Citrus Sinensis ID: 046825

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------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------121

CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLPSESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIETTKCGNCKAKNPRISKPTFGWIHMNGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKDLFSGPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGDSVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAARERGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLLVGKT

cccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHcccHHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccHHHHHHHHHHHcHHHHHHHcccccccccccccccccccEEEEEEcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHccccccccHHHHHHHHHHHHccccccccccEEEEccccccccccHHHHHHHHHHccccccccccccccccccccccEEEEEcccccEEEEcccccccccccccEEEEEccccccEEEccccccccccccccccccccccccHHHHHHHHHHHcccccEEcccccccEEEEHHHHHHHHHHcccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccEEEEEccEEEEEEEEccccccccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHcccHHHHHHHHcccccccccccHHHHHHHHcccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccccccEEcccccHHHHHHHHHccccEEEccccEEcccccEEEEEcccccccccccccHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHcccccccHHHHHHHcHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHccccccccHHHccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccEEEEEcccccc

ccccccccccccccccEEEcccccccHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHcccHHHHHHHHHHccccccccccccccccccccccccccEEHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccEEEEEEccccHcHHHHHHHHHHcccHHccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccEEccHHHHHHHHHHccHHHHHHHccccccccccccccccHcHEEEEEcccccccccccEEccccccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHcccccHcccccccEEcEcEEEEEcccccccEcEccccHHHHHHccccccccHHcHHHHHHHHHcccccccccEEEEEccccEEEcccccHHHHHHHHHHHHHHHHccccccccccccccEEEEEcccccEEEEccccccccccHccEEEEEcccccEEEEEEEcccccccccccccccccccccHHHHHHHHHHHccccccEcccccccEHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccccccccccccccccEEEEcccccEEcccccEEcccccccccEEEEEEEcccccccccEEEccccccccccccccccccEEEEccccccEEEEEccccccccccccccccccccccEEcccccccccccccccEEEEEccEEEEEEEEcHccccccHEHHHHHHccHHHHHHHHHHHHHHHHHHHHHcccEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHEEEEcccccEEEEHHHHHHHccHccccccccccccccccccccccccccccccEEEccccccccHHHHHHHHHccccccHcHHHHHHHHHHHHHHHHHHHcccEEEEcccEEcccccEEEEEEccccccccEEccccccccHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHcccccEEEEEEEcccccccccHEHHHHHHcccccHccccccHHHHHHHHHHHHcccccEEEEEEccccc

cktcgqrqflcpghfghidlvvpvYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAaksldldlpsessnpedsdvsnksscsmvtprgnydnvrnlkpqeWTSLQFAEAKLALLQFLKIEttkcgnckaknpriskptfgwihmngmphaDIRANLirgcnlgetfsggeeekdlgassdvdapethsfngtfpgtqdtaarrhqkgsgavpsgfkkqkdlfsgpllpsdVKDIIEKLWENEFELCSFISDmqqqgfgkkagHSIFFLGVVlvppikfrlpskggdsvmehpQTVLLSKVLQANIYLAnayvnqpdNAKVIVARWMNLQQSVNVLfdgknaagqrDMASGICQLLEKKEGLFRQKLMGKRVNYAcrsvispdpylavneigippyfalrltypervtpwnvVKLRDSiingaeihpgathyldklstmrlppnkkmrISIGrkldtsrgaivqpgkdsdnefeGKMVYRHLQdgdvvlvnrqptlhkpsiMAHVVRVLKGEKTLRMHYAncstynadfdgdemnvhfpqdevsrAEAYNIVnannqyvrpsngdplRSLIQDHIVSAALltkkdtflnRDEFCQLLYSsgvsssglgsftgkpgqrvlisrseqevlpllpaiwkpeplwtgKQVITAVLNHitrgrppfvverggklpqdffktrfnadkqsdrkkndkgklsktnkmhkdksgkkkevvegkpgeekeaeKNKSKEKELSEEKLLIYKNdlvrgvidkaqfadygLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHgftcgvddllILKDKERerknhlhgseeigKRVHlealeledgaeidpiKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLsegllkptgknWISLMTtsgakgskvnFQQISSHlgqqelegkrvprmvsgktlpsfhpwdwapraggfiidrfltglrpqeyyFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLEClkisydysvrdadgsivqfcygedgvdvhqtSFISKFDALAARErgrgrgrnkfcdkgshtfvmgrNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKHKFVlslaqpgepvgllasqsvgepstqmtlntfhlagrgemnvtlgiPRLQEILTIAskdiktpvitcpllvgkt

cktcgqrqflcpghfgHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKgdiiaaksldldlpsessnpedsdvsnksscsmvtprgnydnVRNLKPQEWTSLQFAEAKLALLQFLKIEttkcgnckaknprISKPTFGWIHMNGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETHSFNGTFPGTQDTAARRHQKGsgavpsgfkkqkdlfsgpllPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGDSVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAeihpgathyldklstmrlppNKKMRISigrkldtsrgaivqpgkdsdnefEGKMVYRHLQDGDVVLVNRQptlhkpsimahVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSgvsssglgsFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKtrfnadkqsdrkkndkgklsktnkmhkdksgkkkevvegkpgeekeaeknkskekelseekllIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERerknhlhgseeigkrvhlealeledgaeidpIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHlgqqelegkrvPRMVSGKTlpsfhpwdwaPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAArergrgrgrnkfcdkgshtfvmgrNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILtiaskdiktpvitcpllvgkt

CKTCGQRQFLCPGHFGHIDLVVPVYNPllfnllytllKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLPSESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIETTKCGNCKAKNPRISKPTFGWIHMNGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKDLFSGPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGDSVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQllyssgvsssglgsFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHkdksgkkkevvegkpgeekeaeknkskekelseekllIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAArergrgrgrNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLLVGKT

*****QRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSL*********************************VRNLKPQEWTSLQFAEAKLALLQFLKIETTKCGNCKAKNPRISKPTFGWIHMNGMPHADIRANLIRGCNLGET**********************************************************GPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGDSVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLS*************************************GKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVS***LGSF*****QRVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFF*************************************************************KLLIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILK*********************L****************************DAAVAYFDMK************VINELLSEGLLKPTGKNWISLMT**********************************KTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDA*********************TFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLL***********MTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLLV***

CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLD*************************G***************LQFAEAKLALLQFLKIETTKCGNCKAKNPRISKPTFGWIHMNGMPHADIRANLIRGCNLGETFSGGEEEKDLGA*************************RHQKGSGAVPSGF***KDLFSGPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKF***************TVLLSKVLQANIYLA***********VIVARWMNLQQSVNVL******************LLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRG********SDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAM*GGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAARERGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLLVG**

CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDL********************VTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIETTKCGNCKAKNPRISKPTFGWIHMNGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETHSFNGTFPGT*****************GFKKQKDLFSGPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGDSVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNAD***************************************************SEEKLLIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAARERGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLLVGKT

CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLP*****************SMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIETTKCGNCKAKNPRISKPTFGWIHMNGMPHADIRANLIRGCNLGE**S****************************************SG***********LFSGPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGDSVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSG***EVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAARERGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLLV***

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		1208	2.2.26 [Sep-21-2011]
Q86H36		1615	DNA-directed RNA polymera	yes	no	0.876	0.655	0.384	0.0
P10964		1664	DNA-directed RNA polymera	yes	no	0.913	0.662	0.372	0.0
O35134		1717	DNA-directed RNA polymera	yes	no	0.769	0.541	0.362	1e-179
O95602		1720	DNA-directed RNA polymera	yes	no	0.770	0.541	0.365	1e-176
O54889		1716	DNA-directed RNA polymera	yes	no	0.773	0.544	0.364	1e-174
P91875		1642	DNA-directed RNA polymera	yes	no	0.614	0.451	0.385	1e-154
P16355		1744	DNA-directed RNA polymera	N/A	no	0.555	0.384	0.340	1e-115
P15398		1689	DNA-directed RNA polymera	yes	no	0.542	0.387	0.354	1e-114
O14802		1390	DNA-directed RNA polymera	no	no	0.663	0.576	0.320	1e-112
O94666		1405	DNA-directed RNA polymera	no	no	0.657	0.565	0.306	1e-100

>sp\|Q86H36\|RPA1_DICDI DNA-directed RNA polymerase I subunit rpa1 OS=Dictyostelium discoideum GN=polr1a PE=3 SV=1	Back alignment and function desciption

 Score =  766 bits (1979), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 488/1269 (38%), Positives = 674/1269 (53%), Gaps = 210/1269 (16%)

Query: 1    CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRK 60
            C TC      CPGHFGHI+L +P YNP+ F  ++ LLK  CF CHHFK  +  + + + +
Sbjct: 65   CATCSLDFIECPGHFGHIELAIPCYNPVSFQTIFKLLKNKCFHCHHFKHGKPIINQFIEE 124

Query: 61   LELIIKGDIIAAKSLDL---------DLPSESSNPEDSDV--SNKSSCSMVTPRGNYDNV 109
            L L+ KGD++ A++L           +     SN E  +V  S++S    +    N  N 
Sbjct: 125  LTLLFKGDVVKARNLRERNVLLRGYEEKKKGKSNEEGEEVMESDESDSDKMDTDENKTNG 184

Query: 110  RNLKPQEWTSLQFAEAKLALLQFLKIETTK------------CGNCKAKNPRISKPTFGW 157
            + +    + + +    K   ++  K E  K            CGNC A +PR+       
Sbjct: 185  KIICDGVFNAKEIYSGKATHIEDFKREVFKEFFGSFSGYAIPCGNCGAYSPRLRNGDASK 244

Query: 158  IHMNGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETHSFNGTFPGTQDTAA 217
              +  MP  D  A       L   FS  +E+ +               +GT+        
Sbjct: 245  SKLFIMPLHDKYATKNSAIKLPTNFSSVKEQTE---------------HGTW-------- 281

Query: 218  RRHQKGSGAVPSGFKKQKDLFSGPLLPSDVKDIIEKLWENEFE-----LCSFISDMQQQG 272
                                      P +V D ++KL+ENE E     L   +  +  +G
Sbjct: 282  ------------------------FAPWEVLDNMKKLFENEKEILDMLLGHLVPIVTNKG 317

Query: 273  ---------FGKKAGHSIFFLGVVLVPPIKFRLPSKGGDSVMEHPQTVLLSKVLQANIYL 323
                     F K++     F+ V  V P ++R P+       EHPQ      ++++N  +
Sbjct: 318  GAKKNVGRQFTKESNVDSLFMRVFPVTPARYRPPNFVNGRRSEHPQNSHYKGMVKSNKMI 377

Query: 324  ANAYVNQPDNAKVIVARWMNLQQSVNVLFD-GKNAAGQRDMASGICQLLEKKEGLFRQKL 382
              +       AK +V    +LQ  VN ++D  K+ +   ++A+GI Q+LEKKEGLFR+ +
Sbjct: 378  RQSIDAGEGKAKFLVNSVCDLQMHVNNMYDNSKSNSNTNEVANGIKQILEKKEGLFRKHM 437

Query: 383  MGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHP 442
            MGKRVNYA R+VISPD  L  NE+G+P YFA  LT+P+ VT +N  +L  ++ING E +P
Sbjct: 438  MGKRVNYAARTVISPDISLETNEMGVPQYFAKTLTFPQPVTSFNYNQLAQAVINGPEQYP 497

Query: 443  GATHYLDK---LSTMRLPPNKKMRISIGRKLDTS-----RGAIVQPGKDSDNEFEGKMVY 494
            GA    D+   L  +     +K RI++ + L TS     RG               K VY
Sbjct: 498  GANFIEDENGHLINLSKESQEK-RIALSKTLLTSHPHAPRGV-------------NKKVY 543

Query: 495  RHLQDGDVVLVNRQPTLHKPSIMAHVVRVL-KGEKTLRMHYANCSTYNADFDGDEMNVHF 553
            RHL  GD VL NRQPTLHKP IM H V+VL K EKTLRMHY+NCSTYNADFDGDEMN+HF
Sbjct: 544  RHLLSGDYVLANRQPTLHKPGIMGHRVKVLGKNEKTLRMHYSNCSTYNADFDGDEMNIHF 603

Query: 554  PQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLY 613
            PQ  ++ AE   I   N QY+ P NG PLR LIQDHI++  LLTK+DT   + +F  +LY
Sbjct: 604  PQSLLASAEIREICANNYQYLVPRNGAPLRGLIQDHILTGVLLTKRDTLFTKADFQAILY 663

Query: 614  SSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGR 673
            +S  S +        P                 P I KP PLW+GKQ+I+A LN +T GR
Sbjct: 664  ASCWSVNTKHPIVTPP-----------------PCILKPVPLWSGKQLISAALNQLTIGR 706

Query: 674  PPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGE 733
             P  +E   K+P   + T+                L  T   H                 
Sbjct: 707  APLNLEAPSKIPTKMWGTK---------------GLEITRDSH----------------- 734

Query: 734  EKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQF--ADYGLVHTVQELYGSNTAGTLL 791
                              ++I +N++V G++DK  F  + YGLVHT  ELY  + AG+LL
Sbjct: 735  ------------------VIIRQNEMVAGILDKGHFGASSYGLVHTCYELYDPDVAGSLL 776

Query: 792  SALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEI 851
            + L R+FT +LQ  GFTCGVDDLL+   +E+ R   L  + E G  V   A +  D ++ 
Sbjct: 777  TLLGRMFTNYLQSRGFTCGVDDLLMKNKEEKFRVETLKKANEEGYTV---AAKFADLSKY 833

Query: 852  DPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISL 911
            D  K +    KA++   +  VA  D  +   LN++T S VI+ L+  G  KP  KN  SL
Sbjct: 834  DEQKARDFFSKALQ--SEREVARLDGLLKKGLNQYT-SKVIDTLIPGGQQKPFPKNNFSL 890

Query: 912  MTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFL 971
            MT SGAKGS VNF Q+S  LGQQELEGKRVPRMVSGKTLPSF  +D + RAGGF++DRFL
Sbjct: 891  MTVSGAKGSVVNFSQVSCLLGQQELEGKRVPRMVSGKTLPSFQAYDASARAGGFVMDRFL 950

Query: 972  TGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQ 1031
            TG+RPQ+Y+FHCMAGREGL+DTAVKTSRSGYLQRCLIK+LE L + YD +VR++DGS++Q
Sbjct: 951  TGVRPQDYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLSVQYDNTVRESDGSVIQ 1010

Query: 1032 FCYGEDGVDVHQTSFISKFDALAARERGRGRGRNKFCDKGSHTFVMGRNQEMI-YK---K 1087
            F YGED +++ +T +++KF  +A         +++F           +NQE++ Y    K
Sbjct: 1011 FNYGEDSLEIGKTPYLTKFPIIAENYE---LFKSQF--PMEQLIEQLKNQEVVEYNRSIK 1065

Query: 1088 CSGQLD--------------ASNAYIMELPDALKDNAEKFADKFLSN---EMAKQDFLKL 1130
               +LD               S +++ +L   ++ N +K   K  SN   ++ ++DF  L
Sbjct: 1066 TQPELDPVMSKFNPSSDLGCVSESFMNQLNHYIESNPQKLI-KTTSNRDGKINEKDFRNL 1124

Query: 1131 VKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIA 1190
            +   +  S+  PGE VGLL +QS+GEPSTQMTLNTFHLAGRGE NVTLGIPRL+E++  A
Sbjct: 1125 MYLYYSRSMVSPGESVGLLCAQSIGEPSTQMTLNTFHLAGRGEANVTLGIPRLRELIMTA 1184

Query: 1191 SKDIKTPVI 1199
            +    TP++
Sbjct: 1185 TTKPITPLM 1193

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 I which synthesizes ribosomal RNA precursors. 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 I. A bridging helix emanates from RPA1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol I 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: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6

>sp\|P10964\|RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPA190 PE=1 SV=2	Back alignment and function description

>sp\|O35134\|RPA1_MOUSE DNA-directed RNA polymerase I subunit RPA1 OS=Mus musculus GN=Polr1a PE=1 SV=2	Back alignment and function description

>sp\|O95602\|RPA1_HUMAN DNA-directed RNA polymerase I subunit RPA1 OS=Homo sapiens GN=POLR1A PE=1 SV=2	Back alignment and function description

>sp\|O54889\|RPA1_RAT DNA-directed RNA polymerase I subunit RPA1 OS=Rattus norvegicus GN=Polr1a PE=1 SV=1	Back alignment and function description

>sp\|P91875\|RPA1_DROME DNA-directed RNA polymerase I subunit RPA1 OS=Drosophila melanogaster GN=RpI1 PE=1 SV=2	Back alignment and function description

>sp\|P16355\|RPA1_TRYBB DNA-directed RNA polymerase I subunit RPA1 OS=Trypanosoma brucei brucei GN=TRP11 PE=1 SV=1	Back alignment and function description

>sp\|P15398\|RPA1_SCHPO DNA-directed RNA polymerase I subunit rpa1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpa1 PE=1 SV=2	Back alignment and function description

>sp\|O14802\|RPC1_HUMAN DNA-directed RNA polymerase III subunit RPC1 OS=Homo sapiens GN=POLR3A PE=1 SV=2	Back alignment and function description

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

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		1208
255571576		1686	DNA-directed RNA polymerase I largest su	0.940	0.673	0.649	0.0
225441748		1740	PREDICTED: DNA-directed RNA polymerase I	0.951	0.660	0.648	0.0
297739697		1669	unnamed protein product [Vitis vinifera]	0.942	0.681	0.649	0.0
356537377		1653	PREDICTED: DNA-directed RNA polymerase I	0.923	0.675	0.621	0.0
449437932		1650	PREDICTED: DNA-directed RNA polymerase I	0.923	0.675	0.617	0.0
449517429		1652	PREDICTED: LOW QUALITY PROTEIN: DNA-dire	0.920	0.673	0.613	0.0
224087062		1168	predicted protein [Populus trichocarpa]	0.903	0.934	0.626	0.0
297817092		1678	hypothetical protein ARALYDRAFT_486216 [	0.940	0.676	0.602	0.0
147815227		1350	hypothetical protein VITISV_029145 [Viti	0.912	0.816	0.620	0.0
357475409		1628	DNA-directed RNA polymerase subunit beta	0.918	0.681	0.596	0.0

>gi\|255571576\|ref\|XP_002526734.1\| DNA-directed RNA polymerase I largest subunit, putative [Ricinus communis] gi\|223533923\|gb\|EEF35648.1\| DNA-directed RNA polymerase I largest subunit, putative [Ricinus communis]	Back alignment and taxonomy information

 Score = 1569 bits (4063), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 792/1219 (64%), Positives = 927/1219 (76%), Gaps = 83/1219 (6%)

Query: 1    CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRK 60
            CKTCGQR   CPGH GHIDLV PVYNPLLFN L+ LL+R CF C HF+  R +VEKC+++
Sbjct: 67   CKTCGQRSTNCPGHCGHIDLVSPVYNPLLFNFLHKLLQRTCFLCFHFRMQRGQVEKCIKQ 126

Query: 61   LELIIKGDIIAAKSLDLDLPSESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSL 120
            LELI+KGDI+ AK L+   PSE+  PE+SD+S++S C  +      ++  + + Q WTSL
Sbjct: 127  LELIVKGDIVGAKRLESVSPSEALYPEESDLSHES-CPTIHSGVQCNDGEHTRQQGWTSL 185

Query: 121  QFAEAKLALLQFLKIETTKCGNCKAKNPRISKPTFGWIHMNGMPHADIRANLIRGCNLGE 180
            QF EA   L  FLK +  KC NC++ NP I+KPTFGW H +GM  A IRAN+I G  LG 
Sbjct: 186  QFTEAMSVLNNFLKPKFKKCKNCESSNPNITKPTFGWFHTSGMSDASIRANVITGHQLGG 245

Query: 181  TFSGGEEEKDLGASSDVDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKDLFSG 240
               G E E   G +   DA E        PG Q +  ++H+K        F +QK  FS 
Sbjct: 246  LL-GSEIE---GTTDVEDAAE--------PGDQHSGTKKHKKKERKEVLEFTRQKSTFSK 293

Query: 241  PLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGK-KAGHSIFFLGVVLVPPIKFRLPSK 299
             LLPS+VK+ +E LW+NE  +CSFISD+QQQ FGK KAG ++FFL  +LVPPIKFR P+K
Sbjct: 294  QLLPSEVKEKLELLWKNEARICSFISDLQQQEFGKRKAGPAMFFLETILVPPIKFRPPTK 353

Query: 300  GGDSVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNA-- 357
            GGDSVMEHPQTVLLSKVLQ+NI L +A++N+  +   IV RW++LQQS+N LFD K A  
Sbjct: 354  GGDSVMEHPQTVLLSKVLQSNISLGDAHINKEHSK--IVRRWLDLQQSINTLFDSKTAKG 411

Query: 358  AGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLT 417
             GQR+ A GICQLLEKKEGLFRQK+MGKRVNYACRSVISPDPY+ VNEIGIPP FA++LT
Sbjct: 412  PGQREGAPGICQLLEKKEGLFRQKMMGKRVNYACRSVISPDPYIGVNEIGIPPCFAVKLT 471

Query: 418  YPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAI 477
            YPERVTPWN+ KLR+++ING+E HPGATHY+DKLS  +LPP +K RISI RKL +SRGA+
Sbjct: 472  YPERVTPWNIAKLRNAVINGSECHPGATHYVDKLSINKLPPARKARISISRKLPSSRGAV 531

Query: 478  VQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANC 537
             Q GK S+ EFEGK+VYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANC
Sbjct: 532  TQAGKGSECEFEGKIVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANC 591

Query: 538  S-TYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALL 596
            S TYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQ+VRPSNG+PLR LIQDHIVSA LL
Sbjct: 592  SITYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQFVRPSNGEPLRGLIQDHIVSAVLL 651

Query: 597  TKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLW 656
            TKKDTFL++DEF QLLYSSGVS+ G  SF G+PGQ+VL SRSE E+  L PAIWKP+PLW
Sbjct: 652  TKKDTFLSQDEFNQLLYSSGVSTVGPNSFHGRPGQKVLWSRSEDEIQTLPPAIWKPKPLW 711

Query: 657  TGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMH 716
            TGKQVITA+LNHIT   PPF VE+  K+P +FFK+R N DK    +K+DK          
Sbjct: 712  TGKQVITAILNHITSDHPPFTVEKDAKIPSNFFKSRANEDKPCQEEKSDK---------- 761

Query: 717  KDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFADYGLVH 776
                             +  AEK         EEK+L+YKN+LVRGVIDK QF +YGLVH
Sbjct: 762  -----------------DAPAEKEPD------EEKMLVYKNELVRGVIDKGQFGEYGLVH 798

Query: 777  TVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGK 836
            TV EL GS+TAG LLS LSRLFT +LQMHGFTCGVDDLLIL +K+ ERK  L   E+ G+
Sbjct: 799  TVHELLGSHTAGILLSVLSRLFTAYLQMHGFTCGVDDLLILTNKDEERKKQLEWCEKSGE 858

Query: 837  RVHLEALELED-GAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINEL 895
             VH   + ++D   +IDP+ ++  IEK +R  GD+A+AY D +M+++LN  TSS VI+ L
Sbjct: 859  AVHRNFIGIKDEKIKIDPVAMQLNIEKTIRSDGDSALAYLDRQMSNELNTKTSSGVISNL 918

Query: 896  LSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHP 955
            LS+GLLKP+GKN ISLMTTSGAKGSKVNFQQISS LGQQELEGKRVPRMVSGKTLP FHP
Sbjct: 919  LSDGLLKPSGKNCISLMTTSGAKGSKVNFQQISSFLGQQELEGKRVPRMVSGKTLPCFHP 978

Query: 956  WDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLK 1015
            WDWA R+GG+I DRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLK
Sbjct: 979  WDWAARSGGYITDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLK 1038

Query: 1016 ISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAARERGRGRGRNKFCDKGSHTF 1075
            I YD++VRDADGS+VQF YGEDGVDVHQTSFI+KF  LA                     
Sbjct: 1039 IGYDHTVRDADGSVVQFYYGEDGVDVHQTSFIAKFKELAL-------------------- 1078

Query: 1076 VMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADKF------LSNEMAKQDFLK 1129
                NQ+MIYK+  GQL A N+YI ELP+ALK+ A++F D F       SN + ++D   
Sbjct: 1079 ----NQDMIYKRSGGQLGAFNSYISELPEALKEKADRFLDDFSIMGRIASNLVKREDLYN 1134

Query: 1130 LVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTI 1189
            L+K KF+LSLAQPGEPVG+LA+QSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEIL  
Sbjct: 1135 LMKQKFLLSLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILMT 1194

Query: 1190 ASKDIKTPVITCPLLVGKT 1208
            AS DIKTP++TCPL  G+T
Sbjct: 1195 ASIDIKTPIMTCPLQEGRT 1213

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225441748\|ref\|XP_002277555.1\| PREDICTED: DNA-directed RNA polymerase I subunit RPA1-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297739697\|emb\|CBI29879.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356537377\|ref\|XP_003537204.1\| PREDICTED: DNA-directed RNA polymerase I subunit rpa1-like [Glycine max]	Back alignment and taxonomy information

>gi\|449437932\|ref\|XP_004136744.1\| PREDICTED: DNA-directed RNA polymerase I subunit RPA1-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449517429\|ref\|XP_004165748.1\| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase I subunit RPA1-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|224087062\|ref\|XP_002308049.1\| predicted protein [Populus trichocarpa] gi\|222854025\|gb\|EEE91572.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|297817092\|ref\|XP_002876429.1\| hypothetical protein ARALYDRAFT_486216 [Arabidopsis lyrata subsp. lyrata] gi\|297322267\|gb\|EFH52688.1\| hypothetical protein ARALYDRAFT_486216 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|147815227\|emb\|CAN70028.1\| hypothetical protein VITISV_029145 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|357475409\|ref\|XP_003607990.1\| DNA-directed RNA polymerase subunit beta [Medicago truncatula] gi\|355509045\|gb\|AES90187.1\| DNA-directed RNA polymerase subunit beta [Medicago truncatula]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		1208
TAIR\|locus:2076661		1670	NRPA1 "nuclear RNA polymerase	0.512	0.370	0.572	0.0
DICTYBASE\|DDB_G0275759		1615	rpa1 "RNA polymerase I, larges	0.362	0.271	0.483	9.9e-204
CGD\|CAL0001661		1665	RPA190 [Candida albicans (taxi	0.350	0.254	0.432	1.4e-196
POMBASE\|SPBC4C3.05c		1689	nuc1 "DNA-directed RNA polymer	0.281	0.201	0.457	9.7e-189
UNIPROTKB\|G4NBX7		1719	MGG_01158 "DNA-directed RNA po	0.346	0.243	0.413	7.4e-181
SGD\|S000005868		1664	RPA190 "RNA polymerase I large	0.419	0.304	0.383	3.2e-180
UNIPROTKB\|B9ZVN9		1659	POLR1A "DNA-directed RNA polym	0.247	0.180	0.475	1.2e-178
UNIPROTKB\|O95602		1720	POLR1A "DNA-directed RNA polym	0.247	0.173	0.475	1.9e-178
UNIPROTKB\|G3V7B7		1716	Polr1a "DNA-directed RNA polym	0.247	0.174	0.491	8.7e-176
ZFIN\|ZDB-GENE-030131-5286		1710	polr1a "polymerase (RNA) I pol	0.218	0.154	0.507	2.3e-175

TAIR\|locus:2076661 NRPA1 "nuclear RNA polymerase A1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1811 (642.6 bits), Expect = 0., Sum P(3) = 0.
 Identities = 365/638 (57%), Positives = 456/638 (71%)

Query:    82 ESSNPEDSDVSNKSSCSMVTPRGNYD-NVRNLKPQEWTSLQFAEAKLALLQFLKIETTKC 140
             ES+ P  S  S++S  S+VT   + +    +++ Q WTSLQFAE    L  F+++ +  C
Sbjct:   154 ESNTPTKSKSSDESCESVVTTDSSEECEDSDVEDQRWTSLQFAEVTAVLKNFMRLSSKSC 213

Query:   141 GNCKAKNPRISKPTFGWIHMNGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAP 200
               CK  NP++ KP FGW+ M  M  +D+ AN+IRG  L ++ S   E  D    S +DA 
Sbjct:   214 SRCKGINPKLEKPMFGWVRMRAMKDSDVGANVIRGLKLKKSTSS-VENPDGFDDSGIDA- 271

Query:   201 ETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKDLFSGPLLPSDVKDIIEKLWENEFE 260
                  +    G ++T  +     S  V + F++        LLPS+V++I++ LW+NE E
Sbjct:   272 ----LSEVEDGDKETREK-----STEVAAEFEEHNS--KRDLLPSEVRNILKHLWQNEHE 320

Query:   261 LCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGDSVMEHPQTVLLSKVLQAN 320
              CSFI D+ Q G  +K  +S+FFL  VLVPP KFR P+ GGDSVMEHPQTV L+KV+++N
Sbjct:   321 FCSFIGDLWQSG-SEKIDYSMFFLESVLVPPTKFRPPTTGGDSVMEHPQTVGLNKVIESN 379

Query:   321 IYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAA--GQRDMASGICQLLEKKEGLF 378
               L NA  N+ D +KVI  RW NLQ+SVNVLFD K A    QRD +SGICQLLEKKEGLF
Sbjct:   380 NILGNACTNKLDQSKVIF-RWRNLQESVNVLFDSKTATVQSQRD-SSGICQLLEKKEGLF 437

Query:   379 RQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGA 438
             RQK+MGKRVN+ACRSVISPDPY+AVN+IGIPP FAL+LTYPERVTPWNV KLR++IING 
Sbjct:   438 RQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAIINGP 497

Query:   439 EIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQ 498
             +IHPGATHY DK STM+LP  +K R +I RKL +SRGA  + GK  D  FEGK V+RH++
Sbjct:   498 DIHPGATHYSDKSSTMKLPSTEKARRAIARKLLSSRGATTELGKTCDINFEGKTVHRHMR 557

Query:   499 DGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEV 558
             DGD+VLVNRQPTLHKPS+MAH VRVLKGEKTLR+HYANCSTYNADFDGDEMNVHFPQDE+
Sbjct:   558 DGDIVLVNRQPTLHKPSLMAHKVRVLKGEKTLRLHYANCSTYNADFDGDEMNVHFPQDEI 617

Query:   559 SRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQXXXXXXXX 618
             SRAEAYNIVNANNQY RPSNG+PLR+LIQDHIVS+ LLTK+DTFL++D F Q        
Sbjct:   618 SRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVLLTKRDTFLDKDHFNQLLFSSGVT 677

Query:   619 XXXXXXFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVV 678
                   F+G+ G++V++S S+ E+L + PAI KP PLWTGKQVITAVLN IT+G PPF V
Sbjct:   678 DMVLSTFSGRSGKKVMVSASDAELLTVTPAILKPVPLWTGKQVITAVLNQITKGHPPFTV 737

Query:   679 ERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMH 716
             E+  KLP DFFK R    K +      K ++ ++ K +
Sbjct:   738 EKATKLPVDFFKCRSREVKPNSGDLTKKKEIDESWKQN 775

GO:0003677 "DNA binding" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=ISM;ISS;IDA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005829 "cytosol" evidence=RCA

GO:0009506 "plasmodesma" evidence=IDA

GO:0006354 "DNA-dependent transcription, elongation" evidence=RCA

GO:0006406 "mRNA export from nucleus" evidence=RCA

GO:0006606 "protein import into nucleus" evidence=RCA

DICTYBASE\|DDB_G0275759 rpa1 "RNA polymerase I, largest subunit" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

CGD\|CAL0001661 RPA190 [Candida albicans (taxid:5476)]	Back alignment and assigned GO terms

POMBASE\|SPBC4C3.05c nuc1 "DNA-directed RNA polymerase I complex large subunit Nuc1" [Schizosaccharomyces pombe (taxid:4896)]	Back alignment and assigned GO terms

UNIPROTKB\|G4NBX7 MGG_01158 "DNA-directed RNA polymerase" [Magnaporthe oryzae 70-15 (taxid:242507)]	Back alignment and assigned GO terms

SGD\|S000005868 RPA190 "RNA polymerase I largest subunit A190" [Saccharomyces cerevisiae (taxid:4932)]	Back alignment and assigned GO terms

UNIPROTKB\|B9ZVN9 POLR1A "DNA-directed RNA polymerase" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|O95602 POLR1A "DNA-directed RNA polymerase I subunit RPA1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|G3V7B7 Polr1a "DNA-directed RNA polymerase" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-030131-5286 polr1a "polymerase (RNA) I polypeptide A" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	0.691
4th Layer	2.7.7.6	0.737

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		1208
PRK08566		882	PRK08566, PRK08566, DNA-directed RNA polymerase su	1e-147
TIGR02390		867	TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer	1e-141
PRK14977		1321	PRK14977, PRK14977, bifunctional DNA-directed RNA	1e-132
COG0086		808	COG0086, RpoC, DNA-directed RNA polymerase, beta'	1e-122
smart00663		295	smart00663, RPOLA_N, RNA polymerase I subunit A N-	1e-105
pfam00623		165	pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, do	4e-71
pfam04998		447	pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, do	7e-70
cd02735		309	cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of	9e-43
cd02584		410	cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of	1e-28
cd02736		300	cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) o	2e-27
PRK04309		383	PRK04309, PRK04309, DNA-directed RNA polymerase su	5e-27
TIGR02386		1140	TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase,	2e-26
TIGR02389		367	TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymer	1e-24
cd06528		363	cd06528, RNAP_A'', A'' subunit of Archaeal RNA Pol	2e-24
PRK14906		1460	PRK14906, PRK14906, DNA-directed RNA polymerase su	2e-24
CHL00018		663	CHL00018, rpoC1, RNA polymerase beta' subunit	4e-23
TIGR02387		619	TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase	5e-23
PRK02625		627	PRK02625, rpoC1, DNA-directed RNA polymerase subun	1e-22
pfam05000		108	pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, do	2e-22
PRK14844		2836	PRK14844, PRK14844, bifunctional DNA-directed RNA	4e-22
PRK09603		2890	PRK09603, PRK09603, bifunctional DNA-directed RNA	5e-22
cd00630		158	cd00630, RNAP_largest_subunit_C, Largest subunit o	6e-22
PRK14897		509	PRK14897, PRK14897, unknown domain/DNA-directed RN	7e-19
TIGR02386		1140	TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase,	1e-18
pfam04983		158	pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, do	2e-18
TIGR02388		1227	TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase	2e-14
PRK09603		2890	PRK09603, PRK09603, bifunctional DNA-directed RNA	3e-13
PRK08566		882	PRK08566, PRK08566, DNA-directed RNA polymerase su	8e-12
PRK14906		1460	PRK14906, PRK14906, DNA-directed RNA polymerase su	2e-11
COG0086		808	COG0086, RpoC, DNA-directed RNA polymerase, beta'	2e-10
cd02655		204	cd02655, RNAP_beta'_C, Largest subunit (beta') of	2e-10
PRK00566		1156	PRK00566, PRK00566, DNA-directed RNA polymerase su	1e-09
pfam04997		330	pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, do	6e-09
TIGR02390		867	TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer	1e-08
PRK00566		1156	PRK00566, PRK00566, DNA-directed RNA polymerase su	6e-08
PRK00566		1156	PRK00566, PRK00566, DNA-directed RNA polymerase su	2e-07
COG0086		808	COG0086, RpoC, DNA-directed RNA polymerase, beta'	2e-06
PRK14898		858	PRK14898, PRK14898, DNA-directed RNA polymerase su	3e-06
PRK14898		858	PRK14898, PRK14898, DNA-directed RNA polymerase su	8e-06
CHL00117		1364	CHL00117, rpoC2, RNA polymerase beta'' subunit; Re	1e-05
PRK02597		1331	PRK02597, rpoC2, DNA-directed RNA polymerase subun	1e-05
PRK14977		1321	PRK14977, PRK14977, bifunctional DNA-directed RNA	9e-05
PRK14844		2836	PRK14844, PRK14844, bifunctional DNA-directed RNA	9e-05
PRK14844		2836	PRK14844, PRK14844, bifunctional DNA-directed RNA	9e-05
CHL00117		1364	CHL00117, rpoC2, RNA polymerase beta'' subunit; Re	2e-04
PRK02597		1331	PRK02597, rpoC2, DNA-directed RNA polymerase subun	3e-04
PRK00566		1156	PRK00566, PRK00566, DNA-directed RNA polymerase su	5e-04

>gnl\|CDD\|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated	Back alignment and domain information

 Score =  466 bits (1201), Expect = e-147
 Identities = 251/733 (34%), Positives = 351/733 (47%), Gaps = 164/733 (22%)

Query: 341  WMNLQQSVNVLFD----GKNAAGQRDMASG-----ICQLLEKKEGLFRQKLMGKRVNYAC 391
            W  LQ  V   FD    G   A  R   SG     + Q L+ KEG FR  L GKRVN++ 
Sbjct: 268  WELLQYHVTTYFDNEIPGIPPARHR---SGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSA 324

Query: 392  RSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKL 451
            R+VISPDP L++NE+G+P   A  LT PERVT WN+ +LR+ ++NG E HPGA  Y+ + 
Sbjct: 325  RTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGAN-YVIR- 382

Query: 452  STMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEF------EGKMVYRHLQDGDVVLV 505
                 P  +++++                  D + E        G +V RHL DGD+VL 
Sbjct: 383  -----PDGRRIKL-----------------TDKNKEELAEKLEPGWIVERHLIDGDIVLF 420

Query: 506  NRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYN 565
            NRQP+LH+ SIMAH VRVL G KT R++ A C  YNADFDGDEMN+H PQ E +RAEA  
Sbjct: 421  NRQPSLHRMSIMAHRVRVLPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARI 479

Query: 566  IVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSF 625
            ++      + P  G P+   IQDHI  A LLT+K T   ++E   LL ++G+        
Sbjct: 480  LMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGID------- 532

Query: 626  TGKPGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLP 685
                           E+    PAI   +P WTGKQ+ +                    LP
Sbjct: 533  ---------------ELPEPEPAIENGKPYWTGKQIFSLF------------------LP 559

Query: 686  QDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEK 745
            +D                         N   K K     +  +              KE 
Sbjct: 560  KDL------------------------NLEFKAKICSGCDECK--------------KED 581

Query: 746  ELSEEKLLIYKNDLVRGVIDKAQFADYG--LVHTVQELYGSNTAGTLLSALSRLFTVFLQ 803
               +  ++I    L+ GVIDK         ++  + + YG   A   L +++RL   F+ 
Sbjct: 582  CEHDAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIM 641

Query: 804  MHGFTCGVDDLLILKDKERERKNHLHGSE-------EIGKRVHLEAL---ELEDGAEIDP 853
            + GFT G+DD  I ++ + E    +  +E       E  +   LE L    LE+  E   
Sbjct: 642  LRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLE--- 698

Query: 854  IKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMT 913
            +K+   + KA    G+ A  Y  +          + +VI                   M 
Sbjct: 699  MKIMQVLGKARDEAGEIAEKYLGL---------DNPAVI-------------------MA 730

Query: 914  TSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTG 973
             +GA+GS +N  Q+++ +GQQ + G+R+ R    +TLP F P D    A GF+   + +G
Sbjct: 731  RTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSG 790

Query: 974  LRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFC 1033
            L P E++FH M GREGLVDTAV+TS+SGY+QR LI  L+ LK+ YD +VRD  G+IVQF 
Sbjct: 791  LTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFK 850

Query: 1034 YGEDGVDVHQTSF 1046
            YGEDGVD  ++  
Sbjct: 851  YGEDGVDPMKSDH 863

Length = 882

>gnl\|CDD\|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'	Back alignment and domain information

>gnl\|CDD\|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional	Back alignment and domain information

>gnl\|CDD\|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]	Back alignment and domain information

>gnl\|CDD\|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus	Back alignment and domain information

>gnl\|CDD\|216030 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2	Back alignment and domain information

>gnl\|CDD\|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5	Back alignment and domain information

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

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

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

>gnl\|CDD\|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A''; Validated	Back alignment and domain information

>gnl\|CDD\|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit, predominant form	Back alignment and domain information

>gnl\|CDD\|233842 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A''	Back alignment and domain information

>gnl\|CDD\|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP)	Back alignment and domain information

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

>gnl\|CDD\|214336 CHL00018, rpoC1, RNA polymerase beta' subunit	Back alignment and domain information

>gnl\|CDD\|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma subunit	Back alignment and domain information

>gnl\|CDD\|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma; Provisional	Back alignment and domain information

>gnl\|CDD\|218372 pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, domain 4	Back alignment and domain information

>gnl\|CDD\|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional	Back alignment and domain information

>gnl\|CDD\|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed	Back alignment and domain information

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

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

>gnl\|CDD\|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit, predominant form	Back alignment and domain information

>gnl\|CDD\|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3	Back alignment and domain information

>gnl\|CDD\|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit	Back alignment and domain information

>gnl\|CDD\|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed	Back alignment and domain information

>gnl\|CDD\|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated	Back alignment and domain information

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

>gnl\|CDD\|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]	Back alignment and domain information

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

>gnl\|CDD\|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional	Back alignment and domain information

>gnl\|CDD\|218370 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain 1	Back alignment and domain information

>gnl\|CDD\|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'	Back alignment and domain information

>gnl\|CDD\|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional	Back alignment and domain information

>gnl\|CDD\|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional	Back alignment and domain information

>gnl\|CDD\|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]	Back alignment and domain information

>gnl\|CDD\|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A''; Provisional	Back alignment and domain information

>gnl\|CDD\|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A''; Provisional	Back alignment and domain information

>gnl\|CDD\|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed	Back alignment and domain information

>gnl\|CDD\|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta'; Provisional	Back alignment and domain information

>gnl\|CDD\|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional	Back alignment and domain information

>gnl\|CDD\|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional	Back alignment and domain information

>gnl\|CDD\|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional	Back alignment and domain information

>gnl\|CDD\|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed	Back alignment and domain information

>gnl\|CDD\|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta'; Provisional	Back alignment and domain information

>gnl\|CDD\|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		1208
KOG0262		1640	consensus RNA polymerase I, large subunit [Transcr	100.0
KOG0261		1386	consensus RNA polymerase III, large subunit [Trans	100.0
PRK14977		1321	bifunctional DNA-directed RNA polymerase A'/A'' su	100.0
KOG0260		1605	consensus RNA polymerase II, large subunit [Transc	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
PRK09603		2890	bifunctional DNA-directed RNA polymerase subunit b	100.0
PRK14844		2836	bifunctional DNA-directed RNA polymerase subunit b	100.0
COG0086		808	RpoC DNA-directed RNA polymerase, beta' subunit/16	100.0
smart00663		295	RPOLA_N RNA polymerase I subunit A N-terminus.	100.0
PRK02625		627	rpoC1 DNA-directed RNA polymerase subunit gamma; P	100.0
CHL00018		663	rpoC1 RNA polymerase beta' subunit	100.0
TIGR02387		619	rpoC1_cyan DNA-directed RNA polymerase, gamma subu	100.0
PF00623		166	RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; Int	100.0
PRK02597		1331	rpoC2 DNA-directed RNA polymerase subunit beta'; P	100.0
TIGR02388		1227	rpoC2_cyan DNA-directed RNA polymerase, beta'' sub	100.0
CHL00117		1364	rpoC2 RNA polymerase beta'' subunit; Reviewed	100.0
PF04998		277	RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; Int	100.0
PF04997		337	RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; Int	100.0
cd02735		309	RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic	100.0
TIGR02389		367	RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit	99.97
PRK14897		509	unknown domain/DNA-directed RNA polymerase subunit	99.97
cd02584		410	RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryoti	99.97
cd06528		363	RNAP_A'' A'' subunit of Archaeal RNA Polymerase (R	99.97
PRK04309		383	DNA-directed RNA polymerase subunit A''; Validated	99.96
cd02736		300	RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryot	99.96
PF04983		158	RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; Int	99.96
PF05000		108	RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; Int	99.81
cd02655		204	RNAP_beta'_C Largest subunit (beta') of Bacterial	99.71
cd02737		381	RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher	99.7
PRK14898		858	DNA-directed RNA polymerase subunit A''; Provision	99.54
cd00630		158	RNAP_largest_subunit_C Largest subunit of RNA poly	99.36
PRK14898		858	DNA-directed RNA polymerase subunit A''; Provision	98.68
COG0086		808	RpoC DNA-directed RNA polymerase, beta' subunit/16	97.49

>KOG0262 consensus RNA polymerase I, large subunit [Transcription]	Back alignment and domain information

Probab=100.00  E-value=1.4e-280  Score=2464.20  Aligned_cols=1079  Identities=48%  Similarity=0.775  Sum_probs=914.0

Q ss_pred             CCCCCCCCCCCCCccceeeccccccchhcHHHHHHHHHHhhhhccccccChhhHHHHHHHHHHhhcCChHHHhhhhcccC
Q 046825            1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLP   80 (1208)
Q Consensus         1 C~TCg~~~~~CPGHFGHIELa~PVynP~ff~~l~kLLr~iC~~C~rfll~~~~~~~~~~kL~ll~~G~~~~a~~L~~i~~   80 (1208)
                      |.||++...+||||||||||++|||||+||+.+|++||+.|++||||++++.+++.+.|+||+|++|++.+|.+|+.+..
T Consensus        65 C~TC~~~~~~CPGH~GHIeL~~pvynPlfF~~ly~lLr~sCl~Chhf~~k~~~v~~~~cqLrll~~G~i~ea~~Le~i~~  144 (1640)
T KOG0262|consen   65 CSTCNQDELNCPGHMGHIELPVPVYNPLFFDFLYNLLRGSCLFCHHFRCKNVDVHILFCQLRLLEYGLIEEAEDLESITS  144 (1640)
T ss_pred             hhhhcchhhcCCCccCeeeecccccCHHHHHHHHHHHHHHHHhhhhcccCcHHHHHHHHHHHHHHhchHHHHHHHHHhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999998776


Q ss_pred             CCCCCCCCcc--ccccccccccCCCCCCCCccCCCCcccchhhHHHHHHHHHHHHHhc--ccCCCCCCCCCCceecccce
Q 046825           81 SESSNPEDSD--VSNKSSCSMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIE--TTKCGNCKAKNPRISKPTFG  156 (1208)
Q Consensus        81 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~ii~eflk~~--~~kC~~Cg~~~p~Irk~g~~  156 (1208)
                      ...++.+|..  +....+++++.. +..+..... ...-++...+.+++++.+|++..  .++|++|+..+|++||+++.
T Consensus       145 ~~~~d~~d~~~~~~k~~~~~~v~~-~i~~~~~~~-~~~~t~~~~~~~~~lv~~f~k~~l~~kkC~~C~~~~p~~rk~~~~  222 (1640)
T KOG0262|consen  145 ETVEDNEDESLNEIKSCRAQYVTE-AISEALLDK-SEPNTKNSTELKKKLVTAFLKNALSRKKCPRCKHSNPKLRKDGFR  222 (1640)
T ss_pred             hhhccCcchhHHHHHhhhhhhccH-HHHHHhhcC-CCccchhhHHHHHHHHHHHHHHhhccccCCcccCCCchhhccccc
Confidence            3322212110  111122223332 101100000 11113445678999999999986  78999999999999999999


Q ss_pred             EEEEecCCchhhhhhhhccCCcCCCcCCCccccccCCCCC-CCCCCCCCCCCCCCCCcchhhhhcccCCCCCCCCccccc
Q 046825          157 WIHMNGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSD-VDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQK  235 (1208)
Q Consensus       157 ki~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ed~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  235 (1208)
                      |++...++.+....+...+....+......   +..+-++ .++.++.  .+.+      +++.+.....+..+.     
T Consensus       223 kv~~~~~~~~~~~~~~~~~~i~~~~~~~~~---~d~~~~G~~E~~~~g--~d~~------e~~~~~~~~~~t~~~-----  286 (1640)
T KOG0262|consen  223 KVFIDALSSKVGANVIRGAKIKKDVGSKGF---EDSGIDGSNEVEEDG--KDLF------EKSTEPAEFEKTGKK-----  286 (1640)
T ss_pred             eeeeehhcccccccchhheeeehhcccccc---cccccCCcccccccc--cccc------ccccccccccccccc-----
Confidence            999998875544333333222222221000   0000000 0000000  0000      011111111122233     


Q ss_pred             cccCCCCCHHHHHHHHHhcCHhHHHHccccccccccCCCCCCCCceEEEeeeecCCCcccCCcccCCCccCchhHHHHHH
Q 046825          236 DLFSGPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGDSVMEHPQTVLLSK  315 (1208)
Q Consensus       236 ~~~~~~L~P~eV~~iLkkI~~~d~~lL~ll~~~~~~~~~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~~~~eddlt~~l~~  315 (1208)
                           +|+|.+|+++|+.||.+|.++|.++|+.......+..+-++|||+.|||||+++||+.++++...|+++|..|.+
T Consensus       287 -----~l~~tevR~~l~~lf~ne~~~l~~lf~l~~~~~~k~~p~d~FFld~l~VpPtrfRP~s~~gd~~~en~Qt~~L~k  361 (1640)
T KOG0262|consen  287 -----YLLPTEVREHLRDLFKNEGELLSYLFPLWDSGSGKIDPSDMFFLDNLLVPPTRFRPPSMLGDEVHENPQTLNLNK  361 (1640)
T ss_pred             -----cccHHHHHHHHHHHHhhhHHHHHHhhccccccccccCccceeeeeccccCCcccCCchhcchhhhcChHHHHHHH
Confidence                 999999999999999999999999998321111334555699999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHcC--CCC-------------HHHHHHHHhhHHHHHHhhhcCCCCCc-CCCChhhHHHHhhccccccc
Q 046825          316 VLQANIYLANAYVNQ--PDN-------------AKVIVARWMNLQQSVNVLFDGKNAAG-QRDMASGICQLLEKKEGLFR  379 (1208)
Q Consensus       316 Ii~~n~~l~~~~~~~--~~~-------------~~~i~~~~~~LQ~~v~~~~d~~~~~~-~~~~~~~i~q~L~gK~G~fR  379 (1208)
                      ||+.|..|..+....  +.+             ...++..|.+||.+||.+||+..... +.....||+|.||+|+|+||
T Consensus       362 Vle~s~~i~~~~~~m~~kl~~~~k~~l~~~~g~~~kl~~aw~~LQ~~vn~lfDs~~~~k~~r~~~pGikQiLEKKeGLFR  441 (1640)
T KOG0262|consen  362 VLESSVLIRKLLKDMKGKLDEELKLILERLRGIFSKLINAWLQLQASVNVLFDSKMASKWSRDSPPGIKQILEKKEGLFR  441 (1640)
T ss_pred             HHHHHHHHHHHHHHhhhccCHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccccccccccCCCchHHHHHHHhhhhHH
Confidence            999999999876331  111             23477899999999999999998532 24445899999999999999


Q ss_pred             ccccCccCCccceeeecCCCCccccccCchHHHHhhcCcccccchHHHHHHHHHHHcCCCCCCCceEEecCCCCcccCCC
Q 046825          380 QKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPN  459 (1208)
Q Consensus       380 ~nlmGKRvd~saRsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~  459 (1208)
                      +|||||||||+|||||||||||.+||||||..||++|||||+||+||+++||++|+|||++||||++|++++| .++.|.
T Consensus       442 khMMGKRVN~AaRSVIsPDPnI~tnEIGIP~vFA~KLTyPepVt~~NV~elr~aViNGP~~hPGA~~iqd~dg-~~t~l~  520 (1640)
T KOG0262|consen  442 KHMMGKRVNYAARSVISPDPNIETNEIGIPPVFAKKLTYPEPVTPWNVNELRKAVINGPDVHPGATYIQDEDG-TLTLLS  520 (1640)
T ss_pred             HHhhccccchhhccccCCCCCccccccCCchHHHhhccCCCcCCcccHHHHHHHHhcCCCCCCCcceeecCCC-ceeecC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999 677776


Q ss_pred             ccccccccchhhhcccccccCCCCCCCcccCceeehhhcccceEEEecCCCCCcCcccceeEEEeCCCCeEEEeccCCCC
Q 046825          460 KKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCST  539 (1208)
Q Consensus       460 ~~~~~~~~~r~~~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqPsLHk~simah~v~vl~~~~t~rln~~~c~~  539 (1208)
                      ..   +.++|.++|++| |.|+...+..+.+++||||+++||+||+||||||||+|||||+|||||++|||||||++|++
T Consensus       521 ~~---~~~qR~alA~qL-Ltpst~~~~~~~~K~V~RHvknGDvvlmNRQPTLHKPSimaHkaRVL~gEktlRlHYANCka  596 (1640)
T KOG0262|consen  521 PM---TDEQREALANQL-LTPSTGNPTEFGTKKVHRHVKNGDVVLMNRQPTLHKPSIMAHKARVLPGEKTLRLHYANCKA  596 (1640)
T ss_pred             CC---CHHHHHHHHHHh-hccccCCCcccCCceeeeeccCCcEEEEcCCCccccchhhhhhheecCCcceeeeeeccccc
Confidence            44   678999999999 99887776777899999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCceecccCCCHHHHHHHHHhcccCCceecCCCCCCcccchhhhhhhhhhcccCccccCHHHHHHHHHhcCccC
Q 046825          540 YNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSS  619 (1208)
Q Consensus       540 yNADFDGDemn~h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD~l~g~~lLT~~d~f~~~~~~~~l~~~~~~~~  619 (1208)
                      |||||||||||+|+|||+.|||||++|++++.||++|++|+|++|||||||+++++||.||+||+|++|+||+|.++.  
T Consensus       597 YNADFDGDEMN~HfPQse~araEa~~ian~dsqYLvPt~G~PlrGLIQDHiVsgv~LT~rd~Fftre~y~qLv~~~l~--  674 (1640)
T KOG0262|consen  597 YNADFDGDEMNVHFPQSEIARAEAYNIANTDSQYLVPTDGTPLRGLIQDHIVSGVLLTMRDSFFTREDYQQLVFAGLS--  674 (1640)
T ss_pred             ccCCCCcchhcccCCchhhHHHHHHHHhccCCceeccCCCCchhhhhhhheeeeEEEEecccccCHHHHHHHHHHhhh--
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999998773  


Q ss_pred             CCCCCCCCCCCceeeeecccceeeccCCCccCCCCCCCCCeEEEEeecccc-CCCcceeeccCCCCCccccccccccccc
Q 046825          620 SGLGSFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHIT-RGRPPFVVERGGKLPQDFFKTRFNADKQ  698 (1208)
Q Consensus       620 ~~~~~~~~~~~~~~~~~~~~~~~~~~~PaIlkp~~lwTGKqv~s~~l~~~~-~~~~~~n~~~~~k~~~~~~~~~~~~~~~  698 (1208)
                                       +...+|.++||+|+||.+|||||||||++|.+++ .|+++||+++++|+|.++|+..      
T Consensus       675 -----------------~~~~rI~~lpPtIlkP~~LWTGKQVIsTil~Ni~P~~~p~iNl~~kaKip~~~W~~~------  731 (1640)
T KOG0262|consen  675 -----------------DTFKRIKLLPPTILKPAPLWTGKQVISTILKNIIPEGHPPINLESKAKIPGKAWRVH------  731 (1640)
T ss_pred             -----------------hhccceeccCccccccccccccchHHHHHHHhcCCCCCCcccchhcccCchhhcCCC------
Confidence                             3345789999999999999999999999999987 5799999999999999999520      


Q ss_pred             ccccccccCccccccccccccCCCccccccCCCCchhhhhhhcccccccCCceEEEecceeeeeecCccccC--CccHHH
Q 046825          699 SDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFA--DYGLVH  776 (1208)
Q Consensus       699 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG--~~~Lih  776 (1208)
                                                       ++          +...+|+.|+||+||||+|||||++||  .+||||
T Consensus       732 ---------------------------------s~----------e~~l~Es~v~ir~GellcGVLDKa~~Gat~yGLvH  768 (1640)
T KOG0262|consen  732 ---------------------------------SE----------EPKLNESQVLIREGELLCGVLDKAQFGATAYGLVH  768 (1640)
T ss_pred             ---------------------------------CC----------cccCCcceEEEecCceEEEeechhhcCchhhhhhh
Confidence                                             00          011678999999999999999999999  899999


Q ss_pred             HHHHHhCHHHHHHHHHHHHHHHHHHHHHcCceeeecccccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhH
Q 046825          777 TVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKL  856 (1208)
Q Consensus       777 ~i~~~yG~~~a~~~l~~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l  856 (1208)
                      ++||.||+++++++|+.++|||+.||+++|||||++|+++.++++.+|+++++++...+.++.++++++...  .+++++
T Consensus       769 ~~~ElYG~~~s~~lLs~~srlFT~ylq~~GFT~GvdDlll~~~~D~kR~~il~e~~~vG~qa~~~~~~l~~d--a~~del  846 (1640)
T KOG0262|consen  769 CCHELYGGETSGKLLSVFSRLFTAYLQMHGFTLGVDDLLLDKDADKKRREILRESRNVGNQAAKEAFGLDVD--APPDEL  846 (1640)
T ss_pred             hhhhhhCccchhhHHHHHHHHHHHHHHHhccccccceeeechhhhHHHHHHHHhhhcccHHHHHHHhCCCCC--CCHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999988765  356789


Q ss_pred             HHHHHHHhcCCcchhhHHHHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCcccHHHHHhhcccccc
Q 046825          857 KSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQEL  936 (1208)
Q Consensus       857 ~~~~~~~l~~~~~~~~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~l  936 (1208)
                      ..+++.+...+. ...+.||..+++.+|.++++ |++.|+|.||.+.||.|++..|+.||||||+||++||||+||||++
T Consensus       847 ~~~le~~y~~d~-~~~~~LD~~~k~~~n~~ts~-I~~~cvP~GLlk~FP~N~mqlM~~SGAKGS~VN~~QISclLGQqeL  924 (1640)
T KOG0262|consen  847 RSRLEAIYLKDA-DKLAMLDRVMKSELNGYTSE-IVKKCVPDGLLKKFPENNMQLMIQSGAKGSNVNTSQISCLLGQQEL  924 (1640)
T ss_pred             HHHHHHHHhcch-hHHHHHHHHHHHHHhhhhHH-HHhhhccchhhhcCCcchHHHHHHhcCCcccccHHHHHHhhhhHhh
Confidence            999999888332 22389999999999999999 9999999999999999999999999999999999999999999999


Q ss_pred             cCcccCCCCCCccccCCCCCCCCccccccccccccCCCCchhhhhhcccccccchhccccccCCchhhHHHHhhhceeee
Q 046825          937 EGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKI 1016 (1208)
Q Consensus       937 eG~Rip~~~~grtLP~f~~~d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V 1016 (1208)
                      ||+|||.|+||||||||.++|++|+|+|||.++|++|+.|+|||||||||||||||||||||+|||||||||||||+|+|
T Consensus       925 EGkRvPlMvSGKtLPsF~p~e~spraGGfI~~RFlTGi~PqeyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEgl~V 1004 (1640)
T KOG0262|consen  925 EGKRVPLMVSGKTLPSFAPYETSPRAGGFIDGRFLTGIKPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKV 1004 (1640)
T ss_pred             cCCccceeecCCccCCcCCCCCCCCCCCcccceeecCCCchHHhhhhhccccchhhhHHhcccchHHHHHHHHhhhhcEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccEEEcCCCCEEEeeecCCcceeccccccccchhhhhhhccccccccccccCCCceeeechhHHHHHhhhcchh----
Q 046825         1017 SYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAARERGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQL---- 1092 (1208)
Q Consensus      1017 ~YD~TVR~~~g~IvQF~YGedGld~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~---- 1092 (1208)
                      +||.||||+||+||||.|||||+|++|++++++|++..+                        |++.+...++++.    
T Consensus      1005 ~YD~TVRDsDgsvVQF~YGEDglDitKssfl~~~~f~~~------------------------Ny~avl~~~~~~~v~s~ 1060 (1640)
T KOG0262|consen 1005 HYDLTVRDSDGSVVQFMYGEDGLDITKSSFLNKKEFPTD------------------------NYEAVLLKYKSESVLSA 1060 (1640)
T ss_pred             eccceEEcCCCcEEEEeecCccccccHHhhcchhhhhhh------------------------hHHHHHhhhChHHHhhh
Confidence            999999999999999999999999999999999998876                        4444444333320    


Q ss_pred             ---hhHHHHHHh-------------------------------------------HHHHHHHhHHHHHHhhhcchhHHHH
Q 046825         1093 ---DASNAYIME-------------------------------------------LPDALKDNAEKFADKFLSNEMAKQD 1126 (1208)
Q Consensus      1093 ---~~~~~~~~~-------------------------------------------~~~~~~~~~~~~~~~~~~~~l~~~~ 1126 (1208)
                         .++..++++                                           +..|.+++ .+..+   .+.-+.+.
T Consensus      1061 ~d~~~a~~~~k~i~kw~kk~~w~~~~k~~~cpdpv~~k~~p~~y~gsvsekf~~~i~~f~~~~-~k~~~---s~~~~~~~ 1136 (1640)
T KOG0262|consen 1061 FDIKKASKYIKKILKWKKKHMWFELDKKIACPDPVLAKYNPDKYLGSVSEKFRKKIDDFDDEN-AKKEK---SEEPSEEK 1136 (1640)
T ss_pred             hhhHHHHHHHHHHHHHHhhhccchhhcccCCCChhhhhcchhhhhccccHHHHHHHHHHHHHh-hhhhc---cccchHHH
Confidence               112222222                                           22232222 11111   12233678


Q ss_pred             HHHHHHHHhhhcCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHHhhcCCCCCeEEEecCCC
Q 046825         1127 FLKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLLVG 1206 (1208)
Q Consensus      1127 f~~l~~~~y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~ask~ikTP~~~~~l~~~ 1206 (1208)
                      |+.+++.||++|+++|||+||+||||||||||||||||||||||+|+|||||||||||||||+||++||||+||+|+.++
T Consensus      1137 lr~ll~~K~~~SLa~PGE~VGvlAAQSIGEPSTQMTLNTFHfAGrGemNVTLGIPRLREIlMtASanIkTP~mt~pi~~g 1216 (1640)
T KOG0262|consen 1137 LRRLLQLKYIRSLADPGEPVGVLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASANIKTPSMTVPIKNG 1216 (1640)
T ss_pred             HHHHHHHHHHHHhcCCCCcceeeeecccCCCcceeehhheeeccccceeeeecchHHHHHHHHHhhccCCCceeeeccCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             C
Q 046825         1207 K 1207 (1208)
Q Consensus      1207 ~ 1207 (1208)
                      .
T Consensus      1217 ~ 1217 (1640)
T KOG0262|consen 1217 V 1217 (1640)
T ss_pred             c
Confidence            4

>KOG0261 consensus RNA polymerase III, large subunit [Transcription]	Back alignment and domain information

>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional	Back alignment and domain information

>KOG0260 consensus RNA polymerase II, large subunit [Transcription]	Back alignment and domain information

>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'	Back alignment and domain information

>PRK08566 DNA-directed RNA polymerase subunit A'; Validated	Back alignment and domain information

>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form	Back alignment and domain information

>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional	Back alignment and domain information

>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional	Back alignment and domain information

>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed	Back alignment and domain information

>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional	Back alignment and domain information

>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]	Back alignment and domain information

>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus	Back alignment and domain information

>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional	Back alignment and domain information

>CHL00018 rpoC1 RNA polymerase beta' subunit	Back alignment and domain information

>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit	Back alignment and domain information

>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	Back alignment and domain information

>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional	Back alignment and domain information

>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit	Back alignment and domain information

>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed	Back alignment and domain information

>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA	Back alignment and domain information

>PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 RNA polymerases catalyse the DNA-dependent polymerisation of RNA	Back alignment and domain information

>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain	Back alignment and domain information

>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''	Back alignment and domain information

>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional	Back alignment and domain information

>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain	Back alignment and domain information

>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP)	Back alignment and domain information

>PRK04309 DNA-directed RNA polymerase subunit A''; Validated	Back alignment and domain information

>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain	Back alignment and domain information

>PF04983 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; InterPro: IPR007066 RNA polymerases catalyse the DNA dependent polymerisation of RNA	Back alignment and domain information

>PF05000 RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; InterPro: IPR007083 RNA polymerases catalyse the DNA dependent polymerisation of RNA	Back alignment and domain information

>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain	Back alignment and domain information

>cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain	Back alignment and domain information

>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional	Back alignment and domain information

>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain	Back alignment and domain information

>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional	Back alignment and domain information

>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]	Back alignment and domain information

Homologous Structure Templates