 (858)
T ss_pred             EecCc---hHHHHHHHHHHhcCcEEECCCCccEEEEecCCCCCCceEEEEecCcCHHHHhcCCCCcccccccCCHHHHHH
Confidence            33211   123466677789999999999999999987664444689999999999999999999999999999999999


Q ss_pred             HhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        952 TLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       952 ~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      +|||||||++|++|++++|+.||++||+|||+||||+||++|++.+.+
T Consensus       741 ~lGIEAar~~ii~Ei~~v~~~~gi~V~~rHl~liad~MT~~G~~~~~~  788 (858)
T PRK14898        741 VLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIG  788 (858)
T ss_pred             hhCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHccCCcEEEec
Confidence            999999999999999999999999999999999999999999999864

>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain

Probab=99.82  E-value=8e-21  Score=197.83  Aligned_cols=55  Identities=45%  Similarity=0.654  Sum_probs=53.2

Q ss_pred             chHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        945 NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       945 ~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      ||++|+++|||||||..|++|++++++.||++||+|||+||||+||++|.+.+.+
T Consensus        49 dI~~i~~~lGIEAaR~~iv~El~~v~~~~Gi~V~~rHl~LIAD~MT~~G~~~gin  103 (158)
T cd00630          49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVT  103 (158)
T ss_pred             cHHHHHHHhCHHHHHHHHHHHHHHHHHhcCceecHHHHHHHHHHHhcCCcccccc
Confidence            7899999999999999999999999999999999999999999999999999864

RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe

>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]

Probab=99.73  E-value=3.8e-20  Score=235.71  Aligned_cols=120  Identities=9%  Similarity=-0.108  Sum_probs=106.4

Q ss_pred             CCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCccccc
Q psy13846        311 ELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEM  390 (1423)
Q Consensus       311 ~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m  390 (1423)
                      .+.+++.+++++|.   .|++++.++|.+....                     .+||    |++.+-.+..+.|.-.++
T Consensus       668 m~~~Gs~~n~sq~~---~~iG~~gv~g~r~~~~---------------------~~~~----Fe~~~~~~~a~~~i~s~f  719 (808)
T COG0086         668 MGLSGARMNISQIV---QLIGQQGVMGEKISVL---------------------ARAA----FEVTVKHLEAEGPGESSF  719 (808)
T ss_pred             HhhhhhccCHHHHH---HHhhhheeeccCCCcc---------------------cccc----cccccccceeeeeeeccc
Confidence            45789999999999   9999999999763221                     7899    999999999999999999


Q ss_pred             ccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHHHHHHh
Q psy13846        391 NVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAST  469 (1423)
Q Consensus       391 ~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~  469 (1423)
                      .-+|.+++          ||||+||||+|+++++.+++.|+|.+|+|+...|| +.+.|+.|+++......|+.|..+.
T Consensus       720 ~eGLt~~e----------~f~~~~ggR~GlvDTA~KTa~sGYl~RrLv~~~qd-l~v~~d~~~~~g~~~~~~~~~ged~  787 (808)
T COG0086         720 LEGLTENE----------YFGHPIGGRTGLVDTALKTADSGYLTRRLVDVAQD-LIVQEDDCVTDGIGVVIQFEYGEDG  787 (808)
T ss_pred             CCCCCcce----------EEeecCccccchHHHhhhhcccCcceEEeechhcc-eEEEecCeEeecCceEEEEecCccc
Confidence            99999777          99999999999999999999999999999999999 9999999999977666776664443

>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit

Probab=99.50  E-value=4.3e-15  Score=191.88  Aligned_cols=192  Identities=14%  Similarity=0.115  Sum_probs=111.5

Q ss_pred             HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehhhhh
Q psy13846        167 INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKY  246 (1423)
Q Consensus       167 ~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~  246 (1423)
                      .+++..+...       ++......|+++++.....+..+.+++.++.|.....             .|.   .++    
T Consensus        13 ~~LI~~~~~~-------yG~~~t~~~lD~lk~Lgf~~aT~~G~SigidDl~ip~-------------~K~---~li----   65 (1227)
T TIGR02388        13 KNLISWAYKT-------YGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPP-------------AKQ---DLL----   65 (1227)
T ss_pred             HHHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHHHhcCeEEeeccCCCCH-------------HHH---HHH----
Confidence            5566666666       7888889999999988888888888888888763211             000   011    


Q ss_pred             cccccchhhHHHHHHHHhhhhhcc-Chh---hhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCCCCcceEEEE
Q psy13846        247 KNRTKKKDAIVEDLLAEYNEAVKF-NPE---IEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR  322 (1423)
Q Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~---~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe~liLt~  322 (1423)
                          ++++....+..+.|+.-.-. .+.   +..... ...+. -..++...|+...+ .+++..|+.+|||++..-+.+
T Consensus        66 ----~~a~~~v~~~~~~y~~G~it~~Er~~~ii~~w~-~t~e~-~~~~~~~~~~~~d~-~N~v~mMa~SGARGNisQi~Q  138 (1227)
T TIGR02388        66 ----EAAEKEIRATEERYRRGEITEVERFQKVIDTWN-GTNEE-LKDEVVNNFRQTDP-LNSVYMMAFSGARGNMSQVRQ  138 (1227)
T ss_pred             ----HHHHHHHHHHHHHHHcCCCcchhhHHHHHHHHH-HHHHH-HHHHHHHhhhhcCC-CCcHHHHhhccCcccHHHHHH
Confidence                01111122222222210000 000   000000 00000 12233444444333 478999999999994444444


Q ss_pred             ecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHh
Q psy13846        323 LLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARA  402 (1423)
Q Consensus       323 lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~ara  402 (1423)
                      |      ++.+-.|-. ..|..                   ..+|                  .-..+..+|.+.|    
T Consensus       139 L------vGmrGlma~-p~G~i-------------------i~lP------------------I~snFreGLt~~E----  170 (1227)
T TIGR02388       139 L------VGMRGLMAN-PQGEI-------------------IDLP------------------IKTNFREGLTVTE----  170 (1227)
T ss_pred             H------hcchheecC-CCCcE-------------------eecc------------------chhhhhcCCCHHH----
Confidence            4      344432211 11211                   1123                  3345778888777    


Q ss_pred             cccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEE
Q psy13846        403 EALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFIT  446 (1423)
Q Consensus       403 E~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~  446 (1423)
                            ||||+||||+|++|+|.+|+.|||.+|+|+...||.++
T Consensus       171 ------yF~sa~GaRkGLvDTAlKTAdSGYLTRRLVdv~qDviV  208 (1227)
T TIGR02388       171 ------YVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIV  208 (1227)
T ss_pred             ------hheeccccccchhhcceeccccchHHHHHHHhhceEEE
Confidence                  99999999999999999999999999999999999443

The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.

>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed

Probab=99.45  E-value=1.5e-14  Score=190.49  Aligned_cols=194  Identities=10%  Similarity=0.057  Sum_probs=109.8

Q ss_pred             HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehhhhh
Q psy13846        167 INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKY  246 (1423)
Q Consensus       167 ~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~  246 (1423)
                      .+|+..+...       ++.+....|+++++.....+..+.+++.++.|.....            - |.   +++.   
T Consensus        20 ~~li~~~~~~-------~G~~~t~~~lD~lk~lgf~~at~~G~Sigi~Dl~ip~------------~-K~---~li~---   73 (1364)
T CHL00117         20 KRLISWLIDH-------FGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPP------------S-KG---WLVQ---   73 (1364)
T ss_pred             HHHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHHHhcceEEecCcccCCH------------H-HH---HHHH---
Confidence            4455555555       7888889999999988888888888888887763110            0 00   1111   


Q ss_pred             cccccchhhHHHHHHHHhhhhhccC-hhhhhhhcc--CccccCCHHHHHHHhhccCCCcccccccccCCCCCcceEEEEe
Q psy13846        247 KNRTKKKDAIVEDLLAEYNEAVKFN-PEIEAHKKF--GLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRL  323 (1423)
Q Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~--~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe~liLt~l  323 (1423)
                           +++..+..+.+.|..-.-.. .......+.  ...+.+ ..++...|+... ..++++.|+.+|||++   ++||
T Consensus        74 -----~a~~~v~~~~~~y~~G~it~~er~~~~i~~w~~~~~~l-~~~~~~~~~~~d-~~N~v~mMa~SGARGn---~sQi  143 (1364)
T CHL00117         74 -----DAEQQSLILEKHYHYGNVHAVEKLRQSIEIWYATSEYL-KQEMNPNFRMTD-PLNPVYMMSFSGARGN---ASQV  143 (1364)
T ss_pred             -----HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHhhccCC-CCCcHhhhhhccCccc---HHHH
Confidence                 11111122222221100000 000000000  001111 112333444433 3589999999999994   5555


Q ss_pred             cCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhc
Q psy13846        324 LVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE  403 (1423)
Q Consensus       324 pVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE  403 (1423)
                      -   .+++....|- ...|.                          .|.++           .-..+..+|.+.|     
T Consensus       144 ~---qLvGmRGlma-~p~G~--------------------------iI~~P-----------I~snFreGLs~~E-----  177 (1364)
T CHL00117        144 H---QLVGMRGLMS-DPQGQ--------------------------IIDLP-----------IQSNFREGLSLTE-----  177 (1364)
T ss_pred             H---HHhcccceee-CCCCc--------------------------Eeecc-----------hhhhhhcCCCHHH-----
Confidence            4   4444211110 01111                          11111           3456778888777     


Q ss_pred             ccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEE
Q psy13846        404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITG  447 (1423)
Q Consensus       404 ~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~  447 (1423)
                           ||||+||||+|++|||.+|+.|||.+|+|+...||.++.
T Consensus       178 -----yFis~~GaRkGLvDTAlkTAdSGYLtRRLVdv~qdviV~  216 (1364)
T CHL00117        178 -----YIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVR  216 (1364)
T ss_pred             -----hheeccccccchhhcceecccccchhhHHHhhhccEEEE
Confidence                 999999999999999999999999999999999995543

>PF04983 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; InterPro: IPR007066 RNA polymerases catalyse the DNA dependent polymerisation of RNA

Probab=99.06  E-value=5.7e-12  Score=133.57  Aligned_cols=146  Identities=21%  Similarity=0.356  Sum_probs=102.5

Q ss_pred             ccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhccc--ccceeeeEEEecCCHHHHhhcceeeeecC-
Q psy13846         28 NLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR--KVFFRGLIEGTVTKEDRVQQQSHIQIVSK-  104 (1423)
Q Consensus        28 ~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~--~~~i~~~i~F~~~S~eeIrklSv~eIt~~-  104 (1423)
                      ||+||++|+|++|.+||+++|+|+||++++|++++|++++++|.....  ...+..                  .|..+ 
T Consensus         1 NilSP~~G~Pii~~~QD~vlG~y~LT~~~~f~~~~e~~~~~~~~~~~~~~~~~~~~------------------~I~~~~   62 (158)
T PF04983_consen    1 NILSPANGKPIIGPTQDMVLGAYYLTSEDTFLSRDEAQQALMNGLIDDKKIVLLHP------------------AILKPK   62 (158)
T ss_dssp             GSEETTTTEESSS--SHHHHHHHHHSSTTTEESHHHHHHHHHCSST----CHCSSS------------------SBSSSS
T ss_pred             CccCCCCCCceEEeccceEeEEEEEEecccccchHHHHHHHHcccccccceeccch------------------hhhccc
Confidence            799999999999999999999999999999999999999999643221  111222                  23322 


Q ss_pred             cccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCceeEEeeeccH-------HHHhhhccccc
Q psy13846        105 NLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCV-------INILQSICKNP  177 (1423)
Q Consensus       105 ~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~gffd~v-------~~iL~~iC~~~  177 (1423)
                      +.|    +|+.+.|-++...+-+.... .|..           .+.+.+...+...|.+++.       .+|++.++.. 
T Consensus        63 ~~~----tgk~~~s~il~~~i~~~~~~-~~~~-----------~~~~~i~~g~~l~g~l~k~~lgk~~~~~li~~i~~~-  125 (158)
T PF04983_consen   63 ELW----TGKQTFSRILPNEINPEGFS-NDPD-----------DGYVVINNGELLSGVLDKKTLGKKSLGSLIHQIYRE-  125 (158)
T ss_dssp             SCE----ECHHHHHTTSHTTHHEEEST-SCHS-----------SHSEEECTSSEEEC--SHHHHSCSHTTCHHHHHHHH-
T ss_pred             cce----eeccHHHHhccccccccccc-cccc-----------ccceeecCCccchhheehheecccchhhHHHHHHHH-
Confidence            356    78888888877644333222 1111           6788899999999998743       3566666666 


Q ss_pred             cccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHH
Q psy13846        178 TCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKIL  214 (1423)
Q Consensus       178 ~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~  214 (1423)
                            +++++...|++++++....+..+.+++.++.
T Consensus       126 ------yG~~~~~~~ld~i~~lg~~~~t~~GfSvgi~  156 (158)
T PF04983_consen  126 ------YGPEATVQFLDAIKRLGFRYLTRSGFSVGID  156 (158)
T ss_dssp             ------SHHHHHHHHHHHHHHHHHHHHHHHTBB-SGG
T ss_pred             ------HCHHHHHHHHHHHHHHHHHHHHHcCeeEecc
Confidence                  7888899999999988877777777765543

Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....

>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional

Probab=98.94  E-value=1.2e-09  Score=143.53  Aligned_cols=118  Identities=18%  Similarity=0.288  Sum_probs=96.1

Q ss_pred             cceeeccCchHHHHHH----------------hchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-
Q psy13846        937 KGVKCSSNNTYEVYKT----------------LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-  999 (1423)
Q Consensus       937 D~~~t~SN~i~eV~~~----------------LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-  999 (1423)
                      +.....+.|.|+++.+                +|+||+|..+++|++++++.||++||+|||++++|+||+++.+...| 
T Consensus      1052 ~~lt~g~~~ph~iL~~~f~~~~~~~g~~~aa~~~~~~~~~~lv~evq~Vy~~QGv~I~dkHieiIvrqMt~kV~i~d~Gd 1131 (1331)
T PRK02597       1052 EPLTDGPINPHELLEIFFEDLRDRKGLYEAALEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGD 1131 (1331)
T ss_pred             ccccCCCCCHHHHHhhhhhhhcccchhhHHHHHhHHHHHHHHHHHHHHHHHhcCeEechhhHHhHHHHHhCcEEEeeCCC
Confidence            3334445678888887                89999999999999999999999999999999999999999886544 


Q ss_pred             ------cchhhHHHHHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHHHHH
Q psy13846       1000 ------TPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056 (1423)
Q Consensus      1000 ------~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~~~ 1056 (1423)
                            ..|++.++...++.....+..|+...+.+++++++.|.+++|+++||  |.+-.+-.
T Consensus      1132 t~~lpGeli~~~~~~~~N~~~~~~~~~~a~y~pvLlGItkasl~T~sfis~aS--FqeT~rvL 1192 (1331)
T PRK02597       1132 TTMLPGELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAAS--FQETTRVL 1192 (1331)
T ss_pred             cccCCcceeeHHHHHHHHHHHHhcCCCcceeeeeeeeeeeeccccCChhhhcc--HHHHHHHH
Confidence                  56777888777777666666667666778899999999999998776  66654443

>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional

Probab=98.24  E-value=5.5e-07  Score=110.83  Aligned_cols=49  Identities=29%  Similarity=0.489  Sum_probs=46.2

Q ss_pred             hhHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcc
Q psy13846         10 TLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAF   58 (1423)
Q Consensus        10 ~~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~   58 (1423)
                      -.-+||||||+.||.+++|++||++|+|++|.+||+++|+|+||.+|..
T Consensus       479 PqS~~A~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~LT~~~~~  527 (627)
T PRK02625        479 PLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPG  527 (627)
T ss_pred             CCCHHHHHHHHHHhcCccceEEcCCCceeEeechhhhhheeeeeccCcc
Confidence            3458999999999999999999999999999999999999999999865

>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit

Probab=98.23  E-value=5.5e-07  Score=110.69  Aligned_cols=49  Identities=29%  Similarity=0.465  Sum_probs=45.8

Q ss_pred             hhHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcc
Q psy13846         10 TLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAF   58 (1423)
Q Consensus        10 ~~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~   58 (1423)
                      -.-+||||||++||.+++|++||++|+|++|.+||+++|+|+||.+|.-
T Consensus       472 PqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llg~y~LT~~~~~  520 (619)
T TIGR02387       472 PLSLEAQTEARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPG  520 (619)
T ss_pred             CCCHHHHHHHHHHhhchhcEEecCCCceeEeechhhhhhhheeeccccc
Confidence            3457999999999999999999999999999999999999999999853

The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.

>CHL00018 rpoC1 RNA polymerase beta' subunit

Probab=98.19  E-value=8.1e-07  Score=110.46  Aligned_cols=49  Identities=29%  Similarity=0.394  Sum_probs=45.9

Q ss_pred             hhHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcc
Q psy13846         10 TLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAF   58 (1423)
Q Consensus        10 ~~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~   58 (1423)
                      -.-+||||||+.||++.+|++||++|+|++|.+||+++|+|+||.+|.-
T Consensus       500 PqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~  548 (663)
T CHL00018        500 PLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNRR  548 (663)
T ss_pred             CCCHHHHHHHHHHhcCccceeEcCCCceeEeechhhhhhhheecccCCC
Confidence            3457999999999999999999999999999999999999999999863

>PF05000 RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; InterPro: IPR007083 RNA polymerases catalyse the DNA dependent polymerisation of RNA

Probab=91.13  E-value=0.024  Score=56.53  Aligned_cols=62  Identities=19%  Similarity=0.287  Sum_probs=49.5

Q ss_pred             CcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCc
Q psy13846        301 EDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTP  380 (1423)
Q Consensus       301 ~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~  380 (1423)
                      .+++++.|..+|+|++++++.||.   .|+++|...|.++...+                 ..|+|||    |.+..-.|
T Consensus        47 ~~N~l~~M~~SGaKGs~~ni~Qi~---g~lGqq~~~g~ri~~~~-----------------~~Rtlp~----f~~~~~~~  102 (108)
T PF05000_consen   47 FNNSLLIMINSGAKGSMSNISQIS---GCLGQQSVEGKRIPRGF-----------------SGRTLPH----FKPFDESP  102 (108)
T ss_dssp             TTSHHHHHHHSSSS--HHHHHHHH---ST-EEEEETTSES--SS-----------------TTCSSTT----S-SS-SST
T ss_pred             CCCcHHhhhhccCCCCHHHHHHHH---HHHHHhhccccccccCC-----------------CCCcCCC----cCCCCCCc
Confidence            468899999999999999999999   99999999999877767                 8999999    88888888


Q ss_pred             ccCCCc
Q psy13846        381 YNADFD  386 (1423)
Q Consensus       381 ~nadFd  386 (1423)
                      ...+|.
T Consensus       103 ~~~GFI  108 (108)
T PF05000_consen  103 ESRGFI  108 (108)
T ss_dssp             TTTTEE
T ss_pred             ccCCCC
Confidence            888884

Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This entry, domain 4, represents the funnel domain. The funnel domain contains the binding site for some elongation factors [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Q 3HKZ_I 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2Y0S_W 3IYD_D 3LU0_D ....

>PF04992 RNA_pol_Rpb1_6: RNA polymerase Rpb1, domain 6; InterPro: IPR007075 RNA polymerases catalyse the DNA dependent polymerisation of RNA

Probab=87.94  E-value=0.14  Score=56.20  Aligned_cols=88  Identities=14%  Similarity=0.177  Sum_probs=58.3

Q ss_pred             cchhhHHHHHHHHHhcc--CCCCCCCCHHHHHHHhhhhcCcchhhh-----------hhhHHHHHHHHHHHHHhhhcccc
Q psy13846       1000 TPVELKRLLDDIIAKNS--SRSDPSLSAQEILALSNETLDSKEFLQ-----------DTSENFVRDIKKFLEEFSKKESV 1066 (1423)
Q Consensus      1000 ~~~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~l~~~~~~~-----------~~~~~f~~~~~~~~~~~~~~~~~ 1066 (1423)
                      .||++.|++.+++....  .+....+.|.+++..+++.++.-..+.           .|.-.|.-.|++           
T Consensus        87 LPVNi~RiI~nAq~~f~i~~~~~sdL~P~~Vi~~V~~L~~~L~vv~g~D~ls~Eaq~NAtlLf~i~lRs-----------  155 (187)
T PF04992_consen   87 LPVNIQRIIWNAQKIFHIDPRKPSDLSPIYVIEKVEELLDRLVVVRGDDPLSREAQENATLLFKILLRS-----------  155 (187)
T ss_dssp             EES-HHHHCCCCCCCTT--TTS-BS--HHHHHHHHHHHHTT--SS--SSCCCCHHHHCCCHHHHHHHCC-----------
T ss_pred             CCccHHHHHHHHHHHcCCCCCCcccCCHHHHHHHHHHHHHHHhhccCCCcchHHHHhhHHHHHHHHHHH-----------
Confidence            89999999888776532  455578999999999998876421110           122344433332           


Q ss_pred             ccccccCCchhhhhhhccccccCcccCCCCCChhHHHHHHHHHhhhc
Q psy13846       1067 TSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRA 1113 (1423)
Q Consensus      1067 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~s 1113 (1423)
                               .++.|.+..++++|++++    +  |++++++.+|.+|
T Consensus       156 ---------~LasKrvi~e~rL~~~AF----~--wilgEIe~rF~~a  187 (187)
T PF04992_consen  156 ---------TLASKRVIEEYRLNKEAF----D--WILGEIESRFKKA  187 (187)
T ss_dssp             ---------CSSHHHHHHTSB--HHHH----H--HHHHHHHHHHHCC
T ss_pred             ---------hhhhHHHHHHhCcCHHHH----H--HHHHHHHHHHHcC
Confidence                     356788889999999998    8  9999999999886

Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [, ]. This family appears to be specific to the largest subunit of RNA polymerase II.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 1Y77_A 3CQZ_A 3GTM_A 1TWA_A 4A3I_A 2NVY_A 2NVT_A 1I6H_A 1TWF_A ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	1423
2pmz_C	392	Archaeal Rna Polymerase From Sulfolobus Solfataricu		2e-43
3hkz_C	395	The X-Ray Crystal Structure Of Rna Polymerase From		2e-43
2waq_C	395	The Complete Structure Of The Archaeal 13-Subunit D		3e-41
2y0s_C	395	Crystal Structure Of Sulfolobus Shibatae Rna Polyme		6e-41
2waq_A	880	The Complete Structure Of The Archaeal 13-Subunit D		9e-40
2waq_A	880	The Complete Structure Of The Archaeal 13-Subunit D		1e-17
2pmz_A	880	Archaeal Rna Polymerase From Sulfolobus Solfataricu		1e-39
2pmz_A	880	Archaeal Rna Polymerase From Sulfolobus Solfataricu		1e-17
3h0g_A	1752	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		4e-39
3h0g_A	1752	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		4e-24
4a3c_A	1732	Rna Polymerase Ii Initial Transcribing Complex With		8e-36
4a3c_A	1732	Rna Polymerase Ii Initial Transcribing Complex With		1e-21
4a3c_A	1732	Rna Polymerase Ii Initial Transcribing Complex With		8e-20
1i3q_A	1733	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		9e-36
1i3q_A	1733	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		1e-21
1i3q_A	1733	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		8e-20
3j0k_A	1455	Orientation Of Rna Polymerase Ii Within The Human V		1e-35
3j0k_A	1455	Orientation Of Rna Polymerase Ii Within The Human V		9e-22
3j0k_A	1455	Orientation Of Rna Polymerase Ii Within The Human V		8e-20
3qqc_A	436	Crystal Structure Of Archaeal Spt45 BOUND TO THE RN		4e-25
3iyd_D	1413	Three-Dimensional Em Structure Of An Intact Activat		1e-16
3iyd_D	1413	Three-Dimensional Em Structure Of An Intact Activat		3e-07
3iyd_D	1413	Three-Dimensional Em Structure Of An Intact Activat		4e-05
3lu0_D	1407	Molecular Model Of Escherichia Coli Core Rna Polyme		1e-16
3lu0_D	1407	Molecular Model Of Escherichia Coli Core Rna Polyme		3e-07
3lu0_D	1407	Molecular Model Of Escherichia Coli Core Rna Polyme		4e-05
4gzy_D	1534	Crystal Structures Of Bacterial Rna Polymerase Paus		6e-15
4gzy_D	1534	Crystal Structures Of Bacterial Rna Polymerase Paus		2e-10
1iw7_D	1524	Crystal Structure Of The Rna Polymerase Holoenzyme		6e-15
1iw7_D	1524	Crystal Structure Of The Rna Polymerase Holoenzyme		2e-10
2gho_D	1233	Recombinant Thermus Aquaticus Rna Polymerase For St		6e-15
2gho_D	1233	Recombinant Thermus Aquaticus Rna Polymerase For St		3e-10
1l9u_D	1524	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		6e-15
1l9u_D	1524	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		4e-10
1i6v_D	1264	Thermus Aquaticus Core Rna Polymerase-Rifampicin Co		7e-15
1i6v_D	1264	Thermus Aquaticus Core Rna Polymerase-Rifampicin Co		3e-10
1hqm_D	1265	Crystal Structure Of Thermus Aquaticus Core Rna Pol		7e-15
1hqm_D	1265	Crystal Structure Of Thermus Aquaticus Core Rna Pol		3e-10

>pdb|2PMZ|C Chain C, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 392

Iteration: 1
 Score =  175 bits (443), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 120/374 (32%), Positives = 187/374 (50%), Gaps = 64/374 (17%)
Query: 1072 KVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGE 1131
            K+   L+  IL+ +  +        F  A K      +Y    I P  A+G +AAQS+GE
Sbjct: 24   KIVDDLKNLILNKEIIVTRDEIDKIFDLAIK------EYSEGLIAPGEAIGIVAAQSVGE 77
Query: 1132 PGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFILIKL----DMDRIRLLHL 1176
            PGTQMTL+TFHFAG            + E ++   VP    + I L      DR + L +
Sbjct: 78   PGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMTIYLTDEYKRDRDKALEV 137
Query: 1177 ----------------EVDIDSIRYCIE------RTRGIS--------GHLTVSGHSFLI 1206
                             +DI S+   ++      + +G++        G L +    F+I
Sbjct: 138  ARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLKDKGVTVDDVKKAIGRLKLG--DFMI 195
Query: 1207 LKPKDSSKSFN-------SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 1259
             + +DS+ + N       + +++++  + +  IKG++GI RA++ ++  E    Y +L +
Sbjct: 196  EESEDSTLNINFANIDSIAALFKLRDKILNTKIKGIKGIKRAIVQKKGDE----YIILTD 251
Query: 1260 GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 1319
            G NL  V++  GV   K  +NN  E+ +  GIEAAR  I+ EI  V+   G+ +D RH +
Sbjct: 252  GSNLSGVLSVKGVDVAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDIRHIL 311
Query: 1320 LVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECII 1379
            L+AD+MT  G V  I RHG+   K SVL  A+FE T  HL DAA  G  +   GV E II
Sbjct: 312  LIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENII 371
Query: 1380 MGLPMNVGTGLIKL 1393
            +G P+ +GTG+++L
Sbjct: 372  IGHPIKLGTGMVEL 385

>pdb|3HKZ|C Chain C, The X-Ray Crystal Structure Of Rna Polymerase From Archaea Length = 395

Iteration: 1
 Score =  174 bits (442), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 120/374 (32%), Positives = 187/374 (50%), Gaps = 64/374 (17%)
Query: 1072 KVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGE 1131
            K+   L+  IL+ +  +        F  A K      +Y    I P  A+G +AAQS+GE
Sbjct: 27   KIVDDLKNLILNKEIIVTRDEIDKIFDLAIK------EYSEGLIAPGEAIGIVAAQSVGE 80
Query: 1132 PGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFILIKL----DMDRIRLLHL 1176
            PGTQMTL+TFHFAG            + E ++   VP    + I L      DR + L +
Sbjct: 81   PGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMTIYLTDEYKRDRDKALEV 140
Query: 1177 ----------------EVDIDSIRYCIE------RTRGIS--------GHLTVSGHSFLI 1206
                             +DI S+   ++      + +G++        G L +    F+I
Sbjct: 141  ARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLKDKGVTVDDVKKAIGRLKLG--DFMI 198
Query: 1207 LKPKDSSKSFN-------SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 1259
             + +DS+ + N       + +++++  + +  IKG++GI RA++ ++  E    Y +L +
Sbjct: 199  EESEDSTLNINFANIDSIAALFKLRDKILNTKIKGIKGIKRAIVQKKGDE----YIILTD 254
Query: 1260 GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 1319
            G NL  V++  GV   K  +NN  E+ +  GIEAAR  I+ EI  V+   G+ +D RH +
Sbjct: 255  GSNLSGVLSVKGVDVAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDIRHIL 314
Query: 1320 LVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECII 1379
            L+AD+MT  G V  I RHG+   K SVL  A+FE T  HL DAA  G  +   GV E II
Sbjct: 315  LIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENII 374
Query: 1380 MGLPMNVGTGLIKL 1393
            +G P+ +GTG+++L
Sbjct: 375  IGHPIKLGTGMVEL 388

>pdb|2WAQ|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 395

Iteration: 1
 Score =  167 bits (424), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 110/338 (32%), Positives = 167/338 (49%), Gaps = 58/338 (17%)
Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFV 1156
            ++Y    I P  A+G +AAQS+GEPGTQMTL+TFHFAG            + E ++   V
Sbjct: 57   KEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKV 116
Query: 1157 PDDSFILI------------------KLDMDRIR---------------LLHLE------ 1177
            P    + I                  KL+  +I                +L L+      
Sbjct: 117  PSTPMMTIYLTDEYKHDKEKALEVARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLKD 176
Query: 1178 --VDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGV 1235
              V +D ++  I R +   G   +       L    ++    + +++++  + +  IKG+
Sbjct: 177  KGVTVDDVKKAINRLK--LGEFVIDESEGTTLNISFANIDSIAALFKLRDKILNTKIKGI 234
Query: 1236 QGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 1295
            +GI RA++ ++  E    Y +L +G NL  V++  GV   K  +NN  E+ +  GIEAAR
Sbjct: 235  KGIKRAIVQKKGDE----YIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAR 290
Query: 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
              I+ EI  V+   G+ +D RH +LVAD+MT  G V  I RHG+   K SVL  A+FE T
Sbjct: 291  EIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVT 350
Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
              HL DAA  G  +   GV E II+G P+ +GTG+++L
Sbjct: 351  VKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVEL 388

>pdb|2Y0S|C Chain C, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In P21 Space Group Length = 395

Iteration: 1
 Score =  167 bits (422), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 110/338 (32%), Positives = 167/338 (49%), Gaps = 58/338 (17%)
Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFV 1156
            ++Y    I P  A+G +AAQS+GEPGTQMTL+TFHFAG            + E ++   V
Sbjct: 57   KEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKV 116
Query: 1157 PDDSFILI------------------KLDMDRIR---------------LLHLE------ 1177
            P    + I                  KL+  +I                +L L+      
Sbjct: 117  PSTPMMTIYLTDEYKHDKEKALEVARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLKD 176
Query: 1178 --VDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGV 1235
              V +D ++  I R +   G   +       L    ++    + +++++  + +  IKG+
Sbjct: 177  KGVTVDDVKKAINRLK--LGEFVIDESEGNTLNISFANIDSIAALFKLRDKILNTKIKGI 234
Query: 1236 QGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 1295
            +GI RA++ ++  E    Y +L +G NL  V++  GV   K  +NN  E+ +  GIEAAR
Sbjct: 235  KGIKRAIVQKKGDE----YIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAR 290
Query: 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
              I+ EI  V+   G+ +D RH +LVAD+MT  G V  I RHG+   K SVL  A+FE T
Sbjct: 291  EIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVT 350
Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
              HL DAA  G  +   GV E II+G P+ +GTG+++L
Sbjct: 351  VKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVEL 388

>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 880

Iteration: 1
 Score =  162 bits (411), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 101/272 (37%), Positives = 149/272 (54%), Gaps = 29/272 (10%)
Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DVVLFNRQPSLH++S+MAHR +VL   TFR N  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 412 TDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEE 471
Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A AE              AK +M    N++TPR G  +I A QD+I+G YLLT K     
Sbjct: 472 AIAE--------------AKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLT 517
Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           + +  +I    +AD     G     + R +           +TGKQ+ S  L  + +   
Sbjct: 518 KEEAQQILG--VADVKIDLGEPAILAPREY-----------YTGKQVVSAFLPKDFNFHG 564
Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            AN+ +  R      E C  DSYV+++N  LL G  DK  +G+    ++ + L++++ ++
Sbjct: 565 QANVSSGPR--LCKNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDE 622
Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
                M  L R+   ++  +GF++ + DV+ G
Sbjct: 623 YGKWLMDNLFRVFIRFVELQGFTMRLEDVSLG 654

>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 880

Iteration: 1
 Score = 89.4 bits (220), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 56/73 (76%), Gaps = 2/73 (2%)
Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D++P  +GF+ +SF +GL PTE FFH  GGREGLVDTAV+T+++GYMQRRL+ +L DL  
Sbjct: 773 DISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLRA 832
Query: 666 QYDMSFDAAFYGQ 678
           +YD +   + YG+
Sbjct: 833 EYDGTV-RSLYGE 844

>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 880

Iteration: 1
 Score =  162 bits (410), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 100/271 (36%), Positives = 148/271 (54%), Gaps = 29/271 (10%)
Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+MAHR +VL   TFR N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 413 DGDIVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 472
Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AE              AK +M    N++TPR G  +I A QD+I+G YLLT K     +
Sbjct: 473 IAE--------------AKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTK 518
Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  +I    +AD     G     + R +           +TGKQ+ S  L  + +    
Sbjct: 519 EEAQQILG--VADVKIDLGEPAILAPREY-----------YTGKQVISAFLPKDFNFHGQ 565
Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           AN+ +  R      E C  DSYV+++N  LL G  DK  +G+    ++ + L++++ ++ 
Sbjct: 566 ANVSSGPR--LCKNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEY 623
Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
               M  L R+   ++  +GF++ + DV+ G
Sbjct: 624 GKWLMDNLFRVFIRFVELQGFTMRLEDVSLG 654

>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 880

Iteration: 1
 Score = 89.4 bits (220), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 56/73 (76%), Gaps = 2/73 (2%)
Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D++P  +GF+ +SF +GL PTE FFH  GGREGLVDTAV+T+++GYMQRRL+ +L DL  
Sbjct: 773 DISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLRA 832
Query: 666 QYDMSFDAAFYGQ 678
           +YD +   + YG+
Sbjct: 833 EYDGTV-RSLYGE 844

>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752

Iteration: 1
 Score =  160 bits (405), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 94/268 (35%), Positives = 149/268 (55%), Gaps = 38/268 (14%)
Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVV+FNRQPSLHK+S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 444 DGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSEET 503
Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               ++ M  K  +V+P++ + ++   QD + G    + ++ F  R
Sbjct: 504 RAEI-------------QEITMVPK-QIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTR 549
Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M I    +    D  GI+         P V ++  V+WTGKQI SLI+      P  
Sbjct: 550 NAVMNI----MLWVPDWDGILP--------PPVILKPKVLWTGKQILSLII------PKG 591
Query: 521 ANL-KTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL +   +   +N      DS +++ N E++ G +DK T+G+  +  + + + ++ G +
Sbjct: 592 INLIRDDDKQSLSNPT----DSGMLIENGEIIYGVVDKKTVGA-SQGGLVHTIWKEKGPE 646
Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +       + R+ +++L++ GFSIGIGD
Sbjct: 647 ICKGFFNGIQRVVNYWLLHNGFSIGIGD 674

>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752

Iteration: 1
 Score =  110 bits (276), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 61/174 (35%), Positives = 97/174 (55%), Gaps = 9/174 (5%)
Query: 1225 QLLPSVVIKGVQGINRAVIHEEDV---------EGVTKYKLLVEGDNLRDVMATYGVKGV 1275
             +L S+ ++GV  I R  + E  +         E   ++ L  +G NL + M   GV   
Sbjct: 1272 HMLESISLRGVPNITRVYMMEHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVDAT 1331
Query: 1276 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGIT 1335
            +  SN+  E+ + LGIEA RS ++ E++ V+E  G  +++RH  L+ D+MTS+G ++ IT
Sbjct: 1332 RTYSNSFVEILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAIT 1391
Query: 1336 RHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            RHG+ + +   L   SFE T + L DAA  G+ D   G+SE I++G    +GTG
Sbjct: 1392 RHGINRAETGALMRCSFEETVEILMDAAASGEKDDCKGISENIMLGQLAPMGTG 1445

>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt Dna-Rna Hybrid Length = 1732

Iteration: 1
 Score =  149 bits (377), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 89/267 (33%), Positives = 143/267 (53%), Gaps = 36/267 (13%)
Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 438 DNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 497
Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 L A    +V+P++ +  +   QD + G   LT ++ F   
Sbjct: 498 RAE--------------LSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIEL 543
Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q +     ++    D  G+I         P + ++   +W+GKQI S+ +      P  
Sbjct: 544 DQVL----NMLYWVPDWDGVIP-------TPAI-IKPKPLWSGKQILSVAI------PNG 585
Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            +L+      T       +D+ +++ + +++ G ++K T+GS     + +++ R+ G  V
Sbjct: 586 IHLQRFDEGTTL---LSPKDNGMLIIDGQIIFGVVEKKTVGS-SNGGLIHVVTREKGPQV 641
Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
                  + ++ +F+L++ GFS GIGD
Sbjct: 642 CAKLFGNIQKVVNFWLLHNGFSTGIGD 668

>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt Dna-Rna Hybrid Length = 1732

Iteration: 1
 Score =  102 bits (255), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 54/63 (85%), Gaps = 1/63 (1%)
Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 791 DYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMV 850
Query: 666 QYD 668
            YD
Sbjct: 851 HYD 853

>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt Dna-Rna Hybrid Length = 1732

Iteration: 1
 Score = 96.7 bits (239), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 55/178 (30%), Positives = 97/178 (54%), Gaps = 9/178 (5%)
Query: 1226 LLPSVVIKGVQGINRAVIHEED--VEGVT-------KYKLLVEGDNLRDVMATYGVKGVK 1276
            +L ++ ++GV+ I R V+ + D  V   T       ++ L  +G NL +VM   G+   +
Sbjct: 1267 MLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTR 1326
Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
              +N+  ++ + LGIEA R+ +  E+  V+ + G  +++RH  L+ D+MT++G +  +TR
Sbjct: 1327 IYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTR 1386
Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            HG  +     L   SFE T + LF+A    + D   GVSE +I+G    +GTG   ++
Sbjct: 1387 HGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVM 1444

>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1733

Iteration: 1
 Score =  149 bits (377), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 89/267 (33%), Positives = 143/267 (53%), Gaps = 36/267 (13%)
Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 438 DNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 497
Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 L A    +V+P++ +  +   QD + G   LT ++ F   
Sbjct: 498 RAE--------------LSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIEL 543
Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q +     ++    D  G+I         P + ++   +W+GKQI S+ +      P  
Sbjct: 544 DQVL----NMLYWVPDWDGVIP-------TPAI-IKPKPLWSGKQILSVAI------PNG 585
Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            +L+      T       +D+ +++ + +++ G ++K T+GS     + +++ R+ G  V
Sbjct: 586 IHLQRFDEGTTL---LSPKDNGMLIIDGQIIFGVVEKKTVGS-SNGGLIHVVTREKGPQV 641
Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
                  + ++ +F+L++ GFS GIGD
Sbjct: 642 CAKLFGNIQKVVNFWLLHNGFSTGIGD 668

>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1733

Iteration: 1
 Score =  102 bits (255), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 54/63 (85%), Gaps = 1/63 (1%)
Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 791 DYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMV 850
Query: 666 QYD 668
            YD
Sbjct: 851 HYD 853

>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1733

Iteration: 1
 Score = 96.7 bits (239), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 55/178 (30%), Positives = 97/178 (54%), Gaps = 9/178 (5%)
Query: 1226 LLPSVVIKGVQGINRAVIHEED--VEGVT-------KYKLLVEGDNLRDVMATYGVKGVK 1276
            +L ++ ++GV+ I R V+ + D  V   T       ++ L  +G NL +VM   G+   +
Sbjct: 1267 MLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTR 1326
Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
              +N+  ++ + LGIEA R+ +  E+  V+ + G  +++RH  L+ D+MT++G +  +TR
Sbjct: 1327 IYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTR 1386
Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            HG  +     L   SFE T + LF+A    + D   GVSE +I+G    +GTG   ++
Sbjct: 1387 HGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVM 1444

>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 1455

Iteration: 1
 Score =  149 bits (376), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 89/267 (33%), Positives = 143/267 (53%), Gaps = 36/267 (13%)
Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 438 DNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 497
Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 L A    +V+P++ +  +   QD + G   LT ++ F   
Sbjct: 498 RAE--------------LSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIEL 543
Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q +     ++    D  G+I         P + ++   +W+GKQI S+ +      P  
Sbjct: 544 DQVL----NMLYWVPDWDGVIP-------TPAI-IKPKPLWSGKQILSVAI------PNG 585
Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            +L+      T       +D+ +++ + +++ G ++K T+GS     + +++ R+ G  V
Sbjct: 586 IHLQRFDEGTTL---LSPKDNGMLIIDGQIIFGVVEKKTVGS-SNGGLIHVVTREKGPQV 641
Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
                  + ++ +F+L++ GFS GIGD
Sbjct: 642 CAKLFGNIQKVVNFWLLHNGFSTGIGD 668

>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 1455

Iteration: 1
 Score =  103 bits (256), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 54/63 (85%), Gaps = 1/63 (1%)
Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 791 DYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMV 850
Query: 666 QYD 668
            YD
Sbjct: 851 HYD 853

>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 1455

Iteration: 1
 Score = 96.7 bits (239), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 55/178 (30%), Positives = 98/178 (55%), Gaps = 9/178 (5%)
Query: 1226 LLPSVVIKGVQGINRAVIHEEDV-------EGVTKYKLLVEGD--NLRDVMATYGVKGVK 1276
            +L ++ ++GV+ I R V+ + D        E V + + ++E D  NL +VM   G+   +
Sbjct: 1267 MLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTR 1326
Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
              +N+  ++ + LGIEA R+ +  E+  V+ + G  +++RH  L+ D+MT++G +  +TR
Sbjct: 1327 IYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTR 1386
Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            HG  +     L   SFE T + LF+A    + D   GVSE +I+G    +GTG   ++
Sbjct: 1387 HGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVM 1444

>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP CLAMP DOMAIN Length = 436

Iteration: 1
 Score =  114 bits (285), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 82/289 (28%), Positives = 135/289 (46%), Gaps = 43/289 (14%)
Query: 61  RAQTMRIASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGL 120
           +A  +R    L  G KV   G IE  +     +++ S +++   + Y  D    PI  G+
Sbjct: 52  KAMVIRPKLNLSEGGKVI--GSIEFGILSPQEIRKMSAVEVTVPDTY--DDDGYPIEGGV 107
Query: 121 LDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCA 180
           +D+RMG       C TCG    +C GHFG+I+L  PV H+G+ + +  IL+S C+   C 
Sbjct: 108 MDKRMGVIDPGLRCETCGGRAGECPGHFGHIELARPVIHVGFAKTIYRILESTCRE--CG 165
Query: 181 RVLLGEEKAAGFRAKL---RNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG 237
           R+ L +E+   +  K+   RN    +     + K+I +  K+  VCPHCG     +    
Sbjct: 166 RIKLTDEEIEEYMKKIELARNRRSEF---NEIIKEIHKKAKERMVCPHCGAPQYPI---- 218
Query: 238 LLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEA 297
                  K++  T   +   ++   EY                     L P EV    E 
Sbjct: 219 -------KFEKPTIYWEIRKDEQGNEYR------------------HRLMPTEVRDWLEK 253
Query: 298 IPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVI--SDLKSDNDV 344
           IP +D+PLL ++ E S+P  ++LT L VPP   RPS+   + +++++D+
Sbjct: 254 IPDKDLPLLGLDPEKSRPEWMVLTVLPVPPVTARPSITLETGIRAEDDL 302

>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 1413

Iteration: 1
 Score = 85.9 bits (211), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 42/109 (38%), Positives = 63/109 (57%), Gaps = 14/109 (12%)
Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
           VL NR P+LH+L I A    ++  +  + +  VC  YNADFDGD+M VH+P T EA+ E 
Sbjct: 421 VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLE- 479
Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
                        A+ LM + +N+++P NGE +I  +QD + G Y +T+
Sbjct: 480 -------------ARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTR 515

>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 1413

Iteration: 1
 Score = 54.7 bits (130), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/77 (40%), Positives = 41/77 (53%), Gaps = 13/77 (16%)
Query: 615 VQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA 674
           +  +F  GL   ++F  T G R+GL DTA+KTA +GY+ RRLV   +DL V  D      
Sbjct: 759 ITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTED------ 812
Query: 675 FYGQTDCISGVSECIIM 691
                DC  G  E I+M
Sbjct: 813 -----DC--GTHEGIMM 822

>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 1413

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 19/31 (61%), Positives = 24/31 (77%)
Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            I    A+G +AAQSIGEPGTQ+T++TFH  G
Sbjct: 909  INKGEAIGVIAAQSIGEPGTQLTMRTFHIGG 939

>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1407

Iteration: 1
 Score = 85.9 bits (211), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 42/109 (38%), Positives = 63/109 (57%), Gaps = 14/109 (12%)
Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
           VL NR P+LH+L I A    ++  +  + +  VC  YNADFDGD+M VH+P T EA+ E 
Sbjct: 421 VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLE- 479
Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
                        A+ LM + +N+++P NGE +I  +QD + G Y +T+
Sbjct: 480 -------------ARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTR 515

>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1407

Iteration: 1
 Score = 54.7 bits (130), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/77 (40%), Positives = 41/77 (53%), Gaps = 13/77 (16%)
Query: 615 VQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA 674
           +  +F  GL   ++F  T G R+GL DTA+KTA +GY+ RRLV   +DL V  D      
Sbjct: 759 ITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTED------ 812
Query: 675 FYGQTDCISGVSECIIM 691
                DC  G  E I+M
Sbjct: 813 -----DC--GTHEGIMM 822

>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1407

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 19/31 (61%), Positives = 24/31 (77%)
Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            I    A+G +AAQSIGEPGTQ+T++TFH  G
Sbjct: 909  INKGEAIGVIAAQSIGEPGTQLTMRTFHIGG 939

>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused Elongation Complexes Length = 1534

Iteration: 1
 Score = 80.5 bits (197), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 41/110 (37%), Positives = 64/110 (58%), Gaps = 14/110 (12%)
Query: 344 VVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE 403
           VVL NR P+LH+L I A +  ++  ++ + +  VC  +NADFDGD+M VH+P +  A+AE
Sbjct: 699 VVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE 758
Query: 404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
                         A++ M +  NL++P +GE L   ++D I G Y +TQ
Sbjct: 759 --------------ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQ 794

>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused Elongation Complexes Length = 1534

Iteration: 1
 Score = 65.5 bits (158), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 72/295 (24%), Positives = 136/295 (46%), Gaps = 44/295 (14%)
Query: 1120 AVGALAAQSIGEPGTQMTLKTFHFAG------------EVCEYIEEVFVPDDSFILIKLD 1167
            AVG +AAQSIGEPGTQ+T++TFH  G             V E   E   P    ++ ++D
Sbjct: 1220 AVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELF-EARRPKAKAVISEID 1278
Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD---SSKSFNSKMYQMK 1224
                 ++ +E   + +   +E + G S    +   + L++K  D   + +          
Sbjct: 1279 G----VVRIEETEEKLSVFVE-SEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPH 1333
Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            QLL +   KG + + R ++  E+++ V + + +   D   +++    +K V+ +      
Sbjct: 1334 QLLEA---KGPEAVERYLV--EEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSR 1388
Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
            + +   +E      + E +L+ E  G +     P+L           +G+T+  L+   +
Sbjct: 1389 LLEGQVLEKWDVEALNE-RLIAE--GKTPVAWKPLL-----------MGVTKSALS--TK 1432
Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG--LPMNVGTGLIKLLQAV 1397
            S L+ ASF+NT+  L +AA  G+ D + G+ E +I+G  +P   G+  ++  Q V
Sbjct: 1433 SWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVV 1487

>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 1524

Iteration: 1
 Score = 80.5 bits (197), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 41/110 (37%), Positives = 64/110 (58%), Gaps = 14/110 (12%)
Query: 344 VVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE 403
           VVL NR P+LH+L I A +  ++  ++ + +  VC  +NADFDGD+M VH+P +  A+AE
Sbjct: 699 VVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE 758
Query: 404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
                         A++ M +  NL++P +GE L   ++D I G Y +TQ
Sbjct: 759 --------------ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQ 794

>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 1524

Iteration: 1
 Score = 65.5 bits (158), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 72/295 (24%), Positives = 136/295 (46%), Gaps = 44/295 (14%)
Query: 1120 AVGALAAQSIGEPGTQMTLKTFHFAG------------EVCEYIEEVFVPDDSFILIKLD 1167
            AVG +AAQSIGEPGTQ+T++TFH  G             V E   E   P    ++ ++D
Sbjct: 1220 AVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELF-EARRPKAKAVISEID 1278
Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD---SSKSFNSKMYQMK 1224
                 ++ +E   + +   +E + G S    +   + L++K  D   + +          
Sbjct: 1279 G----VVRIEETEEKLSVFVE-SEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPH 1333
Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            QLL +   KG + + R ++  E+++ V + + +   D   +++    +K V+ +      
Sbjct: 1334 QLLEA---KGPEAVERYLV--EEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSR 1388
Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
            + +   +E      + E +L+ E  G +     P+L           +G+T+  L+   +
Sbjct: 1389 LLEGQVLEKWDVEALNE-RLIAE--GKTPVAWKPLL-----------MGVTKSALS--TK 1432
Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG--LPMNVGTGLIKLLQAV 1397
            S L+ ASF+NT+  L +AA  G+ D + G+ E +I+G  +P   G+  ++  Q V
Sbjct: 1433 SWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVV 1487

>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For Structural Studies Length = 1233

Iteration: 1
 Score = 80.5 bits (197), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 41/110 (37%), Positives = 64/110 (58%), Gaps = 14/110 (12%)
Query: 344 VVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE 403
           VVL NR P+LH+L I A +  ++  ++ + +  VC  +NADFDGD+M VH+P +  A+AE
Sbjct: 408 VVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE 467
Query: 404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
                         A++ M +  NL++P +GE L   ++D I G Y +TQ
Sbjct: 468 --------------ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQ 503

>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For Structural Studies Length = 1233

Iteration: 1
 Score = 64.7 bits (156), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 72/300 (24%), Positives = 135/300 (45%), Gaps = 54/300 (18%)
Query: 1120 AVGALAAQSIGEPGTQMTLKTFHFAG------------EVCEYIEEVFVPDDSFILIKLD 1167
            AVG +AA+SIGEPGTQ+T++TFH  G             V E   E   P    ++ ++D
Sbjct: 929  AVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF-EARRPKAKAVISEID 987
Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD---SSKSFNSKMYQMK 1224
                 ++ +E   D +   +E + G S    +   + L++K  D   + +          
Sbjct: 988  G----VVRIEEGEDRLSVFVE-SEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGAIDPH 1042
Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY- 1283
            QLL +   KG + + R ++ E  ++ V + + +   D   +++    +K V+ +      
Sbjct: 1043 QLLEA---KGPEAVERYLVDE--IQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSR 1097
Query: 1284 ----EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
                +V +   +EA    ++ E K+             P+    L+      +G+T+  L
Sbjct: 1098 LLEGQVLEKWDVEALNERLIAEGKV-------------PVAWKPLL------MGVTKSAL 1138
Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG--LPMNVGTGLIKLLQAV 1397
            +   +S L+ ASF+NT+  L +AA  G+ D + G+ E +I+G  +P   G+  ++  Q V
Sbjct: 1139 S--TKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVV 1196

>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1524

Iteration: 1
 Score = 80.5 bits (197), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 41/110 (37%), Positives = 64/110 (58%), Gaps = 14/110 (12%)
Query: 344 VVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE 403
           VVL NR P+LH+L I A +  ++  ++ + +  VC  +NADFDGD+M VH+P +  A+AE
Sbjct: 699 VVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE 758
Query: 404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
                         A++ M +  NL++P +GE L   ++D I G Y +TQ
Sbjct: 759 --------------ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQ 794

>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1524

Iteration: 1
 Score = 64.7 bits (156), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 72/300 (24%), Positives = 135/300 (45%), Gaps = 54/300 (18%)
Query: 1120 AVGALAAQSIGEPGTQMTLKTFHFAG------------EVCEYIEEVFVPDDSFILIKLD 1167
            AVG +AA+SIGEPGTQ+T++TFH  G             V E   E   P    ++ ++D
Sbjct: 1220 AVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF-EARRPKAKAVISEID 1278
Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD---SSKSFNSKMYQMK 1224
                 ++ +E   D +   +E + G S    +   + L++K  D   + +          
Sbjct: 1279 G----VVRIEEGEDRLSVFVE-SEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGAIDPH 1333
Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY- 1283
            QLL +   KG + + R ++ E  ++ V + + +   D   +++    +K V+ +      
Sbjct: 1334 QLLEA---KGPEAVERYLVDE--IQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSR 1388
Query: 1284 ----EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
                +V +   +EA    ++ E K+             P+    L+      +G+T+  L
Sbjct: 1389 LLEGQVLEKWDVEALNERLIAEGKV-------------PVAWKPLL------MGVTKSAL 1429
Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG--LPMNVGTGLIKLLQAV 1397
            +   +S L+ ASF+NT+  L +AA  G+ D + G+ E +I+G  +P   G+  ++  Q V
Sbjct: 1430 S--TKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVV 1487

>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1264

Iteration: 1
 Score = 80.5 bits (197), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 41/110 (37%), Positives = 64/110 (58%), Gaps = 14/110 (12%)
Query: 344 VVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE 403
           VVL NR P+LH+L I A +  ++  ++ + +  VC  +NADFDGD+M VH+P +  A+AE
Sbjct: 439 VVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE 498
Query: 404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
                         A++ M +  NL++P +GE L   ++D I G Y +TQ
Sbjct: 499 --------------ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQ 534

>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1264

Iteration: 1
 Score = 65.1 bits (157), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 72/300 (24%), Positives = 135/300 (45%), Gaps = 54/300 (18%)
Query: 1120 AVGALAAQSIGEPGTQMTLKTFHFAG------------EVCEYIEEVFVPDDSFILIKLD 1167
            AVG +AA+SIGEPGTQ+T++TFH  G             V E   E   P    ++ ++D
Sbjct: 960  AVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF-EARRPKAKAVISEID 1018
Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD---SSKSFNSKMYQMK 1224
                 ++ +E   D +   +E + G S    +   + L++K  D   + +          
Sbjct: 1019 G----VVRIEEGEDRLSVFVE-SEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGAIDPH 1073
Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY- 1283
            QLL +   KG + + R ++ E  ++ V + + +   D   +++    +K V+ +      
Sbjct: 1074 QLLEA---KGPEAVERYLVDE--IQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSR 1128
Query: 1284 ----EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
                +V +   +EA    ++ E K+             P+    L+      +G+T+  L
Sbjct: 1129 LLEGQVLEKWDVEALNERLIAEGKV-------------PVAWKPLL------MGVTKSAL 1169
Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG--LPMNVGTGLIKLLQAV 1397
            +   +S L+ ASF+NT+  L +AA  G+ D + G+ E +I+G  +P   G+  ++  Q V
Sbjct: 1170 S--TKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVV 1227

>pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase- Includes Complete Structure With Side-Chains (Except For Disordered Regions)-Further Refined From Original Deposition-Contains Additional Sequence Information Length = 1265

Iteration: 1
 Score = 80.5 bits (197), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 41/110 (37%), Positives = 64/110 (58%), Gaps = 14/110 (12%)
Query: 344 VVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE 403
           VVL NR P+LH+L I A +  ++  ++ + +  VC  +NADFDGD+M VH+P +  A+AE
Sbjct: 439 VVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE 498
Query: 404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
                         A++ M +  NL++P +GE L   ++D I G Y +TQ
Sbjct: 499 --------------ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQ 534

>pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase- Includes Complete Structure With Side-Chains (Except For Disordered Regions)-Further Refined From Original Deposition-Contains Additional Sequence Information Length = 1265

Iteration: 1
 Score = 64.7 bits (156), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 72/300 (24%), Positives = 135/300 (45%), Gaps = 54/300 (18%)
Query: 1120 AVGALAAQSIGEPGTQMTLKTFHFAG------------EVCEYIEEVFVPDDSFILIKLD 1167
            AVG +AA+SIGEPGTQ+T++TFH  G             V E   E   P    ++ ++D
Sbjct: 961  AVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF-EARRPKAKAVISEID 1019
Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD---SSKSFNSKMYQMK 1224
                 ++ +E   D +   +E + G S    +   + L++K  D   + +          
Sbjct: 1020 G----VVRIEEGEDRLSVFVE-SEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGAIDPH 1074
Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY- 1283
            QLL +   KG + + R ++ E  ++ V + + +   D   +++    +K V+ +      
Sbjct: 1075 QLLEA---KGPEAVERYLVDE--IQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSP 1129
Query: 1284 ----EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
                +V +   +EA    ++ E K+             P+    L+      +G+T+  L
Sbjct: 1130 LLEGQVLEKWDVEALNERLIAEGKV-------------PVAWKPLL------MGVTKSAL 1170
Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG--LPMNVGTGLIKLLQAV 1397
            +   +S L+ ASF+NT+  L +AA  G+ D + G+ E +I+G  +P   G+  ++  Q V
Sbjct: 1171 S--TKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVV 1228

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	1423
4ayb_A	880	DNA-directed RNA polymerase; transferase, multi-su	5e-80
4ayb_A	880	DNA-directed RNA polymerase; transferase, multi-su	2e-54
4ayb_A	880	DNA-directed RNA polymerase; transferase, multi-su	2e-31
4ayb_A	880	DNA-directed RNA polymerase; transferase, multi-su	7e-10
4ayb_C	395	DNA-directed RNA polymerase; transferase, multi-su	7e-80
4ayb_C	395	DNA-directed RNA polymerase; transferase, multi-su	2e-45
4ayb_C	395	DNA-directed RNA polymerase; transferase, multi-su	5e-08
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	5e-75
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	1e-69
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	2e-54
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	2e-52
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	5e-24
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	2e-11
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	4e-08
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	3e-72
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	5e-71
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	7e-53
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	5e-51
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	2e-24
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	6e-11
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	9e-08
3qqc_A	436	DNA-directed RNA polymerase subunit B, DNA-direct	3e-65
1hqm_D	1265	DNA-directed RNA polymerase; transferase, transcri	9e-21
1hqm_D	1265	DNA-directed RNA polymerase; transferase, transcri	1e-08
1hqm_D	1265	DNA-directed RNA polymerase; transferase, transcri	2e-08
1hqm_D	1265	DNA-directed RNA polymerase; transferase, transcri	8e-04
2a6h_D	1524	DNA-directed RNA polymerase beta' chain; RNA polym	1e-20
2a6h_D	1524	DNA-directed RNA polymerase beta' chain; RNA polym	1e-08
2a6h_D	1524	DNA-directed RNA polymerase beta' chain; RNA polym	2e-08
2a6h_D	1524	DNA-directed RNA polymerase beta' chain; RNA polym	3e-04
3lu0_D	1407	DNA-directed RNA polymerase subunit beta'; E. coli	2e-18
3lu0_D	1407	DNA-directed RNA polymerase subunit beta'; E. coli	6e-09
3lu0_D	1407	DNA-directed RNA polymerase subunit beta'; E. coli	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-06

>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880

 Score =  282 bits (724), Expect = 5e-80
 Identities = 97/273 (35%), Positives = 143/273 (52%), Gaps = 31/273 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++S+MAHR +VL   TFR N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 413 DGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 472

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AE              AK +M    N++TPR G  +I A QD+I+G YLLT K     +
Sbjct: 473 IAE--------------AKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTK 518

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
            +  +I                    +        +     +TGKQ+ S  L  + +   
Sbjct: 519 EEAQQILGV--------------ADVKIDLGEPAILAPREYYTGKQVVSAFLPKDFNFHG 564

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            AN+ +  R      E C  DSYV+++N  LL G  DK  +G+    ++ + L++++ ++
Sbjct: 565 QANVSSGPRLC--KNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDE 622

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
                M  L R+   ++  +GF++ + DV+ G 
Sbjct: 623 YGKWLMDNLFRVFIRFVELQGFTMRLEDVSLGD 655

>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880

 Score =  205 bits (522), Expect = 2e-54
 Identities = 66/257 (25%), Positives = 113/257 (43%), Gaps = 41/257 (15%)

Query: 90  EDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFG 149
            D +++ S   I++ ++Y  D   TPI   ++D R+G  +    C TCG  L +C GHFG
Sbjct: 16  PDEIRKMSVTAIITPDVY--DEDGTPIEGSVMDPRLGVIEPGQKCPTCGNTLGNCPGHFG 73

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209
           +I+L  PV H+G+ + V   L++ C+   C RV + E++   +          +      
Sbjct: 74  HIELVRPVIHVGFVKHVYEFLKATCRR--CGRVKISEDEIEKYSRIYNAIKKRWPSAARR 131

Query: 210 KK-KILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAV 268
               + +T  K  VCPHCGE    +K         E+ +   K                 
Sbjct: 132 LTEYVKKTAMKAQVCPHCGEKQFKIKLEKPYNFYEERKEGVAK----------------- 174

Query: 269 KFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
                            L P ++ +  E +P  D+ +L  +   S+P  +ILT L VPP 
Sbjct: 175 -----------------LTPSDIRERLEKVPESDVEILGYDPTTSRPEWMILTVLPVPPI 217

Query: 329 CIRPSVISD--LKSDND 343
            IRPS++ +  +++++D
Sbjct: 218 TIRPSIMIESGIRAEDD 234

>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880

 Score =  132 bits (334), Expect = 2e-31
 Identities = 36/58 (62%), Positives = 47/58 (81%)

Query: 613 GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           GF+ +SF +GL PTE FFH  GGREGLVDTAV+T+++GYMQRRL+ +L DL  +YD +
Sbjct: 780 GFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLRAEYDGT 837

>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880

 Score = 62.6 bits (152), Expect = 7e-10
 Identities = 18/50 (36%), Positives = 28/50 (56%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           + +M    N++TPR G  +I A QD+I+G YLLT K     + +  +I  
Sbjct: 477 KEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQILG 526

>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C Length = 395

 Score =  268 bits (685), Expect = 7e-80
 Identities = 118/404 (29%), Positives = 178/404 (44%), Gaps = 69/404 (17%)

Query: 1046 SENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKA-- 1103
                    K +LEE  K+ S      K+ + L+  I + +  +                 
Sbjct: 2    ENVIDEKDKSYLEEKVKQAS-NILPQKIVEDLKNLISNKEVLV--------TRDEIDKIF 52

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------ 1145
            +   ++Y    I P  A+G +AAQS+GEPGTQMTL+TFHFAG                  
Sbjct: 53   DLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVD 112

Query: 1146 --------------------------EVCEYIEEVFVPD--------DSFILIKLDMDRI 1171
                                      EV   +E   + +         + + I L +D  
Sbjct: 113  AKKVPSTPMMTIYLTDEYKHDKEKALEVARKLEYTKIENVVSSTSIDIASMSIILQLDNE 172

Query: 1172 RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
             L    V +D ++  I R +     +  S  + L +   +          + K  + +  
Sbjct: 173  MLKDKGVTVDDVKKAINRLKLGEFVIDESEGNTLNISFANIDSIAALFKLRDK--ILNTK 230

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            IKG++GI RA++ ++  E    Y +L +G NL  V++  GV   K  +NN  E+ +  GI
Sbjct: 231  IKGIKGIKRAIVQKKGDE----YIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGI 286

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAAR  I+ EI  V+   G+ +D RH +LVAD+MT  G V  I RHG+   K SVL  A+
Sbjct: 287  EAAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAA 346

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            FE T  HL DAA  G  +   GV E II+G P+ +GTG+++L  
Sbjct: 347  FEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTM 390

>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C Length = 395

 Score =  168 bits (426), Expect = 2e-45
 Identities = 73/236 (30%), Positives = 117/236 (49%), Gaps = 12/236 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP++T YL  +   D + A  V  +LE T +  V          
Sbjct: 103 GLPRLIEIVDAKKVPSTPMMTIYLTDEYKHDKEKALEVARKLEYTKIENVVSSTS----I 158

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           D + + I L +D   L    V +D ++  I R +     +  S  + L +   +      
Sbjct: 159 DIASMSIILQLDNEMLKDKGVTVDDVKKAINRLKLGEFVIDESEGNTLNISFANIDSIAA 218

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
               + K  + +  IKG++GI RA++ ++  E    Y +L +G NL  V++  GV   K 
Sbjct: 219 LFKLRDK--ILNTKIKGIKGIKRAIVQKKGDE----YIILTDGSNLSGVLSVKGVDIAKV 272

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +NN  E+ +  GIEAAR  I+ EI  V+   G+ +D RH +LVAD+MT  G V  
Sbjct: 273 ETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQ 328

>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C Length = 395

 Score = 55.9 bits (134), Expect = 5e-08
 Identities = 15/39 (38%), Positives = 22/39 (56%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
               DAA  G  +   GV E II+G P+ +GTG+++L  
Sbjct: 352 KHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTM 390

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score =  275 bits (703), Expect = 5e-75
 Identities = 106/479 (22%), Positives = 175/479 (36%), Gaps = 124/479 (25%)

Query: 1043 QDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQ------------PLREQILSHQDKIGH 1090
            +  ++    DI   L E   K ++    D++++             LR +    +  + +
Sbjct: 979  KKPTDLLPSDIINGLNELIAKLTIFRGSDRITRDVQNNATLLFQILLRSKFAVKRVIMEY 1038

Query: 1091 GRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----- 1145
                  F           ++ +A + P   VG LAAQSIGEP TQMTL TFH+AG     
Sbjct: 1039 RLNKVAFEWIMGE--VEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKN 1096

Query: 1146 ---------------------------------------EVCEYIE------------EV 1154
                                                    V   IE              
Sbjct: 1097 VTLGVPRLKEILNVAKNIKTPSLTIYLMPWIAANMDLAKNVQTQIEHTTLSTVTSATEIH 1156

Query: 1155 FVPDDSFILIKLDMD------------------------------RIRLLHLEVDIDSIR 1184
            + PD    +I+ D D                              R ++L  ++ +  + 
Sbjct: 1157 YDPDPQDTVIEEDKDFVEAFFAIPDEEVEENLYKQSPWLLRLELDRAKMLDKKLSMSDVA 1216

Query: 1185 YCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK---------------MYQMKQLLPS 1229
              I  +         S  +   L  +      + +                     +L S
Sbjct: 1217 GKIAESFERDLFTIWSEDNADKLIIRCRIIRDDDRKAEDDDNMIEEDVFLKTIEGHMLES 1276

Query: 1230 VVIKGVQGINRAVIHEEDV---------EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSN 1280
            + ++GV  I R  + E  +         E   ++ L  +G NL + M   GV   +  SN
Sbjct: 1277 ISLRGVPNITRVYMMEHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVDATRTYSN 1336

Query: 1281 NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLA 1340
            +  E+ + LGIEA RS ++ E++ V+E  G  +++RH  L+ D+MTS+G ++ ITRHG+ 
Sbjct: 1337 SFVEILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAITRHGIN 1396

Query: 1341 KMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 1399
            + +   L   SFE T + L DAA  G+ D   G+SE I++G    +GTG   +      
Sbjct: 1397 RAETGALMRCSFEETVEILMDAAASGEKDDCKGISENIMLGQLAPMGTGAFDIYLDQDM 1455

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score =  257 bits (658), Expect = 1e-69
 Identities = 95/329 (28%), Positives = 155/329 (47%), Gaps = 61/329 (18%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVV+FNRQPSLHK+S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 444 DGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSEET 503

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               + +      +V+P++ + ++   QD + G    + ++ F  R
Sbjct: 504 RAE--------------IQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTR 549

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M I   +     D  GI+         P V ++  V+WTGKQI SLI+       + 
Sbjct: 550 NAVMNIMLWV----PDWDGIL--------PPPVILKPKVLWTGKQILSLIIPKGI-NLIR 596

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            + K               DS +++ N E++ G +DK T+G+     + + + ++ G ++
Sbjct: 597 DDDKQS--------LSNPTDSGMLIENGEIIYGVVDKKTVGASQG-GLVHTIWKEKGPEI 647

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLV 640
                  + R+ +++L++ GFSIGIGD                        TM      V
Sbjct: 648 CKGFFNGIQRVVNYWLLHNGFSIGIGDTIADA------------------DTMKEVTRTV 689

Query: 641 DTA-------VKTAETGYMQRRLVKSLED 662
             A       ++ A+   ++     +L +
Sbjct: 690 KEARRQVAECIQDAQHNRLKPEPGMTLRE 718

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score =  209 bits (532), Expect = 2e-54
 Identities = 71/290 (24%), Positives = 123/290 (42%), Gaps = 56/290 (19%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N ++NI TP +T YL      ++D A+ V+ ++E TTL  V    E  + P
Sbjct: 1100 GVPRLKEILNVAKNIKTPSLTIYLMPWIAANMDLAKNVQTQIEHTTLSTVTSATEIHYDP 1159

Query: 822  DDSFILIKLDM------------------------------DRIRLLHLEVDIDSIRYCI 851
            D    +I+ D                               DR ++L  ++ +  +   I
Sbjct: 1160 DPQDTVIEEDKDFVEAFFAIPDEEVEENLYKQSPWLLRLELDRAKMLDKKLSMSDVAGKI 1219

Query: 852  ERTRGISGHLTVSGHSFLILKPKDSSKSFNSK---------------MYQMKQLLPSVVI 896
              +         S  +   L  +      + +                     +L S+ +
Sbjct: 1220 AESFERDLFTIWSEDNADKLIIRCRIIRDDDRKAEDDDNMIEEDVFLKTIEGHMLESISL 1279

Query: 897  KGVQGINRAVIHEEDV---------EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY 947
            +GV  I R  + E  +         E   ++ L  +G NL + M   GV   +  SN+  
Sbjct: 1280 RGVPNITRVYMMEHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVDATRTYSNSFV 1339

Query: 948  EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            E+ + LGIEA RS ++ E++ V+E  G  +++RH  L+ D+MTS+G ++ 
Sbjct: 1340 EILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMA 1389

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score =  202 bits (514), Expect = 2e-52
 Identities = 68/258 (26%), Positives = 113/258 (43%), Gaps = 20/258 (7%)

Query: 90  EDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFG 149
            + ++  S  +I       +   + P   GLLD R+GT  ++  C TCG+ ++DC GHFG
Sbjct: 26  PEEIRSMSVAKIEFPETMDESG-QRPRVGGLLDPRLGTIDRQFKCQTCGETMADCPGHFG 84

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209
           +I+L  PVFHIG+   +  IL+ +C N  C ++ +             N    Y   K+ 
Sbjct: 85  HIELAKPVFHIGFLSKIKKILECVCWN--CGKLKIDSSN------PKFNDTQRYRDPKNR 136

Query: 210 KKKILETTKKVSVCPHCGEINGVVKK--CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEA 267
              +    K   VC                   + H         +  I +D L  +   
Sbjct: 137 LNAVWNVCKTKMVCDTGLSAGSDNFDLSNPSANMGHGGCGA---AQPTIRKDGLRLWGSW 193

Query: 268 VKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPP 327
            +   E +  +K    + L+PLEV  +F  I  ED+  L +N + ++P  +I+T L VPP
Sbjct: 194 KRGKDESDLPEK----RLLSPLEVHTIFTHISSEDLAHLGLNEQYARPDWMIITVLPVPP 249

Query: 328 NCIRPSVISD--LKSDND 343
             +RPS+  D   + ++D
Sbjct: 250 PSVRPSISVDGTSRGEDD 267

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score =  109 bits (273), Expect = 5e-24
 Identities = 41/58 (70%), Positives = 51/58 (87%)

Query: 613 GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           GF++NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK++ED+ V+YD +
Sbjct: 804 GFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGT 861

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 68.2 bits (166), Expect = 2e-11
 Identities = 13/72 (18%), Positives = 28/72 (38%)

Query: 13  YATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
             TR   Q +      +V+P++ + ++   QD + G    + ++ F  R   M I   + 
Sbjct: 501 EETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIMLWVP 560

Query: 73  AGRKVFFRGLIE 84
               +    +I 
Sbjct: 561 DWDGILPPPVIL 572

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 57.0 bits (137), Expect = 4e-08
 Identities = 13/43 (30%), Positives = 21/43 (48%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 710
            ++  DAA  G+ D   G+SE I++G    +GTG   +      
Sbjct: 1413 EILMDAAASGEKDDCKGISENIMLGQLAPMGTGAFDIYLDQDM 1455

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score =  266 bits (680), Expect = 3e-72
 Identities = 105/512 (20%), Positives = 199/512 (38%), Gaps = 123/512 (24%)

Query: 1002 VELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFS 1061
            V+ ++ L ++     +     ++ + I+  + +T          S+  ++DI   +++  
Sbjct: 937  VKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDH--TKPSDLTIKDIVLGVKDLQ 994

Query: 1062 KKESVTSHQDKVSQ------------PLREQILSHQDKIGHGRESNPFPSACKAEACREK 1109
            +   V   ++++ Q             LR ++ + +    +      F           +
Sbjct: 995  ENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVL--SNIEAQ 1052

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------------ 1145
            ++R+ + P   VG LAAQSIGEP TQMTL TFHFAG                        
Sbjct: 1053 FLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMK 1112

Query: 1146 --------------------EVCEYIE------------EVFVPDDSFILIKLDMDRIR- 1172
                                 +   IE              + PD    +I  D + I+ 
Sbjct: 1113 TPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQL 1172

Query: 1173 -------------------LLHLEVDIDSIRYCIERTRGISGHLTVSGHSFL-------- 1205
                               LL LE+D  ++         +   +  +  + L        
Sbjct: 1173 HFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDN 1232

Query: 1206 ---------ILKPKDSSKSFNSKMYQM-----KQLLPSVVIKGVQGINRAVIHEEDVEGV 1251
                     +++PK       ++   M       +L ++ ++GV+ I R V+ + D +  
Sbjct: 1233 DEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVP 1292

Query: 1252 T---------KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 1302
            +         ++ L  +G NL +VM   G+   +  +N+  ++ + LGIEA R+ +  E+
Sbjct: 1293 SPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEV 1352

Query: 1303 KLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDA 1362
              V+ + G  +++RH  L+ D+MT++G +  +TRHG  +     L   SFE T + LF+A
Sbjct: 1353 YNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEA 1412

Query: 1363 AFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
                + D   GVSE +I+G    +GTG   ++
Sbjct: 1413 GASAELDDCRGVSENVILGQMAPIGTGAFDVM 1444

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score =  262 bits (670), Expect = 5e-71
 Identities = 90/329 (27%), Positives = 149/329 (45%), Gaps = 61/329 (18%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 438 DNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 497

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 L A    +V+P++ +  +   QD + G   LT ++ F   
Sbjct: 498 RAE--------------LSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIEL 543

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q + +   +      I                 ++   +W+GKQI S+ +       ++
Sbjct: 544 DQVLNMLYWVPDWDGVI------------PTPAIIKPKPLWSGKQILSVAIPNG----IH 587

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
                +G           +D+ +++ + +++ G ++K T+GS     + +++ R+ G  V
Sbjct: 588 LQRFDEG-----TTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNG-GLIHVVTREKGPQV 641

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLV 640
                  + ++ +F+L++ GFS GIGD                        TM      +
Sbjct: 642 CAKLFGNIQKVVNFWLLHNGFSTGIGDTIADG------------------PTMREITETI 683

Query: 641 DTA-------VKTAETGYMQRRLVKSLED 662
             A        K A+   +  +   +L +
Sbjct: 684 AEAKKKVLDVTKEAQANLLTAKHGMTLRE 712

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score =  203 bits (518), Expect = 7e-53
 Identities = 67/287 (23%), Positives = 130/287 (45%), Gaps = 53/287 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N ++N+ TP +T YL+     D + A++++  +E TTL  V    E  + P
Sbjct: 1097 GVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDP 1156

Query: 822  DDSFILIKLDMDRIR--------------------LLHLEVDIDSIRYCIERTRGISGHL 861
            D    +I  D + I+                    LL LE+D  ++         +   +
Sbjct: 1157 DPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERI 1216

Query: 862  TVSGHSFL-----------------ILKPKDSSKSFNSKMYQM-----KQLLPSVVIKGV 899
              +  + L                 +++PK       ++   M       +L ++ ++GV
Sbjct: 1217 KQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGV 1276

Query: 900  QGINRAVIHEEDVEGVT---------KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 950
            + I R V+ + D +  +         ++ L  +G NL +VM   G+   +  +N+  ++ 
Sbjct: 1277 ENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIM 1336

Query: 951  KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            + LGIEA R+ +  E+  V+ + G  +++RH  L+ D+MT++G +  
Sbjct: 1337 EVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTS 1383

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score =  198 bits (503), Expect = 5e-51
 Identities = 63/256 (24%), Positives = 106/256 (41%), Gaps = 20/256 (7%)

Query: 90  EDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFG 149
            + V+  S  +I       +   R     GL D R+G+  +   C TC + +++C GHFG
Sbjct: 24  PEEVRAISVAKIRFPETMDETQTR-AKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFG 82

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209
           +IDL  PVFH+G+   +  + + +C +  C ++LL E        +L   AL+    K  
Sbjct: 83  HIDLAKPVFHVGFIAKIKKVCECVCMH--CGKLLLDEHN------ELMRQALAIKDSKKR 134

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
              I    K   VC           +     +S     N           L+  + +   
Sbjct: 135 FAAIWTLCKTKMVCETDVPSEDDPTQ----LVSRGGCGNTQPTIRKDGLKLVGSWKKDRA 190

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
                E   +      L+  E+L +F+ I ++D   L  N   S+P  +ILT L VPP  
Sbjct: 191 TGDADEPELRV-----LSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPP 245

Query: 330 IRPSVISD--LKSDND 343
           +RPS+  +   + ++D
Sbjct: 246 VRPSISFNESQRGEDD 261

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score =  110 bits (277), Expect = 2e-24
 Identities = 44/58 (75%), Positives = 51/58 (87%)

Query: 613 GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           GFV+NS+  GLTP EFFFH MGGREGL+DTAVKTAETGY+QRRLVK+LED+ V YD +
Sbjct: 798 GFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNT 855

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 66.7 bits (162), Expect = 6e-11
 Identities = 15/72 (20%), Positives = 27/72 (37%)

Query: 13  YATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
             TR     L A    +V+P++ +  +   QD + G   LT ++ F    Q + +   + 
Sbjct: 495 EETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVP 554

Query: 73  AGRKVFFRGLIE 84
               V     I 
Sbjct: 555 DWDGVIPTPAII 566

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 56.3 bits (135), Expect = 9e-08
 Identities = 12/38 (31%), Positives = 21/38 (55%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 705
            ++ F+A    + D   GVSE +I+G    +GTG   ++
Sbjct: 1407 EILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVM 1444

>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus} Length = 436

 Score =  227 bits (581), Expect = 3e-65
 Identities = 70/247 (28%), Positives = 110/247 (44%), Gaps = 33/247 (13%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
             +++ S +++   + Y  D    PI  G++D+RMG       C TCG    +C GHFG+
Sbjct: 80  QEIRKMSAVEVTVPDTY--DDDGYPIEGGVMDKRMGVIDPGLRCETCGGRAGECPGHFGH 137

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  PV H+G+ + +  IL+S C+   C R+ L +E+   +  K+            + 
Sbjct: 138 IELARPVIHVGFAKTIYRILESTCRE--CGRIKLTDEEIEEYMKKIELARNRRSEFNEII 195

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           K+I +  K+  VCPHCG     +K      I  E  K+    +                 
Sbjct: 196 KEIHKKAKERMVCPHCGAPQYPIKFEK-PTIYWEIRKDEQGNEY---------------- 238

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
                          L P EV    E IP +D+PLL ++ E S+P  ++LT L VPP   
Sbjct: 239 ------------RHRLMPTEVRDWLEKIPDKDLPLLGLDPEKSRPEWMVLTVLPVPPVTA 286

Query: 331 RPSVISD 337
           RPS+  +
Sbjct: 287 RPSITLE 293

>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D Length = 1265

 Score = 98.5 bits (246), Expect = 9e-21
 Identities = 40/109 (36%), Positives = 63/109 (57%), Gaps = 14/109 (12%)

Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
           VL NR P+LH+L I A +  ++  ++ + +  VC  +NADFDGD+M VH+P +  A+AE 
Sbjct: 440 VLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE- 498

Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
                        A++ M +  NL++P +GE L   ++D I G Y +TQ
Sbjct: 499 -------------ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQ 534

>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D Length = 1265

 Score = 58.8 bits (143), Expect = 1e-08
 Identities = 20/40 (50%), Positives = 29/40 (72%)

Query: 618 SFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLV 657
           SF  GLT  E+F  + G R+G  DTA++TA++GY+ R+LV
Sbjct: 801 SFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLV 840

>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D Length = 1265

 Score = 58.1 bits (141), Expect = 2e-08
 Identities = 17/24 (70%), Positives = 22/24 (91%)

Query: 1119 TAVGALAAQSIGEPGTQMTLKTFH 1142
             AVG +AA+SIGEPGTQ+T++TFH
Sbjct: 960  EAVGVVAAESIGEPGTQLTMRTFH 983

>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D Length = 1265

 Score = 43.0 bits (102), Expect = 8e-04
 Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 2/65 (3%)

Query: 1326 TSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMN 1385
              K  ++G+T+  L+   +S L+ ASF+NT+  L +AA  G+ D + G+ E +I+G  + 
Sbjct: 1157 AWKPLLMGVTKSALST--KSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIP 1214

Query: 1386 VGTGL 1390
             GTG 
Sbjct: 1215 AGTGS 1219

>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Length = 1524

 Score = 98.3 bits (245), Expect = 1e-20
 Identities = 40/109 (36%), Positives = 63/109 (57%), Gaps = 14/109 (12%)

Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
           VL NR P+LH+L I A +  ++  ++ + +  VC  +NADFDGD+M VH+P +  A+AE 
Sbjct: 700 VLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE- 758

Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
                        A++ M +  NL++P +GE L   ++D I G Y +TQ
Sbjct: 759 -------------ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQ 794

>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Length = 1524

 Score = 58.6 bits (142), Expect = 1e-08
 Identities = 19/31 (61%), Positives = 24/31 (77%)

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +    AVG +AAQSIGEPGTQ+T++TFH  G
Sbjct: 1215 VSIGEAVGIVAAQSIGEPGTQLTMRTFHTGG 1245

>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Length = 1524

 Score = 58.6 bits (142), Expect = 2e-08
 Identities = 20/40 (50%), Positives = 29/40 (72%)

Query: 618  SFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLV 657
            SF  GLT  E+F  + G R+G  DTA++TA++GY+ R+LV
Sbjct: 1060 SFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLV 1099

>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Length = 1524

 Score = 44.4 bits (105), Expect = 3e-04
 Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 2/65 (3%)

Query: 1326 TSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMN 1385
              K  ++G+T+  L+   +S L+ ASF+NT+  L +AA  G+ D + G+ E +I+G  + 
Sbjct: 1416 AWKPLLMGVTKSALST--KSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIP 1473

Query: 1386 VGTGL 1390
             GTG 
Sbjct: 1474 AGTGS 1478

>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* Length = 1407

 Score = 91.2 bits (227), Expect = 2e-18
 Identities = 42/109 (38%), Positives = 63/109 (57%), Gaps = 14/109 (12%)

Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
           VL NR P+LH+L I A    ++  +  + +  VC  YNADFDGD+M VH+P T EA+ E 
Sbjct: 421 VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLE- 479

Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
                        A+ LM + +N+++P NGE +I  +QD + G Y +T+
Sbjct: 480 -------------ARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTR 515

>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* Length = 1407

 Score = 60.0 bits (146), Expect = 6e-09
 Identities = 24/48 (50%), Positives = 32/48 (66%)

Query: 618 SFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           +F  GL   ++F  T G R+GL DTA+KTA +GY+ RRLV   +DL V
Sbjct: 762 NFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVV 809

>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* Length = 1407

 Score = 58.1 bits (141), Expect = 2e-08
 Identities = 20/39 (51%), Positives = 25/39 (64%)

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEE 1153
            I    A+G +AAQSIGEPGTQ+T++TFH  G       E
Sbjct: 909  INKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAE 947

>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 = 68.3 bits (166), Expect = 2e-11
 Identities = 103/689 (14%), Positives = 191/689 (27%), Gaps = 214/689 (31%)

Query: 768  IKEIINASRNI-STPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFI 826
             K++ +  ++I S   I   +     +     +   L       V +++EEV   +  F+
Sbjct: 35   CKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFL 94

Query: 827  LIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ 886
                 M  I+    +  + +  Y  +R R     L      F     K +          
Sbjct: 95   -----MSPIKTEQRQPSMMTRMYIEQRDR-----LYNDNQVF----AKYN---------- 130

Query: 887  MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV--MATYGVKGVKCSSN 944
                           ++R     +    + +  LL     LR    +   GV G      
Sbjct: 131  ---------------VSR----LQPYLKLRQ-ALL----ELRPAKNVLIDGVLG--SG-- 162

Query: 945  NTYEVYKT-LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVE 1003
                  KT + ++   S    +++  M+     ++ ++         S   VL       
Sbjct: 163  ------KTWVALDVCLS---YKVQCKMDFKIFWLNLKN-------CNSPETVLEM----- 201

Query: 1004 LKRLLDDIIAKNSSRSDPS----LSAQEILALSNETLDSKEF------LQDTSENFVRD- 1052
            L++LL  I    +SRSD S    L    I A     L SK +      L +     V++ 
Sbjct: 202  LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLN-----VQNA 256

Query: 1053 --IKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKY 1110
                 F    S K  +T+   +V+  L     +H   I     S       + ++   KY
Sbjct: 257  KAWNAF--NLSCKILLTTRFKQVTDFLSAATTTH---ISLDHHSMTLTPD-EVKSLLLKY 310

Query: 1111 V--RAQIEP--ATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKL 1166
            +  R Q  P             I E                                I+ 
Sbjct: 311  LDCRPQDLPREVLTTNPRRLSIIAE-------------------------------SIRD 339

Query: 1167 DMDRI-RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQ 1225
             +       H  V+ D +   IE              S  +L+P +       KM+    
Sbjct: 340  GLATWDNWKH--VNCDKLTTIIES-------------SLNVLEPAE-----YRKMFDRLS 379

Query: 1226 LLPSVVIKGVQGINRAVI-------HEEDVEGVTKY---KLLVEGDNLRDVMATYGVKGV 1275
            + P         I   ++        + DV  V        LVE         T  +  +
Sbjct: 380  VFP----PSAH-IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKES---TISIPSI 431

Query: 1276 ----KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSID------FRHPMLVADLM 1325
                K    N Y +++++ ++         I    ++  +         + H        
Sbjct: 432  YLELKVKLENEYALHRSI-VDHYN------IPKTFDSDDLIPPYLDQYFYSH-------- 476

Query: 1326 TSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMN 1385
                    I  H L  ++     +  F        D  F  Q       +      + +N
Sbjct: 477  --------IGHH-LKNIEHP-ERMTLFRMV---FLDFRFLEQKIRHDSTAWNASGSI-LN 522

Query: 1386 VGTGLIKLLQAVPRSEPVPRTLLFDNPEF 1414
                L      +  ++P    L+    +F
Sbjct: 523  TLQQLKFYKPYICDNDPKYERLVNAILDF 551

>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 = 66.8 bits (162), Expect = 4e-11
 Identities = 89/576 (15%), Positives = 172/576 (29%), Gaps = 164/576 (28%)

Query: 1   MKNSVIGTLTLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 60
            K++V GTL L+      W  L++ +  +V     E+L     ++    +L++       
Sbjct: 57  SKDAVSGTLRLF------W-TLLSKQEEMVQKFVEEVL---RINY---KFLMSPIKTEQR 103

Query: 61  RAQTMRIASTLIAGRKVFFRG---LIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIP 117
             Q   +    I  R   +       +  V++     +      + + L    P +  + 
Sbjct: 104 --QPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLK------LRQALLELRPAKNVLI 155

Query: 118 HGLLDRRMGTNQKEANCTTC--GQNLSDCVGHFGYID-LPLPVF--HIGYFRC---VINI 169
            G     +  + K     T             +     +   +F  ++        V+ +
Sbjct: 156 DG-----VLGSGK-----TWVALDVCLS----YKVQCKMDFKIFWLNLKNCNSPETVLEM 201

Query: 170 LQSICKN---PTCARV-------LLGEEKAAGFRAKLRNPAL--SYLV------RKSLKK 211
           LQ +         +R        L      A  R  L++       LV       K+   
Sbjct: 202 LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNA 261

Query: 212 -----KILETTKKVSVCPHCGEINGV-VKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY- 264
                KIL TT+   V       + +       + + H      T  +   V+ LL +Y 
Sbjct: 262 FNLSCKILLTTRFKQV------TDFLSAATTTHISLDHHS-MTLTPDE---VKSLLLKYL 311

Query: 265 --------NEAVKFNP---------------------EIEAHKKFGLIQT----LNPLEV 291
                    E +  NP                      +   K   +I++    L P E 
Sbjct: 312 DCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEY 371

Query: 292 LQLFE--AIPLED--IPL----LLMNAELSKPSDLILTRL----LV----PPNCIR-PSV 334
            ++F+  ++      IP     L+    +     +++ +L    LV      + I  PS+
Sbjct: 372 RKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI 431

Query: 335 ISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTP---YNADFDGDEMN 391
             +LK   +      + +LH+ SI+ H       +TF  ++ +      Y     G    
Sbjct: 432 YLELKVKLE-----NEYALHR-SIVDHYN---IPKTFDSDDLIPPYLDQYFYSHIGH--- 479

Query: 392 VHLPQTEEA-RAEALPSLH-KLSIMAHRAKVLMANKSNLVTPRNGELLIAAT-QDFIT-G 447
            HL   E   R      +      +    K+   +     T  N    I  T Q      
Sbjct: 480 -HLKNIEHPERMTLFRMVFLDFRFL--EQKIRHDS-----TAWNASGSILNTLQQLKFYK 531

Query: 448 GYLLTQKNAFFNRAQT-----MRIASTLI-ADTSDI 477
            Y+      +            +I   LI +  +D+
Sbjct: 532 PYICDNDPKYERLVNAILDFLPKIEENLICSKYTDL 567

>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 = 66.4 bits (161), Expect = 5e-11
 Identities = 110/696 (15%), Positives = 200/696 (28%), Gaps = 218/696 (31%)

Query: 786  YLDKDT---DLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEV 842
            ++D +T      Y  I+                E+ FV +     +  DM +  L   E+
Sbjct: 6    HMDFETGEHQYQYKDIL-------------SVFEDAFVDNFDCKDV-QDMPKSILSKEEI 51

Query: 843  D-IDSIRYCIERTRGISGHLTVSG---------------HSFLI--LKPKDSSKSFNSKM 884
            D I   +  +  T  +   L                   + FL+  +K +    S  ++M
Sbjct: 52   DHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRM 111

Query: 885  Y--QMKQLL--PSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV--MATYGVKG 938
            Y  Q  +L     V  K    ++R     +    + +  LL     LR    +   GV G
Sbjct: 112  YIEQRDRLYNDNQVFAKY--NVSR----LQPYLKLRQ-ALL----ELRPAKNVLIDGVLG 160

Query: 939  VKCSSNNTYEVYKT-LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
                        KT + ++   S    +++  M+     ++ ++         S   VL 
Sbjct: 161  --SG--------KTWVALDVCLSY---KVQCKMDFKIFWLNLKN-------CNSPETVLE 200

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPS----LSAQEILALSNETLDSKEF------LQDTSE 1047
                  L++LL  I    +SRSD S    L    I A     L SK +      L +   
Sbjct: 201  M-----LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLN--- 252

Query: 1048 NFVRD---IKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAE 1104
              V++      F    S K  +T+   +V+  L     +H   I     S       + +
Sbjct: 253  --VQNAKAWNAF--NLSCKILLTTRFKQVTDFLSAATTTH---ISLDHHSMTLTPD-EVK 304

Query: 1105 ACREKYV--RAQIEP--ATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDS 1160
            +   KY+  R Q  P             I E                             
Sbjct: 305  SLLLKYLDCRPQDLPREVLTTNPRRLSIIAE----------------------------- 335

Query: 1161 FILIKLDMDRI-RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 1219
               I+  +       H  V+ D +   IE              S  +L+P +       K
Sbjct: 336  --SIRDGLATWDNWKH--VNCDKLTTIIES-------------SLNVLEPAE-----YRK 373

Query: 1220 MYQMKQLLPSVVIKGVQGINRAVI-------HEEDVEGVTKY---KLLVEGDNLRDVMAT 1269
            M+    + P         I   ++        + DV  V        LVE         T
Sbjct: 374  MFDRLSVFP----PSAH-IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKES---T 425

Query: 1270 YGVKGV----KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF---------- 1315
              +  +    K    N Y +++++ ++         I    ++  +   +          
Sbjct: 426  ISIPSIYLELKVKLENEYALHRSI-VDHYN------IPKTFDSDDLIPPYLDQYFYSHIG 478

Query: 1316 RHPMLVADLMTSKGEVLGITRHGL-------AKMKESVLNLASFENTSDHLFDAAFYGQ- 1367
             H +   +      E + + R           K++       +  +  + L    FY   
Sbjct: 479  HH-LKNIEH----PERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPY 533

Query: 1368 -TDCISGVSECI--IMGLPMNVGTGLIK-----LLQ 1395
              D        +  I+     +   LI      LL+
Sbjct: 534  ICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLR 569

>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 = 60.6 bits (146), Expect = 3e-09
 Identities = 76/532 (14%), Positives = 148/532 (27%), Gaps = 168/532 (31%)

Query: 623  LTPTEF-FFHTMGGREGLVDTAVKTAETGYMQRRLVKS-LEDLCVQYDMSFDAAFYGQTD 680
            L P +      + G  G      KT         +         VQ  M F   F+    
Sbjct: 147  LRPAKNVLIDGVLG-SG------KTW--------VALDVCLSYKVQCKMDF-KIFW---- 186

Query: 681  CISGVSECIIMGLPMNVGTGLIKLLQAVPR---SEPVPRTLLFDNPEFHFPQVYYERRRD 737
             ++ +  C       N    ++++LQ +          R+    N +     +  E RR 
Sbjct: 187  -LN-LKNC-------NSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRR- 236

Query: 738  YSVKVTASVKVTLELWNPGDYK---LSQDGVPRIKEIINASRNIS--TPIITAYLDKDTD 792
                          L     Y+   L    V +  +  NA  N+S    + T +      
Sbjct: 237  --------------LLKSKPYENCLLVLLNV-QNAKAWNAF-NLSCKILLTTRFKQVTDF 280

Query: 793  LDYARIVKGRLERTTLGEVCEYIEEVFV------PDD-------------SFI--LIKLD 831
            L  A      L+  ++    + ++ + +      P D             S I   I+  
Sbjct: 281  LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDG 340

Query: 832  MDRI-RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQL 890
            +       H  V+ D +   IE              S  +L+P +       KM+    +
Sbjct: 341  LATWDNWKH--VNCDKLTTIIES-------------SLNVLEPAE-----YRKMFDRLSV 380

Query: 891  LPSVVIKGVQGINRAVI-------HEEDVEGVTKY---KLLVEGDNLRDVMATYGVKGV- 939
             P         I   ++        + DV  V        LVE         T  +  + 
Sbjct: 381  FP----PSAH-IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKES---TISIPSIY 432

Query: 940  ---KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF----------RHPMLVA 986
               K    N Y +++++ ++         I    ++  +   +           H  L  
Sbjct: 433  LELKVKLENEYALHRSI-VDHYN------IPKTFDSDDLIPPYLDQYFYSHIGHH--LKN 483

Query: 987  DLMTSKGEVLGNGTPVELKRLLDD-------IIAKNSSRSDPSLSAQEILALSNETLDSK 1039
                 +            + +  D       I   +++ +        +  L       K
Sbjct: 484  IEHPERMT--------LFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKF----YK 531

Query: 1040 EFLQD---TSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQI-LSHQDK 1087
             ++ D     E  V  I  FL +  +    + + D +      +I L  +D+
Sbjct: 532  PYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLL------RIALMAEDE 577

>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 = 50.2 bits (119), Expect = 5e-06
 Identities = 63/432 (14%), Positives = 137/432 (31%), Gaps = 120/432 (27%)

Query: 1039 KEFLQDTSENFVRDIK-KFLEE-----FSKKE--SVTSHQDKVSQPLR--EQILSHQDKI 1088
            K+ L    + FV +   K +++      SK+E   +   +D VS  LR    +LS Q+++
Sbjct: 19   KDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEM 78

Query: 1089 GHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVC 1148
                               +K+V   +        L +  I     Q ++ T  +     
Sbjct: 79   ------------------VQKFVEEVLRI--NYKFLMSP-IKTEQRQPSMMTRMYI---- 113

Query: 1149 EYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTR--------GISGHLTVS 1200
            E  + ++  +D+ +  K ++ R++          +R  +   R        G+ G    S
Sbjct: 114  EQRDRLY--NDNQVFAKYNVSRLQPYL------KLRQALLELRPAKNVLIDGVLG----S 161

Query: 1201 GHSFL---ILKPKDSSKSFNSKMY---------------QMKQLLPSVVIKGVQGINRAV 1242
            G +++   +          + K++                +++LL  +        + + 
Sbjct: 162  GKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSS 221

Query: 1243 ---IHEEDVEGV-------TKYK--LLVEGDNLRDVMATYGVK--GVKCSSNNTYEVYKT 1288
               +    ++           Y+  LLV    L +V          + C         K 
Sbjct: 222  NIKLRIHSIQAELRRLLKSKPYENCLLV----LLNVQNAKAWNAFNLSC---------KI 268

Query: 1289 L-------GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAK 1341
            L         +   +   T I L   +  ++ D        ++ +   + L      L +
Sbjct: 269  LLTTRFKQVTDFLSAATTTHISLDHHSMTLTPD--------EVKSLLLKYLDCRPQDLPR 320

Query: 1342 --MKESVLNLASF-ENTSDHLFDAAFYGQTDC--ISGVSECIIMGLPMNVGTGLIKLLQA 1396
              +  +   L+   E+  D L     +   +C  ++ + E  +  L       +   L  
Sbjct: 321  EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV 380

Query: 1397 VPRSEPVPRTLL 1408
             P S  +P  LL
Sbjct: 381  FPPSAHIPTILL 392

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	1423
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	100.0
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	100.0
1hqm_D	1265	DNA-directed RNA polymerase; transferase, transcri	100.0
3lu0_D	1407	DNA-directed RNA polymerase subunit beta'; E. coli	100.0
2a6h_D	1524	DNA-directed RNA polymerase beta' chain; RNA polym	100.0
4ayb_A	880	DNA-directed RNA polymerase; transferase, multi-su	100.0
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	100.0
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	100.0
4ayb_C	395	DNA-directed RNA polymerase; transferase, multi-su	100.0
1hqm_D	1265	DNA-directed RNA polymerase; transferase, transcri	100.0
3qqc_A	436	DNA-directed RNA polymerase subunit B, DNA-direct	100.0
2a6h_D	1524	DNA-directed RNA polymerase beta' chain; RNA polym	100.0
3lu0_D	1407	DNA-directed RNA polymerase subunit beta'; E. coli	100.0
4ayb_C	395	DNA-directed RNA polymerase; transferase, multi-su	100.0
4ayb_A	880	DNA-directed RNA polymerase; transferase, multi-su	99.97
3qqc_A	436	DNA-directed RNA polymerase subunit B, DNA-direct	95.63

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=100.00  E-value=6.3e-194  Score=1921.49  Aligned_cols=996  Identities=32%  Similarity=0.544  Sum_probs=772.1

Q ss_pred             ccceeeeEEEecCCHHHHhhcceeeeecCcccccCCC-CCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEcc
Q psy13846         76 KVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQ-RTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLP  154 (1423)
Q Consensus        76 ~~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~-g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~  154 (1423)
                      ..+|.+ |+|+++|||||+++||++|+++++|  |.. |+|+.|||||||||+.++...|+|||++..+||||||||||+
T Consensus        13 ~~~i~~-i~Fg~~S~eeI~~~Sv~~I~~~~~~--d~~~~~P~~~Gl~D~rlG~~~~~~~C~TCg~~~~~CpGHFGHIELa   89 (1752)
T 3h0g_A           13 LRRVEE-VQFGILSPEEIRSMSVAKIEFPETM--DESGQRPRVGGLLDPRLGTIDRQFKCQTCGETMADCPGHFGHIELA   89 (1752)
T ss_dssp             CCCCCC-BEECCCCHHHHHHHCCCCCCCTTCT--TCSSSSSCCSSSSSSSCCCSSSSCCCTTSCCSSSSCCCCCEECCCC
T ss_pred             ceeeee-EEEecCCHHHHHHhCeeEEeccccc--ccccCCCCCCCCcCccccCCCCCCCCCCCCCCCCcCCCcceeeecc
Confidence            367889 9999999999999999999999999  666 799999999999999999999999999999999999999999


Q ss_pred             CceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccC-----------
Q psy13846        155 LPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVC-----------  223 (1423)
Q Consensus       155 ~PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C-----------  223 (1423)
                      +||||||||+++++||+|+|++  |++|++++++. .|.++++...     .+.+++++++.|++++.|           
T Consensus        90 ~PVfHpgF~~~I~kILr~vC~~--C~klll~~~~~-~f~~~lrlrd-----~k~r~~~V~~~ck~k~~Ce~~~~~~~~~~  161 (1752)
T 3h0g_A           90 KPVFHIGFLSKIKKILECVCWN--CGKLKIDSSNP-KFNDTQRYRD-----PKNRLNAVWNVCKTKMVCDTGLSAGSDNF  161 (1752)
T ss_dssp             SCBCCHHHHHHHHHHSSSSCTT--TCCCSCCSCSH-HHHHHHHSSC-----TTTTHHHHHHHHHHCCCCCSSTTCCSSCC
T ss_pred             cceEeehhhHHHHHHHHHHHHH--hcccccccccH-HHHHHHHccC-----HHHHHHHHHHHhccccccCCCCcccccch
Confidence            9999999999999999999999  99999998765 4777655322     124567888888765556           


Q ss_pred             -----------CCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHH
Q psy13846        224 -----------PHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL  292 (1423)
Q Consensus       224 -----------~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~  292 (1423)
                                 ++||+.||.|||+++ +++++ ++..+.  ++                .+       ...+.|+|.+|+
T Consensus       162 ~~~~~~~~~~~~gCG~~qP~IRKegl-kl~~~-~k~~k~--~~----------------~~-------~~k~~LtP~eVl  214 (1752)
T 3h0g_A          162 DLSNPSANMGHGGCGAAQPTIRKDGL-RLWGS-WKRGKD--ES----------------DL-------PEKRLLSPLEVH  214 (1752)
T ss_dssp             CSSCCCCCCSSCSSCCCCCCCEEETT-EEECC-BCCSSS--SC----------------BC-------SSCCCCCHHHHH
T ss_pred             hcccccccccCCCcCCcCCcEEeecc-EEEEE-Eccccc--cc----------------cc-------ccceecCHHHHH
Confidence                       479999999999984 77664 211110  00                00       124689999999


Q ss_pred             HHhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCC-C-------------------------------
Q psy13846        293 QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLK-S-------------------------------  340 (1423)
Q Consensus       293 eiLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~-~-------------------------------  340 (1423)
                      ++|++||++|+.+|++++..+||+||||++|||||+|+||++.+|+. .                               
T Consensus       215 ~ifk~IsdeD~~lLGl~~~~~rPewmiL~vLPVpPp~vRPsv~ldg~~~~edDLt~~l~~II~~N~~Lk~~~~~gap~~~  294 (1752)
T 3h0g_A          215 TIFTHISSEDLAHLGLNEQYARPDWMIITVLPVPPPSVRPSISVDGTSRGEDDLTHKLSDIIKANANVRRCEQEGAPAHI  294 (1752)
T ss_dssp             HHHHHSCHHHHHHSSCCSSSCCGGGSSBSSCEECCGGGSCCCCCSSSCCCCCTTTTHHHHHHHHHHHHHGGGGCCSSSTT
T ss_pred             HHHHhcCHHHHHHhCCCccCCChhheEeeccccCCCCccCceEcCCCccCCChHHHHHHHHHHHHHHHHHHHHhcchhHH
Confidence            99999999999999999999999999999999999999999998764 1                               


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        341 --------------------------------------------------------------------------------  340 (1423)
Q Consensus       341 --------------------------------------------------------------------------------  340 (1423)
                                                                                                      
T Consensus       295 ~~~~~~~LQ~~v~~~~dn~~~~~~~~~~~~~rp~k~~~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~l~~~evGvP~  374 (1752)
T 3h0g_A          295 VSEYEQLLQFHVATYMDNEIAGQPQALQKSGRPLKSIRARLKGKEGRLRGNLMGKRVDFSARTVITGDPNLSLDELGVPR  374 (1752)
T ss_dssp             HHHHHHHHHHHHHHTTCTTCSSCCCCCSSSSCCCCCHHHHHTCSSSSSTTTTSSCCCSSEEEEEEEEETTSCTTBCBCCH
T ss_pred             HHHHHHHHHHHHHHhhcCCCCCCccccccCCCCCcchHhhhhcccccccccccccccCCccceeecCCCCcccceeeChH
Confidence                                                                                            


Q ss_pred             ---------------------------------------------------------------------CCeEEEEecCc
Q psy13846        341 ---------------------------------------------------------------------DNDVVLFNRQP  351 (1423)
Q Consensus       341 ---------------------------------------------------------------------~~d~Vl~nRqP  351 (1423)
                                                                                           +||+|||||||
T Consensus       375 ~~A~~Lt~Pe~vt~~ni~~l~~lv~nG~~~~pga~~v~~~~~~~~~l~~~~~~~~~~l~~g~~v~r~l~~gd~Vl~NRqP  454 (1752)
T 3h0g_A          375 SIAKTLTYPETVTPYNIYQLQELVRNGPDEHPGAKYIIRDTGERIDLRYHKRAGDIPLRYGWRVERHIRDGDVVIFNRQP  454 (1752)
T ss_dssp             HHHTSCCCCCBCCTTTHHHHHHHHHHCTTSSSCEEEEECTTCCBCCTTTTCSCCCCCCCSSCEEEECCCSCCEEEEECSS
T ss_pred             HHHHhcCCCccccHHHHHHHHHHHHcCCccccCceeeecCCCcEeechhhchhhhhhcCcCcEEEeeeccCCeEEEecCc
Confidence                                                                                 68999999999


Q ss_pred             cccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccC
Q psy13846        352 SLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTP  431 (1423)
Q Consensus       352 sLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~  431 (1423)
                      ||||+|||||++|++|+|||||||++|+||||||||||||+|+||+++|||||+              +||.+.+|++||
T Consensus       455 tLHr~sima~~~~v~~gktirlh~~vC~~yNADFDGDeMnvHvPqs~eAraEa~--------------~Lm~~~~nilsP  520 (1752)
T 3h0g_A          455 SLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSEETRAEIQ--------------EITMVPKQIVSP  520 (1752)
T ss_dssp             CCSGGGEEEEECCCCSSSSEEEEGGGSGGGTCCSSSCEEEEECCCSTTHHHHHH--------------HTCCTTTTSEET
T ss_pred             ccchhhcccccceeecCceeeechhhCCCccCccccceeeeeccCCHHHHHHHH--------------HHhcCccceecC
Confidence            999999999999999999999999999999999999999999999999999999              999999999999


Q ss_pred             CCCccccccccceEEEEEeecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecc
Q psy13846        432 RNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLIL  511 (1423)
Q Consensus       432 ~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il  511 (1423)
                      ++|+|+++++||+|+|+|.||.+|.|++++|++++++++.    .+.+        .+|+|||+||.++|||||||+++|
T Consensus       521 ~~G~Pi~~~~QD~vlg~y~lT~~~~f~~~~e~~~l~~~~~----~~~~--------~~~~pai~kp~~~wtGkqifs~il  588 (1752)
T 3h0g_A          521 QSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIMLWVP----DWDG--------ILPPPVILKPKVLWTGKQILSLII  588 (1752)
T ss_dssp             TTTEESCCCCTHHHHHHHHHHSTTCEEETHHHHGGGGCSS----SCCS--------SCCCCSBCSSSCEEETTHHHHTTS
T ss_pred             CCCCceeeecchhhhheeeeccccccCCHHHHHHHHHhhc----ccCC--------ccCccceecCcCCCchhhHHhhhC
Confidence            9999999999999999999999999999999999998763    2332        689999999999999999999999


Q ss_pred             cCCCCcccccceeecccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhh
Q psy13846        512 KPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRM  591 (1423)
Q Consensus       512 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l  591 (1423)
                      |++      +++..+.+   ....++++|+.|+|+|||+++|.+||+.+|+ +.+++||.+|++||++.|+.||++++++
T Consensus       589 p~~------~~~~~~~~---~~~~~~~~d~~v~i~~gell~g~l~K~~lg~-~~~~li~~i~~~~G~~~~~~~ld~~~~l  658 (1752)
T 3h0g_A          589 PKG------INLIRDDD---KQSLSNPTDSGMLIENGEIIYGVVDKKTVGA-SQGGLVHTIWKEKGPEICKGFFNGIQRV  658 (1752)
T ss_dssp             CSS------BCEECCCS---SCCSSCTTTCSEEECBSCEEEECCSHHHHSS-CTTCHHHHSSSSSCTTTHHHHHHHHHHH
T ss_pred             cCC------CCceeccc---cccCcCCCcCeEEEEcCeEEecccchHHhcc-CcccHHHHHHHHHCHHHHHHHHHHHHHH
Confidence            865      33433222   1224678899999999999999999999998 5699999999999999999999999999


Q ss_pred             hhHHHhhcCcceecCCCCCCc-----------------------------------------------------------
Q psy13846        592 TSFYLMNRGFSIGIGDVTPGQ-----------------------------------------------------------  612 (1423)
Q Consensus       592 ~~~~L~~~GfsiGi~D~~~~~-----------------------------------------------------------  612 (1423)
                      +++||+.+|||||++|+++++                                                           
T Consensus       659 ~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~a~~~v~~~~~~~~~g~l~~~~g~~~~e~~e~~v~~~l~~~~~~~~~~  738 (1752)
T 3h0g_A          659 VNYWLLHNGFSIGIGDTIADADTMKEVTRTVKEARRQVAECIQDAQHNRLKPEPGMTLRESFEAKVSRILNQARDNAGRS  738 (1752)
T ss_dssp             HHHHHHHHCCCCCGGGGSCCSHHHHHHHHHHHTTTHHHHHHHTTTTTTCCCCCSSCCTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCceechhhcccCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999997655                                                           


Q ss_pred             -----------------------------------------------------------------cccccccccCCCcee
Q psy13846        613 -----------------------------------------------------------------GFVQNSFFSGLTPTE  627 (1423)
Q Consensus       613 -----------------------------------------------------------------GfI~~sf~~GL~p~E  627 (1423)
                                                                                       |||.+||++||+|+|
T Consensus       739 ~~~~l~~~N~~~~M~~SGakGs~~ni~Q~~~~~Gqq~~~GkrIp~g~~~rtLP~f~k~d~~~~a~GfV~~sF~~GL~p~E  818 (1752)
T 3h0g_A          739 AEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGFKYRTLPHFPKDDDSPESRGFIENSYLRGLTPQE  818 (1752)
T ss_dssp             HHTTSCSSCTTTHHHHHCSSCCHHHHHHHHTCCCCCCSTTSSSCCCSTTSSSTTSCSSCCSTTTSSCCSSCTTTCCCHHH
T ss_pred             HHHhcCCCCcHHHHhhhccccCHHHHHHHHhccCCCccCCccCCCCCCCccCCCCCCCCCCcccCcchhhcccCCCCHHH
Confidence                                                                             899999999999999


Q ss_pred             eeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeecc-------ccCCCccCCCcchheecCCCcccchh
Q psy13846        628 FFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA-------FYGQTDCISGVSECIIMGLPMNVGTG  700 (1423)
Q Consensus       628 fffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s-------~yG~~~~~~~~~~~~~~~~~~~~g~~  700 (1423)
                      ||||||||||||+|||||||+||||||||||+||||+|+||+||||+       .||+|+.+.-..|.            
T Consensus       819 fFfhtmggReGLiDTAvKTA~SGYLqRRLVk~leDv~V~YDgTVRns~g~ivQF~YGeDGlD~~~~e~------------  886 (1752)
T 3h0g_A          819 FFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNAMGDIIQFAYGEDGLDATLVEY------------  886 (1752)
T ss_dssp             HHHHHHHHTTTTTHHHHTTTHHHHHHHHHHHHHTTCEEETTTEEECTTSCEEESSSSSSCBCGGGEEE------------
T ss_pred             HHHHhhhhhhhhhHhhhhcCcCchhHHHHHHHHhheEEeeCCeeEcCCCcEEEEecCCCCcChHHhhc------------
Confidence            99999999999999999999999999999999999999999999998       48887554332221            


Q ss_pred             HHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCC
Q psy13846        701 LIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNIST  780 (1423)
Q Consensus       701 vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikT  780 (1423)
                                  +...++.+++..|.         +.|.+...          ++       .++.  .|++   +.+..
T Consensus       887 ------------q~~~~~~~s~~~f~---------~~~~~~~~----------~~-------~~~~--~~~~---~~l~~  923 (1752)
T 3h0g_A          887 ------------QVFDSLRLSTKQFE---------KKYRIDLM----------ED-------RSLS--LYME---NSIEN  923 (1752)
T ss_dssp             ------------EECTTTSCCHHHHT---------TTSCCCTT----------TT-------CCGG--GTSC---SCCTT
T ss_pred             ------------cccccccCCHHHHH---------HHhccccc----------cc-------cccc--HHHH---HHhcc
Confidence                        11122222221121         00000000          00       0000  0000   00000


Q ss_pred             ceeeeecccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCc
Q psy13846        781 PIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH  860 (1423)
Q Consensus       781 Piitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~  860 (1423)
                         ...+....+.|+.+..+.|-.   |.      .+++...+..+.+++|++|+.            +...+.      
T Consensus       924 ---~~~~~~~l~~E~~~l~~dr~~---lr------~~i~~~~~~~~~lP~N~~R~i------------~~~~~~------  973 (1752)
T 3h0g_A          924 ---DSSVQDLLDEEYTQLVADREL---LC------KFIFPKGDARWPLPVNVQRII------------QNALQI------  973 (1752)
T ss_dssp             ---SCSSTHHHHHHHHHHHHHHTT---SS------SSSSSCSCCEEEEESCHHHHT------------TTTTTT------
T ss_pred             ---CHHHHHHHHHHHHHHHHHHHH---HH------HHhhccccccccCCccHHHHH------------HHHHHh------
Confidence               001112224455544433310   11      112333444555666666541            000000      


Q ss_pred             ccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccccceeeccccee
Q psy13846        861 LTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK  940 (1423)
Q Consensus       861 i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gvD~~~  940 (1423)
                                         |                                                      .+|...
T Consensus       974 -------------------f------------------------------------------------------~~~~~~  980 (1752)
T 3h0g_A          974 -------------------F------------------------------------------------------HLEAKK  980 (1752)
T ss_dssp             -------------------S------------------------------------------------------CCCTTS
T ss_pred             -------------------c------------------------------------------------------CCCcCc
Confidence                               0                                                      000000


Q ss_pred             eccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCCcchhhHHHHHHHHHhccCCCC
Q psy13846        941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSD 1020 (1423)
Q Consensus       941 t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~~~~~~~~~~~~~~~~~~~~~~ 1020 (1423)
                       .| +...           ..++..+++.++               ++...+    |.                     +
T Consensus       981 -~s-~l~p-----------~~~~~~v~~~~~---------------~l~~~~----g~---------------------d 1007 (1752)
T 3h0g_A          981 -PT-DLLP-----------SDIINGLNELIA---------------KLTIFR----GS---------------------D 1007 (1752)
T ss_dssp             -CC-CCCH-----------HHHHHHHHHHHT---------------TCCCSC----CC---------------------S
T ss_pred             -cC-CCCH-----------HHHHHHHHHHHH---------------hhhccc----CC---------------------c
Confidence             00 0000           011222222221               000001    10                     0


Q ss_pred             CCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHHHHHHHHhhhccccccccccCCchhhhhhhccccccCcccCCCCCChh
Q psy13846       1021 PSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSA 1100 (1423)
Q Consensus      1021 ~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1100 (1423)
                       .++.+ .  .           ..+...|...++.+                    ++.+.+...++++++++    +  
T Consensus      1008 -~l~~~-~--~-----------~na~~l~~~~lr~~--------------------l~~k~~~~~~~l~~~~~----~-- 1046 (1752)
T 3h0g_A         1008 -RITRD-V--Q-----------NNATLLFQILLRSK--------------------FAVKRVIMEYRLNKVAF----E-- 1046 (1752)
T ss_dssp             -TTTTH-H--H-----------HTSSHHHHHHHTTS--------------------SSHHHHHHSSCCCHHHH----H--
T ss_pred             -chhhh-h--h-----------hchHHHHHHHHHhh--------------------hhhhhhhhhcCcCHHHH----H--
Confidence             11100 0  0           01112233322222                    12344556678999887    7  


Q ss_pred             HHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc-----------------------------------
Q psy13846       1101 CKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------------------- 1145 (1423)
Q Consensus      1101 ~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG----------------------------------- 1145 (1423)
                      ||+++|+.+|.+|+|+||||||+|||||||||+||||||||||||                                   
T Consensus      1047 ~~~~~~~~~y~~a~v~pGe~VG~iaAQSIgEp~TQMTLnTFHfAGvas~NVTlGVPRLkEIInask~ikTP~mtv~L~~~ 1126 (1752)
T 3h0g_A         1047 WIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNVAKNIKTPSLTIYLMPW 1126 (1752)
T ss_dssp             HHHHHHHHHHHTTBCCSSCCHHHHHHHHHHHHHHHHHHHTTSSCCCCCSSCCCSGGGHHHHHTTCSCCSCCCCEECCCSS
T ss_pred             HHHHHHHHHHHHhccCcccchhhhhhcccCCchhhhhHHhhhhccccccccccCcccHHHHHhhhcCCCCCeEEEEecCc
Confidence            999999999999999999999999999999999999999999999                                   


Q ss_pred             ---------------------cccceeEEEEccCCcEE------------------------------EEEEchHHHHHh
Q psy13846       1146 ---------------------EVCEYIEEVFVPDDSFI------------------------------LIKLDMDRIRLL 1174 (1423)
Q Consensus      1146 ---------------------~i~~~i~~~~~~~~~~~------------------------------~i~l~~~~~~~~ 1174 (1423)
                                           +|++.++++|+|+..+.                              .+++.+++.+++
T Consensus      1127 ~~~d~e~A~~v~~~ie~t~L~~v~~~~~i~~~p~~~~~~i~~d~~~v~~~~~~~~~~~~~~~~~~~~~~~rl~l~~~~~~ 1206 (1752)
T 3h0g_A         1127 IAANMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFVEAFFAIPDEEVEENLYKQSPWLLRLELDRAKML 1206 (1752)
T ss_dssp             SCSSSTTTHHHHTTSSCCSSCSCCSCEEEECCCSTTCCCCSSSCSHHHHHHHTTCSSTTCSSCSCCCCEEEEECCTTSST
T ss_pred             cccCHHHHHHHHHhhccEEHHHheeEEEEEEecCccceEEeecHHHHHHHhccchhhhhcccccccceeEEEEecHHHHH
Confidence                                 45667788888764433                              344444444455


Q ss_pred             cccCCHHHHHHHHHhccccCCceEE--ec----CcEEEEEeCCCC----c------hhhhHHHHHH-hccCCcEEcccCC
Q psy13846       1175 HLEVDIDSIRYCIERTRGISGHLTV--SG----HSFLILKPKDSS----K------SFNSKMYQMK-QLLPSVVIKGVQG 1237 (1423)
Q Consensus      1175 ~~~i~~~~i~~~i~~~k~~~~~~~~--~~----~~~i~i~~~~~~----~------~~~~~l~~l~-~~l~~~~v~Gi~~ 1237 (1423)
                      ++++++++|..+|.+...  .++.+  ++    +..+++++....    +      .....|+.++ ..|++++|+||||
T Consensus      1207 ~~~l~~~~I~~~i~~~~~--~~~~v~~~d~~~~~~~i~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~l~~~~i~Gi~~ 1284 (1752)
T 3h0g_A         1207 DKKLSMSDVAGKIAESFE--RDLFTIWSEDNADKLIIRCRIIRDDDRKAEDDDNMIEEDVFLKTIEGHMLESISLRGVPN 1284 (1752)
T ss_dssp             TTTCCHHHHTTSGGGSST--TSCCEECCCTTCSSCEEEECCCCCSCCCCCSSCCCSCSCHHHHHHHHHHTTCCCSSCCTT
T ss_pred             HcCCCHHHHHHHHHhhcc--CCeeEeecCCCccceeEEEEeccccccccccccccccHHHHHHHHHHhhccceEEecCCC
Confidence            667899999888754321  22222  11    224566553210    0      1224578887 4689999999999


Q ss_pred             ccEEEEecccc---------cceeeEEEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhc
Q psy13846       1238 INRAVIHEEDV---------EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMEN 1308 (1423)
Q Consensus      1238 i~r~~i~~~~~---------~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~ 1308 (1423)
                      |+||+|.+++.         ...++|.|.|||+||+++|.+++||++||+||||+||+++|||||||++|++||+.||+.
T Consensus      1285 I~rv~i~~~~~~~~~~~g~~~~~~~~~l~teG~nL~~v~~~~gVD~~rt~sNdI~ei~~vlGIEAAR~~Ii~Ei~~v~~~ 1364 (1752)
T 3h0g_A         1285 ITRVYMMEHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVDATRTYSNSFVEILQILGIEATRSALLKELRNVIEF 1364 (1752)
T ss_dssp             CCCCCEEEEEEEEECSSSCEEEEEEEEEECCSCCCSTTTSSSSCCTTTCCCSCHHHHHHHSCHHHHHHHHHHHHHTTSCS
T ss_pred             ccEEEEecccceeecCCCcccccceEEEEecccCHHHHhCcCCCccccCeeCCHHHHHHHHhHHHHHHHHHHHHHHHHHh
Confidence            99999976431         124589999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeecccccccc
Q psy13846       1309 HGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388 (1423)
Q Consensus      1309 ~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GT 1388 (1423)
                      ||++||+|||+||||+||++|++++||||||+++++|||++||||+|+++|++||++|+.|+|+|||||||+|+++++||
T Consensus      1365 ~G~~Vd~RHl~LlaD~MT~~G~~~~itR~Gi~~~~~s~l~~aSFE~T~~~L~~Aa~~g~~D~l~gvse~Ii~G~~~~~GT 1444 (1752)
T 3h0g_A         1365 DGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGALMRCSFEETVEILMDAAASGEKDDCKGISENIMLGQLAPMGT 1444 (1752)
T ss_dssp             SSCCCCHHHHHHHHHHHTSSSSCCCCCTTSCSCCCSHHHHHHHHSCCTHHHHHHGGGTCCBCCCCSTTGGGTCSCCCSBT
T ss_pred             cCCCCCHHHHHHHHHHhccCCeEEeechhhhccCCCCHHHHhhHHHHHHHHHHHHHhcCcccccChhHHhhcCCCcCCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEeecCCC
Q psy13846       1389 GLIKLLQAVPR 1399 (1423)
Q Consensus      1389 G~~~l~~~~~~ 1399 (1423)
                      |+|||+++.++
T Consensus      1445 G~fdll~~~~~ 1455 (1752)
T 3h0g_A         1445 GAFDIYLDQDM 1455 (1752)
T ss_dssp             TSCEECCCHHH
T ss_pred             ceEEEEeCHHH
Confidence            99999998554

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...

Probab=100.00  E-value=9.6e-183  Score=1816.76  Aligned_cols=991  Identities=31%  Similarity=0.502  Sum_probs=765.1

Q ss_pred             ccceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccC
Q psy13846         76 KVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL  155 (1423)
Q Consensus        76 ~~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~  155 (1423)
                      ..++.+ |+|+++||||||++||++|+++++|+ +.+.+|..|||+|||||+.++...|.|||....+||||||||||+.
T Consensus        11 ~~~i~~-I~f~l~SpeeIr~~Sv~eI~~pet~~-~~~~~P~~~GL~d~rlG~~~~~~~C~tCg~~~~~C~GHfGHIELa~   88 (1733)
T 1twf_A           11 LRTVKE-VQFGLFSPEEVRAISVAKIRFPETMD-ETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAK   88 (1733)
T ss_dssp             BCCCCE-EECCBCCHHHHHHTCCCCCCCSCCSC-TTSCCSCCSSSSCSSSCCCTTCCCSSSCCCCTTSCCCCCCCEEEEE
T ss_pred             ccccce-EEEEeCCHHHHHHhCeeEEecccccc-cccCCCCcCCCcCcccCcccCCCEeCCCCCCCCcCCCccceeeccc
Confidence            467889 99999999999999999999999995 3455999999999999999999999999999999999999999999


Q ss_pred             ceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccC------------
Q psy13846        156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVC------------  223 (1423)
Q Consensus       156 PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C------------  223 (1423)
                      ||||||||+.++++|+|+|++  |+++++++.+. .|.+.++...     .+.+++++++.|++++.|            
T Consensus        89 PV~HigF~k~i~kiLe~VC~~--Cskllld~~~~-~~~~~L~~~~-----pk~r~~~v~e~ck~k~~Ce~~~~~~~e~~~  160 (1733)
T 1twf_A           89 PVFHVGFIAKIKKVCECVCMH--CGKLLLDEHNE-LMRQALAIKD-----SKKRFAAIWTLCKTKMVCETDVPSEDDPTQ  160 (1733)
T ss_dssp             EEECGGGHHHHHHHHHHBCTT--TCCBSCCTTSH-HHHHHHTCCS-----HHHHHHHHHHHHTTCCBCCSEECCSSCTTS
T ss_pred             ccccHHHHhhHHHHHHHHhHh--cceeeeccchH-HHHHHHHhcC-----HHHHHHHHHHHhcccccccccccchhcccc
Confidence            999999999999999999999  99999987765 4666554331     145567789998876666            


Q ss_pred             ----CCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccC
Q psy13846        224 ----PHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIP  299 (1423)
Q Consensus       224 ----~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~  299 (1423)
                          .+||+.++.+||.++ ++.++ ++....  +.              ..       .....+.++|.+|+++|++|+
T Consensus       161 ~~~~~gCGa~qp~irk~gl-~l~~e-~k~~~~--~~--------------e~-------~~~~k~~Ltp~eV~eifk~I~  215 (1733)
T 1twf_A          161 LVSRGGCGNTQPTIRKDGL-KLVGS-WKKDRA--TG--------------DA-------DEPELRVLSTEEILNIFKHIS  215 (1733)
T ss_dssp             CEECCSCCCBCCCCEECSS-CEEEE-ECSSSS--CT--------------TS-------CSCEEEEECHHHHHHHHTTSC
T ss_pred             ccccCCCCCccHHHHhcCC-ceEEe-eccccc--cc--------------cc-------chhhhccCCHHHHHHHHHhCC
Confidence                499999999999884 44432 211110  00              00       002356899999999999999


Q ss_pred             CCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCC-C--------------------------------------
Q psy13846        300 LEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLK-S--------------------------------------  340 (1423)
Q Consensus       300 ~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~-~--------------------------------------  340 (1423)
                      ++|+.+|++++..+||+||||++|||||+|+||++.+++. .                                      
T Consensus       216 deD~~lLgl~p~~~rPewmiLtvLPVpPp~vRPsv~ldg~~~~edDLT~~l~~II~~N~~Lk~~~~~gap~~ii~e~~~~  295 (1733)
T 1twf_A          216 VKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESL  295 (1733)
T ss_dssp             HHHHHHTTCBTTTBCGGGGEEEEECCCCTTTSCCCCCSSSCCCCCHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHH
T ss_pred             HHHHHHhCCCccCCChheeeeeeeccCCCCccCceecCCCcccCCHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHH
Confidence            9999999999999999999999999999999999988763 1                                      


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        341 --------------------------------------------------------------------------------  340 (1423)
Q Consensus       341 --------------------------------------------------------------------------------  340 (1423)
                                                                                                      
T Consensus       296 LQ~~v~~~~dn~~~~~~~~~~~~~rp~k~i~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~L~~~evGvP~~~A~~Lt  375 (1733)
T 1twf_A          296 LQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLT  375 (1733)
T ss_dssp             HHHHHHHHHCCCSSCCCCCSSCTTCCCCCSTTSCTTTTTTSSGGGTTCSCCSEEEEEEEECTTSCTTEEEEEHHHHTTCE
T ss_pred             HHHHHHHHhccCccCCCccccCCCccchhHHHHhccccchhhhcccccccCcccceEEeCCCCcccccccCcHHHHHhCC
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------------CCeEEEEecCcccccccc
Q psy13846        341 --------------------------------------------------------------DNDVVLFNRQPSLHKLSI  358 (1423)
Q Consensus       341 --------------------------------------------------------------~~d~Vl~nRqPsLHk~Si  358 (1423)
                                                                                    +||+|||||||||||+||
T Consensus       376 ~Pe~vt~~ni~~l~~lv~~g~~~~~ga~~~~~~~g~~~~l~~~~~~~~~~l~~g~~v~r~l~~gd~VllNRqPTLHr~si  455 (1733)
T 1twf_A          376 YPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSM  455 (1733)
T ss_dssp             EEEECCTTTHHHHHHHHHHTTTSSSCEEEEECTTCCEEETTSCTTTTCCCCCTTCEEEEECCTTCEEEEECSSCCSGGGE
T ss_pred             CCccccHHHHHHHHHHHHcCCccCCCceeEEcCCCcEEeccccchhhhhhcccCCEEEeeeccCCEEEEeCCCccccccc
Confidence                                                                          678999999999999999


Q ss_pred             ceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCcccc
Q psy13846        359 MAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLI  438 (1423)
Q Consensus       359 mah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~  438 (1423)
                      |||++|++|++||||||++|+||||||||||||+|+||+++|||||+              .||.+.+|++||++|+|++
T Consensus       456 ~a~~~~v~~~~tirlnp~vC~~yNADFDGDeMnvHvPqs~eAraEa~--------------~Lm~~~~nilsP~~G~Pi~  521 (1733)
T 1twf_A          456 MAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELS--------------QLCAVPLQIVSPQSNKPCM  521 (1733)
T ss_dssp             EEEEEEEESSSSEEECGGGHHHHTCCSSSCEEEEECCCSHHHHHHHH--------------HHTBGGGGSEETTTTEESC
T ss_pred             eeEEEEEccCCeEEeChhhcCCCCccchhhhhhhhcCCCHHHHHHHH--------------HHhcCcccEEecCCCCeeE
Confidence            99999999999999999999999999999999999999999999999              9999999999999999999


Q ss_pred             ccccceEEEEEeecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcc
Q psy13846        439 AATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCP  518 (1423)
Q Consensus       439 ~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~  518 (1423)
                      +++||+|+|+|.||.+|.|++++|++++++++.    .+.+        .+|+|+|+||.++|||||||+++||++    
T Consensus       522 ~~~QD~v~g~y~lT~~~~f~~~~e~~~~~~~~~----~~~~--------~~~~pai~kp~~~wtGkqifs~ilp~~----  585 (1733)
T 1twf_A          522 GIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVP----DWDG--------VIPTPAIIKPKPLWSGKQILSVAIPNG----  585 (1733)
T ss_dssp             CCCHHHHHHHHHHHSTTCEEEHHHHHHHHHHST----TCCS--------CCCCCSBCSSSCEEEHHHHHHHHSCTT----
T ss_pred             eeeccccccceeeecCcccCCHHHHHHHHHhhh----hhcC--------ccCCccccCcccCccHHHHHHHhCCCC----
Confidence            999999999999999999999999999998873    2333        578999999999999999999999875    


Q ss_pred             cccceeecccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhh
Q psy13846        519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMN  598 (1423)
Q Consensus       519 ~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~  598 (1423)
                        +++..+..   ...+.+..|+.|+|+|||+++|++||+.+|+ +.+++||.+|++||++.|+.||+++++++++|++.
T Consensus       586 --~~~~~~~~---~~~~~~~~d~~v~i~~gel~~g~ldKk~lg~-~~~~li~~i~~~~G~~~a~~~ld~l~~l~~~~l~~  659 (1733)
T 1twf_A          586 --IHLQRFDE---GTTLLSPKDNGMLIIDGQIIFGVVEKKTVGS-SNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLH  659 (1733)
T ss_dssp             --CCEEECCT---TCCTTCTTCCSEEEETTEEEESCCCHHHHSS-CTTSHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             --CceeecCC---CcccCCcccceEEEeCCcEEEeecchHHhcc-ChhHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHH
Confidence              33433221   1234567789999999999999999999998 56899999999999999999999999999999999


Q ss_pred             cCcceecCCCCCCc------------------------------------------------------------------
Q psy13846        599 RGFSIGIGDVTPGQ------------------------------------------------------------------  612 (1423)
Q Consensus       599 ~GfsiGi~D~~~~~------------------------------------------------------------------  612 (1423)
                      +|||||++|+++++                                                                  
T Consensus       660 ~GfSigi~D~~~~~~~~~~i~~~i~~a~~~v~~~~~~~~~g~l~~~pg~~~~e~~e~~v~~il~~~~d~~~~~~~~~l~~  739 (1733)
T 1twf_A          660 NGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKD  739 (1733)
T ss_dssp             TCBCCCGGGGCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSCT
T ss_pred             cceEEehhhcCcCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            99999999997655                                                                  


Q ss_pred             ----------------------------------------------------------cccccccccCCCceeeeeeccc
Q psy13846        613 ----------------------------------------------------------GFVQNSFFSGLTPTEFFFHTMG  634 (1423)
Q Consensus       613 ----------------------------------------------------------GfI~~sf~~GL~p~Efffh~ma  634 (1423)
                                                                                |||.+||++||+|+||||||||
T Consensus       740 ~N~i~~Ma~SGAKGs~~Ni~Q~~~~~Gqq~~~Gkrip~g~~~RtLPhf~k~d~~p~s~GfI~ssF~~GLtp~EyFfh~mg  819 (1733)
T 1twf_A          740 LNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMG  819 (1733)
T ss_dssp             TCHHHHHHHHTSSCCHHHHHHHHSCCEECCBTTBSCCCCBTTBSSTTSCTTCCSTTTTTEECSCTTTCCCHHHHHHHHHH
T ss_pred             CCCeEEEeeccCcccHHhHHHHHhCcCCcccCCccCCCCCCCCCCCCCCCCCCCccccchhhhhhhcccchHHHhhhhhc
Confidence                                                                      7899999999999999999999


Q ss_pred             ccccchhcccccCCCCcchHHHHHHHhhhhhcccceeecc-------ccCCCccCCCcchheecCCCcccchhHHHHhhh
Q psy13846        635 GREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA-------FYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA  707 (1423)
Q Consensus       635 GReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s-------~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aq  707 (1423)
                      |||||||||||||+||||||||||+||||+|+||+||||+       .||+|+.+....+..                  
T Consensus       820 gReGLiDTAvKTA~SGYLqRRLVk~ledv~V~yDgTVR~s~g~IvQF~YGeDGlD~~~~e~~------------------  881 (1733)
T 1twf_A          820 GREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQ------------------  881 (1733)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTCEECTTSCEECTTCCEEESSGGGTTBCGGGEEEE------------------
T ss_pred             cccchhhhceecccCCcceeehhhhhcceEEEecCcEecCCCCEEEEEeccccCCcceeecc------------------
Confidence            9999999999999999999999999999999999999987       255543221100000                  


Q ss_pred             cCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeeec
Q psy13846        708 VPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYL  787 (1423)
Q Consensus       708 sige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L  787 (1423)
                                      .|                                        +                    +
T Consensus       882 ----------------~~----------------------------------------~--------------------~  885 (1733)
T 1twf_A          882 ----------------SL----------------------------------------D--------------------T  885 (1733)
T ss_dssp             ----------------EC----------------------------------------G--------------------G
T ss_pred             ----------------cc----------------------------------------c--------------------c
Confidence                            00                                        0                    0


Q ss_pred             ccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccc
Q psy13846        788 DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHS  867 (1423)
Q Consensus       788 ~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~  867 (1423)
                      ....+..+.+..+...                 .++..                                          
T Consensus       886 ~~~~~~~f~~~~~~~~-----------------~~~~~------------------------------------------  906 (1733)
T 1twf_A          886 IGGSDAAFEKRYRVDL-----------------LNTDH------------------------------------------  906 (1733)
T ss_dssp             GSSCHHHHHHHHCCCT-----------------TCTTT------------------------------------------
T ss_pred             cccCHHHHHHHhcccc-----------------ccccc------------------------------------------
Confidence            0000001110000000                 00000                                          


Q ss_pred             cccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccccceeecccceeeccCchH
Q psy13846        868 FLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY  947 (1423)
Q Consensus       868 ~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~  947 (1423)
                       + ..+                           ++.                                 +.         
T Consensus       907 -~-l~~---------------------------~~~---------------------------------~~---------  915 (1733)
T 1twf_A          907 -T-LDP---------------------------SLL---------------------------------ES---------  915 (1733)
T ss_dssp             -S-CCT---------------------------TTB---------------------------------TT---------
T ss_pred             -c-CCH---------------------------HHH---------------------------------HH---------
Confidence             0 000                           000                                 00         


Q ss_pred             HHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCCcchhhHHHHHHHHHhccC--CCCCCCCH
Q psy13846        948 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSS--RSDPSLSA 1025 (1423)
Q Consensus       948 eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~~~~~~~~~~~~~~~~~~~--~~~~~l~~ 1025 (1423)
                       ....++-+..+..+-.|.....+      |.+   .|-..+ ..|.-. ...|+++.+++.+.......  .....+.|
T Consensus       916 -~~~~~~~~~~~~~l~~e~~~l~~------~r~---~lr~i~-~~~~~~-~~~P~ni~r~i~~~~~~f~~~~~~~s~l~p  983 (1733)
T 1twf_A          916 -GSEILGDLKLQVLLDEEYKQLVK------DRK---FLREVF-VDGEAN-WPLPVNIRRIIQNAQQTFHIDHTKPSDLTI  983 (1733)
T ss_dssp             -HHHHTTCHHHHHHHHHHHHHHHH------HHH---HHHHHT-TTCCCE-EEEESCHHHHHHHHHHHTTCCTTSCBCCCH
T ss_pred             -HHHhhccHHHHHHHHHHHHHHHH------HHH---HHHHhh-cccccc-ccCChhHHHHHHHHHHHhcccccccccCCH
Confidence             00000000011111111111100      000   000000 011100 11588899988777665321  22345778


Q ss_pred             HHHHHHhhhhcCcchh------h-----hhhhHHHHHHHHHHHHHhhhccccccccccCCchhhhhhhccccccCcccCC
Q psy13846       1026 QEILALSNETLDSKEF------L-----QDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRES 1094 (1423)
Q Consensus      1026 ~~~~~~~~~~l~~~~~------~-----~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1094 (1423)
                      ..+.+.+++.+.....      +     ..+...|.-.+++++                    +.+.+...++++++++ 
T Consensus       984 ~~~~~~v~~~~~~~~~~~g~d~l~~~~~~n~~~l~~~~~rs~L--------------------~~k~~~~~~~l~~~~~- 1042 (1733)
T 1twf_A          984 KDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRL--------------------ATRRVLQEYRLTKQAF- 1042 (1733)
T ss_dssp             HHHHHHHHHHHTTCCSCCCCSHHHHHHHHHTTHHHHHHHHHHS--------------------CHHHHHHTSCCCHHHH-
T ss_pred             HHHHHHHHHHHHhhhcccCCcchhhhhhhchHHHHHHHhhhhh--------------------hhhhhhhhcCCCHHHH-
Confidence            8888877776653210      0     011223433334332                    2234445678898887 


Q ss_pred             CCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc-----------------------------
Q psy13846       1095 NPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------------- 1145 (1423)
Q Consensus      1095 ~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG----------------------------- 1145 (1423)
                         +  +|+++|+.||.+|+|+||||||+|||||||||+||||||||||||                             
T Consensus      1043 ---~--~~l~~i~~ky~~a~v~pGe~VG~iaAQSigEp~TQMTLnTFHfAGva~~NVTLGVPRLkEIinask~ikTP~mt 1117 (1733)
T 1twf_A         1043 ---D--WVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLT 1117 (1733)
T ss_dssp             ---H--HHHHHHHHHHHHHBCCTTCCHHHHHHHHHHHHHTTCCC----------CCSCCHHHHHHHHTTTCSSCSSCEEE
T ss_pred             ---H--HHHHHHHHHHHhccCCCCchhhhHhhhhcCCccccccccccccccccccCcccCcHHHHHHHHhccCCCCCeEE
Confidence               7  999999999999999999999999999999999999999999999                             


Q ss_pred             ---------------------------cccceeEEEEccCC-------------c-----------------EEEEEEch
Q psy13846       1146 ---------------------------EVCEYIEEVFVPDD-------------S-----------------FILIKLDM 1168 (1423)
Q Consensus      1146 ---------------------------~i~~~i~~~~~~~~-------------~-----------------~~~i~l~~ 1168 (1423)
                                                 +|++.++++|+|+.             .                 .+.++|++
T Consensus      1118 v~L~~~~~~~~e~A~~v~~~ie~ttL~dv~~~i~i~~dp~~~~tvi~ed~~~~~~y~~i~~~d~~~~~~~~~~~~lrl~l 1197 (1733)
T 1twf_A         1118 VYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLEL 1197 (1733)
T ss_dssp             EEBCSSSSSCHHHHHHHHHHHSCEEGGGTEEEEEEEECCCSSSCSSGGGHHHHHTSSCC----------CCCSEEEEEEE
T ss_pred             EEeCCcccccHHHHHHHHHhhceeEHHHhhheEEEEEccCccceeeecchhhhhhhhcccHHhhcchhhhcccceeEEEe
Confidence                                       45566777787761             0                 13457778


Q ss_pred             HHHHHhcccCCHHHHHHHHHhccccCCceEE--ecC----cEEEEEeCCCCc-------hhhhHHHHH-HhccCCcEEcc
Q psy13846       1169 DRIRLLHLEVDIDSIRYCIERTRGISGHLTV--SGH----SFLILKPKDSSK-------SFNSKMYQM-KQLLPSVVIKG 1234 (1423)
Q Consensus      1169 ~~~~~~~~~i~~~~i~~~i~~~k~~~~~~~~--~~~----~~i~i~~~~~~~-------~~~~~l~~l-~~~l~~~~v~G 1234 (1423)
                      ++.+++...+++++|..+|.+...  .++.+  .++    ..++++.....+       .....++.+ ++.+.+++|+|
T Consensus      1198 ~~~~~~~~~l~~~~I~~~i~~~~~--~~~~~~~~d~~~~~~~~~i~~~~~~~~~~~~~~~~~~~l~~l~~~~l~~~~v~G 1275 (1733)
T 1twf_A         1198 DRAAMNDKDLTMGQVGERIKQTFK--NDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRG 1275 (1733)
T ss_dssp             CHHHHHHTTCCHHHHHHHHHHHHG--GGEEEEECCTTSSSCEEEEEEC----------CCTTHHHHHHHHHHHHHCEEES
T ss_pred             cHHHHHhcCCCHHHHHHHHHHhhC--CCcceecCCcccchhheeeeeccCccccccccchhHHHHHHHHHHhhhheEEec
Confidence            887787888999999998854211  12221  111    133444421110       001124444 77788999999


Q ss_pred             cCCccEEEEec-------ccc--cceeeEEEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHHHHHHHH
Q psy13846       1235 VQGINRAVIHE-------EDV--EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 1305 (1423)
Q Consensus      1235 i~~i~r~~i~~-------~~~--~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v 1305 (1423)
                      +|||+||+|.+       ++.  +..++|+|.|||+||.++|.+++||++||+||||+||+++|||||||++|++||++|
T Consensus      1276 i~~I~r~~i~~~~~~~~~~~g~~~~~~~~~L~teG~nL~~vl~~~~VD~~rt~SNdI~eI~~vlGIEAAR~~Ii~Ei~~V 1355 (1733)
T 1twf_A         1276 VENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNV 1355 (1733)
T ss_dssp             CTTCCCEEEEEEEEEEECTTSSEEEEEEEEEEEESCCHHHHTTSTTBCTTTCBCSCHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             CCCccEEEEecccceeecCCCccccCcceEEEeecccHHHHhccCCcccccceeccHHHHHHHhhHHHHHHHHHHHHHHH
Confidence            99999999863       111  235689999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeeccccc
Q psy13846       1306 MENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMN 1385 (1423)
Q Consensus      1306 ~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~ 1385 (1423)
                      |+.||++||+|||+||||+||++|.++|||||||+++++|||++||||+|+++|++||++|+.|+|+|||||||+|+++|
T Consensus      1356 ~~~~Gi~Vd~RHl~LlaD~MT~~G~~~~itR~Gi~~~~~S~L~~aSFE~T~~~L~~Aa~~g~~D~l~gvsenII~G~~~~ 1435 (1733)
T 1twf_A         1356 IASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAP 1435 (1733)
T ss_dssp             HHTTTCCCCHHHHHHHHHHTTTBSSCCCSSSCSSSCSSCCTTSSCCSSCSHHHHHHHHHHTCEECCCSHHHHHHTTCCCS
T ss_pred             HhhcCccccchhhhhhhhhhccCceecccchhhhcccCCCchhhcchhhhHHHHHHHHhccCcCcccccccccccCCCCC
Confidence            99999999999999999999999999999999999989999999999999999999999999999999999999999999


Q ss_pred             cccceEEEeecCCCCC
Q psy13846       1386 VGTGLIKLLQAVPRSE 1401 (1423)
Q Consensus      1386 ~GTG~~~l~~~~~~~~ 1401 (1423)
                      +|||+|||+++.+...
T Consensus      1436 ~GTG~FdLl~~~~~~~ 1451 (1733)
T 1twf_A         1436 IGTGAFDVMIDEESLV 1451 (1733)
T ss_dssp             SGGGSSEEEECSCCC-
T ss_pred             CCCccEEEEEchhhcc
Confidence            9999999999987643

>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D

Probab=100.00  E-value=8.4e-136  Score=1323.00  Aligned_cols=520  Identities=22%  Similarity=0.305  Sum_probs=356.8

Q ss_pred             ceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCC-CCC--------------CCCCccCCCCCCCc
Q psy13846         78 FFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRM-GTN--------------QKEANCTTCGQNLS  142 (1423)
Q Consensus        78 ~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rL-G~~--------------~~~~~C~TCg~~~~  142 (1423)
                      .+.+ |+|+++|||+|+++|+.+|++|++|+ +.+++|..+||+|+|| ||.              ++...|.|||....
T Consensus         4 ~~~~-i~~gl~Spe~Ir~~S~geV~~pet~n-y~t~kP~~~GLfd~rifGp~k~~~C~Cgkyk~~~~~~~~C~~Cg~~~~   81 (1265)
T 1hqm_D            4 EVRK-VRIALASPEKIRSWSYGEVEKPETIN-YRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVT   81 (1265)
T ss_dssp             CBCC-CCCCCCCTTTHHHHTTTCCCCCCC--------------------------------------CCSCSSSSSSSSC
T ss_pred             ccce-EEEecCCHHHHHHhhEEEEcchhhee-cCCCcccCCCCcCccccCCCccceecCCCccccCCCCCCCCCCCCccc
Confidence            4778 99999999999999999999999994 3699999999999999 775              37789999999999


Q ss_pred             cc---CCccceEEccCceeEEeeeccH-----------HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHH
Q psy13846        143 DC---VGHFGYIDLPLPVFHIGYFRCV-----------INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKS  208 (1423)
Q Consensus       143 eC---pGHfGhIeL~~PV~h~gffd~v-----------~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~  208 (1423)
                      +|   |||||||+|+.||||+|||+.+           .+.|+|+|++  |+++++++..  .+..++....     .+.
T Consensus        82 ~~~vrrg~~GhIeLa~PV~Hi~y~k~~~s~l~~lL~~~~k~le~v~y~--~s~v~~~~~~--~l~~~l~~~~-----~~~  152 (1265)
T 1hqm_D           82 RSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLFATELEQVLYF--NKYIVLDPKG--AVLDGVPVEK-----RQL  152 (1265)
T ss_dssp             CSSSCCCSCCCCCCCSCCCSTTSTTHHHHTTTCTTTHHHHTTSSSCCC--CSCCCCSSSC--CCTTCCCCTT-----HHH
T ss_pred             ccccccCccceEEecCceeeeeecccchHHHHHHhcCCHHhhccEeee--cceEeecCCc--hHhhhcCHHH-----HHH
Confidence            99   8999999999999999999974           5677778888  8888865430  0000111100     000


Q ss_pred             HH----HHHHHHccCCccCCCCCCCCCceeecCcceehhhhhccccc-c-hhhHHHHHHHHhhhhhccChhhhhhhccCc
Q psy13846        209 LK----KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTK-K-KDAIVEDLLAEYNEAVKFNPEIEAHKKFGL  282 (1423)
Q Consensus       209 ~~----~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~-~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  282 (1423)
                      +.    +++...+...+.|  |.......   + .+..++.+..... . -.+....+++..+-.. ...+..     ..
T Consensus       153 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~---~-~~~~~~~~~~~~~~~~G~~~~~~~l~~~~l~~-~~~~~~-----~~  220 (1265)
T 1hqm_D          153 LTDXXXXXXXXXXXXXXXX--XXXXXXXX---X-XXXXXXXXXXXIDARMGAEAIQELLKELDLEK-LERELL-----EE  220 (1265)
T ss_dssp             HTCCCCCCCCCCCCSSCCC--CCCCCTTS---C-CCCCCCCCCCCCCCCCSHHHHHHHHTHHHHCH-HHHHHH-----TT
T ss_pred             Hhhhccccccccccccccc--cccccccc---c-cccccccchhhhhcccCchhHHHHHHhcCHHH-HHHHHH-----HH
Confidence            00    0000000001112  11111110   0 1111111110000 0 0011111111111000 000001     11


Q ss_pred             cccCCHHHHHHHhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCC----------------------
Q psy13846        283 IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS----------------------  340 (1423)
Q Consensus       283 ~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~----------------------  340 (1423)
                      .+..++....++|+++..    +-.+.++++||+||||++|||||+++||++.+++..                      
T Consensus       221 ~~~~~~~~~~~~~krl~~----~~~f~~~~~~Pewmil~~lPVpPp~~RP~v~l~gg~~~~~Dln~~~~~Ii~~N~~L~~  296 (1265)
T 1hqm_D          221 MKHPSRARRAKARKRLEV----VRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKK  296 (1265)
T ss_dssp             TCCSSHHHHHHHHHHHHH----HHHHHSSSCSSCCSCSSCCCCCSCC------------CCCGGGTHHHHTHHHHHHHHT
T ss_pred             HhhccHHHHHHHhhhhhh----hhhhcccCCCcceEeeeccCCCCCcCccceecCCCceecChhHHHHHHHHHHHHHHHH
Confidence            222355666666666532    112344578999999999999999999999886631                      


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        341 --------------------------------------------------------------------------------  340 (1423)
Q Consensus       341 --------------------------------------------------------------------------------  340 (1423)
                                                                                                      
T Consensus       297 ~~~~~ap~~ii~~~~~~LQ~~V~~l~Dn~~~g~~~~~~~~rp~lksl~~~LkGK~GrfR~NLmGKRVdfSaRSVI~pdP~  376 (1265)
T 1hqm_D          297 LLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQ  376 (1265)
T ss_dssp             SSSSCCCSTTTSTTTTTTGGGTTTTSSCCSSCCCSSCSSCCCCCCCSTTTSSSTTCTTTTTTSCCEETTCCCCBEEECCS
T ss_pred             HHHcCCchhHHHHHHHHHHHHHHHHhCCCCCCCCccCCCCCccccchhhhcccchhhhhhhhcccccCcccceeEecCCC
Confidence                                                                                            


Q ss_pred             -----------------------------------------------------------CCeEEEEecCcccccccccee
Q psy13846        341 -----------------------------------------------------------DNDVVLFNRQPSLHKLSIMAH  361 (1423)
Q Consensus       341 -----------------------------------------------------------~~d~Vl~nRqPsLHk~Simah  361 (1423)
                                                                                 +||+|||||||||||+|||||
T Consensus       377 L~i~evGvP~~~A~~L~~P~~~~~lv~~g~~~~i~~ak~~i~~~~~~~~~~~~v~~~v~~gd~VLlNRqPTLHr~sIma~  456 (1265)
T 1hqm_D          377 LKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAF  456 (1265)
T ss_dssp             SSSSBCCCBHHHHHHHHHHHHHHHHHHTTCSSCSHHHHHHHCSSSCCCHHHHTTTTTTTTTCCEECCCSSCCSGGGSCEE
T ss_pred             cccccccChHHHHHHhCcHHHHHHHHHcCCcchhhhhhhhhhhccccCCccceeEEEeccCcEEEEecCcccccccccce
Confidence                                                                       789999999999999999999


Q ss_pred             eeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccc
Q psy13846        362 RAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAAT  441 (1423)
Q Consensus       362 ~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~  441 (1423)
                      +++++|++||||||++|+||||||||||||+|+|||++|||||+              .||.+.+|++||++|+|+++++
T Consensus       457 ~~~l~~~ktirlhp~vC~~yNADFDGDeMnvHvPqs~eA~aEa~--------------~Lm~~~~nilsP~~G~Pi~~~~  522 (1265)
T 1hqm_D          457 QPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEAR--------------IQMLSAHNLLSPASGEPLAKPS  522 (1265)
T ss_dssp             BCCCBSSSSEEECGGGHHHHCCCSSSCBCCCCCCCSTHHHHTTS--------------SSSBSSSSSSSCSSSSCSSCCC
T ss_pred             eEEecCCCeEEechhhcCCcCCCcccceEEEecCCCHHHHHHHH--------------HHhCccccEecCCCCCeeEeee
Confidence            99999999999999999999999999999999999999999999              9999999999999999999999


Q ss_pred             cceEEEEEeecccc--------cCCCHHHHHHHHHhhccCCccccceEe-eee------cc-ccCCce------------
Q psy13846        442 QDFITGGYLLTQKN--------AFFNRAQTMRIASTLIADTSDICGIIK-RFS------WR-SWNPVV------------  493 (1423)
Q Consensus       442 qD~~~~~~~~t~~~--------~~~~~~~~~~l~~~~~~~~~~~~~~~~-~~~------~~-~l~~p~------------  493 (1423)
                      ||+++|+|.||.+|        .|++++|++++++...   .+.+..++ +..      |. .+++|+            
T Consensus       523 QD~vlg~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~~---i~l~a~i~~~~~~~~~g~~k~~~t~P~k~I~~~~~g~~~  599 (1265)
T 1hqm_D          523 RDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGE---VALNAPIVVAGRETSVGRLKFVFANPDEALLAVAHGLLD  599 (1265)
T ss_dssp             TTHHHHHHHTTCCCCCCCCCCCCSSCCTHHHHHTTSSC---CSSCCCSSSCCSTTSSCCCCCTTTCSHHHHHHHHTTSSC
T ss_pred             ccccceeEEeccccCCccCCCcccCCHHHHHHHHHCCC---CCCCCceEEecccccccccccccccccccccccccCccc
Confidence            99999999999999        7999999998654322   23333332 110      00 112121            


Q ss_pred             -------eecc--eeeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEEEeccccccccccccCCcCCCC
Q psy13846        494 -------FVRT--AVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGG  564 (1423)
Q Consensus       494 -------i~kp--~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~  564 (1423)
                             .++|  ...|+|||+|+.++|++..         .   +.     .+++-.+       +.|++||+.+|   
T Consensus       600 ~q~~~~~~~k~~~~~t~~Gr~if~~~lp~~~~---------~---~~-----~p~~~~~-------~ngvldKk~lG---  652 (1265)
T 1hqm_D          600 LQDTVTTRYLGRRLETNPGRILFARIVGEAVG---------D---EK-----VAQELIQ-------MDVPQEKNSLK---  652 (1265)
T ss_dssp             SSSCCCCEESSSEECCCHHHHHHHHHHHHHTT---------C---TT-----TTTTSSC-------CSSCCCSSHHH---
T ss_pred             cccccceeccccceeccCCceEEeeecccccc---------c---cC-----CCCCCce-------EeeeecHHHHH---
Confidence                   1244  6889999999999975422         0   00     1221111       45899999997   


Q ss_pred             CCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcC-cceecCCCCCCc-------------------------------
Q psy13846        565 KANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRG-FSIGIGDVTPGQ-------------------------------  612 (1423)
Q Consensus       565 ~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~G-fsiGi~D~~~~~-------------------------------  612 (1423)
                        +++|.+|++||++.|+.||+++++++++|++.+| ||+|++|+++.+                               
T Consensus       653 --~LI~~i~~~~G~~~a~~~ld~l~~l~~~~lt~~G~fSigi~D~~~~~~k~~~i~~a~~~v~~i~~~y~~g~lt~~e~~  730 (1265)
T 1hqm_D          653 --DLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGIITIGIDDAVIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERY  730 (1265)
T ss_dssp             --HHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHTTCCCCSSSSCCCCSTTTTHHHHHHHHHHHHHTTTTSSSSCHHHHH
T ss_pred             --HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhCCCceEeeccccCCHHHHHHHHHHHHHHHHHHHHHHcCCCcHHHHH
Confidence              6999999999999999999999999999999999 999999997544                               


Q ss_pred             -----------------------------------------------------------------cccccccccCCCcee
Q psy13846        613 -----------------------------------------------------------------GFVQNSFFSGLTPTE  627 (1423)
Q Consensus       613 -----------------------------------------------------------------GfI~~sf~~GL~p~E  627 (1423)
                                                                                       +||.+||++||+|+|
T Consensus       731 ~~v~~~~~~~~d~~~~~~~~~l~~~~~~N~i~~Ma~SGAKGS~~ni~Ql~g~~G~ma~~~G~~i~~pI~ssF~eGLtp~E  810 (1265)
T 1hqm_D          731 DQVIQLWTETTEKVTQAVFNNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRGLMQKPSGETFEVPVRSSFREGLTVLE  810 (1265)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSCSSSCTTTTTTTSSSCCHHHHHHHSSCCCCCCCTTSCCCSCCCCCCBTTBCTTCT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccCCCCcHHHHHHhcCCcCHHHHHHHHhhccccccCCCCccCcccccccccCCChHH
Confidence                                                                             789999999999999


Q ss_pred             eeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccce
Q psy13846        628 FFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS  670 (1423)
Q Consensus       628 fffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~t  670 (1423)
                      ||||||||||||+|||||||+||||||||||++||++|+||++
T Consensus       811 yFfhtmggReGLiDTAvKTA~SGYLqRRLVkv~qDv~V~~ddc  853 (1265)
T 1hqm_D          811 YFISSHGARKGGADTALRTADSGYLTRKLVDVAHEIVVREADC  853 (1265)
T ss_dssp             HHHHHHHHTTHHHHHTHHHHTSSSTHHHHHHHSCSCCCCSCCC
T ss_pred             hheecccccccchhhhhhcccCCcceeeeeeecceEEEEECCC
Confidence            9999999999999999999999999999999999999999886

>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D*

Probab=100.00  E-value=6.9e-125  Score=1195.76  Aligned_cols=499  Identities=26%  Similarity=0.370  Sum_probs=376.4

Q ss_pred             cccceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCC-CCC--------------CCCCccCCCCC
Q psy13846         75 RKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRM-GTN--------------QKEANCTTCGQ  139 (1423)
Q Consensus        75 ~~~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rL-G~~--------------~~~~~C~TCg~  139 (1423)
                      ....+.. +++++.|||+|+++|+.||++|++++ +.+.+|..+||+++|+ ||.              .+...|.+||-
T Consensus        13 ~~~~~~~-i~i~laSpe~I~~ws~GEV~kpetin-yrt~kPe~dGLFcerIFGp~kd~eC~Cgkyk~~~~~g~~C~~Cgv   90 (1407)
T 3lu0_D           13 KTEEFDA-IKIALASPDMIRSWSFGEVKKPETIN-YRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGV   90 (1407)
T ss_dssp             -CCCCCC-EEECCCCHHHHHHHBCSCCCSCCCCC-SSCCSCCSSSSSCTTTTCCSSSSCCSSCSCCSTTCSSSCCSSSCC
T ss_pred             ccCccce-EEEEeCCHHHHHhhcCeEECCccccc-cCCCCCCCCCccchhhcCCCcCcEEeCccccccccCCCCCCCCCC
Confidence            3467888 99999999999999999999999996 6799999999999998 987              25678999999


Q ss_pred             CCcccC---CccceEEccCceeEEeeeccH----HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHH
Q psy13846        140 NLSDCV---GHFGYIDLPLPVFHIGYFRCV----INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK  212 (1423)
Q Consensus       140 ~~~eCp---GHfGhIeL~~PV~h~gffd~v----~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~  212 (1423)
                      ...+|.   .|||||+|+.||.|+|||+.+    ..+|.+.|+.  |.++++-....      +..+....+.+.++..+
T Consensus        91 evt~~~vRr~rmGhI~La~PV~Hiwy~k~~ps~i~~lL~~~~k~--le~viy~~~~i------v~~~~~~~l~~~~~~~~  162 (1407)
T 3lu0_D           91 EVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRD--IERVLYFESYV------VIEGGMTNLERQQILTE  162 (1407)
T ss_dssp             CCCCTTHHHHCBCEEEEEEEECCTHHHHSSSCTTTTTTTSCSST--THHHHSSSCCC------EECCSSSCSCSSCCCCS
T ss_pred             ccccCcchhhhcceeeecCceeEeeeccCCchHHHHHhCCCHHH--hhhheecceeE------eecCCCCccchhcccCH
Confidence            999998   999999999999999999987    7899999999  99888654321      11221111111111000


Q ss_pred             HHHHccCCccCCCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHH
Q psy13846        213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL  292 (1423)
Q Consensus       213 i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~  292 (1423)
                        +.+.....|..-    ....+.|. +.+.+.+....  -+...+.+.+++.....   .    .  +..+.+.-.++.
T Consensus       163 --~~~~~~~~~~~~----~~~~~~Ga-eai~~lL~~~d--l~~~~~~l~~~~~~~~~---~----~--k~~~~~krl~~v  224 (1407)
T 3lu0_D          163 --EQYLDALEEFGD----EFDAKMGA-EAIQALLKSMD--LEQECEQLREELNETNS---E----T--KRKKLTKRIKLL  224 (1407)
T ss_dssp             --TTCCCCCSSSCC----CCCEECSS-HHHHHHHHTCC--HHHHHHTHHHHHHHCCC---T----T--TTTTTTTSSTTH
T ss_pred             --HHHHHHHHhhch----hhhccccH-HHHHHHHHhcC--HHHHHHHHHHHHHhccc---H----H--HHHHHHHHHHHH
Confidence              011111111110    11111110 11111110000  01111112122111000   0    0  000111111111


Q ss_pred             HHhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCC--------------------------------
Q psy13846        293 QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS--------------------------------  340 (1423)
Q Consensus       293 eiLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~--------------------------------  340 (1423)
                      +             .+..+++||+||||++|||||+++||++.+++..                                
T Consensus       225 ~-------------~F~~s~~rPewmil~~lPVpPp~lRP~v~l~gg~~~~~DLn~ly~~II~~N~~Lk~~~~~~ap~~i  291 (1407)
T 3lu0_D          225 E-------------AFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDII  291 (1407)
T ss_dssp             H-------------HHHSSSCCGGGSSEEEEECCCSTTSCCCBCSTTCBCCCTTTTTHHHHHHTTTTTGGGTSSCCCTTT
T ss_pred             H-------------HHHhcCCCHHHhhhheeecCCCCCCCcEEeCCCccccCchHHHHHHHHHHHHHHHHHHHcCCcHHH
Confidence            1             2334678999999999999999999999987631                                


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        341 --------------------------------------------------------------------------------  340 (1423)
Q Consensus       341 --------------------------------------------------------------------------------  340 (1423)
                                                                                                      
T Consensus       292 i~~~~~~LQ~~V~~l~Dn~~~g~~~~~~~~rplksl~qrLkGKeGrfR~NLmGKRVDfSaRSVIspdP~L~i~evGvP~~  371 (1407)
T 3lu0_D          292 VRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKK  371 (1407)
T ss_dssp             HHHHHHHHHHHHHHHHCSSSSCCCCBTTBCCCCCCTTHHHHTSSSTHHHHTTCCCCSSBCEEEEEECSSCCTTEEEEESH
T ss_pred             HHHHHHHHHHHHHHhcCCCCCCCcccCCCCCcccchHHHhccccchhhcccccCCCCCcCceEEeCCCCccceeeeCCHH
Confidence                                                                                            


Q ss_pred             ---------------------------------------------CCeEEEEecCccccccccceeeeEEecCCceeecc
Q psy13846        341 ---------------------------------------------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNE  375 (1423)
Q Consensus       341 ---------------------------------------------~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~  375 (1423)
                                                                   +||+|||||||||||+|||||+++++|++|||+||
T Consensus       372 ~A~~L~~Pf~i~~L~~~g~~~~i~~ak~~v~~~~~~v~~vl~~vi~gd~VLlNRqPTLHr~sIma~~~~l~~~ktirlnp  451 (1407)
T 3lu0_D          372 MALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHP  451 (1407)
T ss_dssp             HHHHHTCHHHHHHHTTSSSCSSTTTTTTTTTSSCSSHHHHHHTTTTSCCEEEEESSCCSGGGEEEEEEEEESSSSEEECT
T ss_pred             HHHHhcchHHHHHHHHcCccccHHHHHHHHHhcCCchhhHHHHHhhceeeeecCCcccccccceeeeEEecCCceEEeCh
Confidence                                                         78999999999999999999999999999999999


Q ss_pred             CCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccc
Q psy13846        376 CVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN  455 (1423)
Q Consensus       376 ~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~  455 (1423)
                      ++|+||||||||||||+|+|||++|||||+              .||.+.+|++||++|+|+++++||+++|+|.||.+|
T Consensus       452 ~vC~~yNADFDGDeMnvHvPqs~eAraEa~--------------~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~lT~~~  517 (1407)
T 3lu0_D          452 LVCAAYNADFDGDQMAVHVPLTLEAQLEAR--------------ALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDC  517 (1407)
T ss_dssp             GGGGTTTCCSSSCEEEEECCCSSHHHHTTT--------------TSSBTTTCCSCSSSSSCSSCCCSHHHHHHHHHSCCC
T ss_pred             hhcccccCCcccceeeeecCCCHHHHHHHH--------------HHHhCccccccCCCCCceeeecccchheeEEeeccc
Confidence            999999999999999999999999999999              999999999999999999999999999999999999


Q ss_pred             c--------CCCHHHHHHHHHhhccCCccccceEeeeeccccCC------ceeecceeeeecceeeeecccCCCCccccc
Q psy13846        456 A--------FFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNP------VVFVRTAVIWTGKQIFSLILKPNRDCPVNA  521 (1423)
Q Consensus       456 ~--------~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~------p~i~kp~~~wtGKqi~s~il~~~~~~~~~~  521 (1423)
                      .        |.+.++++.++...   .+..+.+++ +.++.+.+      |...++.+.|+|||+|+.+||++..     
T Consensus       518 ~~~~~~~~~F~~~~ev~~al~~g---~v~l~a~i~-vr~~~~~~~~~g~~~~~~~~~~tt~Gr~ifs~ilP~~~~-----  588 (1407)
T 3lu0_D          518 VNAKGEGMVLTGPKEAERLYRSG---LASLHARVK-VRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLP-----  588 (1407)
T ss_dssp             CCSCCSCCCCSSCSHHHHHHHHS---SSSSSSCSS-SSCCCCSCSHHHHHHHTTTSCCSSSHHHHHHHHGGGSSC-----
T ss_pred             ccccCCcceeCCHHHHHHHHHcC---CCCCCCeeE-EecCccccCcCCcccccceeeecCCccccHHhhCCCCCC-----
Confidence            6        66788877765432   124444442 00101000      1123456789999999999986421     


Q ss_pred             ceeecccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCc
Q psy13846        522 NLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGF  601 (1423)
Q Consensus       522 ~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~Gf  601 (1423)
                                                .+++.|.++|+.+|     ++|+.+|++||.+.|..||++++++..+|++.+||
T Consensus       589 --------------------------~~~ing~l~KK~lg-----~LI~~i~~~~G~~~t~~flD~lk~Lgf~~at~~Gf  637 (1407)
T 3lu0_D          589 --------------------------YSIVNQALGKKAIS-----KMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGA  637 (1407)
T ss_dssp             --------------------------CTTTTTCCSSSTTT-----THHHHHHHHSCSHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             --------------------------ceeeecccchhhHH-----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCe
Confidence                                      12567899999986     69999999999999999999999999999999999


Q ss_pred             ceecCCCCCCc---------------------------------------------------------------------
Q psy13846        602 SIGIGDVTPGQ---------------------------------------------------------------------  612 (1423)
Q Consensus       602 siGi~D~~~~~---------------------------------------------------------------------  612 (1423)
                      |+|++|+++.+                                                                     
T Consensus       638 SIgI~D~~ip~~K~~iI~~A~~eV~ei~~~y~~G~lt~~er~~kVi~iw~~a~e~v~~~m~~~l~~~~~~d~~G~~~~l~  717 (1407)
T 3lu0_D          638 SVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQV  717 (1407)
T ss_dssp             CCCSTTSCCCTTHHHHHHHHHTHHHHHHHHHHHTSCCSSTTTTTHHHHHHTHHHHHHHHHHTTHHHH------------C
T ss_pred             EEeeccCccChHHHHHHHHHHHHHHHHHHHHHcCCCccchHHHHHHHHHHHHHHHHHHHHHHhccccccccccccccccC
Confidence            99999996433                                                                     


Q ss_pred             ---------------------------------------cccccccccCCCceeeeeecccccccchhcccccCCCCcch
Q psy13846        613 ---------------------------------------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQ  653 (1423)
Q Consensus       613 ---------------------------------------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlq  653 (1423)
                                                             ++|.+||++||+|.|||||||||||||+|||||||+|||||
T Consensus       718 ~~N~i~mMa~SGARGS~~qI~QLaGmrGlmakpdG~iie~PI~ssFreGLtp~EyFfst~GaRKGL~DTALKTAdSGYLT  797 (1407)
T 3lu0_D          718 SFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLT  797 (1407)
T ss_dssp             SCCHHHHHHHSSSSCCTTHHHHHSSCCCCCBCSSSCBCSSCCCCCSSSCCCHHHHHHHHHHHHHHHHHTTTTTTCTTTTT
T ss_pred             CCCChheeeeccccCCHHHHHHHHHhcCCccCCCCCCcchhhhcccccCCCHHHhhhhcccchhhhhhhhhhcccchhHH
Confidence                                                   67889999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhhhccc
Q psy13846        654 RRLVKSLEDLCVQYD  668 (1423)
Q Consensus       654 RrLvk~ledl~v~yD  668 (1423)
                      |||||++||++|.++
T Consensus       798 RRLVdv~QDviV~e~  812 (1407)
T 3lu0_D          798 RRLVDVAQDLVVTED  812 (1407)
T ss_dssp             HHHHTTSTTCCBCCC
T ss_pred             HHHHHhhcceEEEec
Confidence            999999999998864

>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D

Probab=100.00  E-value=1.2e-124  Score=1212.11  Aligned_cols=292  Identities=28%  Similarity=0.419  Sum_probs=239.0

Q ss_pred             CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846        341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV  420 (1423)
Q Consensus       341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~  420 (1423)
                      +||+|||||||||||+|||||+++++|++||||||++|+||||||||||||+|+|||++|||||+              .
T Consensus       696 dgd~VLlNRqPTLHRlSIqAf~~kl~~gkTiRLhplVC~pyNADFDGDEMnvHvPqS~eAraEA~--------------~  761 (1524)
T 2a6h_D          696 HGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEAR--------------I  761 (1524)
T ss_dssp             TTCCEEEECSSCCSGGGEEEEEEEEESSSCEEECSGGGTTTTCCTTTCEEEEECCCSHHHHHHHH--------------H
T ss_pred             cCceEEEccCCcccccccceeEEEEcCCccceeChhhcCCccCCcccceeeEecCCCHHHHHHHH--------------H
Confidence            68999999999999999999999999999999999999999999999999999999999999999              9


Q ss_pred             hhccccccccCCCCccccccccceEEEEEeecccc--------cCCCHHHHHHHHHhhccCCccccceEe-eee-c----
Q psy13846        421 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN--------AFFNRAQTMRIASTLIADTSDICGIIK-RFS-W----  486 (1423)
Q Consensus       421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~--------~~~~~~~~~~l~~~~~~~~~~~~~~~~-~~~-~----  486 (1423)
                      ||.+.+|++||++|+|+++++||+++|+|.||.++        .|++.++++.+.+.-..   +.+.+++ ++. |    
T Consensus       762 LM~~~~nilsP~~G~Pi~~~~QD~vlG~y~LT~~~~~~~~~g~~F~~~~e~~~ay~~~~~---~l~~~i~v~~~~~~~~~  838 (1524)
T 2a6h_D          762 QMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEV---ALNAPIKVAGRETSVGR  838 (1524)
T ss_dssp             HSBTTTCCBCSSSSSBSSCCCHHHHHHHHHHHCCCCCCCCSCCCTTSCHHHHHHHHHHHH---TTSSCSSCCCSSCCHHH
T ss_pred             HhCCccceecCCCCCeeeeecccchhhheecccccccccCCCceeCCHHHHHHHHhcCCc---CcCCceEEecccccccc
Confidence            99999999999999999999999999999999984        78899998876543211   2222221 100 0    


Q ss_pred             --cccCCce--eecceeeeecceeeeec----ccCCCCcccccceeecccc-ccc------CcccccCCcEEEecccccc
Q psy13846        487 --RSWNPVV--FVRTAVIWTGKQIFSLI----LKPNRDCPVNANLKTKGRA-YTA------NEEFCHRDSYVILRNSELL  551 (1423)
Q Consensus       487 --~~l~~p~--i~kp~~~wtGKqi~s~i----l~~~~~~~~~~~~~~~~~~-~~~------~~~~~~~d~~v~i~~~ell  551 (1423)
                        ..+|||+  |+||   |||||+++.+    ++.+.      .....++. +..      .....|++-       ..+
T Consensus       839 ~~~~~p~P~~aIlKp---wtGKQi~~~~~~~~I~~~~------~~tt~Gr~ifn~~lp~~l~~~~~P~d~-------~~i  902 (1524)
T 2a6h_D          839 LKYVFANPDEALLAV---AHGIVDLQDVVTVRYMGKR------LETSPGRILFARIVAEAVEDEKVAWEL-------IQL  902 (1524)
T ss_dssp             HHCEESSHHHHHHHH---HTTSSCTTSCCEEECSSCE------ECCCHHHHHHHHHHHHHSSCHHHHHHT-------CCT
T ss_pred             cccccCCchhhhcCC---CCCccccccccccceecce------eecccchhhHHHHhhhhcccccCCCcc-------cce
Confidence              0234554  7787   9999998842    11100      00001110 000      000012111       123


Q ss_pred             ccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCc-------------------
Q psy13846        552 AGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ-------------------  612 (1423)
Q Consensus       552 ~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~-------------------  612 (1423)
                      .|++||+.+|     +++|.+|++||++.|+.||+++++++++|++.+|||||++|+++++                   
T Consensus       903 nGvLdKk~LG-----~LI~~i~~~yG~~~t~~fLD~lk~Lg~~~lt~~GfSIGI~Dlii~~~K~eiI~eA~~~v~~i~~~  977 (1524)
T 2a6h_D          903 DVPQEKNSLK-----DLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQA  977 (1524)
T ss_dssp             TSCCCHHHHH-----HHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHTCCCCSTTSCCCTTHHHHHHHHHHHHHHHHHH
T ss_pred             eceecHHHHH-----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCceeehhhccCCHHHHHHHHHHHHHHHHHHHH
Confidence            5899999997     5999999999999999999999999999999999999999998764                   


Q ss_pred             -----------------------------------------------------------------------------ccc
Q psy13846        613 -----------------------------------------------------------------------------GFV  615 (1423)
Q Consensus       613 -----------------------------------------------------------------------------GfI  615 (1423)
                                                                                                   .+|
T Consensus       978 y~~G~lt~~Er~~~Vi~iw~~a~d~v~~~~~~~L~~~~~~N~i~~Ma~SGAKGS~~NI~Ql~gmrGqma~p~GkiIp~PI 1057 (1524)
T 2a6h_D          978 YEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPV 1057 (1524)
T ss_dssp             HHTTCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHSSSSCCHHHHHHHTSCCCCCBCSSSCBCSSCC
T ss_pred             HHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCHHHHHHhcCCcCHHHHHHHHhhccccccCCCCCccccc
Confidence                                                                                         369


Q ss_pred             ccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccce
Q psy13846        616 QNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS  670 (1423)
Q Consensus       616 ~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~t  670 (1423)
                      .+||++||+|+|||||||||||||+|||||||+||||||||||++||++|.||.+
T Consensus      1058 ~ssF~eGLtp~EyFfhtmGgReGLvDTAvKTAdSGYLqRRLVkv~qDviVr~dDc 1112 (1524)
T 2a6h_D         1058 RSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADC 1112 (1524)
T ss_dssp             CCCSSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCBCCSCC
T ss_pred             ccccccCCChHHhheecccccCCccccceeeccCCcceeeeeeecceeEEEeCCC
Confidence            9999999999999999999999999999999999999999999999999999876

>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A

Probab=100.00  E-value=1.7e-118  Score=1154.76  Aligned_cols=538  Identities=38%  Similarity=0.657  Sum_probs=469.8

Q ss_pred             cceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCc
Q psy13846         77 VFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP  156 (1423)
Q Consensus        77 ~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~P  156 (1423)
                      .+|.+ |+||++||||||++||++|++|++|  |.+|+|++|||+|||||+.++...|+|||....+||||||||+|+.|
T Consensus         4 k~i~~-I~f~l~SpeeIr~~S~~eV~~p~t~--n~~g~p~~ggl~D~~lG~~~~~~~C~tCg~~~~~c~ghfGhIeLa~P   80 (880)
T 4ayb_A            4 KNIKG-IKFGILSPDEIRKMSVTAIITPDVY--DEDGTPIEGSVMDPRLGVIEPGQKCPTCGNTLGNCPGHFGHIELVRP   80 (880)
T ss_dssp             EEEEE-EEEECCCHHHHHHHTCSCBCCSCCC--BSSSSSBCSSSSCGGGCCCSSSCCCTTTCCCGGGCCCCCEEEEEEEE
T ss_pred             ceece-EEEEeCCHHHHHHhcceEEeCcceE--CCCCCccCCCCCChhhCCCCCCCCCCCCCCCCCCCCCCCeeeccccc
Confidence            56889 9999999999999999999999999  67999999999999999999999999999999999999999999999


Q ss_pred             eeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCch-hHHHHHHHHHHHHHHccCCccCCCCCCCCCceee
Q psy13846        157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPAL-SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKK  235 (1423)
Q Consensus       157 V~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~-~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk  235 (1423)
                      ||||+||+.+.++|+++|++  |+++++.+++...|......... .....+.+...+.+.+.+.+.|++||+.++.+++
T Consensus        81 V~h~~f~~~i~~lL~~~c~~--C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~cg~~~~~i~~  158 (880)
T 4ayb_A           81 VIHVGFVKHVYEFLKATCRR--CGRVKISEDEIEKYSRIYNAIKKRWPSAARRLTEYVKKTAMKAQVCPHCGEKQFKIKL  158 (880)
T ss_dssp             EECGGGTTHHHHHHHTSCTT--SSCCCSSCCHHHHHHHHHHHHGGGCHHHHHHHHHHHHHHHTTCSSCTTTTCCCCCCEE
T ss_pred             ccchhHHHHHHHHHhCcccc--ccCCcCCHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHhcccccchhccchhhhhhh
Confidence            99999999999999999999  99999998887766554322111 1122344555566677888999999999998887


Q ss_pred             cCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCCCC
Q psy13846        236 CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP  315 (1423)
Q Consensus       236 ~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arP  315 (1423)
                      .....+..+.                                 + .....++|.+++++|++|+++|+.+++++++++||
T Consensus       159 ~~~~~~~~~~---------------------------------~-~~~~~l~~~~~~~~l~~i~~~~~~~l~~~~~~~~P  204 (880)
T 4ayb_A          159 EKPYNFYEER---------------------------------K-EGVAKLTPSDIRERLEKVPESDVEILGYDPTTSRP  204 (880)
T ss_dssp             EETTEEEEEE---------------------------------T-TEEEECCHHHHHHHHTTCCHHHHHHTTCCTTTCCS
T ss_pred             cCcCCHHHHH---------------------------------H-HHHHhcCHHHHHHHHHHhHHHHHHHhCCCCcCCCc
Confidence            6433322110                                 0 12346899999999999999999999999999999


Q ss_pred             cceEEEEecCCCCCCCCcEEcCCCC-------------------------------------------------------
Q psy13846        316 SDLILTRLLVPPNCIRPSVISDLKS-------------------------------------------------------  340 (1423)
Q Consensus       316 e~liLt~lpVPP~~vRPsv~~g~~~-------------------------------------------------------  340 (1423)
                      +||||++|||||+++||++.+++..                                                       
T Consensus       205 ewmil~~lPV~Pp~~RP~v~l~~g~~~~~dl~~~~~~ii~~N~~lk~~~~~~ap~~i~~~~~~~LQ~~V~~l~dn~~~g~  284 (880)
T 4ayb_A          205 EWMILTVLPVPPITIRPSIMIESGIRAEDDLTHKLVDIVRINERLKESIDAGAPQLIIEDLWDLLQYHVATYFDNEIPGL  284 (880)
T ss_dssp             GGGEEEEEEECCSSSSCC-----CCCCCCSSHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHCSCCSSS
T ss_pred             hheEEeeeeCCCCCCCchhhcCCcccccchHHHHHHHHHHhhhhhhhhhhcCCchhHHHHHHHHHHHHHHHHHhccCCCC
Confidence            9999999999999999999887642                                                       


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        341 --------------------------------------------------------------------------------  340 (1423)
Q Consensus       341 --------------------------------------------------------------------------------  340 (1423)
                                                                                                      
T Consensus       285 ~~~~~~~~rp~ksl~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~l~~~e~GvP~~~A~~Lt~Pe~vt~~N~~~l~~~  364 (880)
T 4ayb_A          285 PPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSSRTVISPDPNISIDEVGVPEIIARTLTVPERITPWNIEKLRQF  364 (880)
T ss_dssp             CCCCCTTSCCCCCHHHHHHSSSSTHHHHTSSEECSSEEEEEEEECTTSCSSEEEECHHHHTTSEEEEECCTTTHHHHHHH
T ss_pred             CccCCCCCCcccchhhhhcccchhhhhcccceeecccCceeeeCCCCccccccCCcHHHHHhCCCCeEEcHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             ------------------------------------------------CCeEEEEecCccccccccceeeeEEecCCcee
Q psy13846        341 ------------------------------------------------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFR  372 (1423)
Q Consensus       341 ------------------------------------------------~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir  372 (1423)
                                                                      +||+|||||||||||+|||||+++++|++|||
T Consensus       365 v~ng~~~~pga~~~i~~~~~~~~l~~~~~~~~~~~~l~~g~~V~rhl~dgd~VLlNRqPTLHr~si~a~~~~l~~gktir  444 (880)
T 4ayb_A          365 VINGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYVVERHLTDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFR  444 (880)
T ss_dssp             HHHTTSSSSCEEEEECSSCCEEEGGGCSSCTTHHHHCCTTCEEEEECCTTCEEEEECSSCCSGGGEEEEEEEECSSSSEE
T ss_pred             HHcCCccccchhhhhhccceEEEeecchhhhHHHHhccccceEeeeeecCcEEEecCCCcccccceeeeeeecccCceee
Confidence                                                            78999999999999999999999999999999


Q ss_pred             eccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeec
Q psy13846        373 FNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLT  452 (1423)
Q Consensus       373 ~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t  452 (1423)
                      +||++|+||||||||||||+|+|||++|||||+              .||.+.+|++||++|+|+++++||+++|+|.||
T Consensus       445 lhp~vC~~yNADFDGDeMnvHvPqS~eA~aEa~--------------~Lm~~~~nilsP~~G~Pii~~~QD~vlg~y~lT  510 (880)
T 4ayb_A          445 LNLLVCPPYNADFDGDEMNLHVPQSEEAIAEAK--------------EIMLVHKNIITPRYGGPIIGAAQDYISGAYLLT  510 (880)
T ss_dssp             ECGGGHHHHTCCSSSCEEEEECCCSHHHHHHHH--------------HHSBSGGGCBCSSSSSBCSCCCSHHHHHHHHHT
T ss_pred             eccccccccccCcccceeEEeccCCHHHHHHHH--------------HHHhChhccccCCCCCccccccccHHHHhHHhh
Confidence            999999999999999999999999999999999              999999999999999999999999999999999


Q ss_pred             ccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeeccccccc
Q psy13846        453 QKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTA  532 (1423)
Q Consensus       453 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~  532 (1423)
                      .+|.|+++.+++++++...     +  ++      .+++|+|.+|.++|||||+|++++|++.......+....++..  
T Consensus       511 ~~~~~~~~~~~~~~~~~~~-----~--~~------~~~~p~i~~~~~~~tgkqi~s~~lp~~~~~~~~~~~~~~~~~~--  575 (880)
T 4ayb_A          511 VKTTLLTKEEAQQILGVAD-----V--KI------DLGEPAILAPREYYTGKQVVSAFLPKDFNFHGQANVSSGPRLC--  575 (880)
T ss_dssp             SSSCEECHHHHHHHHTTSC-----C--CC------CCCSCSEESSSEEEEHHHHHHTTSCTTCCEEEECTTCSGGGCC--
T ss_pred             cCcccCCHHHHhhhhcccc-----e--ec------ccCccceecceeEeccceEEEEEecccccccceeEeecCCccc--
Confidence            9999999999999876543     1  12      7899999999999999999999998764322222222222211  


Q ss_pred             CcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCc
Q psy13846        533 NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ  612 (1423)
Q Consensus       533 ~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~  612 (1423)
                      ..+.++.|..|+|+||++++|.+||+.+|++..++++|.+|++||+..|..||+++++++++|++.+|||+|++|+++++
T Consensus       576 ~~~~~~~~~~v~i~~g~l~~g~ldk~~lg~~~~~~li~~i~~~~G~~~t~~~ld~l~~lg~~~lt~~GfSigi~Di~i~~  655 (880)
T 4ayb_A          576 KNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNLFRVFIRFVELQGFTMRLEDVSLGD  655 (880)
T ss_dssp             SSSCCTTSCEEEEETTEEEECCCSTTTSSTTCTTSHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHCCCCCGGGGCCCH
T ss_pred             cCccCCCcceEEEeCceeeeeeecchhhcccccceeeehhhhhcccHHHHHHHHHHHHHHHHHHHhcCCcccccccccch
Confidence            23457788999999999999999999999866789999999999999999999999999999999999999999997543


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        613 --------------------------------------------------------------------------------  612 (1423)
Q Consensus       613 --------------------------------------------------------------------------------  612 (1423)
                                                                                                      
T Consensus       656 ~~~~~i~~~i~~a~~~v~~i~~~~~~g~l~~~~g~~~~e~~e~~v~~~l~~~~~~~~~~~~~~l~~~N~i~mMa~SGARG  735 (880)
T 4ayb_A          656 DVKKEIYNEIDRAKVEVDNLIQKYKNGELEPIPGRTLEESLENYILDTLDKLRSTAGDIASKYLDPFNFAYVMARTGARG  735 (880)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTSSC
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHcCCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHhhcCccC
Confidence                                                                                            


Q ss_pred             --------------------------------------------cccccccccCCCceeeeeecccccccchhcccccCC
Q psy13846        613 --------------------------------------------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAE  648 (1423)
Q Consensus       613 --------------------------------------------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~  648 (1423)
                                                                  |||.+||++||+|+|||||||||||||+|||||||+
T Consensus       736 S~~ni~Qlagm~Gqq~~~G~RIprg~~~rtLP~f~~~d~~p~a~GfI~ssF~eGLtp~EyF~ht~ggRkGL~DTAlKTA~  815 (880)
T 4ayb_A          736 SVLNITQMAAMLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQ  815 (880)
T ss_dssp             CSTTHHHHHTCCEECBSSSSBSCCSBTTBSSTTSCTTCCSTTTTSEECSCTTTCCCHHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred             CHHHHHHHHhcccccccCCccCcCCCccCCCCCCCCCCCCcccCCeEhhcccCCCCHHHHHHhhhhhhhhHHhcchhhch
Confidence                                                        789999999999999999999999999999999999


Q ss_pred             CCcchHHHHHHHhhhhhcccceeecc-------ccCCCccC
Q psy13846        649 TGYMQRRLVKSLEDLCVQYDMSFDAA-------FYGQTDCI  682 (1423)
Q Consensus       649 sGYlqRrLvk~ledl~v~yD~tVR~s-------~yG~~~~~  682 (1423)
                      ||||||||||++|||+|+||+|||++       .||+|+.+
T Consensus       816 SGYLtRRLVdv~qDv~V~yDgTVR~~~g~ivqf~YGeDgld  856 (880)
T 4ayb_A          816 SGYMQRRLINALSDLRAEYDGTVRSLYGEVIQVAYGDDGVF  856 (880)
T ss_dssp             HHHHHHHHHHHHTTEEECTTSCEEETTTEEEESSTTTTCBC
T ss_pred             hhHHHHHHHHHHcCEEEecCCCccCCCCcEEEEecCCcccc
Confidence            99999999999999999999999987       37777543

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=100.00  E-value=8.4e-87  Score=890.75  Aligned_cols=780  Identities=20%  Similarity=0.255  Sum_probs=522.3

Q ss_pred             hHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEecCCH
Q psy13846         11 LYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKE   90 (1423)
Q Consensus        11 ~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~~S~   90 (1423)
                      .-+||||||++||+|++||+||++|+||||++||+|+|+|+||+||+|++++|++++++|+... ...+..        |
T Consensus       499 qs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~lT~~~~f~~~~e~~~l~~~~~~~-~~~~~~--------p  569 (1752)
T 3h0g_A          499 QSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIMLWVPDW-DGILPP--------P  569 (1752)
T ss_dssp             CSTTHHHHHHHTCCTTTTSEETTTTEESCCCCTHHHHHHHHHHSTTCEEETHHHHGGGGCSSSC-CSSCCC--------C
T ss_pred             CCHHHHHHHHHHhcCccceecCCCCCceeeecchhhhheeeeccccccCCHHHHHHHHHhhccc-CCccCc--------c
Confidence            4479999999999999999999999999999999999999999999999999999999985211 111111        1


Q ss_pred             HHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCceeEEeeeccHH---
Q psy13846         91 DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVI---  167 (1423)
Q Consensus        91 eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~gffd~v~---  167 (1423)
                      .        -+....+|    +||++.+-++++.++...+..    |.   ..+|-+.+++.+....+..|.+++..   
T Consensus       570 a--------i~kp~~~w----tGkqifs~ilp~~~~~~~~~~----~~---~~~~~~d~~v~i~~gell~g~l~K~~lg~  630 (1752)
T 3h0g_A          570 V--------ILKPKVLW----TGKQILSLIIPKGINLIRDDD----KQ---SLSNPTDSGMLIENGEIIYGVVDKKTVGA  630 (1752)
T ss_dssp             S--------BCSSSCEE----ETTHHHHTTSCSSBCEECCCS----SC---CSSCTTTCSEEECBSCEEEECCSHHHHSS
T ss_pred             c--------eecCcCCC----chhhHHhhhCcCCCCceeccc----cc---cCcCCCcCeEEEEcCeEEecccchHHhcc
Confidence            1        12334678    899999999988776554321    21   24566789999999999999998541   


Q ss_pred             ---HHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehhh
Q psy13846        168 ---NILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHE  244 (1423)
Q Consensus       168 ---~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e  244 (1423)
                         .|++.++..       ++.++...|++++++....++.+.+|+.++.|......                ..+...+
T Consensus       631 ~~~~li~~i~~~-------~G~~~~~~~ld~~~~l~~~~l~~~GfSigi~D~~~~~~----------------~~~~~~~  687 (1752)
T 3h0g_A          631 SQGGLVHTIWKE-------KGPEICKGFFNGIQRVVNYWLLHNGFSIGIGDTIADAD----------------TMKEVTR  687 (1752)
T ss_dssp             CTTCHHHHSSSS-------SCTTTHHHHHHHHHHHHHHHHHHHCCCCCGGGGSCCSH----------------HHHHHHH
T ss_pred             CcccHHHHHHHH-------HCHHHHHHHHHHHHHHHHHHHHhcCceechhhcccCHH----------------HHHHHHH
Confidence               345555555       78888999999999888888888888888877642110                0000111


Q ss_pred             hhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHh--------------------hccCCCccc
Q psy13846        245 KYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLF--------------------EAIPLEDIP  304 (1423)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiL--------------------e~I~~~d~~  304 (1423)
                      .+    ++..+.++++.+.|+.              +.++..++..+++.|                    +.+. .+++
T Consensus       688 ~i----~~a~~~v~~~~~~~~~--------------g~l~~~~g~~~~e~~e~~v~~~l~~~~~~~~~~~~~~l~-~~N~  748 (1752)
T 3h0g_A          688 TV----KEARRQVAECIQDAQH--------------NRLKPEPGMTLRESFEAKVSRILNQARDNAGRSAEHSLK-DSNN  748 (1752)
T ss_dssp             HH----HTTTHHHHHHHTTTTT--------------TCCCCCSSCCTTHHHHHHHHHHHHHHHHHHHHHHHTTSC-SSCT
T ss_pred             HH----HHHHHHHHHHHHHHHc--------------CCCccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCc
Confidence            11    1111222233322221              111222211111111                    2232 3578


Q ss_pred             ccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCC
Q psy13846        305 LLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNAD  384 (1423)
Q Consensus       305 lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nad  384 (1423)
                      ++.|..+|+|+++.+++||.   +|++||.+.|.+++.++                 +.|.|||    |.+.+.+|...+
T Consensus       749 ~~~M~~SGakGs~~ni~Q~~---~~~Gqq~~~GkrIp~g~-----------------~~rtLP~----f~k~d~~~~a~G  804 (1752)
T 3h0g_A          749 VKQMVAAGSKGSFINISQMS---ACVGQQIVEGKRIPFGF-----------------KYRTLPH----FPKDDDSPESRG  804 (1752)
T ss_dssp             TTHHHHHCSSCCHHHHHHHH---TCCCCCCSTTSSSCCCS-----------------TTSSSTT----SCSSCCSTTTSS
T ss_pred             HHHHhhhccccCHHHHHHHH---hccCCCccCCccCCCCC-----------------CCccCCC----CCCCCCCcccCc
Confidence            89999999999999999999   99999999999988888                 8899999    999999999999


Q ss_pred             CcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHH
Q psy13846        385 FDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM  464 (1423)
Q Consensus       385 Fdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~  464 (1423)
                      |+-+++..+|.+.|          ||||+||||||+++||++|+.|||.+|+|+..+|| |.+.||+|+||+.+++.||.
T Consensus       805 fV~~sF~~GL~p~E----------fFfhtmggReGLiDTAvKTA~SGYLqRRLVk~leD-v~V~YDgTVRns~g~ivQF~  873 (1752)
T 3h0g_A          805 FIENSYLRGLTPQE----------FFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMED-VMVRYDGTVRNAMGDIIQFA  873 (1752)
T ss_dssp             CCSSCTTTCCCHHH----------HHHHHHHHTTTTTHHHHTTTHHHHHHHHHHHHHTT-CEEETTTEEECTTSCEEESS
T ss_pred             chhhcccCCCCHHH----------HHHHhhhhhhhhhHhhhhcCcCchhHHHHHHHHhh-eEEeeCCeeEcCCCcEEEEe
Confidence            99999999999666          99999999999999999999999999999999999 99999999999999999999


Q ss_pred             HHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEEE
Q psy13846        465 RIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVI  544 (1423)
Q Consensus       465 ~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~  544 (1423)
                      |+.++++.  ..++.+                         -+..+-..+      ..+   .+.|.-  +. .+...  
T Consensus       874 YGeDGlD~--~~~e~q-------------------------~~~~~~~s~------~~f---~~~~~~--~~-~~~~~--  912 (1752)
T 3h0g_A          874 YGEDGLDA--TLVEYQ-------------------------VFDSLRLST------KQF---EKKYRI--DL-MEDRS--  912 (1752)
T ss_dssp             SSSSCBCG--GGEEEE-------------------------ECTTTSCCH------HHH---TTTSCC--CT-TTTCC--
T ss_pred             cCCCCcCh--HHhhcc-------------------------ccccccCCH------HHH---HHHhcc--cc-ccccc--
Confidence            98887742  122211                         000000000      000   000000  00 00000  


Q ss_pred             eccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHH---------------HhhhhhhHHHhhcCcceecCCCC
Q psy13846        545 LRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMW---------------RLSRMTSFYLMNRGFSIGIGDVT  609 (1423)
Q Consensus       545 i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~---------------~l~~l~~~~L~~~GfsiGi~D~~  609 (1423)
                      +      .-.+.+...++.....++..-|+..-.  ...++.               +++|+....  ...|.+  +   
T Consensus       913 ~------~~~~~~~l~~~~~~~~~l~~E~~~l~~--dr~~lr~~i~~~~~~~~~lP~N~~R~i~~~--~~~f~~--~---  977 (1752)
T 3h0g_A          913 L------SLYMENSIENDSSVQDLLDEEYTQLVA--DRELLCKFIFPKGDARWPLPVNVQRIIQNA--LQIFHL--E---  977 (1752)
T ss_dssp             G------GGTSCSCCTTSCSSTHHHHHHHHHHHH--HHTTSSSSSSSCSCCEEEEESCHHHHTTTT--TTTSCC--C---
T ss_pred             c------cHHHHHHhccCHHHHHHHHHHHHHHHH--HHHHHHHHhhccccccccCCccHHHHHHHH--HHhcCC--C---
Confidence            0      000001122221111222222221100  000000               011111000  011111  0   


Q ss_pred             CCccccccccccCCCceeee------ee---cccccccchhcccccCCCCcchHHHHHHH-----h--hhhhcccceeec
Q psy13846        610 PGQGFVQNSFFSGLTPTEFF------FH---TMGGREGLVDTAVKTAETGYMQRRLVKSL-----E--DLCVQYDMSFDA  673 (1423)
Q Consensus       610 ~~~GfI~~sf~~GL~p~Eff------fh---~maGReGLiDTAvKTa~sGYlqRrLvk~l-----e--dl~v~yD~tVR~  673 (1423)
                             .+=.+.|+|.+++      +.   ..-|-..|...|-+.|.      .|.+.+     .  .+...|-.|-..
T Consensus       978 -------~~~~s~l~p~~~~~~v~~~~~~l~~~~g~d~l~~~~~~na~------~l~~~~lr~~l~~k~~~~~~~l~~~~ 1044 (1752)
T 3h0g_A          978 -------AKKPTDLLPSDIINGLNELIAKLTIFRGSDRITRDVQNNAT------LLFQILLRSKFAVKRVIMEYRLNKVA 1044 (1752)
T ss_dssp             -------TTSCCCCCHHHHHHHHHHHHTTCCCSCCCSTTTTHHHHTSS------HHHHHHHTTSSSHHHHHHSSCCCHHH
T ss_pred             -------cCccCCCCHHHHHHHHHHHHHhhhcccCCcchhhhhhhchH------HHHHHHHHhhhhhhhhhhhcCcCHHH
Confidence                   0011223332211      00   00011111100110000      011110     0  000001000000


Q ss_pred             cccCCCccCCCcchheecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeeccc
Q psy13846        674 AFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELW  753 (1423)
Q Consensus       674 s~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~  753 (1423)
                      -     ++.-+..+..|.++.++||++||++||||||||+|||||    +|||||||             +++|+||   
T Consensus      1045 ~-----~~~~~~~~~~y~~a~v~pGe~VG~iaAQSIgEp~TQMTL----nTFHfAGv-------------as~NVTl--- 1099 (1752)
T 3h0g_A         1045 F-----EWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTL----NTFHYAGV-------------SSKNVTL--- 1099 (1752)
T ss_dssp             H-----HHHHHHHHHHHHTTBCCSSCCHHHHHHHHHHHHHHHHHH----HTTSSCCC-------------CCSSCCC---
T ss_pred             H-----HHHHHHHHHHHHHhccCcccchhhhhhcccCCchhhhhH----Hhhhhccc-------------ccccccc---
Confidence            0     000011123357899999999999999999999999999    99999999             8999999   


Q ss_pred             CCCCCccCCCCchhhHHHHhhhcCCCCceeeeecccCC--hHHHHHHHhhhhcccchhhhhhhheeeecCCCcceee---
Q psy13846        754 NPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILI---  828 (1423)
Q Consensus       754 ~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~--~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i---  828 (1423)
                                |||||||||||||+||||+|+++|.++.  +.+.|+.++++||+++|+||+++++++|+++..+..+   
T Consensus      1100 ----------GVPRLkEIInask~ikTP~mtv~L~~~~~~d~e~A~~v~~~ie~t~L~~v~~~~~i~~~p~~~~~~i~~d 1169 (1752)
T 3h0g_A         1100 ----------GVPRLKEILNVAKNIKTPSLTIYLMPWIAANMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEED 1169 (1752)
T ss_dssp             ----------SGGGHHHHHTTCSCCSCCCCEECCCSSSCSSSTTTHHHHTTSSCCSSCSCCSCEEEECCCSTTCCCCSSS
T ss_pred             ----------CcccHHHHHhhhcCCCCCeEEEEecCccccCHHHHHHHHHhhccEEHHHheeEEEEEEecCccceEEeec
Confidence                      9999999999999999999999999884  7899999999999999999999999999887544444   


Q ss_pred             ---------------------------ehhhhHHHhhccccchhhhhHHhhhcccccCcccccc----cccccccCCCCc
Q psy13846        829 ---------------------------KLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSG----HSFLILKPKDSS  877 (1423)
Q Consensus       829 ---------------------------~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~----~~~~~~~~~~~~  877 (1423)
                                                 ++.+++.++++++++++.|...|.+.+..+..+....    ...+.++.....
T Consensus      1170 ~~~v~~~~~~~~~~~~~~~~~~~~~~~rl~l~~~~~~~~~l~~~~I~~~i~~~~~~~~~v~~~d~~~~~~~i~i~~~~~~ 1249 (1752)
T 3h0g_A         1170 KDFVEAFFAIPDEEVEENLYKQSPWLLRLELDRAKMLDKKLSMSDVAGKIAESFERDLFTIWSEDNADKLIIRCRIIRDD 1249 (1752)
T ss_dssp             CSHHHHHHHTTCSSTTCSSCSCCCCEEEEECCTTSSTTTTCCHHHHTTSGGGSSTTSCCEECCCTTCSSCEEEECCCCCS
T ss_pred             HHHHHHHhccchhhhhcccccccceeEEEEecHHHHHHcCCCHHHHHHHHHhhccCCeeEeecCCCccceeEEEEecccc
Confidence                                       4444455556667778888888866543222222211    112223221110


Q ss_pred             ----c------ccchhhhhhh-hcCCceEEccccccceeeeecccc-----cc----eeEEeeeccCccccccceeeccc
Q psy13846        878 ----K------SFNSKMYQMK-QLLPSVVIKGVQGINRAVIHEEDV-----EG----VTKYKLLVEGDNLRDVMATYGVK  937 (1423)
Q Consensus       878 ----~------~~~~~l~~l~-~~l~~v~IkGi~~I~r~~i~~~~~-----~~----~~~~~l~~eG~nL~~vl~~~gvD  937 (1423)
                          +      .....++.++ ..+++++|+|++||+|++|++++.     +|    ..+|.|.|||+||+++|.++|||
T Consensus      1250 ~~~~~~~~~~~~~~~~l~~l~~~~l~~~~i~Gi~~I~rv~i~~~~~~~~~~~g~~~~~~~~~l~teG~nL~~v~~~~gVD 1329 (1752)
T 3h0g_A         1250 DRKAEDDDNMIEEDVFLKTIEGHMLESISLRGVPNITRVYMMEHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVD 1329 (1752)
T ss_dssp             CCCCCSSCCCSCSCHHHHHHHHHHTTCCCSSCCTTCCCCCEEEEEEEEECSSSCEEEEEEEEEECCSCCCSTTTSSSSCC
T ss_pred             ccccccccccccHHHHHHHHHHhhccceEEecCCCccEEEEecccceeecCCCcccccceEEEEecccCHHHHhCcCCCc
Confidence                0      1112356666 468999999999999999976542     22    46899999999999999999999


Q ss_pred             ceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       938 ~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      +.+|+||||+||+++|||||||++|++||+.||+.||++||+|||+||||+||++|++++++
T Consensus      1330 ~~rt~sNdI~ei~~vlGIEAAR~~Ii~Ei~~v~~~~G~~Vd~RHl~LlaD~MT~~G~~~~it 1391 (1752)
T 3h0g_A         1330 ATRTYSNSFVEILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAIT 1391 (1752)
T ss_dssp             TTTCCCSCHHHHHHHSCHHHHHHHHHHHHHTTSCSSSCCCCHHHHHHHHHHHTSSSSCCCCC
T ss_pred             cccCeeCCHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccCCeEEeec
Confidence            99999999999999999999999999999999999999999999999999999999999975

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...

Probab=100.00  E-value=4.6e-82  Score=846.45  Aligned_cols=788  Identities=20%  Similarity=0.234  Sum_probs=505.1

Q ss_pred             hHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcc-cccceeeeEEEecCC
Q psy13846         11 LYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG-RKVFFRGLIEGTVTK   89 (1423)
Q Consensus        11 ~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~-~~~~i~~~i~F~~~S   89 (1423)
                      .-+||||||++||++++||+||++|+||||++||+|+|+|+||++|+|++++|++++++|+-.. +....+.        
T Consensus       493 qs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~v~g~y~lT~~~~f~~~~e~~~~~~~~~~~~~~~~~pa--------  564 (1733)
T 1twf_A          493 QSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPA--------  564 (1733)
T ss_dssp             CSHHHHHHHHHHTBGGGGSEETTTTEESCCCCHHHHHHHHHHHSTTCEEEHHHHHHHHHHSTTCCSCCCCCS--------
T ss_pred             CCHHHHHHHHHHhcCcccEEecCCCCeeEeeeccccccceeeecCcccCCHHHHHHHHHhhhhhcCccCCcc--------
Confidence            4589999999999999999999999999999999999999999999999999999999986211 1111122        


Q ss_pred             HHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCceeEEeeeccH---
Q psy13846         90 EDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCV---  166 (1423)
Q Consensus        90 ~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~gffd~v---  166 (1423)
                                -+....+|    +|+++.+-++++.++...+...+       ..|+..++++.+..+.+..|.+++-   
T Consensus       565 ----------i~kp~~~w----tGkqifs~ilp~~~~~~~~~~~~-------~~~~~~d~~v~i~~gel~~g~ldKk~lg  623 (1733)
T 1twf_A          565 ----------IIKPKPLW----SGKQILSVAIPNGIHLQRFDEGT-------TLLSPKDNGMLIIDGQIIFGVVEKKTVG  623 (1733)
T ss_dssp             ----------BCSSSCEE----EHHHHHHHHSCTTCCEEECCTTC-------CTTCTTCCSEEEETTEEEESCCCHHHHS
T ss_pred             ----------ccCcccCc----cHHHHHHHhCCCCCceeecCCCc-------ccCCcccceEEEeCCcEEEeecchHHhc
Confidence                      12334678    89999999998766554322111       2344468999999999999999944   


Q ss_pred             ---HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehh
Q psy13846        167 ---INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISH  243 (1423)
Q Consensus       167 ---~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~  243 (1423)
                         ..|+..++..       ++.+....|++++++....++.+.+|+.++.|.....                    ...
T Consensus       624 ~~~~~li~~i~~~-------~G~~~a~~~ld~l~~l~~~~l~~~GfSigi~D~~~~~--------------------~~~  676 (1733)
T 1twf_A          624 SSNGGLIHVVTRE-------KGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADG--------------------PTM  676 (1733)
T ss_dssp             SCTTSHHHHHHHH-------HCHHHHHHHHHHHHHHHHHHHHTTCBCCCGGGGCCCH--------------------HHH
T ss_pred             cChhHHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHHHHcceEEehhhcCcCH--------------------HHH
Confidence               1344444444       7888888999999887777777777777776653111                    010


Q ss_pred             hhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHh--------------------hccCCCcc
Q psy13846        244 EKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLF--------------------EAIPLEDI  303 (1423)
Q Consensus       244 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiL--------------------e~I~~~d~  303 (1423)
                      +.+.+..++....+.++.+.|..              +.++.+++.+..+.|                    +.+. .++
T Consensus       677 ~~i~~~i~~a~~~v~~~~~~~~~--------------g~l~~~pg~~~~e~~e~~v~~il~~~~d~~~~~~~~~l~-~~N  741 (1733)
T 1twf_A          677 REITETIAEAKKKVLDVTKEAQA--------------NLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLK-DLN  741 (1733)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH--------------TCCCCCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSC-TTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHh--------------CCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-cCC
Confidence            11111111112223333333332              222222222222222                    1232 357


Q ss_pred             cccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccC
Q psy13846        304 PLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNA  383 (1423)
Q Consensus       304 ~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~na  383 (1423)
                      +++.|..+|+|+++.+++||.   +|+++|...|.+++.+|                 +.|.|||    |.+.+.+|...
T Consensus       742 ~i~~Ma~SGAKGs~~Ni~Q~~---~~~Gqq~~~Gkrip~g~-----------------~~RtLPh----f~k~d~~p~s~  797 (1733)
T 1twf_A          742 NVKQMVMAGSKGSFINIAQMS---ACVGQQSVEGKRIAFGF-----------------VDRTLPH----FSKDDYSPESK  797 (1733)
T ss_dssp             HHHHHHHHTSSCCHHHHHHHH---SCCEECCBTTBSCCCCB-----------------TTBSSTT----SCTTCCSTTTT
T ss_pred             CeEEEeeccCcccHHhHHHHH---hCcCCcccCCccCCCCC-----------------CCCCCCC----CCCCCCCcccc
Confidence            888999999999999999999   99999999888888888                 8999999    99999999999


Q ss_pred             CCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHH
Q psy13846        384 DFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQT  463 (1423)
Q Consensus       384 dFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~  463 (1423)
                      +|.-+.+..+|.+.|          ||||+||||||+++++++|+.|||.+|+|+..+|| +.+.||+|+||+.+++.||
T Consensus       798 GfI~ssF~~GLtp~E----------yFfh~mggReGLiDTAvKTA~SGYLqRRLVk~led-v~V~yDgTVR~s~g~IvQF  866 (1733)
T 1twf_A          798 GFVENSYLRGLTPQE----------FFFHAMGGREGLIDTAVKTAETGYIQRRLVKALED-IMVHYDNTTRNSLGNVIQF  866 (1733)
T ss_dssp             TEECSCTTTCCCHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CEECTTSCEECTTCCEEES
T ss_pred             chhhhhhhcccchHH----------HhhhhhccccchhhhceecccCCcceeehhhhhcc-eEEEecCcEecCCCCEEEE
Confidence            999999999999666          99999999999999999999999999999999999 9999999999999999999


Q ss_pred             HHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEE
Q psy13846        464 MRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYV  543 (1423)
Q Consensus       464 ~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v  543 (1423)
                      .|+.++++..  ..+.                         |-+..+-..+      ..+   .+.|.-  .. .++..+
T Consensus       867 ~YGeDGlD~~--~~e~-------------------------~~~~~~~~~~------~~f---~~~~~~--~~-~~~~~~  907 (1733)
T 1twf_A          867 IYGEDGMDAA--HIEK-------------------------QSLDTIGGSD------AAF---EKRYRV--DL-LNTDHT  907 (1733)
T ss_dssp             SGGGTTBCGG--GEEE-------------------------EECGGGSSCH------HHH---HHHHCC--CT-TCTTTS
T ss_pred             EeccccCCcc--eeec-------------------------ccccccccCH------HHH---HHHhcc--cc-cccccc
Confidence            9988876421  1110                         0010000000      000   000000  00 000000


Q ss_pred             Eeccccccccccc--cCCcCCCCCCchHHHHHHHhCHHHH-HHHHHHhhhhhhHHHhhcCcceecCCC-----CC--Ccc
Q psy13846        544 ILRNSELLAGSMD--KSTLGSGGKANVFYILLRDFGEDVA-VTAMWRLSRMTSFYLMNRGFSIGIGDV-----TP--GQG  613 (1423)
Q Consensus       544 ~i~~~ell~g~ld--K~~~g~~~~~~li~~i~~~~G~~~a-~~~l~~l~~l~~~~L~~~GfsiGi~D~-----~~--~~G  613 (1423)
                            +-..+.+  +...++   ..+...+.++|..-.. ..++..        +...|-..-...+     +.  ..-
T Consensus       908 ------l~~~~~~~~~~~~~~---~~~~~~l~~e~~~l~~~r~~lr~--------i~~~~~~~~~~P~ni~r~i~~~~~~  970 (1733)
T 1twf_A          908 ------LDPSLLESGSEILGD---LKLQVLLDEEYKQLVKDRKFLRE--------VFVDGEANWPLPVNIRRIIQNAQQT  970 (1733)
T ss_dssp             ------CCTTTBTTHHHHTTC---HHHHHHHHHHHHHHHHHHHHHHH--------HTTTCCCEEEEESCHHHHHHHHHHH
T ss_pred             ------CCHHHHHHHHHhhcc---HHHHHHHHHHHHHHHHHHHHHHH--------hhccccccccCChhHHHHHHHHHHH
Confidence                  0000000  011111   1122222222210000 011110        0011110000000     00  000


Q ss_pred             c-cccccccCCCceeeeeecccccccchhccc-ccCC---CCcch-------HHHHHH-Hhh--hhhcccceeeccccCC
Q psy13846        614 F-VQNSFFSGLTPTEFFFHTMGGREGLVDTAV-KTAE---TGYMQ-------RRLVKS-LED--LCVQYDMSFDAAFYGQ  678 (1423)
Q Consensus       614 f-I~~sf~~GL~p~Efffh~maGReGLiDTAv-KTa~---sGYlq-------RrLvk~-led--l~v~yD~tVR~s~yG~  678 (1423)
                      | +..+..+.|+|.+++-.   =|+ +.+..+ +...   +-+.|       ++++.. |..  +...|..+-..  +  
T Consensus       971 f~~~~~~~s~l~p~~~~~~---v~~-~~~~~~~~~g~d~l~~~~~~n~~~l~~~~~rs~L~~k~~~~~~~l~~~~--~-- 1042 (1733)
T 1twf_A          971 FHIDHTKPSDLTIKDIVLG---VKD-LQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQA--F-- 1042 (1733)
T ss_dssp             TTCCTTSCBCCCHHHHHHH---HHH-HHTTCCSCCCCSHHHHHHHHHTTHHHHHHHHHHSCHHHHHHTSCCCHHH--H--
T ss_pred             hcccccccccCCHHHHHHH---HHH-HHHhhhcccCCcchhhhhhhchHHHHHHHhhhhhhhhhhhhhcCCCHHH--H--
Confidence            0 00011123333322100   000 000000 0000   00111       111110 000  00011001000  0  


Q ss_pred             CccCCCcchheecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCC
Q psy13846        679 TDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDY  758 (1423)
Q Consensus       679 ~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~  758 (1423)
                       +..-+..+..|.+++++|||+||++||||||||+|||||    +||||||+             |++|+||        
T Consensus      1043 -~~~l~~i~~ky~~a~v~pGe~VG~iaAQSigEp~TQMTL----nTFHfAGv-------------a~~NVTL-------- 1096 (1733)
T 1twf_A         1043 -DWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTL----NTFHFAGV-------------ASKKVTS-------- 1096 (1733)
T ss_dssp             -HHHHHHHHHHHHHHBCCTTCCHHHHHHHHHHHHHTTCCC---------------------------CCSCC--------
T ss_pred             -HHHHHHHHHHHHhccCCCCchhhhHhhhhcCCccccccc----cccccccc-------------cccCccc--------
Confidence             000000112356789999999999999999999999999    99999999             8999999        


Q ss_pred             ccCCCCchhhHHHHhhhcCCCCceeeeecccCC--hHHHHHHHhhhhcccchhhhhhhheeeecCCC-------------
Q psy13846        759 KLSQDGVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVPDD-------------  823 (1423)
Q Consensus       759 ~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~--~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~-------------  823 (1423)
                           |||||+|||||||+||||+|+++|.++.  +.+.|+.++++||+++|+||+++++++|+++.             
T Consensus      1097 -----GVPRLkEIinask~ikTP~mtv~L~~~~~~~~e~A~~v~~~ie~ttL~dv~~~i~i~~dp~~~~tvi~ed~~~~~ 1171 (1733)
T 1twf_A         1097 -----GVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQ 1171 (1733)
T ss_dssp             -----HHHHHHHHTTTCSSCSSCEEEEEBCSSSSSCHHHHHHHHHHHSCEEGGGTEEEEEEEECCCSSSCSSGGGHHHHH
T ss_pred             -----CcHHHHHHHHhccCCCCCeEEEEeCCcccccHHHHHHHHHhhceeEHHHhhheEEEEEccCccceeeecchhhhh
Confidence                 9999999999999999999999999874  78999999999999999999999999887761             


Q ss_pred             c-----------------ceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccc----c--ccccCCCC--c-
Q psy13846        824 S-----------------FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHS----F--LILKPKDS--S-  877 (1423)
Q Consensus       824 ~-----------------~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~----~--~~~~~~~~--~-  877 (1423)
                      .                 .+.+++++++.+++.++++++.|...|.+..+....+...+++    .  +.+.....  + 
T Consensus      1172 ~y~~i~~~d~~~~~~~~~~~~lrl~l~~~~~~~~~l~~~~I~~~i~~~~~~~~~~~~~d~~~~~~~~~i~~~~~~~~~~~ 1251 (1733)
T 1twf_A         1172 LHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAE 1251 (1733)
T ss_dssp             TSSCC----------CCCSEEEEEEECHHHHHHTTCCHHHHHHHHHHHHGGGEEEEECCTTSSSCEEEEEEC--------
T ss_pred             hhhcccHHhhcchhhhcccceeEEEecHHHHHhcCCCHHHHHHHHHHhhCCCcceecCCcccchhheeeeeccCcccccc
Confidence            1                 2356777888888888888888888886543211111111110    1  11111000  0 


Q ss_pred             -cc-cchhhhhh-hhcCCceEEccccccceeeeecc-------cc--cceeEEeeeccCccccccceeecccceeeccCc
Q psy13846        878 -KS-FNSKMYQM-KQLLPSVVIKGVQGINRAVIHEE-------DV--EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNN  945 (1423)
Q Consensus       878 -~~-~~~~l~~l-~~~l~~v~IkGi~~I~r~~i~~~-------~~--~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~  945 (1423)
                       +. ....+..+ .+.+++++|+|+++|+|++|.+.       +.  +...+|+|.|+|+||+++|.+++||+.+|+|||
T Consensus      1252 ~~~~~~~~l~~l~~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~g~~~~~~~~~L~teG~nL~~vl~~~~VD~~rt~SNd 1331 (1733)
T 1twf_A         1252 TEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNS 1331 (1733)
T ss_dssp             --CCTTHHHHHHHHHHHHHCEEESCTTCCCEEEEEEEEEEECTTSSEEEEEEEEEEEESCCHHHHTTSTTBCTTTCBCSC
T ss_pred             ccchhHHHHHHHHHHhhhheEEecCCCccEEEEecccceeecCCCccccCcceEEEeecccHHHHhccCCcccccceecc
Confidence             00 00013334 66778999999999999998631       11  134689999999999999999999999999999


Q ss_pred             hHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        946 TYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       946 i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      |+||+++|||||||++|++|++.||+.||++||+|||+||||+||++|++++++
T Consensus      1332 I~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHl~LlaD~MT~~G~~~~it 1385 (1733)
T 1twf_A         1332 FIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVT 1385 (1733)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTTBSSCCCSS
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHHhhcCccccchhhhhhhhhhccCceecccc
Confidence            999999999999999999999999999999999999999999999999999985

>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C

Probab=100.00  E-value=3.1e-64  Score=603.86  Aligned_cols=291  Identities=36%  Similarity=0.560  Sum_probs=232.1

Q ss_pred             hhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc--------------cccce--------eE----
Q psy13846       1099 SACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEY--------IE---- 1152 (1423)
Q Consensus      1099 ~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG--------------~i~~~--------i~---- 1152 (1423)
                      |.++.+.|..||.|++|+||||||+|||||||||+|||||||||+||              |+.+.        +.    
T Consensus        48 ~~~~~~~~~~~y~r~lv~pGEAVGiIAAQSIGEPgTQlTLrTFH~gGva~~nvT~GlPRl~Ei~~a~k~~~tp~~~i~l~  127 (395)
T 4ayb_C           48 IDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMTIYLT  127 (395)
T ss_dssp             HHHHHHHHHHHHHHTBCCTTCCHHHHHHHHHHHHHHTCC-------------CCCSHHHHHHHHTCCSSCSSCEEEECCT
T ss_pred             HHHHHHHHHHHHHHhcCCCCchHhHHHHhhcCCchhhhccccceeeeecceeeecCccceEEecccccCCCCCceEEEec
Confidence            34999999999999999999999999999999999999999999999              11110        00    


Q ss_pred             ----------------------------EEEccCCcEEEEEEchHHHHHhcccCCHHHHHHHHHhccccCCceEEecCcE
Q psy13846       1153 ----------------------------EVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSF 1204 (1423)
Q Consensus      1153 ----------------------------~~~~~~~~~~~i~l~~~~~~~~~~~i~~~~i~~~i~~~k~~~~~~~~~~~~~ 1204 (1423)
                                                  ....+....+.+.++...++  ...++++++..++.+++.....+..++...
T Consensus       128 ~~~~~~~e~~~~~~~~ie~~~~~~~~~~~~i~~~~~~~~~~~d~~~~~--~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~  205 (395)
T 4ayb_C          128 DEYKHDKEKALEVARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLK--DKGVTVDDVKKAINRLKLGEFVIDESEGNT  205 (395)
T ss_dssp             TTGGGCHHHHHHHHHHHHCCCHHHHEEEEEEETTTTEEEEEECGGGGB--TTBCHHHHHHHHHHHSCCSSEEEEECSSEE
T ss_pred             ccccccHHHHHhhccceeEEEccceeeeeEEeecccceeeehhhhhhh--hcCccHHHHHHHHhhhccCcEEEecccCcE
Confidence                                        01122233344555554433  346788899988877654222222333344


Q ss_pred             EEEEeCCCCchhhhHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhcccccceecccccHHH
Q psy13846       1205 LILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284 (1423)
Q Consensus      1205 i~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~ 1284 (1423)
                      +.+.+...  +....|..+++.+.++.|+|++||.|+.+.+.    .++|.+.|+|.|+.++|..+++|+++++||||++
T Consensus       206 ~~~~~~~~--~~v~~l~~~~~~~~~~~i~gi~gi~r~~~~~~----~~~~~~~t~g~~l~~~~~~~~vd~~~~~sn~i~e  279 (395)
T 4ayb_C          206 LNISFANI--DSIAALFKLRDKILNTKIKGIKGIKRAIVQKK----GDEYIILTDGSNLSGVLSVKGVDIAKVETNNIRE  279 (395)
T ss_dssp             EEEECCSS--CCCCCTHHHHHHHHHHCCCSSSSCCEEEEEEE----TTEEEEEEESCCHHHHTTSTTCCTTTCEESCTTH
T ss_pred             EEeecCCC--chHHHHHHHHhhccccEEecccceeEEEEecc----CCEEEEEecCCCceeeeEeecccccccccCcchh
Confidence            55554321  11223444555666789999999999998754    3589999999999999999999999999999999


Q ss_pred             HHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcc
Q psy13846       1285 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAF 1364 (1423)
Q Consensus      1285 i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~ 1364 (1423)
                      |+++|||||||++|++|+++||..||++||+|||+||||+||++|.+.+++|+|++.+++|||++||||+|+++|++||+
T Consensus       280 I~~vlGiEAar~~iv~Ei~~V~~~~Gv~In~rHi~li~d~Mt~~G~~~~igr~g~s~~t~S~LsaASFqeTt~vLteAAi  359 (395)
T 4ayb_C          280 IEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAA  359 (395)
T ss_dssp             HHHHHCHHHHHHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHGGGSCCCSSSSSHHHHCSCHHHHHHHSCTHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHhHHHHHhccCceechHHhhhhhhhhhccceEeccCcccccCCCCCHHHHhcChhHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999888999999999999999999999


Q ss_pred             cCCcccccccccceeeccccccccceEEEeecC
Q psy13846       1365 YGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 1397 (1423)
Q Consensus      1365 ~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~ 1397 (1423)
                      +|++|+|+|+|||||+|+++|+|||+|+|+++.
T Consensus       360 ~Gk~D~L~GlkENVIvGklipaGTG~f~l~~~p  392 (395)
T 4ayb_C          360 RGDVEEFKGVVENIIIGHPIKLGTGMVELTMRP  392 (395)
T ss_dssp             TTCBCCCCSHHHHHHHTCCCSSGGGTCEEEECS
T ss_pred             cCCCCCCCChHHHeecCCCCCCCcCceEEEecc
Confidence            999999999999999999999999999999874

>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D

Probab=100.00  E-value=1.4e-52  Score=545.12  Aligned_cols=639  Identities=16%  Similarity=0.149  Sum_probs=362.3

Q ss_pred             hHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCC--------cccCHHHHHHHHHHhhcccccceeee
Q psy13846         11 LYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN--------AFFNRAQTMRIASTLIAGRKVFFRGL   82 (1423)
Q Consensus        11 ~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~--------~~~~~~~~~~~~~~~~~~~~~~i~~~   82 (1423)
                      .-+||||||++||++++||+||++|+|+||++||+++|+|+||++|        +|++++|++++++.   + ...++..
T Consensus       491 qs~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~---~-~i~l~a~  566 (1265)
T 1hqm_D          491 LSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYER---G-EVALNAP  566 (1265)
T ss_dssp             CSTHHHHTTSSSSBSSSSSSSCSSSSCSSCCCTTHHHHHHHTTCCCCCCCCCCCCSSCCTHHHHHTTS---S-CCSSCCC
T ss_pred             CCHHHHHHHHHHhCccccEecCCCCCeeEeeeccccceeEEeccccCCccCCCcccCCHHHHHHHHHC---C-CCCCCCc
Confidence            4579999999999999999999999999999999999999999999        79999999987652   2 1111110


Q ss_pred             EEE-----------ecCC-HH-HHh-----hc---ceeeee-c---CcccccCCCCCCcCCccccCCCCCCCCCCccCCC
Q psy13846         83 IEG-----------TVTK-ED-RVQ-----QQ---SHIQIV-S---KNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTC  137 (1423)
Q Consensus        83 i~F-----------~~~S-~e-eIr-----kl---Sv~eIt-~---~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TC  137 (1423)
                      +..           ..++ |+ .|.     ++   .+..+. .   -.+|    +|+++.+-++++.+.           
T Consensus       567 i~~~~~~~~~g~~k~~~t~P~k~I~~~~~g~~~~q~~~~~~~k~~~~~t~----~Gr~if~~~lp~~~~-----------  631 (1265)
T 1hqm_D          567 IVVAGRETSVGRLKFVFANPDEALLAVAHGLLDLQDTVTTRYLGRRLETN----PGRILFARIVGEAVG-----------  631 (1265)
T ss_dssp             SSSCCSTTSSCCCCCTTTCSHHHHHHHHTTSSCSSSCCCCEESSSEECCC----HHHHHHHHHHHHHTT-----------
T ss_pred             eEEecccccccccccccccccccccccccCccccccccceeccccceecc----CCceEEeeecccccc-----------
Confidence            000           0111 11 111     00   000000 0   1233    455555544433332           


Q ss_pred             CCCCcccCCccceEEccCceeEEeeecc--HHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHH-HHHHHH
Q psy13846        138 GQNLSDCVGHFGYIDLPLPVFHIGYFRC--VINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKS-LKKKIL  214 (1423)
Q Consensus       138 g~~~~eCpGHfGhIeL~~PV~h~gffd~--v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~-~~~~i~  214 (1423)
                         ...+|..++++       + |.+++  +..|+..+...       ++.+....|++++++....++.+.+ |+.++.
T Consensus       632 ---~~~~p~~~~~~-------n-gvldKk~lG~LI~~i~~~-------~G~~~a~~~ld~l~~l~~~~lt~~G~fSigi~  693 (1265)
T 1hqm_D          632 ---DEKVAQELIQM-------D-VPQEKNSLKDLVYQAFLR-------LGMEKTARLLDALKYYGFTLSTTSGIITIGID  693 (1265)
T ss_dssp             ---CTTTTTTSSCC-------S-SCCCSSHHHHHHHHHHHH-------SCHHHHHHHHHHHHHHHHHHHHHTTCCCCSSS
T ss_pred             ---ccCCCCCCceE-------e-eeecHHHHHHHHHHHHHH-------HCHHHHHHHHHHHHHHHHHHHHhCCCceEeec
Confidence               01234444431       1 44553  23455554444       7888899999999988777777777 777766


Q ss_pred             HHccCCccCCCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChh----hhhhhccCccccCCHHH
Q psy13846        215 ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPE----IEAHKKFGLIQTLNPLE  290 (1423)
Q Consensus       215 ~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~L~p~~  290 (1423)
                      |......             |....+..           +..+++..+.|..-.-...+    +-.... . ....-+..
T Consensus       694 D~~~~~~-------------k~~~i~~a-----------~~~v~~i~~~y~~g~lt~~e~~~~v~~~~~-~-~~d~~~~~  747 (1265)
T 1hqm_D          694 DAVIPEE-------------KQRYLEEA-----------DRKLRQIEQAYEMGFLTDRERYDQVIQLWT-E-TTEKVTQA  747 (1265)
T ss_dssp             SCCCCST-------------TTTHHHHH-----------HHHHHHHHTTTTSSSSCHHHHHHHHHHHHH-H-HHHHHHHH
T ss_pred             cccCCHH-------------HHHHHHHH-----------HHHHHHHHHHHHcCCCcHHHHHHHHHHHHH-H-HHHHHHHH
Confidence            6532110             00111111           11111111111100000000    000000 0 00001233


Q ss_pred             HHHHhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCc
Q psy13846        291 VLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRT  370 (1423)
Q Consensus       291 V~eiLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~t  370 (1423)
                      +.+.|..- ..+++++.|..+|||+++.+++||.   +|+++++..++++                         ++   
T Consensus       748 ~~~~l~~~-~~~N~i~~Ma~SGAKGS~~ni~Ql~---g~~G~ma~~~G~~-------------------------i~---  795 (1265)
T 1hqm_D          748 VFNNFEEN-YPFNPLYVMAQSGARGNPQQIRQLC---GMRGLMQKPSGET-------------------------FE---  795 (1265)
T ss_dssp             HHHHHHHS-CSSSCTTTTTTTSSSCCHHHHHHHS---SCCCCCCCTTSCC-------------------------CS---
T ss_pred             HHHHhccc-CCCCcHHHHHHhcCCcCHHHHHHHH---hhccccccCCCCc-------------------------cC---
Confidence            44444422 2357899999999999999999999   9999876443331                         11   


Q ss_pred             eeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEe
Q psy13846        371 FRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYL  450 (1423)
Q Consensus       371 ir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~  450 (1423)
                                   .|.-+++..+|.+.|          ||||+||||||++|||.+|+.|||.+|+|+...|| +++.|+
T Consensus       796 -------------~pI~ssF~eGLtp~E----------yFfhtmggReGLiDTAvKTA~SGYLqRRLVkv~qD-v~V~~d  851 (1265)
T 1hqm_D          796 -------------VPVRSSFREGLTVLE----------YFISSHGARKGGADTALRTADSGYLTRKLVDVAHE-IVVREA  851 (1265)
T ss_dssp             -------------CCCCCCBTTBCTTCT----------HHHHHHHHTTHHHHHTHHHHTSSSTHHHHHHHSCS-CCCCSC
T ss_pred             -------------cccccccccCCChHH----------hheecccccccchhhhhhcccCCcceeeeeeecce-EEEEEC
Confidence                         247778889999776          99999999999999999999999999999999999 666655


Q ss_pred             ecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeeccccc
Q psy13846        451 LTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAY  530 (1423)
Q Consensus       451 ~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~  530 (1423)
                      -+.-+                      .+ +        .+..+.      .|+.+.+..+....      .+.  .+.+
T Consensus       852 dc~t~----------------------dG-i--------~v~~~~------~~~~i~~~~~~~~~------~L~--~ri~  886 (1265)
T 1hqm_D          852 DCGTT----------------------KY-I--------SVPLFQ------MDEVTRTLRLRKRS------DIE--SGLY  886 (1265)
T ss_dssp             CCCCC----------------------CC-E--------ECCSEE------CCSTTCCCEECCTT------TTH--HHHT
T ss_pred             CCCCC----------------------CC-E--------EEEEee------cCceeechhhhhhh------HHH--HHHH
Confidence            54210                      00 0        011110      02111111110000      000  0000


Q ss_pred             ccCcccccCCcE---EEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCC
Q psy13846        531 TANEEFCHRDSY---VILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD  607 (1423)
Q Consensus       531 ~~~~~~~~~d~~---v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D  607 (1423)
                        +... ..+..   +--..++++        .   ..+..+                 ...++     ...    |+..
T Consensus       887 --gr~~-~~~i~~~~~~p~~~~~i--------~---~~~~~i-----------------~~~~i-----~~~----gi~~  926 (1265)
T 1hqm_D          887 --GRVL-AREVEALGRRLEEGRYL--------S---LEDVHF-----------------LIKAA-----EAG----EVRE  926 (1265)
T ss_dssp             --TCEE-SSCEEETTEEECSSCBC--------C---TTHHHH-----------------HHHHH-----HTT----SCSS
T ss_pred             --hhhh-hhcccccccCCCCccEE--------e---cCcchh-----------------hHHHH-----HHc----CCCE
Confidence              0000 00000   000001110        0   000111                 00011     001    1110


Q ss_pred             CCCCccccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeeccccCCCccCCCcch
Q psy13846        608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSE  687 (1423)
Q Consensus       608 ~~~~~GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~~~~~  687 (1423)
                      +..                         |      ++-|-++                  -..|=..|||.+        
T Consensus       927 v~i-------------------------R------s~ltc~s------------------~~gvc~~CYgr~--------  949 (1265)
T 1hqm_D          927 VPV-------------------------R------SPLTCQT------------------RYGVCQKCYGYD--------  949 (1265)
T ss_dssp             CEE-------------------------E------CGGGCSC------------------TTSCCSSSSCSC--------
T ss_pred             EEe-------------------------e------cCcCHHH------------------HHHHHHHHhhhh--------
Confidence            000                         0      0001111                  001112267776        


Q ss_pred             heecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCcccccccccccccccc-ccceeecccCCCCCccCCCCch
Q psy13846        688 CIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTA-SVKVTLELWNPGDYKLSQDGVP  766 (1423)
Q Consensus       688 ~~~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~a-s~~itl~~~~~g~~~~~~~GvP  766 (1423)
                       ++.+.+++||+|||++||||||||+||+||    +|||++|+             | +++|||             |+|
T Consensus       950 -La~~~lV~~GEaVGiIAAQSIGEPGTQlTL----rTFH~gGv-------------as~~dIT~-------------GLP  998 (1265)
T 1hqm_D          950 -LSMARPVSIGEAVGVVAAESIGEPGTQLTM----RTFHTGGV-------------AVGTDITQ-------------GLP  998 (1265)
T ss_dssp             -SSSSSCCCTTCCHHHHHHHHHHGGGTTSCC----CC---------------------CCTTSS-------------HHH
T ss_pred             -hccCCEeccCceeeeeeccccCCCCceeee----EEEEEcce-------------eccccccc-------------Cch
Confidence             456789999999999999999999999999    99999999             7 489999             999


Q ss_pred             hhHHHHhhhcCCCCceeeeecccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhh
Q psy13846        767 RIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDS  846 (1423)
Q Consensus       767 RlkEIinaSk~ikTPiitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~  846 (1423)
                      |++||++|++ ||||.|.+++.....               +++         ..+...+.+.                 
T Consensus       999 Rv~El~eArk-pk~p~i~a~~~g~v~---------------~~~---------~~~~~~i~i~----------------- 1036 (1265)
T 1hqm_D          999 RVIELFEARR-PKAKAVISEIDGVVR---------------IEE---------GEDRLSVFVE----------------- 1036 (1265)
T ss_dssp             HHHHHHHCCC-CSSCBCCCSSSCBCC---------------CCC---------CSSCCCCCCB-----------------
T ss_pred             hHHHHHhhcC-CCCceEEEeccceEE---------------Eee---------cCCccEEEEE-----------------
Confidence            9999999876 999999887754211               000         0000000000                 


Q ss_pred             hhHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCcc
Q psy13846        847 IRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN  926 (1423)
Q Consensus       847 I~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~n  926 (1423)
                                                .......+                 -++...++.+++.+.  .      ..|  
T Consensus      1037 --------------------------~~g~~~~~-----------------~ip~~~~l~v~~g~~--v------~~g-- 1063 (1265)
T 1hqm_D         1037 --------------------------SEGFSKEY-----------------KLPKDARLLVKDGDY--V------EAG-- 1063 (1265)
T ss_dssp             --------------------------CSSCCCCC-----------------CCSSCCCCCCCSCCS--S------TTC--
T ss_pred             --------------------------ECCcEEEE-----------------EcCCceEEEEecCCE--E------ecC--
Confidence                                      00000000                 012223333332111  0      011  


Q ss_pred             ccccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------
Q psy13846        927 LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-------  999 (1423)
Q Consensus       927 L~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-------  999 (1423)
                                +.....+||++||++++||||+|..|++|++++++.||++||.|||+||||+||++++|...|       
T Consensus      1064 ----------~~lteG~~~~~eil~v~Giea~~~~lv~EIq~vyr~QGv~I~dkHievivrqM~~kv~i~~~g~t~~l~G 1133 (1265)
T 1hqm_D         1064 ----------QPLTRGAIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSPLLEG 1133 (1265)
T ss_dssp             ----------SCCCCSBSHHHHHHHTTHHHHHHHHHHHHHHHHHHTTSCCCCSSTHHHHHHHHTTEECBSSCCSSCCSCC
T ss_pred             ----------ceeeccCccHHHHHHHhhHHHHHHHHHHHHHHHHHHcCccccHHHHHHHHHHHhcceEEecCCCcCCCCC
Confidence                      122233589999999999999999999999999999999999999999999999999998644       


Q ss_pred             cchhhHHHHHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhh
Q psy13846       1000 TPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTS 1046 (1423)
Q Consensus      1000 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~ 1046 (1423)
                      ..|+..++.+.+++....+.+|+.....+++++++.|++++|+++||
T Consensus      1134 e~v~~~~~~~~n~~~~~~g~~~~~~~~~llGITkasl~t~SflsaAS 1180 (1265)
T 1hqm_D         1134 QVLEKWDVEALNERLIAEGKVPVAWKPLLMGVTKSALSTKSWLSAAS 1180 (1265)
T ss_dssp             CEEGGGTTTTTTTTTTC---CCCCBCCCCCCTHHHHTSCSCHHHHTT
T ss_pred             ceecHHHHHHHHHHHHhcCCCcceeeeeeecceecccccCChhhccc
Confidence            56777777777766666666777777778899999999999998877

>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus}

Probab=100.00  E-value=5.8e-49  Score=468.60  Aligned_cols=248  Identities=31%  Similarity=0.535  Sum_probs=200.2

Q ss_pred             HHHHHHHHhh-cccccceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCC
Q psy13846         63 QTMRIASTLI-AGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNL  141 (1423)
Q Consensus        63 ~~~~~~~~~~-~~~~~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~  141 (1423)
                      .+|+|..|+. .....+|.+ |+||++|||||+++||++|+++++|  |.+|+|+.|||||||||++++...|+|||++.
T Consensus        52 ~smnI~~rl~~~d~~~~i~~-i~F~~~s~eeI~~~Sv~~I~~~~~~--d~~~~P~~gGl~D~rlG~~~~~~~C~TCg~~~  128 (436)
T 3qqc_A           52 KAMVIRPKLNLSEGGKVIGS-IEFGILSPQEIRKMSAVEVTVPDTY--DDDGYPIEGGVMDKRMGVIDPGLRCETCGGRA  128 (436)
T ss_dssp             HHTTBCCEEEEEC--CEEEE-EECCBCCHHHHHHTEEEECCBCCCC--C----CCCSBSSCSSSCCCSSCCCCSSSCCCS
T ss_pred             HhCCeeceeecccccceeee-eeeccCCHHHHHHhCCeEEeccccc--CCCCCccCCCccCccccCCCCCCCCCCCCCCC
Confidence            3445555544 223478899 9999999999999999999999999  77899999999999999999999999999999


Q ss_pred             cccCCccceEEccCceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCc
Q psy13846        142 SDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVS  221 (1423)
Q Consensus       142 ~eCpGHfGhIeL~~PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k  221 (1423)
                      .+||||||||+|+.||||||||+++++||+|+|++  |+++++++++...|.++++++......++.+.+.+++.|++.+
T Consensus       129 ~~CpGHfGhIeL~~PVfh~gF~~~I~kILr~vC~~--C~klll~~~~~~~f~~~lr~~~~~~~~~k~~~~~i~~~~k~~~  206 (436)
T 3qqc_A          129 GECPGHFGHIELARPVIHVGFAKTIYRILESTCRE--CGRIKLTDEEIEEYMKKIELARNRRSEFNEIIKEIHKKAKERM  206 (436)
T ss_dssp             SSCCCCEEEEEEEEEEECGGGHHHHHHHHHHSCST--TCCCSSCHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHTCC
T ss_pred             CcCCCCceeEeechHHHHHHHHHHHHHHHHHHHHH--hcccccccccHHHHHHHHHhhhhccccHHHHHHHHHHHcccCC
Confidence            99999999999999999999999999999999999  9999999988888999888765555567888999999999999


Q ss_pred             cCCCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCC
Q psy13846        222 VCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLE  301 (1423)
Q Consensus       222 ~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~  301 (1423)
                      +|++||+.||.||+++.... .+   .. +  +++                  +   . ...+.|+|.+|+++|++|+++
T Consensus       207 ~C~gCG~~qp~Ir~e~~~~~-~~---~~-~--~~~------------------~---~-~~k~~LtP~~vl~ifk~Isde  257 (436)
T 3qqc_A          207 VCPHCGAPQYPIKFEKPTIY-WE---IR-K--DEQ------------------G---N-EYRHRLMPTEVRDWLEKIPDK  257 (436)
T ss_dssp             SCC-------CCCBCSSSCE-EE---EC-C--C------------------------C-CCEEEECHHHHHHHHHHSCTT
T ss_pred             cCcccCCcCceEEEecceee-ee---cc-c--ccc------------------c---c-ccccccCHHHHHHHHHhCCHH
Confidence            99999999999999874221 11   00 0  000                  0   0 235689999999999999999


Q ss_pred             cccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCC--CCCeE
Q psy13846        302 DIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLK--SDNDV  344 (1423)
Q Consensus       302 d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~--~~~d~  344 (1423)
                      |+.+||++++.+||+||||++|||||+++||++.+++.  .++|.
T Consensus       258 D~~lLGl~~~~~rPewmIlt~LPVpPp~vRPsv~~~~g~~~edDL  302 (436)
T 3qqc_A          258 DLPLLGLDPEKSRPEWMVLTVLPVPPVTARPSITLETGIRAEDDL  302 (436)
T ss_dssp             TGGGSSCCTTTCCGGGGEEEEEEECCGGGSCCBCC---CCBCCHH
T ss_pred             HHHHhcccccCCCcceeEeeccccCCCcCcccEEeCCCcCCCChH
Confidence            99999999999999999999999999999999998643  45565

>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D

Probab=100.00  E-value=2.6e-50  Score=521.45  Aligned_cols=632  Identities=16%  Similarity=0.133  Sum_probs=368.5

Q ss_pred             hhHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccC--------CcccCHHHHHHHHHHh-hc-ccccce
Q psy13846         10 TLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQK--------NAFFNRAQTMRIASTL-IA-GRKVFF   79 (1423)
Q Consensus        10 ~~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~--------~~~~~~~~~~~~~~~~-~~-~~~~~i   79 (1423)
                      -.-+||||||++||++++||+||++|+|+||.+||+++|+|+||++        ++|+++++++++++.- +. .....+
T Consensus       750 PqS~eAraEA~~LM~~~~nilsP~~G~Pi~~~~QD~vlG~y~LT~~~~~~~~~g~~F~~~~e~~~ay~~~~~~l~~~i~v  829 (1524)
T 2a6h_D          750 PLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKV  829 (1524)
T ss_dssp             CCSHHHHHHHHHHSBTTTCCBCSSSSSBSSCCCHHHHHHHHHHHCCCCCCCCSCCCTTSCHHHHHHHHHHHHTTSSCSSC
T ss_pred             CCCHHHHHHHHHHhCCccceecCCCCCeeeeecccchhhheecccccccccCCCceeCCHHHHHHHHhcCCcCcCCceEE
Confidence            3458999999999999999999999999999999999999999998        4899999999876521 10 111111


Q ss_pred             --eeeE-----EEecCCHHH-HhhcceeeeecCcccccCCCCCCcCC----------------------ccccCCCCCCC
Q psy13846         80 --RGLI-----EGTVTKEDR-VQQQSHIQIVSKNLYCQDPQRTPIPH----------------------GLLDRRMGTNQ  129 (1423)
Q Consensus        80 --~~~i-----~F~~~S~ee-IrklSv~eIt~~~~y~~D~~g~P~~g----------------------GLlD~rLG~~~  129 (1423)
                        +. |     .+.+..|.+ |.+-          |    +|+++.+                      .+++..++   
T Consensus       830 ~~~~-~~~~~~~~~~p~P~~aIlKp----------w----tGKQi~~~~~~~~I~~~~~~tt~Gr~ifn~~lp~~l~---  891 (1524)
T 2a6h_D          830 AGRE-TSVGRLKYVFANPDEALLAV----------A----HGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVE---  891 (1524)
T ss_dssp             CCSS-CCHHHHHCEESSHHHHHHHH----------H----TTSSCTTSCCEEECSSCEECCCHHHHHHHHHHHHHSS---
T ss_pred             eccc-ccccccccccCCchhhhcCC----------C----CCccccccccccceecceeecccchhhHHHHhhhhcc---
Confidence              11 1     111223332 2210          3    3333322                      22211111   


Q ss_pred             CCCccCCCCCCCcccCCccceEEccCceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHH
Q psy13846        130 KEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSL  209 (1423)
Q Consensus       130 ~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~  209 (1423)
                                 ...+|..++++       + |.++  ++-|..+...  |++. ++.+....|++++++....++.+.+|
T Consensus       892 -----------~~~~P~d~~~i-------n-GvLd--Kk~LG~LI~~--i~~~-yG~~~t~~fLD~lk~Lg~~~lt~~Gf  947 (1524)
T 2a6h_D          892 -----------DEKVAWELIQL-------D-VPQE--KNSLKDLVYQ--AFLR-LGMEKTARLLDALKYYGFTFSTTSGI  947 (1524)
T ss_dssp             -----------CHHHHHHTCCT-------T-SCCC--HHHHHHHHHH--HHHH-TCHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             -----------cccCCCcccce-------e-ceec--HHHHHHHHHH--HHHH-hCHHHHHHHHHHHHHHHHHHHHhcCc
Confidence                       11224333332       1 5566  4444444444  4443 78888999999999888888888888


Q ss_pred             HHHHHHHccCCccCCCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhh----hhhccCcccc
Q psy13846        210 KKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIE----AHKKFGLIQT  285 (1423)
Q Consensus       210 ~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~  285 (1423)
                      +.++.|......             |.   +++.    +    ....+++..+.|+.-.-...+..    ...+ ... .
T Consensus       948 SIGI~Dlii~~~-------------K~---eiI~----e----A~~~v~~i~~~y~~G~lt~~Er~~~Vi~iw~-~a~-d 1001 (1524)
T 2a6h_D          948 TIGIDDAVIPEE-------------KK---QYLE----E----ADRKLLQIEQAYEMGFLTDRERYDQILQLWT-ETT-E 1001 (1524)
T ss_dssp             CCCSTTSCCCTT-------------HH---HHHH----H----HHHHHHHHHHHHHTTCSCHHHHHHHHHHHHH-HHH-H
T ss_pred             eeehhhccCCHH-------------HH---HHHH----H----HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH-HHH-H
Confidence            888877642110             00   1111    0    11112222222221000000000    0000 000 0


Q ss_pred             CCHHHHHHHhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEE
Q psy13846        286 LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKV  365 (1423)
Q Consensus       286 L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~  365 (1423)
                      .-+..+.+.|..- ..+++++.|..+|||+++.+++||.   +|++++....++                         +
T Consensus      1002 ~v~~~~~~~L~~~-~~~N~i~~Ma~SGAKGS~~NI~Ql~---gmrGqma~p~Gk-------------------------i 1052 (1524)
T 2a6h_D         1002 KVTQAVFKNFEEN-YPFNPLYVMAQSGARGNPQQIRQLC---GLRGLMQKPSGE-------------------------T 1052 (1524)
T ss_dssp             HHHHHHHHHHHHT-CTTCHHHHHHHSSSSCCHHHHHHHT---SCCCCCBCSSSC-------------------------B
T ss_pred             HHHHHHHHhhccc-CCCCCHHHHHHhcCCcCHHHHHHHH---hhccccccCCCC-------------------------C
Confidence            0122333344322 2357889999999999999999999   999986533222                         1


Q ss_pred             ecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceE
Q psy13846        366 LPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFI  445 (1423)
Q Consensus       366 ~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~  445 (1423)
                      +|     +           +.-+++..+|.+.|          ||||+||||+|+++|+.+|+.|||.+|+|+...|| +
T Consensus      1053 Ip-----~-----------PI~ssF~eGLtp~E----------yFfhtmGgReGLvDTAvKTAdSGYLqRRLVkv~qD-v 1105 (1524)
T 2a6h_D         1053 FE-----V-----------PVRSSFREGLTVLE----------YFISSHGARKGGADTALRTADSGYLTRKLVDVTHE-I 1105 (1524)
T ss_dssp             CS-----S-----------CCCCCSSSCCCSHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-C
T ss_pred             cc-----c-----------ccccccccCCChHH----------hheecccccCCccccceeeccCCcceeeeeeecce-e
Confidence            11     1           16677888999776          99999999999999999999999999999999999 5


Q ss_pred             EEEEeecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceee
Q psy13846        446 TGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKT  525 (1423)
Q Consensus       446 ~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~  525 (1423)
                      ++.|+-+.                 .     ..+ +        .+..+      -.|+.                    
T Consensus      1106 iVr~dDcg-----------------t-----~dG-i--------~v~~~------~~g~~-------------------- 1128 (1524)
T 2a6h_D         1106 VVREADCG-----------------T-----TNY-I--------SVPLF------QPDEV-------------------- 1128 (1524)
T ss_dssp             CBCCSCCC-----------------C-----CCC-E--------EEESB------CSCSS--------------------
T ss_pred             EEEeCCCC-----------------C-----CCC-e--------EEEEe------ecCCc--------------------
Confidence            44443331                 0     000 0        00000      00000                    


Q ss_pred             cccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceec
Q psy13846        526 KGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGI  605 (1423)
Q Consensus       526 ~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi  605 (1423)
                                    +            +.++         ..++..+..               ++.-++        -.
T Consensus      1129 --------------~------------~~~~---------~~~i~~l~~---------------ri~gR~--------~~ 1150 (1524)
T 2a6h_D         1129 --------------T------------RSLR---------LRKRADIEA---------------GLYGRV--------LA 1150 (1524)
T ss_dssp             --------------S------------SCCC---------BCCHHHHHH---------------HHTTCB--------BS
T ss_pred             --------------c------------ccch---------hHHHHHHHH---------------HHhccc--------ch
Confidence                          0            0000         001111111               111111        11


Q ss_pred             CCCCCCccccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeecc-----------
Q psy13846        606 GDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA-----------  674 (1423)
Q Consensus       606 ~D~~~~~GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s-----------  674 (1423)
                      .|+.          +.+..|.       .|       .+.-...-|+   +++.+....+. ...||+.           
T Consensus      1151 ~di~----------~~~~~p~-------~~-------e~i~~~~~~I---~~~~i~~~gi~-~v~iRS~ltC~s~~gvc~ 1202 (1524)
T 2a6h_D         1151 REVE----------VLGVRLE-------EG-------RYLSMDDVHL---LIKAAEAGEIQ-EVPVRSPLTCQTRYGVCQ 1202 (1524)
T ss_dssp             SCEE----------CSSCEEC-------TT-------CBCCTTTTTH---HHHHHHHTSCS-EEEECCGGGCCCSSCBCH
T ss_pred             hhhh----------hhccCCC-------cC-------cEEeCCCCee---hHHHHHHcCCC-cccccccccHHHHHHHHH
Confidence            1110          0011110       00       0000111133   33333332221 1344532           


Q ss_pred             -ccCCCccCCCcchheecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCcccccccccccccccc-ccceeecc
Q psy13846        675 -FYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTA-SVKVTLEL  752 (1423)
Q Consensus       675 -~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~a-s~~itl~~  752 (1423)
                       |||.+         ++.+.+++||+|||++||||||||+||+||    +|||++|+             + +++|||  
T Consensus      1203 ~CYgr~---------La~~~~v~~GeaVGiiaAQSIGEPgTQlTl----rTFH~gGv-------------~~~~dIt~-- 1254 (1524)
T 2a6h_D         1203 KCYGYD---------LSMARPVSIGEAVGIVAAQSIGEPGTQLTM----RTFHTGGV-------------AGAADITQ-- 1254 (1524)
T ss_dssp             HHHCSC---------SSSSSSCCTTCCHHHHHHHHHHSGGGTCCC----C------------------------CCCC--
T ss_pred             HHhccc---------cccCCccccccceeehhhhccCCCcccccc----eeeeeccc-------------cccccccc--
Confidence             47765         456789999999999999999999999999    99999998             6 689999  


Q ss_pred             cCCCCCccCCCCchhhHHHHhhhcCCCCceeeeecccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhh
Q psy13846        753 WNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDM  832 (1423)
Q Consensus       753 ~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~  832 (1423)
                                 |+||++||++|++...+++++- .            ..+++   +++         ..+.         
T Consensus      1255 -----------GlPRv~El~eARkpk~~aiI~e-i------------~G~V~---i~~---------~~~~--------- 1289 (1524)
T 2a6h_D         1255 -----------GLPRVIELFEARRPKAKAVISE-I------------DGVVR---IEE---------TEEK--------- 1289 (1524)
T ss_dssp             -----------SHHHHHHHHTTCCCSSBCCBCS-S------------CEEEE---ECC---------CSSC---------
T ss_pred             -----------cCcchhhheecccCCCcceEEE-e------------ceEEE---Eee---------cCCc---------
Confidence                       9999999999998888877541 1            11110   000         0000         


Q ss_pred             hHHHhhccccchhhhhHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccc
Q psy13846        833 DRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDV  912 (1423)
Q Consensus       833 ~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~  912 (1423)
                                                        ..+.+.+.+..                 .--.+|..+++.+++.+.
T Consensus      1290 ----------------------------------r~i~i~~~~~~-----------------~~~~ip~~~~l~V~~gd~ 1318 (1524)
T 2a6h_D         1290 ----------------------------------LSVFVESEGFS-----------------KEYKLPKEARLLVKDGDY 1318 (1524)
T ss_dssp             ----------------------------------EEEEEECSSCE-----------------EEEEECTTCCCCCCTTSE
T ss_pred             ----------------------------------eEEEEEcCCce-----------------eEEecCCceEEEEecCCe
Confidence                                              00111111000                 001234444444433211


Q ss_pred             cceeEEeeeccCccccccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccc
Q psy13846        913 EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK  992 (1423)
Q Consensus       913 ~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~  992 (1423)
                        ...+...++                  .+||++||++++||||||++|++|+++||+.||++||.|||+||||+||++
T Consensus      1319 --v~~g~~lte------------------G~~~~~dil~v~Giea~~~~iv~Eiq~Vyr~QGv~I~dKHIevIvrqM~~k 1378 (1524)
T 2a6h_D         1319 --VEAGQPLTR------------------GAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKY 1378 (1524)
T ss_dssp             --ECTTCBSSS------------------SBCCHHHHHHHHCHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTSE
T ss_pred             --eecCeEEec------------------CCCCchhheeecCHHHHHHHHHHHHHHHHHhcCcccchhHHHHHHHHHhce
Confidence              011122233                  358999999999999999999999999999999999999999999999999


Q ss_pred             cccccCC-------cchhhHHHHHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHHH
Q psy13846        993 GEVLGNG-------TPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIK 1054 (1423)
Q Consensus       993 G~i~g~~-------~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~ 1054 (1423)
                      ++|...|       ..|+..++.+.+.+...++..|+.....+++++++.|++++|+++||  |.+..+
T Consensus      1379 v~i~~~Gdt~~l~Ge~v~~~~~~~~n~~~~~~g~~~a~~~~~llGITkasL~t~SfLsaAS--FqeTtr 1445 (1524)
T 2a6h_D         1379 VEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAAS--FQNTTH 1445 (1524)
T ss_dssp             EEEEECSSSCSSCEEEHHHHHHHHHHHHTTSCSCCCCEEEECCCCHHHHHHSCSCHHHHHH--SSCHHH
T ss_pred             eEEecCCCccCCCCceeeHHHHHHHHHHHHHcCCCcceeeeeeeeeeecccccCChhhhcC--hHHHHH
Confidence            9998755       56788889999988888888888888888999999999999998776  544433

>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D*

Probab=100.00  E-value=1.9e-47  Score=487.44  Aligned_cols=119  Identities=16%  Similarity=0.256  Sum_probs=104.7

Q ss_pred             eecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------cchhhH
Q psy13846        933 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-------TPVELK 1005 (1423)
Q Consensus       933 ~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-------~~~~~~ 1005 (1423)
                      +...|...-.+.|++||++++||||+|++|++|+++|++.||++||+|||++++++||++++|...|       ..|+..
T Consensus      1204 v~~G~~l~~G~~~p~dil~v~Giea~~~ylv~Evq~VYr~QGV~IndKHIEvIvrqM~~kv~I~d~Gdt~fl~Ge~vd~~ 1283 (1407)
T 3lu0_D         1204 VERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYS 1283 (1407)
T ss_dssp             CCTTCCCSSSCCCHHHHHHHSCHHHHHHHTTTTTHHHHHHHTCCCCSHHHHTTTGGGTSBCEESSCSSSCSCCCCBSHHH
T ss_pred             EcCCCCccCCCCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHHHhCceEEeeCCCcccCCcceecHH
Confidence            3334666667889999999999999999999999999999999999999999999999999998755       568888


Q ss_pred             HHHHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHH
Q psy13846       1006 RLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDI 1053 (1423)
Q Consensus      1006 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~ 1053 (1423)
                      ++.+.+.+...++..|+...+.+++++++.|++++|+++||  |++..
T Consensus      1284 ~~~~~N~~~~~~g~~pa~~~p~llGITkasl~t~SflSaAS--FQeTt 1329 (1407)
T 3lu0_D         1284 RVKIANRELEANGKVGATYSRDLLGITKASLATESFISAAS--FQETT 1329 (1407)
T ss_dssp             HHHHHHHHTTSSSCCCCCEECCCCCTTTTTTSCSCTTTGGG--SSCHH
T ss_pred             HHHHHHHHHHHcCCCCceeeeeeeceeeccccCCCchhhcc--hhhHH
Confidence            99999999888888888887778899999999999998877  54443

>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C

Probab=100.00  E-value=1.3e-40  Score=399.21  Aligned_cols=270  Identities=30%  Similarity=0.438  Sum_probs=204.6

Q ss_pred             ecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhH
Q psy13846        690 IMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIK  769 (1423)
Q Consensus       690 ~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlk  769 (1423)
                      |.+++++||||||.+||||||||+|||||    +|||+||+             |++|+||             |+||++
T Consensus        59 y~r~lv~pGEAVGiIAAQSIGEPgTQlTL----rTFH~gGv-------------a~~nvT~-------------GlPRl~  108 (395)
T 4ayb_C           59 YSEGLIAPGEAIGIVAAQSVGEPGTQMTL----RTFHFAGI-------------RELNVTL-------------GLPRLI  108 (395)
T ss_dssp             HHHTBCCTTCCHHHHHHHHHHHHHHTCC------------------------------CCC-------------SHHHHH
T ss_pred             HHHhcCCCCchHhHHHHhhcCCchhhhcc----ccceeeee-------------cceeeec-------------CccceE
Confidence            56778999999999999999999999999    99999999             8999999             999999


Q ss_pred             HHHhhhcCCCCceeeeecccC--ChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhh
Q psy13846        770 EIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI  847 (1423)
Q Consensus       770 EIinaSk~ikTPiitv~L~~~--~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I  847 (1423)
                      ||+||+|+++||.++++|.++  .+.+.++.++.+++++++.+++...+..+  ....+.+.+|...  +....++.+.+
T Consensus       109 Ei~~a~k~~~tp~~~i~l~~~~~~~~e~~~~~~~~ie~~~~~~~~~~~~i~~--~~~~~~~~~d~~~--~~~~~~~~~~i  184 (395)
T 4ayb_C          109 EIVDAKKVPSTPMMTIYLTDEYKHDKEKALEVARKLEYTKIENVVSSTSIDI--ASMSIILQLDNEM--LKDKGVTVDDV  184 (395)
T ss_dssp             HHHTCCSSCSSCEEEECCTTTGGGCHHHHHHHHHHHHCCCHHHHEEEEEEET--TTTEEEEEECGGG--GBTTBCHHHHH
T ss_pred             EecccccCCCCCceEEEecccccccHHHHHhhccceeEEEccceeeeeEEee--cccceeeehhhhh--hhhcCccHHHH
Confidence            999999999999999999876  46789999999999999999987655433  2233344444433  34566777888


Q ss_pred             hHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccc
Q psy13846        848 RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL  927 (1423)
Q Consensus       848 ~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL  927 (1423)
                      ...+.+.+.....+.......+.+......  -...++.+.+.+.+..|+|++||.|+.+....    ++|.+.++|+|+
T Consensus       185 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~v~~l~~~~~~~~~~~i~gi~gi~r~~~~~~~----~~~~~~t~g~~l  258 (395)
T 4ayb_C          185 KKAINRLKLGEFVIDESEGNTLNISFANID--SIAALFKLRDKILNTKIKGIKGIKRAIVQKKG----DEYIILTDGSNL  258 (395)
T ss_dssp             HHHHHHSCCSSEEEEECSSEEEEEECCSSC--CCCCTHHHHHHHHHHCCCSSSSCCEEEEEEET----TEEEEEEESCCH
T ss_pred             HHHHhhhccCcEEEecccCcEEEeecCCCc--hHHHHHHHHhhccccEEecccceeEEEEeccC----CEEEEEecCCCc
Confidence            888876543222111111111111111100  01124455666667889999999999887543    479999999999


Q ss_pred             cccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        928 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       928 ~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      .+++.++++|..++.|||++||+++|||||||++|++|++++|..||++||+|||+|+||+||++|++.+.+
T Consensus       259 ~~~~~~~~vd~~~~~sn~i~eI~~vlGiEAar~~iv~Ei~~V~~~~Gv~In~rHi~li~d~Mt~~G~~~~ig  330 (395)
T 4ayb_C          259 SGVLSVKGVDIAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIG  330 (395)
T ss_dssp             HHHTTSTTCCTTTCEESCTTHHHHHHCHHHHHHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHGGGSCCCSS
T ss_pred             eeeeEeecccccccccCcchhhhhhhhHHHHHHHHHHhHHHHHhccCceechHHhhhhhhhhhccceEeccC
Confidence            999999999999999999999999999999999999999999999999999999999999999999999865

>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A

Probab=99.97  E-value=1.9e-34  Score=372.83  Aligned_cols=373  Identities=16%  Similarity=0.171  Sum_probs=264.4

Q ss_pred             hHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEecCCH
Q psy13846         11 LYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKE   90 (1423)
Q Consensus        11 ~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~~S~   90 (1423)
                      .-+||||||++||++++||+||++|+||||.+||+++|+|+||.+|+|++++++++++++  +.....+..        |
T Consensus       468 qS~eA~aEa~~Lm~~~~nilsP~~G~Pii~~~QD~vlg~y~lT~~~~~~~~~~~~~~~~~--~~~~~~~~~--------p  537 (880)
T 4ayb_A          468 QSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQILGV--ADVKIDLGE--------P  537 (880)
T ss_dssp             CSHHHHHHHHHHSBSGGGCBCSSSSSBCSCCCSHHHHHHHHHTSSSCEECHHHHHHHHTT--SCCCCCCCS--------C
T ss_pred             CCHHHHHHHHHHHhChhccccCCCCCccccccccHHHHhHHhhcCcccCCHHHHhhhhcc--cceecccCc--------c
Confidence            458999999999999999999999999999999999999999999999999999999874  111111111        0


Q ss_pred             HHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCceeEEeeeccH----
Q psy13846         91 DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCV----  166 (1423)
Q Consensus        91 eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~gffd~v----  166 (1423)
                      .        -+....+|    +|+++.+.++++.+....+............+-+.+.+++.+....+-.|.|++-    
T Consensus       538 ~--------i~~~~~~~----tgkqi~s~~lp~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~~g~l~~g~ldk~~lg~  605 (880)
T 4ayb_A          538 A--------ILAPREYY----TGKQVVSAFLPKDFNFHGQANVSSGPRLCKNEDCPHDSYVVIKNGILLEGVFDKKAIGN  605 (880)
T ss_dssp             S--------EESSSEEE----EHHHHHHTTSCTTCCEEEECTTCSGGGCCSSSCCTTSCEEEEETTEEEECCCSTTTSST
T ss_pred             c--------eecceeEe----ccceEEEEEecccccccceeEeecCCccccCccCCCcceEEEeCceeeeeeecchhhcc
Confidence            0        11234456    7888887777665543322222222222222333356788899999999988753    


Q ss_pred             ---HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehh
Q psy13846        167 ---INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISH  243 (1423)
Q Consensus       167 ---~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~  243 (1423)
                         ..|++.+...       ++.+....|++++++....++.+.+++.++.|....                    ....
T Consensus       606 ~~~~~li~~i~~~-------~G~~~t~~~ld~l~~lg~~~lt~~GfSigi~Di~i~--------------------~~~~  658 (880)
T 4ayb_A          606 QQPESILHWLIKE-------YSDEYGKWLMDNLFRVFIRFVELQGFTMRLEDVSLG--------------------DDVK  658 (880)
T ss_dssp             TCTTSHHHHHHHT-------SCHHHHHHHHHHHHHHHHHHHHHHCCCCCGGGGCCC--------------------HHHH
T ss_pred             cccceeeehhhhh-------cccHHHHHHHHHHHHHHHHHHHhcCCcccccccccc--------------------hhhH
Confidence               2456665555       788888899999988777777777777776665210                    0000


Q ss_pred             hhhcccccchhhHHHHHHHHhhhhhccC-------hhhhhhhccCccccCC--HHHHHHHhhccCCCcccccccccCCCC
Q psy13846        244 EKYKNRTKKKDAIVEDLLAEYNEAVKFN-------PEIEAHKKFGLIQTLN--PLEVLQLFEAIPLEDIPLLLMNAELSK  314 (1423)
Q Consensus       244 e~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~L~--p~~V~eiLe~I~~~d~~lL~m~~~~ar  314 (1423)
                      +.+.+..++....+++..+.|+...-..       .+.+...    .+.++  -.++-+....--+.+++++.|+.+|||
T Consensus       659 ~~i~~~i~~a~~~v~~i~~~~~~g~l~~~~g~~~~e~~e~~v----~~~l~~~~~~~~~~~~~~l~~~N~i~mMa~SGAR  734 (880)
T 4ayb_A          659 KEIYNEIDRAKVEVDNLIQKYKNGELEPIPGRTLEESLENYI----LDTLDKLRSTAGDIASKYLDPFNFAYVMARTGAR  734 (880)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCCCCCSSSCHHHHHHHHH----HHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTSS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCCcccccchHHHHHHHHH----HHHHHHHHHHHHHHHHhhCCCCCCHHHHhhcCcc
Confidence            0000001111222333334443211000       0000000    00000  011111222222345788899999999


Q ss_pred             CcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCccccccccc
Q psy13846        315 PSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHL  394 (1423)
Q Consensus       315 Pe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~  394 (1423)
                      ++..+++||.   .|++||...|.+++.++                 ..|+|||    |.+...+|...+|.-+.+..+|
T Consensus       735 GS~~ni~Qla---gm~Gqq~~~G~RIprg~-----------------~~rtLP~----f~~~d~~p~a~GfI~ssF~eGL  790 (880)
T 4ayb_A          735 GSVLNITQMA---AMLGQQSVRGERIKRGY-----------------MTRTLPH----FKPYDISPEARGFIYSSFRTGL  790 (880)
T ss_dssp             CCSTTHHHHH---TCCEECBSSSSBSCCSB-----------------TTBSSTT----SCTTCCSTTTTSEECSCTTTCC
T ss_pred             CCHHHHHHHH---hcccccccCCccCcCCC-----------------ccCCCCC----CCCCCCCcccCCeEhhcccCCC
Confidence            9999999999   99999999999998888                 7899999    9999999999999999999999


Q ss_pred             CCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHHHHHHhhc
Q psy13846        395 PQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI  471 (1423)
Q Consensus       395 p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~  471 (1423)
                      .+.|          ||||+||||+|++|||.+|+.|||.+|+|+...|| |.+.|++|+||+.+++.||.|+.++++
T Consensus       791 tp~E----------yF~ht~ggRkGL~DTAlKTA~SGYLtRRLVdv~qD-v~V~yDgTVR~~~g~ivqf~YGeDgld  856 (880)
T 4ayb_A          791 KPTE----------LFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSD-LRAEYDGTVRSLYGEVIQVAYGDDGVF  856 (880)
T ss_dssp             CHHH----------HHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHTT-EEECTTSCEEETTTEEEESSTTTTCBC
T ss_pred             CHHH----------HHHhhhhhhhhHHhcchhhchhhHHHHHHHHHHcC-EEEecCCCccCCCCcEEEEecCCcccc
Confidence            9666          99999999999999999999999999999999999 888999999999999999999877764

>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus}

Probab=95.63  E-value=0.0025  Score=76.53  Aligned_cols=68  Identities=34%  Similarity=0.404  Sum_probs=36.4

Q ss_pred             CCchhhhhcccc-----ceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeecccc
Q psy13846       1315 FRHPMLVADLMT-----SKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM 1384 (1423)
Q Consensus      1315 ~rHl~LiaD~Mt-----~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~ 1384 (1423)
                      -|-+.=|+|...     |+|.++| =|--.+. ++|+|.+|+||.+.+||.+|+.+|++|+++||.|+|++|+.-
T Consensus       359 ~rp~ksi~~rLkGKeGRfR~NL~G-KRVdy~~-~~s~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  431 (436)
T 3qqc_A          359 GRPLKTLAQRLKGKEGRFRGNLSG-GAGSGAG-SGSVLARAAFEITVQHLFEAAEKGEVDNLNGVIENVLIGQKH  431 (436)
T ss_dssp             SCBCCCHHHHHCC-----------------------------CCCCHHHHHHHHHHTCEEECCSSCCTTSCC---
T ss_pred             CCCccchHhhhccccceecCcCCC-CCCCccc-chhHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhhhcccc
Confidence            444555556555     4455555 3555543 679999999999999999999999999999999999999853

---

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	1423
d1twfa_	1449	e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c	7e-59
d1twfa_	1449	e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c	1e-46
d1twfa_	1449	e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c	4e-39
d1twfa_	1449	e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c	8e-35
d1twfa_	1449	e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c	2e-13
d1twfa_	1449	e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c	1e-07
d1twfa_	1449	e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c	2e-07
d1twfa_	1449	e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c	6e-05
d1smyd_	1504	e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t	5e-50
d1smyd_	1504	e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t	7e-43
d1smyd_	1504	e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t	4e-17
d1smyd_	1504	e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t	7e-15
d1smyd_	1504	e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t	3e-07
d1smyd_	1504	e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t	9e-05

>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  221 bits (563), Expect = 7e-59
 Identities = 75/342 (21%), Positives = 149/342 (43%), Gaps = 27/342 (7%)

Query: 1080 QILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTL- 1138
            +IL+    +     +        A+  + K +R+ IE  T      A  I       +  
Sbjct: 1102 EILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTV 1161

Query: 1139 -----KTFHFAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI 1193
                 +       + +   E      S  L++L++DR  +   ++ +  +   I++T   
Sbjct: 1162 IPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKN 1221

Query: 1194 SGHLTVSGHS-------FLILKPKDSSKSFNSKMYQM-----KQLLPSVVIKGVQGINRA 1241
               +  S  +         +++PK       ++   M       +L ++ ++GV+ I R 
Sbjct: 1222 DLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERV 1281

Query: 1242 VIHEEDVEGVT---------KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            V+ + D +  +         ++ L  +G NL +VM   G+   +  +N+  ++ + LGIE
Sbjct: 1282 VMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIE 1341

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            A R+ +  E+  V+ + G  +++RH  L+ D+MT++G +  +TRHG  +     L   SF
Sbjct: 1342 AGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSF 1401

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            E T + LF+A    + D   GVSE +I+G    +GTG   ++
Sbjct: 1402 EETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVM 1443

>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  181 bits (461), Expect = 1e-46
 Identities = 64/247 (25%), Positives = 107/247 (43%), Gaps = 18/247 (7%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + V+  S  +I       +   R     GL D R+G+  +   C TC + +++C GHFG+
Sbjct: 24  EEVRAISVAKIRFPETMDETQTR-AKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGH 82

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL  PVFH+G+   +  + + +C +  C ++LL E        +L   AL+    K   
Sbjct: 83  IDLAKPVFHVGFIAKIKKVCECVCMH--CGKLLLDEHN------ELMRQALAIKDSKKRF 134

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
             I    K   VC    ++        L+          T +KD +   L+  + +    
Sbjct: 135 AAIWTLCKTKMVCET--DVPSEDDPTQLVSRGGCGNTQPTIRKDGL--KLVGSWKKDRAT 190

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
               E   +      L+  E+L +F+ I ++D   L  N   S+P  +ILT L VPP  +
Sbjct: 191 GDADEPELRV-----LSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPV 245

Query: 331 RPSVISD 337
           RPS+  +
Sbjct: 246 RPSISFN 252

>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  157 bits (397), Expect = 4e-39
 Identities = 70/293 (23%), Positives = 133/293 (45%), Gaps = 53/293 (18%)

Query: 758  YKLSQDGVPRIKEIINASRNISTPIITAYLDK--DTDLDYARIVKGRLERTTLGEVCEYI 815
             K    GVPR+KEI+N ++N+ TP +T YL+     D + A++++  +E TTL  V    
Sbjct: 1090 SKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIAS 1149

Query: 816  EEVFVPDDSFILIKLDMDRIR--------------------LLHLEVD----------ID 845
            E  + PD    +I  D + I+                    LL LE+D          + 
Sbjct: 1150 EIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMG 1209

Query: 846  SIRYCIERTRGISGHLTVSGHS-------FLILKPKDSSKSFNSKMYQM-----KQLLPS 893
             +   I++T      +  S  +         +++PK       ++   M       +L +
Sbjct: 1210 QVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLEN 1269

Query: 894  VVIKGVQGINRAVIHEEDVEGVT---------KYKLLVEGDNLRDVMATYGVKGVKCSSN 944
            + ++GV+ I R V+ + D +  +         ++ L  +G NL +VM   G+   +  +N
Sbjct: 1270 ITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTN 1329

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  ++ + LGIEA R+ +  E+  V+ + G  +++RH  L+ D+MT++G +  
Sbjct: 1330 SFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTS 1382

>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  143 bits (361), Expect = 8e-35
 Identities = 89/270 (32%), Positives = 140/270 (51%), Gaps = 36/270 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 437 DNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 496

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 L A    +V+P++ +  +   QD + G   LT ++ F   
Sbjct: 497 RAE--------------LSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIEL 542

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q + +   +     D  G+I   +     P        +W+GKQI S+ + PN      
Sbjct: 543 DQVLNMLYWV----PDWDGVIPTPAIIKPKP--------LWSGKQILSVAI-PNGIHLQR 589

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            +  T             +D+ +++ + +++ G ++K T+GS     + +++ R+ G  V
Sbjct: 590 FDEGTT--------LLSPKDNGMLIIDGQIIFGVVEKKTVGS-SNGGLIHVVTREKGPQV 640

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
                  + ++ +F+L++ GFS GIGD   
Sbjct: 641 CAKLFGNIQKVVNFWLLHNGFSTGIGDTIA 670

>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 73.3 bits (179), Expect = 2e-13
 Identities = 44/58 (75%), Positives = 51/58 (87%)

Query: 613 GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           GFV+NS+  GLTP EFFFH MGGREGL+DTAVKTAETGY+QRRLVK+LED+ V YD +
Sbjct: 797 GFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNT 854

>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 54.1 bits (129), Expect = 1e-07
 Identities = 12/35 (34%), Positives = 19/35 (54%)

Query: 671  FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 705
            F+A    + D   GVSE +I+G    +GTG   ++
Sbjct: 1409 FEAGASAELDDCRGVSENVILGQMAPIGTGAFDVM 1443

>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 53.7 bits (128), Expect = 2e-07
 Identities = 49/251 (19%), Positives = 98/251 (39%), Gaps = 33/251 (13%)

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV----MENHGMSIDFRH 981
             L   +    V     + N+   V + +  E        E + +      +      +R 
Sbjct: 839  RLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRV 898

Query: 982  PMLVAD------LMTSKGEVLGN-----------GTPVELKRLLDDIIAKNSSRSDPSLS 1024
             +L  D      L+ S  E+LG+              V+ ++ L ++     +     ++
Sbjct: 899  DLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVN 958

Query: 1025 AQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSH 1084
             + I+  + +T          S+  ++DI   +++  +   V   ++++ Q  +   ++ 
Sbjct: 959  IRRIIQNAQQTFHIDH--TKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTL 1016

Query: 1085 -----QDKIGHGRESNPFPSACKA-----EACREKYVRAQIEPATAVGALAAQSIGEPGT 1134
                 + ++   R    +    +A          +++R+ + P   VG LAAQSIGEP T
Sbjct: 1017 FCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPAT 1076

Query: 1135 QMTLKTFHFAG 1145
            QMTL TFHFAG
Sbjct: 1077 QMTLNTFHFAG 1087

>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.2 bits (106), Expect = 6e-05
 Identities = 18/97 (18%), Positives = 32/97 (32%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFF 79
             L A    +V+P++ +  +   QD + G   LT ++ F    Q + +   +     V  
Sbjct: 501 SQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIP 560

Query: 80  RGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPI 116
              I          Q  S       +L   D   T +
Sbjct: 561 TPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLL 597

>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RNA-polymerase beta-prime
species: Thermus thermophilus [TaxId: 274]

 Score =  192 bits (489), Expect = 5e-50
 Identities = 72/305 (23%), Positives = 130/305 (42%), Gaps = 48/305 (15%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCE--------YIEEVF--- 1155
             +  +   +    AVG +AAQSIGEPGTQ+T++TFH  G             + E+F   
Sbjct: 1206 YDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELFEAR 1265

Query: 1156 VPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD---S 1212
             P    ++ ++D     ++ +E   + +   +E + G S    +   + L++K  D   +
Sbjct: 1266 RPKAKAVISEID----GVVRIEETEEKLSVFVE-SEGFSKEYKLPKEARLLVKDGDYVEA 1320

Query: 1213 SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHE----EDVEGVTKYKLLVEGDNLRDVMA 1268
             +          QLL     KG + + R ++ E       +GV  +   +E   +R +M 
Sbjct: 1321 GQPLTRGAIDPHQLLE---AKGPEAVERYLVEEIQKVYRAQGVKLHDKHIE-IVVRQMMK 1376

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
               V     S     +V +   +EA    ++ E K                     +  K
Sbjct: 1377 YVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGK-------------------TPVAWK 1417

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
              ++G+T+  L+   +S L+ ASF+NT+  L +AA  G+ D + G+ E +I+G  +  GT
Sbjct: 1418 PLLMGVTKSALST--KSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGT 1475

Query: 1389 GLIKL 1393
            G   +
Sbjct: 1476 GSDFV 1480

>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RNA-polymerase beta-prime
species: Thermus thermophilus [TaxId: 274]

 Score =  169 bits (429), Expect = 7e-43
 Identities = 61/277 (22%), Positives = 102/277 (36%), Gaps = 25/277 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
              VVL NR P+LH+L I A +  ++  ++ + +  VC  +NADFDGD+M VH+P +  A
Sbjct: 695 HGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFA 754

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ-----KN 455
           +AE              A++ M +  NL++P +GE L   ++D I G Y +TQ     K 
Sbjct: 755 QAE--------------ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKG 800

Query: 456 AFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNR 515
           A    A        L A       +            V     V     +    +     
Sbjct: 801 AGLEFATPEEA---LAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAVAHGIV 857

Query: 516 DCPVNANLKTKGRAY-TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKA--NVFYIL 572
           D      ++  G+   T+                E +A  + +  +     +  ++ Y  
Sbjct: 858 DLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQA 917

Query: 573 LRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
               G +     +  L      +    G +IGI D  
Sbjct: 918 FLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAV 954

>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RNA-polymerase beta-prime
species: Thermus thermophilus [TaxId: 274]

 Score = 85.2 bits (210), Expect = 4e-17
 Identities = 22/63 (34%), Positives = 37/63 (58%)

Query: 613  GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFD 672
              V++SF  GLT  E+F  + G R+G  DTA++TA++GY+ R+LV    ++ V+      
Sbjct: 1054 VPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGT 1113

Query: 673  AAF 675
              +
Sbjct: 1114 TNY 1116

>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RNA-polymerase beta-prime
species: Thermus thermophilus [TaxId: 274]

 Score = 77.9 bits (191), Expect = 7e-15
 Identities = 34/234 (14%), Positives = 74/234 (31%), Gaps = 65/234 (27%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            G+PR+ E+  A R  +  +I+  +D        RI +   + +   E   + +E  +P +
Sbjct: 1254 GLPRVIELFEARRPKAKAVIS-EIDG-----VVRIEETEEKLSVFVESEGFSKEYKLPKE 1307

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 883
            + +L+K D D +             + +   +G                           
Sbjct: 1308 ARLLVK-DGDYVEAGQPLTRGAIDPHQLLEAKGPEA------------------------ 1342

Query: 884  MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 943
                   +   +++ +Q + R        +GV  +   +E   +R +M    V     S 
Sbjct: 1343 -------VERYLVEEIQKVYR-------AQGVKLHDKHIE-IVVRQMMKYVEVTDPGDSR 1387

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
                +V +   +EA    ++ E K                     +  K  ++G
Sbjct: 1388 LLEGQVLEKWDVEALNERLIAEGK-------------------TPVAWKPLLMG 1422

>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RNA-polymerase beta-prime
species: Thermus thermophilus [TaxId: 274]

 Score = 52.9 bits (126), Expect = 3e-07
 Identities = 11/34 (32%), Positives = 19/34 (55%)

Query: 671  FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 704
             +AA  G+ D + G+ E +I+G  +  GTG   +
Sbjct: 1447 TEAAIAGKKDELIGLKENVILGRLIPAGTGSDFV 1480

>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RNA-polymerase beta-prime
species: Thermus thermophilus [TaxId: 274]

 Score = 44.8 bits (105), Expect = 9e-05
 Identities = 18/93 (19%), Positives = 41/93 (44%), Gaps = 2/93 (2%)

Query: 245 KYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIP 304
           +   R  +   I   + AE  + +    ++EA +K  L++ +      +  +A    ++ 
Sbjct: 440 RNVVRVVESYDIDARMGAEAIQQLLKELDLEALEKE-LLEEMKHPSRARRAKARKRLEVV 498

Query: 305 LLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
              +++  ++P  +IL  + V P  +RP V  D
Sbjct: 499 RAFLDSG-NRPEWMILEAVPVLPPDLRPMVQVD 530

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	1423
d1twfa_	1449	RBP1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	100.0
d1smyd_	1504	RNA-polymerase beta-prime {Thermus thermophilus [T	100.0
d1twfa_	1449	RBP1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	100.0
d1smyd_	1504	RNA-polymerase beta-prime {Thermus thermophilus [T	99.78

>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=8.8e-167  Score=1691.06  Aligned_cols=997  Identities=30%  Similarity=0.497  Sum_probs=741.5

Q ss_pred             cceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCc
Q psy13846         77 VFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP  156 (1423)
Q Consensus        77 ~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~P  156 (1423)
                      .+|.+ |+|+++||||||++|++||++|++|+ +.+++|..|||||||||+.++...|.|||++..+||||||||+|+.|
T Consensus        11 ~~i~~-i~f~~~s~eeIr~~S~~ei~~~~~~~-~~~~~p~~~Gl~d~rlG~~~~~~~C~tC~~~~~~CpGHfGhIeL~~P   88 (1449)
T d1twfa_          11 RTVKE-VQFGLFSPEEVRAISVAKIRFPETMD-ETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKP   88 (1449)
T ss_dssp             CCCCE-EECCBCCHHHHHHTCCCCCCCSCCSC-TTSCCSCCSSSSCSSSCCCTTCCCSSSCCCCTTSCCCCCCCEEEEEE
T ss_pred             ceece-EEEEecCHHHHHHhcceEEcCCCccc-CCCCCCCCCCCcchhhCCCCCcCCCCCCCCCCcCCCCCCEeeEeccc
Confidence            56889 99999999999999999999999994 34678999999999999999999999999999999999999999999


Q ss_pred             eeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCc---------------
Q psy13846        157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVS---------------  221 (1423)
Q Consensus       157 V~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k---------------  221 (1423)
                      ||||+||+.++++|+++|++  ||+++++.... .+...+....     .+....++.+.++...               
T Consensus        89 V~h~~f~~~~~~~L~~~C~~--C~~l~l~~~~~-~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (1449)
T d1twfa_          89 VFHVGFIAKIKKVCECVCMH--CGKLLLDEHNE-LMRQALAIKD-----SKKRFAAIWTLCKTKMVCETDVPSEDDPTQL  160 (1449)
T ss_dssp             EECGGGHHHHHHHHHHBCTT--TCCBSCCTTSH-HHHHHHTCCS-----HHHHHHHHHHHHTTCCBCCSEECCSSCTTSC
T ss_pred             chhHHHHHHHHHHHHHhhhc--cCCEeecccHH-HHHHHHhhcc-----hhhhhHHHHHHhhhheeccccccchhhhhhh
Confidence            99999999999999999999  99999986653 2333332221     1233445555554443               


Q ss_pred             -cCCCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCC
Q psy13846        222 -VCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPL  300 (1423)
Q Consensus       222 -~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~  300 (1423)
                       +|++|++.++.+++.+. ++..........  .                  +    ........++|.+++++|++||+
T Consensus       161 ~~~~~c~~~~~~~~~~~~-~~~~~~~~~~~~--~------------------~----~~~~~~~~l~~~~~~~i~~~i~~  215 (1449)
T d1twfa_         161 VSRGGCGNTQPTIRKDGL-KLVGSWKKDRAT--G------------------D----ADEPELRVLSTEEILNIFKHISV  215 (1449)
T ss_dssp             EECCSCCCBCCCCEECSS-CEEEEECSSSSC--T------------------T----SCSCEEEEECHHHHHHHHTTSCH
T ss_pred             hhcCCCCcCChhhhhhhH-HHHHHHHHhhhc--c------------------c----ccchhheeCCHHHHHHHHHhCCH
Confidence             45899999999998763 332211000000  0                  0    00023457899999999999999


Q ss_pred             CcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCC----------------------------------------
Q psy13846        301 EDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS----------------------------------------  340 (1423)
Q Consensus       301 ~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~----------------------------------------  340 (1423)
                      +|+..+++++..+||+||||++|||||+|+||++..++..                                        
T Consensus       216 ~~~~~l~~~~~~~~p~~~~l~~lpV~P~~~RP~~~~~~~~~~~~dlt~~~~~Ii~~n~~l~~~~~~~~~~~~~~~~~~~L  295 (1449)
T d1twfa_         216 KDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLL  295 (1449)
T ss_dssp             HHHHHTTCBTTTBCGGGGEEEEECCCCTTTSCCCCCSSSCCCCCHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHH
T ss_pred             hHHHHhCCCcCCCChHHEEeeeeecCCCCcCCceEeCCCcccCChHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence            9999999999999999999999999999999998877641                                        


Q ss_pred             --------------------------------------------------------------------------------
Q psy13846        341 --------------------------------------------------------------------------------  340 (1423)
Q Consensus       341 --------------------------------------------------------------------------------  340 (1423)
                                                                                                      
T Consensus       296 Q~~v~~~~dn~~~~~~~~~~~~~~~~k~i~~~L~gK~GrfR~nl~GKRVd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~  375 (1449)
T d1twfa_         296 QFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTY  375 (1449)
T ss_dssp             HHHHHHHHCCCSSCCCCCSSCTTCCCCCSTTSCTTTTTTSSGGGTTCSCCSEEEEEEEECTTSCTTEEEEEHHHHTTCEE
T ss_pred             HHHHHHhccccccCCchhccccCCCccchhhHhccchhhhhhhccccccccccceeeccCCccceeecccHHHHHhhCCC
Confidence                                                                                            


Q ss_pred             -------------------------------------------------------------CCeEEEEecCccccccccc
Q psy13846        341 -------------------------------------------------------------DNDVVLFNRQPSLHKLSIM  359 (1423)
Q Consensus       341 -------------------------------------------------------------~~d~Vl~nRqPsLHk~Sim  359 (1423)
                                                                                   +||+|||||||||||+|||
T Consensus       376 pe~v~~~n~~~l~~~v~ng~~~~pga~~~~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~Vl~NRqPtLHr~si~  455 (1449)
T d1twfa_         376 PEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMM  455 (1449)
T ss_dssp             EEECCTTTHHHHHHHHHHTTTSSSCEEEEECTTCCEEETTSCTTTTCCCCCTTCEEEEECCTTCEEEEECSSCCSGGGEE
T ss_pred             CeeecHHHHHHHHHHHHcCCccCCcccceecccCceEEEecchhhhhhhcccccEEEEEEecCeeEEecCccchhhhccc
Confidence                                                                         7999999999999999999


Q ss_pred             eeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccc
Q psy13846        360 AHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIA  439 (1423)
Q Consensus       360 ah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~  439 (1423)
                      ||++|++|++||||||++|+||||||||||||+|+|||++|||||+              .||.+.+|++||++|+|+++
T Consensus       456 a~~~~v~~~ktirl~~~vc~~yNADFDGDeMnvhvPqs~~A~aEa~--------------~Lm~~~~nilsp~~G~pi~~  521 (1449)
T d1twfa_         456 AHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELS--------------QLCAVPLQIVSPQSNKPCMG  521 (1449)
T ss_dssp             EEEEEEESSSSEEECGGGHHHHTCCSSSCEEEEECCCSHHHHHHHH--------------HHTBGGGGSEETTTTEESCC
T ss_pred             cceeEeecCceEEeccccccccccccccceEEEEccCCHHHHHHHH--------------HHhhhhcccccccCCceeee
Confidence            9999999999999999999999999999999999999999999999              99999999999999999999


Q ss_pred             cccceEEEEEeecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCccc
Q psy13846        440 ATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV  519 (1423)
Q Consensus       440 ~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~  519 (1423)
                      ++||+++|+|.||.+|+|+++.+++++++++.    +..+        .+|+|++.+|.++|||||+||+++|...    
T Consensus       522 ~~QD~~lg~y~LT~~~~f~~~~~~~~~~~~~~----~~~~--------~~~~p~~~~~~~~~tgkqi~s~~l~~~~----  585 (1449)
T d1twfa_         522 IVQDTLCGIRKLTLRDTFIELDQVLNMLYWVP----DWDG--------VIPTPAIIKPKPLWSGKQILSVAIPNGI----  585 (1449)
T ss_dssp             CCHHHHHHHHHHHSTTCEEEHHHHHHHHHHST----TCCS--------CCCCCSBCSSSCEEEHHHHHHHHSCTTC----
T ss_pred             eccchhhhhhhhhcccccCCHHHHHHHHHhcc----cccc--------cccCCeEEeeeeccccceEEEEEccCCc----
Confidence            99999999999999999999999999999874    2222        6789999999999999999999998542    


Q ss_pred             ccceeecccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhc
Q psy13846        520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNR  599 (1423)
Q Consensus       520 ~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~  599 (1423)
                        ++......   ...++..+..++|++|+++.|.+||+++|+ +.++++|.+|++||++.|..||+.+++++++|++.+
T Consensus       586 --~~~~~~~~---~~~~~~~~~~~~i~~g~l~~g~l~k~~~g~-~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~  659 (1449)
T d1twfa_         586 --HLQRFDEG---TTLLSPKDNGMLIIDGQIIFGVVEKKTVGS-SNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHN  659 (1449)
T ss_dssp             --CEEECCTT---CCTTCTTCCSEEEETTEEEESCCCHHHHSS-CTTSHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             --eeeeccCC---ccccccCCceEEEECCeeeeccchhhhccc-ccccccccccccccHHHHHHHHHHHHHHHHHHHHhc
Confidence              22211111   223466788899999999999999999998 678999999999999999999999999999999999


Q ss_pred             CcceecCCCCCCc-------------------------------------------------------------------
Q psy13846        600 GFSIGIGDVTPGQ-------------------------------------------------------------------  612 (1423)
Q Consensus       600 GfsiGi~D~~~~~-------------------------------------------------------------------  612 (1423)
                      |||+|++|++++.                                                                   
T Consensus       660 Gfs~gi~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~v~~~~~~~~~~~~~~~~~~~~~~  739 (1449)
T d1twfa_         660 GFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDL  739 (1449)
T ss_dssp             CBCCCGGGGCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             chheeeccccccchhhHHHHHHHHHHhhhHHHHHHHHHHhhhccccCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcc
Confidence            9999999998754                                                                   


Q ss_pred             ---------------------------------------------------------cccccccccCCCceeeeeecccc
Q psy13846        613 ---------------------------------------------------------GFVQNSFFSGLTPTEFFFHTMGG  635 (1423)
Q Consensus       613 ---------------------------------------------------------GfI~~sf~~GL~p~Efffh~maG  635 (1423)
                                                                               |||.+||++||+|+|||||||||
T Consensus       740 N~~~~M~~SGakGs~~n~~Qi~g~~Gqq~~~g~ri~~~~~~r~lp~f~~~~~~~~~~GfI~~sf~~GL~p~Eyf~h~~~g  819 (1449)
T d1twfa_         740 NNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGG  819 (1449)
T ss_dssp             CHHHHHHHHTSSCCHHHHHHHHSCCEECCBTTBSCCCCBTTBSSTTSCTTCCSTTTTTEECSCTTTCCCHHHHHHHHHHH
T ss_pred             cchHhheeccccCCccchHHHHhhhhhhcccCccccccccccccccCCCCCCCccccCcccchhhhhhcchheeeeeccc
Confidence                                                                     88999999999999999999999


Q ss_pred             cccchhcccccCCCCcchHHHHHHHhhhhhcccceeecc-------ccCCCccCCCcchheecCCCcccchhHHHHhhhc
Q psy13846        636 REGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA-------FYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV  708 (1423)
Q Consensus       636 ReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s-------~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aqs  708 (1423)
                      ||||+|||+|||+||||||||||+|||++|+||+|||++       .||+|+.+....+.                    
T Consensus       820 ReGLiDTAvkTa~sGYl~RrLvk~ledv~v~yD~tvr~~~g~IiQf~YGeDg~d~~~~e~--------------------  879 (1449)
T d1twfa_         820 REGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEK--------------------  879 (1449)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCEECTTSCEECTTCCEEESSGGGTTBCGGGEEE--------------------
T ss_pred             hhhhhhhcccccccHHHHHHHHHHhcCeEEEecCccCcCCceEEEEEEcCccccceEEEE--------------------
Confidence            999999999999999999999999999999999999987       25554322110000                    


Q ss_pred             CCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeeecc
Q psy13846        709 PRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLD  788 (1423)
Q Consensus       709 ige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~  788 (1423)
                                                               +             .++.+                    
T Consensus       880 -----------------------------------------~-------------~~~~~--------------------  885 (1449)
T d1twfa_         880 -----------------------------------------Q-------------SLDTI--------------------  885 (1449)
T ss_dssp             -----------------------------------------E-------------ECGGG--------------------
T ss_pred             -----------------------------------------e-------------eccee--------------------
Confidence                                                     0             00000                    


Q ss_pred             cCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCccccccccc
Q psy13846        789 KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSF  868 (1423)
Q Consensus       789 ~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~~  868 (1423)
                      ...+..+.+..+.        ++..       .+           .                                  
T Consensus       886 ~~~~~~~~~~~~~--------~~~~-------~~-----------~----------------------------------  905 (1449)
T d1twfa_         886 GGSDAAFEKRYRV--------DLLN-------TD-----------H----------------------------------  905 (1449)
T ss_dssp             SSCHHHHHHHHCC--------CTTC-------TT-----------T----------------------------------
T ss_pred             ccchHHhhhhhhh--------cccc-------cc-----------c----------------------------------
Confidence            0000000000000        0000       00           0                                  


Q ss_pred             ccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccccceeecccceeeccCchHH
Q psy13846        869 LILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE  948 (1423)
Q Consensus       869 ~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~e  948 (1423)
                                .                                                        .+..     ....
T Consensus       906 ----------~--------------------------------------------------------~~~~-----~~~~  914 (1449)
T d1twfa_         906 ----------T--------------------------------------------------------LDPS-----LLES  914 (1449)
T ss_dssp             ----------S--------------------------------------------------------CCTT-----TBTT
T ss_pred             ----------c--------------------------------------------------------cChh-----Hhhh
Confidence                      0                                                        0000     0000


Q ss_pred             HHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCCcchhhHHHHHHHHHhc--cCCCCCCCCHH
Q psy13846        949 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKN--SSRSDPSLSAQ 1026 (1423)
Q Consensus       949 V~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~~~~~~~~~~~~~~~~~--~~~~~~~l~~~ 1026 (1423)
                      ..+.++..+++..+-.|.+..++..         .++.+..+. +.. ....|+++.++.+......  .......+.+.
T Consensus       915 ~~ei~~~~~~~~i~~~~~~~l~~~r---------~~l~~~~~~-~~~-~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~  983 (1449)
T d1twfa_         915 GSEILGDLKLQVLLDEEYKQLVKDR---------KFLREVFVD-GEA-NWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIK  983 (1449)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHH---------HHHHHHTTT-CCC-EEEEESCHHHHHHHHHHHTTCCTTSCBCCCHH
T ss_pred             hHHHhhhHHHHHHHHHHHHHHHHHH---------HHHHHHhcC-ccc-cccCcchHHHHHHhhhhhcccccCccccccHH
Confidence            1112333344444444444443310         011111111 110 1125677777777666542  22233445666


Q ss_pred             HHHHHhhhhcCcchhh---hhhhHHHHHH-HHHHHHHhhhccccccccccCCchhhhhhhccccccCcccCCCCCChhHH
Q psy13846       1027 EILALSNETLDSKEFL---QDTSENFVRD-IKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACK 1102 (1423)
Q Consensus      1027 ~~~~~~~~~l~~~~~~---~~~~~~f~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1102 (1423)
                      ++....++........   ....+.+... ...+...             ....+..+.+...++++++.+    .  ++
T Consensus       984 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~l~~~~~~~~~~l~~~~~----~--~~ 1044 (1449)
T d1twfa_         984 DIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCL-------------LRSRLATRRVLQEYRLTKQAF----D--WV 1044 (1449)
T ss_dssp             HHHHHHHHHHTTCCSCCCCSHHHHHHHHHTTHHHHHH-------------HHHHSCHHHHHHTSCCCHHHH----H--HH
T ss_pred             HHHHHHHHHHhhhheecccchhhhhhcccccceeeee-------------eccccchhhhhhhcccCHHHH----H--HH
Confidence            6655554443321110   0000111000 0000000             001122334456677888766    6  89


Q ss_pred             HHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc-------------------------------------
Q psy13846       1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------------------------- 1145 (1423)
Q Consensus      1103 ~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG------------------------------------- 1145 (1423)
                      +..|..+|.+++|+||||||+|||||||||+|||||||||+||                                     
T Consensus      1045 ~~~~~~ky~~slv~pGEaVGiiAAQSIGEP~TQmTLnTFH~AG~~~~nvT~GiPRl~EIl~ask~iktp~~~v~l~~~~~ 1124 (1449)
T d1twfa_        1045 LSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHA 1124 (1449)
T ss_dssp             HHHHHHHHHHHBCCTTCCHHHHHHHHHHHHHTTCCC----------CCSCCHHHHHHHHTTTCSSCSSCEEEEEBCSSSS
T ss_pred             HHHHHHHHhhhhhhccCcchhhhhhhhccchhhhhhhhhhhcceeeecccccchhhhhheeeecccCCcceeEEeccccc
Confidence            9999999999999999999999999999999999999999999                                     


Q ss_pred             -------------------cccceeEEEEccCCcE------------------------------EEEEEchHHHHHhcc
Q psy13846       1146 -------------------EVCEYIEEVFVPDDSF------------------------------ILIKLDMDRIRLLHL 1176 (1423)
Q Consensus      1146 -------------------~i~~~i~~~~~~~~~~------------------------------~~i~l~~~~~~~~~~ 1176 (1423)
                                         ++....+.+|+|+...                              +.+++.++.......
T Consensus      1125 ~~~~~~k~~~~~i~~~~l~~vv~~~~v~~~~~~~~~~i~~~~~~i~~~~~~~~~~~~~~~~~~~~~ilrl~l~~~~~~~k 1204 (1449)
T d1twfa_        1125 ADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDK 1204 (1449)
T ss_dssp             SCHHHHHHHHHHHSCEEGGGTEEEEEEEECCCSSSCSSGGGHHHHHTSSCC----------CCCSEEEEEEECHHHHHHT
T ss_pred             hhHHHHHhhhheeeeeeccceeeeeEEEEcCCCceEEEEEecceeeEEEEeccchheeeecccCCceEEEEEchhhcccC
Confidence                               1222334455554221                              234555555555556


Q ss_pred             cCCHHHHHHHHHhccccCCceEEec----CcEEEEEeCC-------CCchhhhHHHHH-HhccCCcEEcccCCccEEEEe
Q psy13846       1177 EVDIDSIRYCIERTRGISGHLTVSG----HSFLILKPKD-------SSKSFNSKMYQM-KQLLPSVVIKGVQGINRAVIH 1244 (1423)
Q Consensus      1177 ~i~~~~i~~~i~~~k~~~~~~~~~~----~~~i~i~~~~-------~~~~~~~~l~~l-~~~l~~~~v~Gi~~i~r~~i~ 1244 (1423)
                      ++++.++...+.+....+.....++    ...++.....       ........+..+ ...+.++.|+|+++|+|+++.
T Consensus      1205 ~i~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~l~~i~~~~l~~~~v~Gi~~I~rv~i~ 1284 (1449)
T d1twfa_        1205 DLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMM 1284 (1449)
T ss_dssp             TCCHHHHHHHHHHHHGGGEEEEECCTTSSSCEEEEEEC----------CCTTHHHHHHHHHHHHHCEEESCTTCCCEEEE
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEecCCCcceEEEecccCCccccccccccchHHHHHHHHhhccCCcEEeCCCCeEEEEEe
Confidence            7888888777753211111111111    1123332211       000112233333 345678899999999999875


Q ss_pred             cccc---------cceeeEEEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccC
Q psy13846       1245 EEDV---------EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 1315 (1423)
Q Consensus      1245 ~~~~---------~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~ 1315 (1423)
                      ..+.         .+.++|++.|||+||.++|..++||+++++||||++|+++|||||||++|++||++||+.||++||+
T Consensus      1285 ~~~~~~~~~~~~~~~~~~~vl~teG~nl~~~l~~~~iD~~~~~sNdI~dil~~lGIEAar~~ii~EI~~V~~~~Gi~Id~ 1364 (1449)
T d1twfa_        1285 KYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNY 1364 (1449)
T ss_dssp             EEEEEEECTTSSEEEEEEEEEEEESCCHHHHTTSTTBCTTTCBCSCHHHHHHHHCHHHHHHHHHHHHHHHHHTTTCCCCH
T ss_pred             cccceeeCCCCcCccCCcEEEEcCcCCHHHHhccCCcccccCccCcHHHHHHHHhHHHHHHHHHHHHHHHHHhcCcEECH
Confidence            3211         1356899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeeccccccccceEEEee
Q psy13846       1316 RHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395 (1423)
Q Consensus      1316 rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~ 1395 (1423)
                      |||+||||+||++|.++||||+||++++.|||++||||+|+++|++||++|++|+|+|||||||+|+++|+|||+|||++
T Consensus      1365 rHi~LIad~MT~~G~~~~i~R~gi~~~~~S~l~~aSFEeT~~vL~~AAi~g~~D~L~G~senIi~G~~ip~GTG~fdll~ 1444 (1449)
T d1twfa_        1365 RHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMI 1444 (1449)
T ss_dssp             HHHHHHHHHTTTBSSCCCSSSCSSSCSSCCTTSSCCSSCSHHHHHHHHHHTCEECCCSHHHHHHTTCCCSSGGGSSEEEE
T ss_pred             HHHHHHHHHHCcCCeEeeccHHHhccCCcCHHHHhhchhHHHHHHHHHhcCCcccCCCcHHHeecCCCCCCcccccEEEe
Confidence            99999999999999999999999988889999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q psy13846       1396 AVPR 1399 (1423)
Q Consensus      1396 ~~~~ 1399 (1423)
                      |.+.
T Consensus      1445 d~~~ 1448 (1449)
T d1twfa_        1445 DEES 1448 (1449)
T ss_dssp             CSCC
T ss_pred             chhh
Confidence            9765

>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]}

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RNA-polymerase beta-prime
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=9.8e-120  Score=1203.20  Aligned_cols=379  Identities=26%  Similarity=0.377  Sum_probs=303.9

Q ss_pred             CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846        341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV  420 (1423)
Q Consensus       341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~  420 (1423)
                      +||+|||||||||||+|||||++|++|++||||||++|+||||||||||||+|+|||++|||||+              .
T Consensus       695 ~GD~VL~NRQPTLHR~SImAh~~~l~~gkTiRLnp~vC~pyNADFDGDEMNvHvPQS~eAraEa~--------------~  760 (1504)
T d1smyd_         695 HGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEAR--------------I  760 (1504)
T ss_dssp             SSCCEEEECSSCCSGGGEEEEEECCBSSSSEEECSGGGTTTTCCSSSCEEEEECCCSHHHHHHHH--------------H
T ss_pred             cCCEEEecCCCccccceeeEEEEEEcCCceeeecccccccccCCCCCceEEEecCCCHHHHHHHH--------------H
Confidence            79999999999999999999999999999999999999999999999999999999999999999              9


Q ss_pred             hhccccccccCCCCccccccccceEEEEEeecc-----cccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceee
Q psy13846        421 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQ-----KNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFV  495 (1423)
Q Consensus       421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~-----~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~  495 (1423)
                      ||.+.+|++||++|+|+++++||+++|+|.||.     ++.++....+..++.++.      .+.+      .+|+|+++
T Consensus       761 LM~~~~nilsP~~G~PIi~~iQD~ilG~ylLT~~~~~~k~~~~~f~~~~e~l~a~~------~~~i------~l~~pi~~  828 (1504)
T d1smyd_         761 QMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHE------RGEV------ALNAPIKV  828 (1504)
T ss_dssp             HSBSTTCCBCSSSSSBSSCCCSHHHHHHHHHSCCCCCCCCSCCCTTSCSHHHHHHH------HHHH------TTSSCSSC
T ss_pred             HhccccccccCCCCCeeeehhhhhhhhheeeeeeecccccceeEecCHHHHHhhhh------cccc------ccCCCccc
Confidence            999999999999999999999999999999997     445444444444444443      1223      78999999


Q ss_pred             cceeeeecceeeeecccCCCCccc---ccceeecccccccCcccccCCcEEEecccccccc-----------------cc
Q psy13846        496 RTAVIWTGKQIFSLILKPNRDCPV---NANLKTKGRAYTANEEFCHRDSYVILRNSELLAG-----------------SM  555 (1423)
Q Consensus       496 kp~~~wtGKqi~s~il~~~~~~~~---~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g-----------------~l  555 (1423)
                      +|.++|||||+++...|.......   ..++...       .........+....|.++.+                 .+
T Consensus       829 k~k~l~tGkq~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~k~~~tt~G~i~~~~~~~~~v~~~~~~~~~~~~  901 (1504)
T d1smyd_         829 AGRETSVGRLKYVFANPDEALLAVAHGIVDLQDV-------VTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQL  901 (1504)
T ss_dssp             CCSSCCHHHHHCEESSHHHHHHHHHTTSSCTTSC-------CEEEETTEEECCCHHHHHHHHHHHHHSSCHHHHHHSCCT
T ss_pred             ccccccccceeeeecccccccccccCCccccccc-------cccccCCccccCCCCeeeccccccccccccccccccccc
Confidence            999999999999887653210000   0000000       00001111222333333332                 22


Q ss_pred             ccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCc-----------------------
Q psy13846        556 DKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ-----------------------  612 (1423)
Q Consensus       556 dK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~-----------------------  612 (1423)
                      ++...+. +.++++|.+|++||+..++.||++++++.++|++.+|||+|++|+...+                       
T Consensus       902 ~~~~~k~-~l~~LI~~i~~~yG~~~t~~fLd~lk~Lg~~~l~~~GfSiGI~Di~~~~~k~~~I~~a~~~v~~i~~~~~~G  980 (1504)
T d1smyd_         902 DVPQEKN-SLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMG  980 (1504)
T ss_dssp             TSCCCHH-HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHTCCCCGGGSCCCTHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cccccCc-cHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHhcCCcccccccccCHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            3333332 3357999999999999999999999999999999999999999997655                       


Q ss_pred             -------------------------------------------------------------------------ccccccc
Q psy13846        613 -------------------------------------------------------------------------GFVQNSF  619 (1423)
Q Consensus       613 -------------------------------------------------------------------------GfI~~sf  619 (1423)
                                                                                               |||.+||
T Consensus       981 ~lt~~er~~~v~~~~~~~~~~v~~~~~~~L~~~~p~N~l~~Mv~SGAKGS~~NIsQl~G~rGL~~~PsG~~ie~pI~sSF 1060 (1504)
T d1smyd_         981 FLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSF 1060 (1504)
T ss_dssp             CSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHSSSSCCHHHHHHHTTCCCCCBCSSSCBCSSCCCCCS
T ss_pred             cCchhHHHHHHHHHHHHHHHHHhhhhhhhhhhcCCCCceEEEeccccccCHHHHHHHhcccccccCCCCcccCCcccccc
Confidence                                                                                     8999999


Q ss_pred             ccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeeccc-------cCCCcc-----------
Q psy13846        620 FSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAF-------YGQTDC-----------  681 (1423)
Q Consensus       620 ~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~-------yG~~~~-----------  681 (1423)
                      ++||+|+|||||||||||||||||||||+||||||||||++||++|.||.++|++.       ||+..-           
T Consensus      1061 ~eGLtP~EFFFHtMGGREGLIDTAVKTA~SGYLqRRLVKvlEDl~V~~dd~~~~~~~~i~~~~~~e~~~~l~~~~~~d~~ 1140 (1504)
T d1smyd_        1061 REGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIE 1140 (1504)
T ss_dssp             SSCCCHHHHHHHHHHHHHHHHHHHHHHSCSHHHHHHHHHTTTTCBCCCSCCSCCCCEECCCEECTTSSSCCEECCHHHHH
T ss_pred             cccCCHHHHHhhcCCCcchhhhhhccccccchhhHHHHHHhccceEEEeeccccCceEEEEeeCCccchhhhhhhcchhh
Confidence            99999999999999999999999999999999999999999999999999999761       222100           


Q ss_pred             -------------------CC-------------------Cc-----------------ch-----heecCCCcccchhH
Q psy13846        682 -------------------IS-------------------GV-----------------SE-----CIIMGLPMNVGTGL  701 (1423)
Q Consensus       682 -------------------~~-------------------~~-----------------~~-----~~~~~~~~~~g~~v  701 (1423)
                                         ..                   ++                 -+     .++.+.+++|||||
T Consensus      1141 ~~~~~r~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~i~~v~vrs~ltc~~~~gvc~kcyg~~la~~~~V~pGEaV 1220 (1504)
T d1smyd_        1141 AGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAV 1220 (1504)
T ss_dssp             HHHTTCBBSSCEECSSCEECTTCBCCHHHHHHHHHHHHHSSCSCCEECCGGGCSSTTBCCHHHHCSCSSSSSCCCSSCCH
T ss_pred             hhhhhhhhhhhHhhcccccccccccchhhHHHHHHHHHhcCccEEeccCccchhhHhhHHHHHHHHHHhhCCcCCCCCHH
Confidence                               00                   00                 00     01245578999999


Q ss_pred             HHHhhhcCCCCCCccccccCCCCcccCcccccccccccccccc-ccceeecccCCCCCccCCCCchhhHHHHhhhcCCCC
Q psy13846        702 IKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTA-SVKVTLELWNPGDYKLSQDGVPRIKEIINASRNIST  780 (1423)
Q Consensus       702 g~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~a-s~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikT  780 (1423)
                      |++||||||||+|||||    +|||+|||             | ++|||+             |||||+||+||++...+
T Consensus      1221 GiIAAQSIGEPgTQMTL----nTFH~aGV-------------ag~~nIT~-------------GvPRl~EIi~a~kpk~~ 1270 (1504)
T d1smyd_        1221 GIVAAQSIGEPGTQLTM----RTFHTGGV-------------AGAADITQ-------------GLPRVIELFEARRPKAK 1270 (1504)
T ss_dssp             HHHHHHHHHHHHTTSCC----SCTTCSCS-------------STTCCCCC-------------HHHHHHHHHTTCCCTTB
T ss_pred             HHHHhhccCchHHhHHH----hhhhhccc-------------CCCCcccC-------------CCchHHHHHhccCCCCC
Confidence            99999999999999999    99999998             6 689999             99999999999876666


Q ss_pred             cee
Q psy13846        781 PII  783 (1423)
Q Consensus       781 Pii  783 (1423)
                      |++
T Consensus      1271 ~ii 1273 (1504)
T d1smyd_        1271 AVI 1273 (1504)
T ss_dssp             CCB
T ss_pred             ceE
Confidence            654

>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.4e-65  Score=694.25  Aligned_cols=798  Identities=20%  Similarity=0.234  Sum_probs=467.6

Q ss_pred             HHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccc-cceeeeEEEecCCH
Q psy13846         12 YYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRK-VFFRGLIEGTVTKE   90 (1423)
Q Consensus        12 ~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~-~~i~~~i~F~~~S~   90 (1423)
                      -+||||||++||++++||+||++|+|++|.+||+++|+|+||.+|+|+++++++++++|+..... ...+.         
T Consensus       493 s~~A~aEa~~Lm~~~~nilsp~~G~pi~~~~QD~~lg~y~LT~~~~f~~~~~~~~~~~~~~~~~~~~~~p~---------  563 (1449)
T d1twfa_         493 SEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPA---------  563 (1449)
T ss_dssp             SHHHHHHHHHHTBGGGGSEETTTTEESCCCCHHHHHHHHHHHSTTCEEEHHHHHHHHHHSTTCCSCCCCCS---------
T ss_pred             CHHHHHHHHHHhhhhcccccccCCceeeeeccchhhhhhhhhcccccCCHHHHHHHHHhcccccccccCCe---------
Confidence            48999999999999999999999999999999999999999999999999999999998632211 11111         


Q ss_pred             HHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCceeEEeeeccH----
Q psy13846         91 DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCV----  166 (1423)
Q Consensus        91 eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~gffd~v----  166 (1423)
                               -+....+|    +|+++.+.+++..+...... .+.+.     -|+ -.+.+.+....+-.|.+++.    
T Consensus       564 ---------~~~~~~~~----tgkqi~s~~l~~~~~~~~~~-~~~~~-----~~~-~~~~~~i~~g~l~~g~l~k~~~g~  623 (1449)
T d1twfa_         564 ---------IIKPKPLW----SGKQILSVAIPNGIHLQRFD-EGTTL-----LSP-KDNGMLIIDGQIIFGVVEKKTVGS  623 (1449)
T ss_dssp             ---------BCSSSCEE----EHHHHHHHHSCTTCCEEECC-TTCCT-----TCT-TCCSEEEETTEEEESCCCHHHHSS
T ss_pred             ---------EEeeeecc----ccceEEEEEccCCceeeecc-CCccc-----ccc-CCceEEEECCeeeeccchhhhccc
Confidence                     22445667    78888877776654332111 11111     122 25668889999999999843    


Q ss_pred             --HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehhh
Q psy13846        167 --INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHE  244 (1423)
Q Consensus       167 --~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e  244 (1423)
                        ..+.+++-..       ++++....|++++.+....++...+|+.++.|.....                   + ..+
T Consensus       624 ~~~~li~~i~~~-------~G~~~~~~~l~~~~~l~~~~l~~~Gfs~gi~D~~~~~-------------------~-~~~  676 (1449)
T d1twfa_         624 SNGGLIHVVTRE-------KGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADG-------------------P-TMR  676 (1449)
T ss_dssp             CTTSHHHHHHHH-------HCHHHHHHHHHHHHHHHHHHHHTTCBCCCGGGGCCCH-------------------H-HHH
T ss_pred             cccccccccccc-------ccHHHHHHHHHHHHHHHHHHHHhcchheeeccccccc-------------------h-hhH
Confidence              1133333333       6777777888877765444444444443333321100                   0 000


Q ss_pred             hhcccccchhhHHHHHHHHhhhhhc-cCh------hhhhhhccCccccCC--HHHHHHHhhccCCCcccccccccCCCCC
Q psy13846        245 KYKNRTKKKDAIVEDLLAEYNEAVK-FNP------EIEAHKKFGLIQTLN--PLEVLQLFEAIPLEDIPLLLMNAELSKP  315 (1423)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~------~~~~~~~~~~~~~L~--p~~V~eiLe~I~~~d~~lL~m~~~~arP  315 (1423)
                      ...+...+......++..+|....- .++      ..+...    ...++  -..+.+........+++++.|..+|||+
T Consensus       677 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~v----~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGakG  752 (1449)
T d1twfa_         677 EITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNV----VRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKG  752 (1449)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHH----HHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHTSSC
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHhhhccccCCcHHHHHHHHH----HHHHHHHHHHHHHHHhhhhhcccchHhheeccccC
Confidence            0000000011111222222221100 000      000000    00000  0112222222233467888898899999


Q ss_pred             cceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccC
Q psy13846        316 SDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLP  395 (1423)
Q Consensus       316 e~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p  395 (1423)
                      ++.++.||.   .|+++|...|+++...+                 ..|++||    |.+..++|...+|..+.+..+|.
T Consensus       753 s~~n~~Qi~---g~~Gqq~~~g~ri~~~~-----------------~~r~lp~----f~~~~~~~~~~GfI~~sf~~GL~  808 (1449)
T d1twfa_         753 SFINIAQMS---ACVGQQSVEGKRIAFGF-----------------VDRTLPH----FSKDDYSPESKGFVENSYLRGLT  808 (1449)
T ss_dssp             CHHHHHHHH---SCCEECCBTTBSCCCCB-----------------TTBSSTT----SCTTCCSTTTTTEECSCTTTCCC
T ss_pred             CccchHHHH---hhhhhhcccCccccccc-----------------ccccccc----CCCCCCCccccCcccchhhhhhc
Confidence            999999999   99999999998877776                 7899999    99999999999999999999999


Q ss_pred             CCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHHHHHHhhccCCc
Q psy13846        396 QTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTS  475 (1423)
Q Consensus       396 ~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~  475 (1423)
                      +.|          ||||+||||+|+++++.+|+.|||.+|+|+..+|| +...|+.|+||..+++.||.|+.++++..  
T Consensus       809 p~E----------yf~h~~~gReGLiDTAvkTa~sGYl~RrLvk~led-v~v~yD~tvr~~~g~IiQf~YGeDg~d~~--  875 (1449)
T d1twfa_         809 PQE----------FFFHAMGGREGLIDTAVKTAETGYIQRRLVKALED-IMVHYDNTTRNSLGNVIQFIYGEDGMDAA--  875 (1449)
T ss_dssp             HHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CEECTTSCEECTTCCEEESSGGGTTBCGG--
T ss_pred             chh----------eeeeeccchhhhhhhcccccccHHHHHHHHHHhcC-eEEEecCccCcCCceEEEEEEcCccccce--
Confidence            666          99999999999999999999999999999999999 88899999999999999999988877521  


Q ss_pred             cccceEe------------eeeccccCCceeecceeeeecceeeee-----cccCCCCcccccceeecccccccCccccc
Q psy13846        476 DICGIIK------------RFSWRSWNPVVFVRTAVIWTGKQIFSL-----ILKPNRDCPVNANLKTKGRAYTANEEFCH  538 (1423)
Q Consensus       476 ~~~~~~~------------~~~~~~l~~p~i~kp~~~wtGKqi~s~-----il~~~~~~~~~~~~~~~~~~~~~~~~~~~  538 (1423)
                      ..+....            ++.+..+.+-....+.-++.++++...     ++.+.     ...+.. .+.+- ...+..
T Consensus       876 ~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~~~i~~~~-----~~~l~~-~r~~l-~~~~~~  948 (1449)
T d1twfa_         876 HIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEE-----YKQLVK-DRKFL-REVFVD  948 (1449)
T ss_dssp             GEEEEECGGGSSCHHHHHHHHCCCTTCTTTSCCTTTBTTHHHHTTCHHHHHHHHHH-----HHHHHH-HHHHH-HHHTTT
T ss_pred             EEEEeecceeccchHHhhhhhhhcccccccccChhHhhhhHHHhhhHHHHHHHHHH-----HHHHHH-HHHHH-HHHhcC
Confidence            1111100            000000000011111111112111100     00000     000000 00000 000000


Q ss_pred             C-CcEEEecccc-cccc-----ccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCC
Q psy13846        539 R-DSYVILRNSE-LLAG-----SMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG  611 (1423)
Q Consensus       539 ~-d~~v~i~~~e-ll~g-----~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~  611 (1423)
                      . ...+.--+-. ++..     ..+....+.-    ....++.            .++.+.......++..    .++  
T Consensus       949 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~------------~~~~l~~~~~~~~~~~----~~~-- 1006 (1449)
T d1twfa_         949 GEANWPLPVNIRRIIQNAQQTFHIDHTKPSDL----TIKDIVL------------GVKDLQENLLVLRGKN----EII-- 1006 (1449)
T ss_dssp             CCCEEEEESCHHHHHHHHHHHTTCCTTSCBCC----CHHHHHH------------HHHHHHTTCCSCCCCS----HHH--
T ss_pred             ccccccCcchHHHHHHhhhhhcccccCccccc----cHHHHHH------------HHHHHHhhhheecccc----hhh--
Confidence            0 0111100100 0000     0011111100    0000000            0000000000000000    000  


Q ss_pred             ccccccccccCCCceee-eeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeeccccCCCccCCCcchhee
Q psy13846        612 QGFVQNSFFSGLTPTEF-FFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECII  690 (1423)
Q Consensus       612 ~GfI~~sf~~GL~p~Ef-ffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~~~~~~~~  690 (1423)
                          ...........-. ..+..+.+.-+       .+.|--..++-..+..+..+|                       
T Consensus      1007 ----~~~~~~~~~~~~~~~~~~l~~~~~~-------~~~~l~~~~~~~~~~~~~~ky----------------------- 1052 (1449)
T d1twfa_        1007 ----QNAQRDAVTLFCCLLRSRLATRRVL-------QEYRLTKQAFDWVLSNIEAQF----------------------- 1052 (1449)
T ss_dssp             ----HHHHHHTTHHHHHHHHHHSCHHHHH-------HTSCCCHHHHHHHHHHHHHHH-----------------------
T ss_pred             ----hhhcccccceeeeeeccccchhhhh-------hhcccCHHHHHHHHHHHHHHH-----------------------
Confidence                0000000000000 00000000000       000000111111122222222                       


Q ss_pred             cCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHH
Q psy13846        691 MGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKE  770 (1423)
Q Consensus       691 ~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkE  770 (1423)
                      .+++++||++||.+||||||||+|||||    +|||+||+             +++|+|+             |+||++|
T Consensus      1053 ~~slv~pGEaVGiiAAQSIGEP~TQmTL----nTFH~AG~-------------~~~nvT~-------------GiPRl~E 1102 (1449)
T d1twfa_        1053 LRSVVHPGEMVGVLAAQSIGEPATQMTL----NTFHFAGV-------------ASKKVTS-------------GVPRLKE 1102 (1449)
T ss_dssp             HHHBCCTTCCHHHHHHHHHHHHHTTCCC---------------------------CCSCC-------------HHHHHHH
T ss_pred             hhhhhhccCcchhhhhhhhccchhhhhh----hhhhhcce-------------eeecccc-------------cchhhhh
Confidence            4568899999999999999999999999    99999998             7888888             9999999


Q ss_pred             HHhhhcCCCCceeeeecccC--ChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeee-------------------
Q psy13846        771 IINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIK-------------------  829 (1423)
Q Consensus       771 IinaSk~ikTPiitv~L~~~--~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~-------------------  829 (1423)
                      |++++++++||.|+++|.+.  .+.+.++.++..++++++++++...+.+|+++.....+.                   
T Consensus      1103 Il~ask~iktp~~~v~l~~~~~~~~~~~k~~~~~i~~~~l~~vv~~~~v~~~~~~~~~~i~~~~~~i~~~~~~~~~~~~~ 1182 (1449)
T d1twfa_        1103 ILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQ 1182 (1449)
T ss_dssp             HTTTCSSCSSCEEEEEBCSSSSSCHHHHHHHHHHHSCEEGGGTEEEEEEEECCCSSSCSSGGGHHHHHTSSCC-------
T ss_pred             heeeecccCCcceeEEeccccchhHHHHHhhhheeeeeeccceeeeeEEEEcCCCceEEEEEecceeeEEEEeccchhee
Confidence            99999999999999999876  467889999999999999999999888888765443333                   


Q ss_pred             -----------hhhhHHHhhccccchhhhhHHhhhcccccCcccccc----cccccc---cCCC----Cccccchhhhhh
Q psy13846        830 -----------LDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSG----HSFLIL---KPKD----SSKSFNSKMYQM  887 (1423)
Q Consensus       830 -----------ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~----~~~~~~---~~~~----~~~~~~~~l~~l  887 (1423)
                                 +.+++..+....+.+..+...+.+....+.......    ...+..   +...    ........+..+
T Consensus      1183 ~~~~~~~~ilrl~l~~~~~~~k~i~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~l~~i 1262 (1449)
T d1twfa_        1183 SFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKI 1262 (1449)
T ss_dssp             ---CCCSEEEEEEECHHHHHHTTCCHHHHHHHHHHHHGGGEEEEECCTTSSSCEEEEEEC----------CCTTHHHHHH
T ss_pred             eecccCCceEEEEEchhhcccCCCCHHHHHHHHHHhcCCCeEEEecCCCcceEEEecccCCccccccccccchHHHHHHH
Confidence                       333333333334444445444433222111110000    000000   0000    000011112222


Q ss_pred             -hhcCCceEEccccccceeeeecccc---------cceeEEeeeccCccccccceeecccceeeccCchHHHHHHhchHH
Q psy13846        888 -KQLLPSVVIKGVQGINRAVIHEEDV---------EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEA  957 (1423)
Q Consensus       888 -~~~l~~v~IkGi~~I~r~~i~~~~~---------~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~eV~~~LGIEA  957 (1423)
                       ...++++.|+|+++|+|+.+...+.         ....+|.+.++|.+|.+++..+++|+.+++||||++|+++|||||
T Consensus      1263 ~~~~l~~~~v~Gi~~I~rv~i~~~~~~~~~~~~~~~~~~~~vl~teG~nl~~~l~~~~iD~~~~~sNdI~dil~~lGIEA 1342 (1449)
T d1twfa_        1263 ENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEA 1342 (1449)
T ss_dssp             HHHHHHHCEEESCTTCCCEEEEEEEEEEECTTSSEEEEEEEEEEEESCCHHHHTTSTTBCTTTCBCSCHHHHHHHHCHHH
T ss_pred             HhhccCCcEEeCCCCeEEEEEecccceeeCCCCcCccCCcEEEEcCcCCHHHHhccCCcccccCccCcHHHHHHHHhHHH
Confidence             2355678999999999998764321         124679999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846        958 ARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG  999 (1423)
Q Consensus       958 AR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~  999 (1423)
                      ||++|++|++.||+.||++||+|||+||||+||++|+++|+.
T Consensus      1343 ar~~ii~EI~~V~~~~Gi~Id~rHi~LIad~MT~~G~~~~i~ 1384 (1449)
T d1twfa_        1343 GRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVT 1384 (1449)
T ss_dssp             HHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTTBSSCCCSS
T ss_pred             HHHHHHHHHHHHHHhcCcEECHHHHHHHHHHHCcCCeEeecc
Confidence            999999999999999999999999999999999999999975

>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]}

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RNA-polymerase beta-prime
species: Thermus thermophilus [TaxId: 274]

Probab=99.78  E-value=7.8e-23  Score=271.40  Aligned_cols=88  Identities=31%  Similarity=0.428  Sum_probs=80.4

Q ss_pred             HHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcc
Q psy13846       1285 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAF 1364 (1423)
Q Consensus      1285 i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~ 1364 (1423)
                      +.+++||||||+.++.|+                   .|.||++|.++||||+|++  ++|||++||||+|+++|++||+
T Consensus      1393 ~v~~~~ie~~~~~~~~e~-------------------~~~~t~~g~llgITr~gl~--~~s~Ls~ASFeeT~~vL~~AAi 1451 (1504)
T d1smyd_        1393 VLEKWDVEALNERLIAEG-------------------KTPVAWKPLLMGVTKSALS--TKSWLSAASFQNTTHVLTEAAI 1451 (1504)
T ss_dssp             EHHHHHHHHHHHHHTSCS-------------------CCCCCEEECCCCHHHHHHT--CSCHHHHTTSTTHHHHHHHHHH
T ss_pred             eeehhhHHHHHHHHHHcC-------------------CCcceeceEEeeeccCccc--ccCHHHHhhhhhHHHHHHHHHH
Confidence            446789999999887664                   5789999999999999998  4899999999999999999999


Q ss_pred             cCCcccccccccceeeccccccccceEEE
Q psy13846       1365 YGQTDCISGVSECIIMGLPMNVGTGLIKL 1393 (1423)
Q Consensus      1365 ~g~~D~l~g~s~~ii~G~~~~~GTG~~~l 1393 (1423)
                      +|++|.|.|||||||+|+++|+|||++.+
T Consensus      1452 ~g~~D~l~GvsEnVI~G~liP~GTG~~~~ 1480 (1504)
T d1smyd_        1452 AGKKDELIGLKENVILGRLIPAGTGSDFV 1480 (1504)
T ss_dssp             HTCEEECCSHHHHHHTTCCCSSSTTCTTT
T ss_pred             hcCCCcCcChhHHHhCCCCccCCCCchHH
Confidence            99999999999999999999999998543