Citrus Sinensis ID: 001532

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------106
MGLMQVEGSPKDEQLPDKQKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGFP
ccccccccccccccccccccccccccccccHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccEEEEEEEEEEEccEEcccccccccccHHHHHccccccccEEEEEEEEEccccccEEEEEccEEEcccccEEcccccccccccHHHHHHccccccccccEEEEcccEEEEEEEEEccccEEEEEEcccccEEEEEEEcccccccEEEEEEEccEEEEEEccccccccEEEHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccccccHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHcccccccccccccccEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHcccccccccccccccEEEEccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccHHHHHccEEEEEEcccccHHHHHHHHHcccEEcccccccccccccEEEEEEccEEEEEEccHHHHHHHHHHHHHccccccccEEEEcccccEEEEEEccccccccEEEEEcccccccHHHHHHHHcccccHHHHHHcccEEEEcHHHHHccccccccccccccccEEccccccHHHHcccccccccccccccHHHHHHccccccccccccccccccccccEEcccccccccccccccccccccccccEEEEEEEEccccccccHHHHcccccccccEEEEEEEEEHHHHHccccccccEEccccccccccccccccccccccccccEEccccEEEEEEcccccccccccccccccccEEEEEEEEEccccccEEEEEEEEEEcccccEEEEEEEcccccccccccccccccccccccccccccccccccccccccEEEccccccccccHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccEEEEEEEEEEEHHccccccccccccccccccccccccccccccccccccc
cccccccccccccccccccccccccccHHHHHHHHHHHHHHHcHHHHHHHcHHHHHHHHHHHHHHHcccEEEcccccEEEEEEEEEEcccccccccccccccccHHEHccccccccEEEEEEEEEcccccccEEEEccEEEccEEEEEEcccEEcccccHHHHHHHcccccccccEEEEEccHHEEEEEHHHcccEEEEEEcccccEEEEEEEcccccccEEEEEEEccEEEEEcccccccccEEEEEEHcccccHHHHHHHHcccHHHHHHHcccHHHHHHcccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHcccccccccHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHccHHHHHHHHHHHHHcccccHHHHHHHHcHHHHHHHHHHHHHHHHHHHHccccccccccccccHHccccccccEccccccccccHHHHHHHHHHHEEccccccHHHHHHHHHcccccHHHccHHHHcccccEEEEEEcEEEEEcccHHHHHHHHHHHHHccccccEEEEEEEccccEEEEEcccccEEccEEEEEcccEEccHHHHHHHHcccccHHHHHHccEEEEEEccccccEEEEEcHHHccccccEEcEEEEEEEcccccccccHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccEEEEEEEEEccccccccccEEEEEEEEccccHHHEEEEcHcHHcccccHHHHHHcccHHHHHcccccEHEccccccccccccHHHHccccccccccEEEccccEEEEcEcccccccccccccccccccccccccEEEcccccccEEEEEEEEEcccccEEEEEEEEEEEccccccccccccccccEEEEEEEccccccccccccccEEEccccccccHHHHHHHHHHHcHHHHHcccccccccccccccccccHHHHHHHHHHccccccccEEEEccccccccEEEEEEcHHHHHHHHHHHHHHHHHcccccEEEEEcccccccccccccc
mglmqvegspkdeqlpdkqklaapvksVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKivrandrivsgidpsiflrfkdvrigqpsmtvdgvseklnphmcrlsdmtyaaPILVNIEYvqgshtekttmekndvvigRIPIMLRSCrcvlygkdeaelarlgecpldpggyfiiKGTEKVLLIQEQLsknrviidtdkkgninasvtsstetvkskTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVgrdprysalllpsieecanldIYTQEKALEYLEGkvkrstfgsppndregraFSILRDVFlanvpvhnnnfrpkCFYVAVMLRRMVEAMLNKdamddkdyvgnkrleLSGQLVSLLFEDLFKTMISEVQKTVDIIlskpsrssrfdlsqfiVRDSITVGlertlstgnfdvkRFKMHRKGMTQVLARLSFIgtlghmtrvspqfeksrkvsgpralqpsqwgmlcpcdtpegeacglvKNLALMThvttdeeegplisLCYClgvedlellsgeelhnpnsfLVIFNglilgkhrrpkCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIasdggrvcrplviadKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALyegdatpdtthieiepfTILGVIaglipyphhnqsprntyqcamgkqamgnIAFNQLCRMDSLLYLlvypqrpllttrtIELVgydklgagqNATVAVMSYSGYDIEDAIVMNKssldrgfgrcIVVKKYTAINQKYanstsdrilrpdrtgpgaermqildddglaapgeiikpndvyinkespletrgsimsptgqtdsryrsarqtykgpdgetcVVDRVAlcsdkngdLCIKFLIRhtrrpelgdkfssrhgqkgvcgtivqqedfpfsergicpdlimnphgfpsrmTVGKMIELLGgkagvscgrfhygsafgepsghadtvESISETLVKHgfsyngkdmiysgitgcplqayifmgpIYYQKLKHMVLDKmhargsgprvmltrqptegrarnggfp
mglmqvegspkdeqlpdkqKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKivrandrivsgidpsiflrfkdvrigqpsmtvdgvseklnPHMCRLSDMTYAAPILVNIEYVQGshtekttmekndvvigrIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSknrviidtdkkgninasvtsstetvksktviqmekgKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGkvkrstfgsppndREGRAFSILRDVFLAnvpvhnnnfrpKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVdiilskpsrssrfdlsqfivrdsitvglertlstgnfdvkrfkMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVyiasdggrvcrpLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTainqkyanstsdrilrpdRTGPGAERMQILDDdglaapgeiikpndvyinkespletrgsimsptgqtdsryRSARQtykgpdgetcVVDRVALCSDKNGDLCIKFLIrhtrrpelgdkfssrhgqkgvcgTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARgsgprvmltrqptegrarnggfp
MGLMQVEGSPKDEQLPDKQKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINAsvtsstetvksktvIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGFP
************************VKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKK****************KTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKV**************RAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTR********************QWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYA*********************************II***DVY************************************ETCVVDRVALCSDKNGDLCIKFLIRHTRRPELG******HGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDK***************************
***************PDKQKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMT****SEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINA************TVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTF*SPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP**********PRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTA********************PGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETR***************SARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGR**NGG**
********************LAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVS**************LQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGFP
************EQLPDKQKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLET**************YRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQP***********
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MGLMQVEGSPKDEQLPDKQKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGFP
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 ?
Query1058 2.2.26 [Sep-21-2011]
Q102331165 DNA-directed RNA polymera yes no 0.968 0.879 0.576 0.0
Q9NW081133 DNA-directed RNA polymera yes no 0.969 0.905 0.570 0.0
P594701133 DNA-directed RNA polymera yes no 0.969 0.905 0.570 0.0
P222761149 DNA-directed RNA polymera yes no 0.965 0.889 0.566 0.0
P251671137 DNA-directed RNA polymera yes no 0.980 0.912 0.531 0.0
Q54IZ91608 DNA-directed RNA polymera yes no 0.522 0.343 0.607 0.0
P318141122 DNA-directed RNA polymera N/A no 0.938 0.885 0.383 0.0
Q54J751170 DNA-directed RNA polymera no no 0.946 0.855 0.361 0.0
Q10578 1193 DNA-directed RNA polymera no no 0.950 0.843 0.359 0.0
Q42877 1191 DNA-directed RNA polymera N/A no 0.949 0.843 0.382 0.0
>sp|Q10233|RPC2_SCHPO DNA-directed RNA polymerase III subunit RPC2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc2 PE=2 SV=1 Back     alignment and function desciption
 Score = 1253 bits (3241), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 607/1053 (57%), Positives = 787/1053 (74%), Gaps = 28/1053 (2%)

Query: 19   QKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSI 78
            +KLA PV ++ DK+QLLP FLKV+GLVKQHLDS+NYFV+  ++KIV+AN+++ S ++P  
Sbjct: 38   KKLADPVPTIEDKWQLLPAFLKVKGLVKQHLDSYNYFVDVDLKKIVQANEKVTSDVEPWF 97

Query: 79   FLRFKDVRIGQPSMT-VDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKN 137
            +L++ D+R+G P  T  D +   ++PH CRL D+TY A I V+IEY +G    K  + + 
Sbjct: 98   YLKYLDIRVGAPVRTDADAIQASISPHECRLRDLTYGANIYVDIEYTRG----KQVVRRR 153

Query: 138  DVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRV 197
            +V IGR+P+MLRS +CVL GK+E E+A L ECPLDPGGYFI+KGTEKV+L+QEQLSKNR+
Sbjct: 154  NVPIGRMPVMLRSNKCVLSGKNEMEMAALNECPLDPGGYFIVKGTEKVILVQEQLSKNRI 213

Query: 198  IIDTD-KKGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESD 256
            I++ + KKG   ASVTSST   KSKT +  + GK+YL  N     IPI+VV+KAMG++SD
Sbjct: 214  IVEAEPKKGLWQASVTSSTHERKSKTYVITKNGKLYLKHNSVADDIPIVVVLKAMGLQSD 273

Query: 257  QEVVQMV-GRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGS----PPNDR 311
            QE+ ++V G +  Y  L  PSIEECA L+IYT ++ALEY+  +VK +        PP++ 
Sbjct: 274  QEIFELVAGAEASYQDLFAPSIEECAKLNIYTAQQALEYIGARVKVNRRAGANRLPPHEE 333

Query: 312  EGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLEL 371
               A  +L  V LA++ V N  FRPK  Y+ +M RR++ AM++   +DD+DYVGNKRLEL
Sbjct: 334  ---ALEVLAAVVLAHINVFNLEFRPKAVYIGIMARRVLMAMVDPLQVDDRDYVGNKRLEL 390

Query: 372  SGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFD-LSQFIVR-DSITVGLERTLST 429
            +GQL++LLFEDLFK   S+++  +D +L KP R+  FD  +Q  V  D IT G+ R LST
Sbjct: 391  AGQLLALLFEDLFKKFNSDLKLNIDKVLKKPHRTQEFDAYNQLTVHSDHITQGMVRALST 450

Query: 430  GNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCP 489
            GN+ +KRFKM R G+T VL+RLS+I  LG MTR++ QFEK+RKVSGPR+LQ SQ+GMLC 
Sbjct: 451  GNWSLKRFKMERAGVTHVLSRLSYISALGMMTRITSQFEKTRKVSGPRSLQASQFGMLCT 510

Query: 490  CDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIF 549
             DTPEGEACGLVKNLALMTH+TTDEEE P+I L Y  G+ED+ ++SG ELH+  ++LV  
Sbjct: 511  SDTPEGEACGLVKNLALMTHITTDEEEEPIIKLAYAFGIEDIHVISGRELHSHGTYLVYL 570

Query: 550  NGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADK 609
            NG ILG  R P  F    RKLRR+GKI  F+ +F+N  QR V+I++DGGR+CRPL+I   
Sbjct: 571  NGAILGISRYPSLFVASFRKLRRSGKISPFIGIFINTHQRAVFISTDGGRICRPLIIVQN 630

Query: 610  GISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEP 669
            G+ +++  H++ L +G   F+DFL++GL+EY+DVNEEN++LI++YE D TPDTTH+EIEP
Sbjct: 631  GLPKVESKHIRLLKEGKWGFEDFLKQGLVEYVDVNEENDSLISVYERDITPDTTHLEIEP 690

Query: 670  FTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLT 729
            FTILG +AGLIPYPHHNQSPRNTYQCAMGKQA+G IA+NQL R+D+LLYL+VYPQ+P++ 
Sbjct: 691  FTILGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQLQRIDTLLYLMVYPQQPMVK 750

Query: 730  TRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQK 789
            T+TIEL+GYDKL AGQNATVA+MSYSGYDIEDA+V+NKSS+DRGFGRC V  K++ I +K
Sbjct: 751  TKTIELIGYDKLPAGQNATVAIMSYSGYDIEDALVLNKSSIDRGFGRCQVFHKHSVIVRK 810

Query: 790  YANSTSDRILRPDR---TGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGS-- 844
            Y N T DRI  P R   TG    +  +++DDGLA  G  ++P  +Y+NK++P     +  
Sbjct: 811  YPNGTHDRIGDPQRDPETGEVVWKHGVVEDDGLAGVGCRVQPGQIYVNKQTPTNALDNSI 870

Query: 845  IMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKF 904
             +  T   +S Y++   TYK P  E   +D+V L +  +    IK L+R TRRPELGDKF
Sbjct: 871  TLGHTQTVESGYKATPMTYKAP--EPGYIDKVMLTTTDSDQTLIKVLMRQTRRPELGDKF 928

Query: 905  SSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGR 964
            SSRHGQKGVCG IVQQED PF+++GICPD+IMNPHGFPSRMTVGKMIELL GK GV  G 
Sbjct: 929  SSRHGQKGVCGVIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELLSGKVGVLRGT 988

Query: 965  FHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKL 1024
              YG+ FG        VE  S  LV+HG++Y+GKDM+ SGITG  L+AYIFMGPIYYQKL
Sbjct: 989  LEYGTCFG-----GTKVEDASRILVEHGYNYSGKDMLTSGITGETLEAYIFMGPIYYQKL 1043

Query: 1025 KHMVLDKMHARGSGPRVMLTRQPTEGRARNGGF 1057
            KHMV+DKMHAR  GPR +LTRQPTEGR+R+GG 
Sbjct: 1044 KHMVMDKMHARARGPRAVLTRQPTEGRSRDGGL 1076
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol III is composed of mobile elements and RPC2 is part of the core element with the central large cleft and probably a clamp element that moves to open and close the cleft.
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6
>sp|Q9NW08|RPC2_HUMAN DNA-directed RNA polymerase III subunit RPC2 OS=Homo sapiens GN=POLR3B PE=1 SV=2 Back     alignment and function description
>sp|P59470|RPC2_MOUSE DNA-directed RNA polymerase III subunit RPC2 OS=Mus musculus GN=Polr3b PE=2 SV=2 Back     alignment and function description
>sp|P22276|RPC2_YEAST DNA-directed RNA polymerase III subunit RPC2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RET1 PE=1 SV=2 Back     alignment and function description
>sp|P25167|RPC2_DROME DNA-directed RNA polymerase III subunit RPC2 OS=Drosophila melanogaster GN=RpIII128 PE=2 SV=2 Back     alignment and function description
>sp|Q54IZ9|RPC2_DICDI DNA-directed RNA polymerase III subunit rpc2 OS=Dictyostelium discoideum GN=polr3b PE=3 SV=1 Back     alignment and function description
>sp|P31814|RPOB_THECE DNA-directed RNA polymerase subunit B OS=Thermococcus celer GN=rpoB PE=3 SV=1 Back     alignment and function description
>sp|Q54J75|RPB2_DICDI DNA-directed RNA polymerase II subunit rpb2 OS=Dictyostelium discoideum GN=polr2b PE=3 SV=1 Back     alignment and function description
>sp|Q10578|RPB2_CAEEL DNA-directed RNA polymerase II subunit RPB2 OS=Caenorhabditis elegans GN=rpb-2 PE=2 SV=2 Back     alignment and function description
>sp|Q42877|RPB2_SOLLC DNA-directed RNA polymerase II subunit RPB2 OS=Solanum lycopersicum GN=RPB2 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 ?
Query1058
2254640231142 PREDICTED: DNA-directed RNA polymerase I 0.979 0.907 0.859 0.0
2555691451139 DNA-directed RNA polymerase III subunit, 0.983 0.913 0.842 0.0
2241325761141 predicted protein [Populus trichocarpa] 0.984 0.913 0.838 0.0
4494477991158 PREDICTED: DNA-directed RNA polymerase I 0.988 0.903 0.828 0.0
297791275 1165 hypothetical protein ARALYDRAFT_917015 [ 0.985 0.895 0.791 0.0
79529842 1161 DNA-directed RNA polymerase III subunit 0.985 0.898 0.786 0.0
9759599 1194 DNA-directed RNA polymerase subunit [Ara 0.985 0.873 0.790 0.0
3565208241152 PREDICTED: DNA-directed RNA polymerase I 0.969 0.890 0.790 0.0
356495051 1166 PREDICTED: DNA-directed RNA polymerase I 0.982 0.891 0.785 0.0
29788820 1174 putative RNA polymerase III [Oryza sativ 0.977 0.880 0.725 0.0
>gi|225464023|ref|XP_002265454.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2 [Vitis vinifera] Back     alignment and taxonomy information
 Score = 1881 bits (4873), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 893/1039 (85%), Positives = 972/1039 (93%), Gaps = 3/1039 (0%)

Query: 22   AAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLR 81
            A PVK  VDKF LLPEFLKVRGLVKQHLDSFNYFV T I+KIVRANDRIVS +DPSI+LR
Sbjct: 12   ADPVKQAVDKFPLLPEFLKVRGLVKQHLDSFNYFVKTDIKKIVRANDRIVSSVDPSIYLR 71

Query: 82   FKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVI 141
            FKDVRIG+PS+TVDG+SEKLNPH CRLSDMTYAAPILVNIEY+ GSH +KT +EKNDVVI
Sbjct: 72   FKDVRIGEPSITVDGISEKLNPHTCRLSDMTYAAPILVNIEYITGSHVQKTRVEKNDVVI 131

Query: 142  GRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDT 201
            GR+PIMLRSC CVLY KDEAELARLGECPLDPGGYF++KGTEKV+LIQEQLSKNR+IIDT
Sbjct: 132  GRMPIMLRSCCCVLYKKDEAELARLGECPLDPGGYFVVKGTEKVILIQEQLSKNRIIIDT 191

Query: 202  DKKGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQ 261
            DKKGNINASVTSSTE+ KSKTVI MEK K++L LNQF  KIPIM+VMKAMGMESDQEVVQ
Sbjct: 192  DKKGNINASVTSSTESTKSKTVIVMEKEKIWLQLNQFTSKIPIMIVMKAMGMESDQEVVQ 251

Query: 262  MVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRD 321
            MVGR+PRYSALLLPS+EECA+  IYTQ++ALE+LE KVK+  F +P  ++EGR  +ILRD
Sbjct: 252  MVGRNPRYSALLLPSMEECASHGIYTQQQALEFLERKVKKLPFYNPSLEKEGRGMAILRD 311

Query: 322  VFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFE 381
             F+ANVPV  NNFRPKC YVAVMLRRM++A+LNKDAMDDKDYVGNKRLELSGQL+SLLFE
Sbjct: 312  TFIANVPVRQNNFRPKCLYVAVMLRRMMDAILNKDAMDDKDYVGNKRLELSGQLISLLFE 371

Query: 382  DLFKTMISEVQKTVDIILSKPSRSSRFDLSQ---FIVRDSITVGLERTLSTGNFDVKRFK 438
            DLFKTMISEV+KT+D IL+KPSRSSRFD SQ   FIVRDSITVGLERTLSTGN+DVKRF+
Sbjct: 372  DLFKTMISEVKKTIDAILAKPSRSSRFDFSQCLRFIVRDSITVGLERTLSTGNWDVKRFR 431

Query: 439  MHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEAC 498
            MHRKGM+QV+ARLS+IG+LGHMT++SPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEAC
Sbjct: 432  MHRKGMSQVVARLSYIGSLGHMTKISPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEAC 491

Query: 499  GLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHR 558
            GLVKNLALMTHVTTDEEE PLISLCY LGVEDLELLSGEELH PNSFL+IFNGLILGKHR
Sbjct: 492  GLVKNLALMTHVTTDEEESPLISLCYSLGVEDLELLSGEELHTPNSFLIIFNGLILGKHR 551

Query: 559  RPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHH 618
            RP+ FA+ +RKLRRAGKIGEFVSVFVNEKQ CVYIASDGGRVCRP+VIADKG SRIKEHH
Sbjct: 552  RPQRFANALRKLRRAGKIGEFVSVFVNEKQHCVYIASDGGRVCRPVVIADKGKSRIKEHH 611

Query: 619  MKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAG 678
            MKEL+DGVR+FDDFLR+GLIEYLDVNEENNALIALYE DA P+TTHIEIEPFTILGV AG
Sbjct: 612  MKELIDGVRTFDDFLRDGLIEYLDVNEENNALIALYEADAKPETTHIEIEPFTILGVCAG 671

Query: 679  LIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGY 738
            LIP+PHHNQSPRNTYQCAMGKQAMGNIA+NQLCRMDSLLYLLVYPQRPLLTTRTIELVGY
Sbjct: 672  LIPFPHHNQSPRNTYQCAMGKQAMGNIAYNQLCRMDSLLYLLVYPQRPLLTTRTIELVGY 731

Query: 739  DKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRI 798
            DKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIV+KK++A+NQ+Y N+ SDRI
Sbjct: 732  DKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVMKKFSAVNQRYENNASDRI 791

Query: 799  LRPDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRS 858
            +RP + G  AERMQILDDDGLAAPGEIIKPND+YINKESP+ T+G ++SP G  DS Y+ 
Sbjct: 792  VRPLKVGHDAERMQILDDDGLAAPGEIIKPNDIYINKESPIITKGPLISPVGLPDSAYKP 851

Query: 859  ARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIV 918
            +RQT+KGP+GE  VVDRVALCSDKN +LCIKFLIRHTRRPE+GDKFSSRHGQKGVCGTI+
Sbjct: 852  SRQTFKGPEGEASVVDRVALCSDKNSNLCIKFLIRHTRRPEVGDKFSSRHGQKGVCGTII 911

Query: 919  QQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHA 978
            QQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHA
Sbjct: 912  QQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHA 971

Query: 979  DTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSG 1038
            D VE+IS+TLVKHGFSY+GKD IYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSG
Sbjct: 972  DKVETISKTLVKHGFSYSGKDFIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSG 1031

Query: 1039 PRVMLTRQPTEGRARNGGF 1057
            PRVMLTRQPTEGRARNGG 
Sbjct: 1032 PRVMLTRQPTEGRARNGGL 1050

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255569145|ref|XP_002525541.1| DNA-directed RNA polymerase III subunit, putative [Ricinus communis] gi|223535120|gb|EEF36800.1| DNA-directed RNA polymerase III subunit, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|224132576|ref|XP_002321356.1| predicted protein [Populus trichocarpa] gi|222868352|gb|EEF05483.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449447799|ref|XP_004141655.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297791275|ref|XP_002863522.1| hypothetical protein ARALYDRAFT_917015 [Arabidopsis lyrata subsp. lyrata] gi|297309357|gb|EFH39781.1| hypothetical protein ARALYDRAFT_917015 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|79529842|ref|NP_199327.4| DNA-directed RNA polymerase III subunit C2 [Arabidopsis thaliana] gi|332007826|gb|AED95209.1| DNA-directed RNA polymerase III subunit C2 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|9759599|dbj|BAB11387.1| DNA-directed RNA polymerase subunit [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|356520824|ref|XP_003529060.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2-like [Glycine max] Back     alignment and taxonomy information
>gi|356495051|ref|XP_003516394.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2-like [Glycine max] Back     alignment and taxonomy information
>gi|29788820|gb|AAP03366.1| putative RNA polymerase III [Oryza sativa Japonica Group] 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 ?
Query1058
TAIR|locus:21533231161 NRPC2 "nuclear RNA polymerase 0.995 0.906 0.771 0.0
POMBASE|SPAC4G9.08c1165 rpc2 "DNA-directed RNA polymer 0.967 0.878 0.570 0.0
UNIPROTKB|E1BRJ41132 POLR3B "DNA-directed RNA polym 0.968 0.905 0.562 1.50000009901e-317
UNIPROTKB|E2RHZ21133 POLR3B "DNA-directed RNA polym 0.968 0.904 0.563 1.80000021762e-317
UNIPROTKB|E1BPX61133 POLR3B "Uncharacterized protei 0.968 0.904 0.563 2.60000020455e-317
UNIPROTKB|Q9NW081133 POLR3B "DNA-directed RNA polym 0.968 0.904 0.563 3.99999993464e-317
RGD|15653111133 Polr3b "polymerase (RNA) III ( 0.968 0.904 0.564 3.99999993464e-317
MGI|MGI:19176781133 Polr3b "polymerase (RNA) III ( 0.968 0.904 0.563 1.10000000673e-316
ZFIN|ZDB-GENE-030131-28871129 polr3b "polymerase (RNA) III ( 0.965 0.905 0.561 4.89999999997e-314
DICTYBASE|DDB_G02884491608 rpc2 "RNA polymerase III, seco 0.521 0.343 0.608 3.3e-312
TAIR|locus:2153323 NRPC2 "nuclear RNA polymerase C2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 4348 (1535.6 bits), Expect = 0., P = 0.
 Identities = 826/1071 (77%), Positives = 938/1071 (87%)

Query:     1 MGLMQVE-GSPKDEQLPDKQKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTG 59
             MGL Q +     D+   DK+KL+AP+KS  DKFQL+PEFLKVRGLVKQHLDSFNYF+N G
Sbjct:     1 MGLDQEDLDLTNDDHFIDKEKLSAPIKSTADKFQLVPEFLKVRGLVKQHLDSFNYFINVG 60

Query:    60 IRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILV 119
             I KIV+AN RI S +DPSI+LRFK VR+G+PS+      E +NPHMCRL+DMTYAAPI V
Sbjct:    61 IHKIVKANSRITSTVDPSIYLRFKKVRVGEPSIINVNTVENINPHMCRLADMTYAAPIFV 120

Query:   120 NIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFII 179
             NIEYV GSH  K    K++V+IGR+PIMLRSCRCVL+GKDE ELARLGECPLDPGGYFII
Sbjct:   121 NIEYVHGSHGNKAKSAKDNVIIGRMPIMLRSCRCVLHGKDEEELARLGECPLDPGGYFII 180

Query:   180 KGTEKVLLIQEQLSKNRVIIDTDKKGNINAXXXXXXXXXXXXXXIQMEKGKMYLLLNQFV 239
             KGTEKVLLIQEQLSKNR+IID+DKKGNINA              IQMEK K+YL L++FV
Sbjct:   181 KGTEKVLLIQEQLSKNRIIIDSDKKGNINASVTSSTEMTKSKTVIQMEKEKIYLFLHRFV 240

Query:   240 KKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKV 299
             KKIPI++V+KAMGMESDQE+VQMVGRDPR+SA LLPSIEEC +  + TQ++AL+YLE KV
Sbjct:   241 KKIPIIIVLKAMGMESDQEIVQMVGRDPRFSASLLPSIEECVSEGVNTQKQALDYLEAKV 300

Query:   300 KRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMD 359
             K+ ++G+PP +++GRA SILRD+FLA+VPV +NNFR KCFYV VMLRRM+EAMLNKDAMD
Sbjct:   301 KKISYGTPP-EKDGRALSILRDLFLAHVPVPDNNFRQKCFYVGVMLRRMIEAMLNKDAMD 359

Query:   360 DKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDS- 418
             DKDYVGNKRLELSGQL+SLLFEDLFKTM+SE  K VD IL+KP R+SRFD SQ + +DS 
Sbjct:   360 DKDYVGNKRLELSGQLISLLFEDLFKTMLSEAIKNVDHILNKPIRASRFDFSQCLNKDSR 419

Query:   419 --ITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGP 476
               I++GLERTLSTGNFD+KRF+MHRKGMTQVL RLSFIG++G +T++SPQFEKSRKVSGP
Sbjct:   420 YSISLGLERTLSTGNFDIKRFRMHRKGMTQVLTRLSFIGSMGFITKISPQFEKSRKVSGP 479

Query:   477 RALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSG 536
             R+LQPSQWGMLCPCDTPEGE+CGLVKNLALMTHVTTDEEEGPL+++CY LGV DLE+LS 
Sbjct:   480 RSLQPSQWGMLCPCDTPEGESCGLVKNLALMTHVTTDEEEGPLVAMCYKLGVTDLEVLSA 539

Query:   537 EELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASD 596
             EELH P+SFLVI NGLILGKH RP+ FA+ +R+LRRAGKIGEFVSVF NEKQ CVY+ASD
Sbjct:   540 EELHTPDSFLVILNGLILGKHSRPQYFANSLRRLRRAGKIGEFVSVFTNEKQHCVYVASD 599

Query:   597 GGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEG 656
              GRVCRPLVIADKGISR+K+HHMKEL DGVR+FDDF+R+GLIEYLDVNEENNALIALYE 
Sbjct:   600 VGRVCRPLVIADKGISRVKQHHMKELQDGVRTFDDFIRDGLIEYLDVNEENNALIALYES 659

Query:   657 DATP-----------DTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNI 705
             D T            DTTHIEIEPFTILGV+AGLIPYPHHNQSPRNTYQCAMGKQAMGNI
Sbjct:   660 DGTTELDEGAEAAKADTTHIEIEPFTILGVVAGLIPYPHHNQSPRNTYQCAMGKQAMGNI 719

Query:   706 AFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVM 765
             A+NQL RMD+LLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMS+SGYDIEDAIVM
Sbjct:   720 AYNQLNRMDTLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSFSGYDIEDAIVM 779

Query:   766 NKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQILDDDGLAAPGEI 825
             NKSSLDRGFGRCIV+KK  A++QKY N T+DRIL P RTGP AE+MQILDDDGLA PGEI
Sbjct:   780 NKSSLDRGFGRCIVMKKIVAMSQKYDNCTADRILIPQRTGPDAEKMQILDDDGLATPGEI 839

Query:   826 IKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGD 885
             I+PND+YINK+ P++T     S    +DS+YR AR+ +KGP+GET VVDRVALCSDK G 
Sbjct:   840 IRPNDIYINKQVPVDTVTKFTSAL--SDSQYRPAREYFKGPEGETQVVDRVALCSDKKGQ 897

Query:   886 LCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRM 945
             LCIK++IRHTRRPELGDKFSSRHGQKGVCG I+QQEDFPFSE GICPDLIMNPHGFPSRM
Sbjct:   898 LCIKYIIRHTRRPELGDKFSSRHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGFPSRM 957

Query:   946 TVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGI 1005
             TVGKMIELLG KAGVSCGRFHYGSAFGE SGHAD VE+IS TLV+ GFSY+GKD++YSGI
Sbjct:   958 TVGKMIELLGSKAGVSCGRFHYGSAFGERSGHADKVETISATLVEKGFSYSGKDLLYSGI 1017

Query:  1006 TGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGG 1056
             +G P++AYIFMGPIYYQKLKHMVLDKMHARGSGPRVM+TRQPTEG+++NGG
Sbjct:  1018 SGEPVEAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSKNGG 1068
GO:0003677 "DNA binding" evidence=IEA;ISS
GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISS
GO:0006351 "transcription, DNA-dependent" evidence=IEA;ISS
GO:0009507 "chloroplast" evidence=ISM
GO:0032549 "ribonucleoside binding" evidence=IEA
GO:0009560 "embryo sac egg cell differentiation" evidence=RCA
POMBASE|SPAC4G9.08c rpc2 "DNA-directed RNA polymerase III complex subunit Rpc2" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
UNIPROTKB|E1BRJ4 POLR3B "DNA-directed RNA polymerase" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|E2RHZ2 POLR3B "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|E1BPX6 POLR3B "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|Q9NW08 POLR3B "DNA-directed RNA polymerase III subunit RPC2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
RGD|1565311 Polr3b "polymerase (RNA) III (DNA directed) polypeptide B" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
MGI|MGI:1917678 Polr3b "polymerase (RNA) III (DNA directed) polypeptide B" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-2887 polr3b "polymerase (RNA) III (DNA directed) polypeptide B" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0288449 rpc2 "RNA polymerase III, second largest subunit" [Dictyostelium discoideum (taxid:44689)] 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

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
P22276RPC2_YEAST2, ., 7, ., 7, ., 60.56690.96590.8894yesno
Q9NW08RPC2_HUMAN2, ., 7, ., 7, ., 60.57030.96970.9055yesno
P59470RPC2_MOUSE2, ., 7, ., 7, ., 60.57030.96970.9055yesno
Q03587RPOB_THEAC2, ., 7, ., 7, ., 60.32480.93570.8284yesno
P25167RPC2_DROME2, ., 7, ., 7, ., 60.53180.98010.9120yesno
Q10233RPC2_SCHPO2, ., 7, ., 7, ., 60.57640.96880.8798yesno
P11513RPOB_SULAC2, ., 7, ., 7, ., 60.36030.94230.8854yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.70.963
4th Layer2.7.7.60.946

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 ?
Query1058
PRK085651103 PRK08565, PRK08565, DNA-directed RNA polymerase su 0.0
COG00851060 COG0085, RpoB, DNA-directed RNA polymerase, beta s 0.0
cd00653866 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun 0.0
TIGR03670599 TIGR03670, rpoB_arch, DNA-directed RNA polymerase 0.0
PRK07225605 PRK07225, PRK07225, DNA-directed RNA polymerase su 0.0
pfam00562373 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, do 1e-174
cd00653866 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun 1e-123
PRK09606494 PRK09606, PRK09606, DNA-directed RNA polymerase su 1e-100
pfam04563394 pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta sub 1e-85
TIGR020131065 TIGR02013, rpoB, DNA-directed RNA polymerase, beta 1e-40
CHL002071077 CHL00207, rpoB, RNA polymerase beta subunit; Provi 3e-36
CHL000011070 CHL00001, rpoB, RNA polymerase beta subunit 4e-30
PRK004051112 PRK00405, rpoB, DNA-directed RNA polymerase subuni 9e-26
pfam04561185 pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, do 3e-23
pfam0456568 pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, do 2e-20
pfam0456663 pfam04566, RNA_pol_Rpb2_4, RNA polymerase Rpb2, do 7e-19
TIGR020131065 TIGR02013, rpoB, DNA-directed RNA polymerase, beta 1e-15
pfam0456746 pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, do 1e-12
CHL002071077 CHL00207, rpoB, RNA polymerase beta subunit; Provi 9e-12
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 1e-10
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 5e-10
PRK004051112 PRK00405, rpoB, DNA-directed RNA polymerase subuni 6e-09
CHL000011070 CHL00001, rpoB, RNA polymerase beta subunit 2e-08
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 6e-07
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 2e-06
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 3e-06
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 2e-04
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 0.003
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B; Provisional Back     alignment and domain information 
 Score =  920 bits (2380), Expect = 0.0
 Identities = 416/1046 (39%), Positives = 605/1046 (57%), Gaps = 71/1046 (6%)

Query: 38   FLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSM-TVDG 96
            + K +GLV+QHLDS+N F+  G+++IV     I + I P + +    +R+G+P +   DG
Sbjct: 8    YFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEI-PGLKIVLGKIRVGEPEIKEADG 66

Query: 97   VSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLY 156
                + P   RL ++TYAAP+ + +  V+     +       V IG +PIM++S  C L 
Sbjct: 67   SERPITPMEARLRNLTYAAPLYLTMIPVENGIEYEPEE----VKIGDLPIMVKSKICPLS 122

Query: 157  GKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNIN---ASVTS 213
            G    EL  +GE P DPGGYFII G+E+V++ QE L+ NRV++D  + G+     A V S
Sbjct: 123  GLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVIS 182

Query: 214  STETVKSKTVIQMEK-GKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSAL 272
            S    +++  ++  K G +Y+       KIP +++M+A+G+E+D+++V  V  DP     
Sbjct: 183  SRAGYRAQVTVERRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPEIQQE 242

Query: 273  LLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNN 332
            LLPS+E+ +++   T E AL+Y+    KR   G P   R  RA  IL    L ++     
Sbjct: 243  LLPSLEQASSIAA-TVEDALDYIG---KRVAIGQPREYRIERAEQILDKYLLPHLGTSPE 298

Query: 333  NFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQ 392
            +   K +++  M  +++E  L +   DDKD+  NKRL L+G L++ LF   FK ++ +++
Sbjct: 299  DRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLK 358

Query: 393  KTVDIILSKPSRSSRFDLSQFIVR-DSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARL 451
              ++   +   R  + DL + IVR D IT  +   L+TGN+        R G++Q+L R 
Sbjct: 359  YQLEKSYA---RGRKLDL-RAIVRPDIITERIRHALATGNW-----VGGRTGVSQLLDRT 409

Query: 452  SFIGTLGHMTRV-------SPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNL 504
            +++ TL H+ RV        P FE        R L  +QWG +CP +TPEG  CGLVKNL
Sbjct: 410  NYLSTLSHLRRVVSPLSRGQPHFEA-------RDLHGTQWGRICPFETPEGPNCGLVKNL 462

Query: 505  ALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFA 564
            ALM  ++   +E  +  + Y LGV  +E    EE    +   V  NG ++G H   +  A
Sbjct: 463  ALMAQISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELA 520

Query: 565  DVMRKLRRAGKIGEFVSV--FVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKEL 622
            + +R+LRR+GKI + V+V      +   VY+  D GRV RPL++ + G  ++   H+++L
Sbjct: 521  EKIRELRRSGKISDEVNVAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKL 580

Query: 623  LDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPY 682
              G  +FDD ++ G+IEYLD  EE NA +AL   D TP+ TH+EI P  ILG+ A +IPY
Sbjct: 581  KKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEHTHLEIWPPAILGITASIIPY 640

Query: 683  PHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLG 742
            P HNQSPRNTYQ AM KQ++G  A N   R D+  +LL YPQRPL+ TR +E++GY+   
Sbjct: 641  PEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRP 700

Query: 743  AGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPD 802
            AGQNA VAV+SY+GY+IEDAI+MNK+S++RG  R    + Y    +KY     D+I  P+
Sbjct: 701  AGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPE 760

Query: 803  ---RTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESP----LETRGSIMSPTGQTDS- 854
               R   G E  + LD+DG+ +P   +K  DV I K SP     E     +    + D+ 
Sbjct: 761  PNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGLQERRDTS 820

Query: 855  ---RYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQK 911
               R+           GE  +VD V +     G+  +K  +R  R PELGDKF+SRHGQK
Sbjct: 821  VTVRH-----------GEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQK 869

Query: 912  GVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAF 971
            GV G +V QED PF+E GI PDLI+NPH  PSRMTVG+++E + GK     GRF   + F
Sbjct: 870  GVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF 929

Query: 972  -GEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLD 1030
             GEP       E + + L+K G+  +G +++Y G TG  ++A IF+G +YYQKL HMV D
Sbjct: 930  YGEP------EEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVAD 983

Query: 1031 KMHARGSGPRVMLTRQPTEGRARNGG 1056
            K+HAR  GP  +LTRQPTEGRAR GG
Sbjct: 984  KIHARARGPVQILTRQPTEGRAREGG 1009

Length = 1103
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] Back     alignment and domain information
>gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit Back     alignment and domain information
>gnl|CDD|132709 TIGR03670, rpoB_arch, DNA-directed RNA polymerase subunit B Back     alignment and domain information
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B'; Validated Back     alignment and domain information
>gnl|CDD|215994 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6 Back     alignment and domain information
>gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit Back     alignment and domain information
>gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B''; Validated Back     alignment and domain information
>gnl|CDD|191028 pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta subunit Back     alignment and domain information
>gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit Back     alignment and domain information
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional Back     alignment and domain information
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit Back     alignment and domain information
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed Back     alignment and domain information
>gnl|CDD|218151 pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, domain 2 Back     alignment and domain information
>gnl|CDD|146955 pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, domain 3 Back     alignment and domain information
>gnl|CDD|113341 pfam04566, RNA_pol_Rpb2_4, RNA polymerase Rpb2, domain 4 Back     alignment and domain information
>gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit Back     alignment and domain information
>gnl|CDD|191029 pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, domain 5 Back     alignment and domain information
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta 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|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed Back     alignment and domain information
>gnl|CDD|214330 CHL00001, rpoB, 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|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|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/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 1058
PRK085651103 DNA-directed RNA polymerase subunit B; Provisional 100.0
KOG02141141 consensus RNA polymerase II, second largest subuni 100.0
KOG02151153 consensus RNA polymerase III, second largest subun 100.0
KOG02161111 consensus RNA polymerase I, second largest subunit 100.0
COG00851060 RpoB DNA-directed RNA polymerase, beta subunit/140 100.0
TIGR020131065 rpoB DNA-directed RNA polymerase, beta subunit. Th 100.0
cd00653866 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA po 100.0
PRK004051112 rpoB DNA-directed RNA polymerase subunit beta; Rev 100.0
CHL000011070 rpoB RNA polymerase beta subunit 100.0
CHL002071077 rpoB RNA polymerase beta subunit; Provisional 100.0
PRK09603 2890 bifunctional DNA-directed RNA polymerase subunit b 100.0
PRK14844 2836 bifunctional DNA-directed RNA polymerase subunit b 100.0
PRK07225605 DNA-directed RNA polymerase subunit B'; Validated 100.0
TIGR03670599 rpoB_arch DNA-directed RNA polymerase subunit B. T 100.0
PF00562386 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; Int 100.0
PRK09606494 DNA-directed RNA polymerase subunit B''; Validated 100.0
PF04563203 RNA_pol_Rpb2_1: RNA polymerase beta subunit; Inter 100.0
PF0456568 RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; Int 99.92
PF04561190 RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; Int 99.85
PF0456663 RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; Int 99.7
PF0456748 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; Int 98.76
KOG02151153 consensus RNA polymerase III, second largest subun 98.75
COG0085 1060 RpoB DNA-directed RNA polymerase, beta subunit/140 97.6
KOG0214 1141 consensus RNA polymerase II, second largest subuni 97.47
PF0688358 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific do 97.43
PHA03394865 lef-8 DNA-directed RNA polymerase subunit beta-lik 95.89
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional Back     alignment and domain information 
Probab=100.00  E-value=2.8e-245  Score=2295.61  Aligned_cols=999  Identities=40%  Similarity=0.680  Sum_probs=912.5

Q ss_pred             ccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcCcceecCCCcEEEEEeEEEEcCCccccCC-ccCCCChhhHhhc
Q 001532           31 KFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDG-VSEKLNPHMCRLS  109 (1058)
Q Consensus        31 ~~~~i~~~f~~~~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~~~~~~l~~~~i~i~~P~~~~~~-~~~~l~P~EcR~r  109 (1058)
                      .|.++++||+.++|++||+||||+|+++||++++++++||+.. ++++.|+|++++|++|.+.+++ ...+|+|+|||+|
T Consensus         1 ~~~li~~~~~~~~Lv~~qidSFn~Fi~~gL~~iv~~~~pI~~~-~~~~~L~f~~i~l~~P~~~~~~~~~~~l~P~ecR~r   79 (1103)
T PRK08565          1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTE-IPGLKIVLGKIRVGEPEIKEADGSERPITPMEARLR   79 (1103)
T ss_pred             CchHHHHHhcccChHHHHHHHHHHHHHHhHHHHHHhcCCEEec-CCCEEEEEEEEEECCCcccccccccCCCCHHHHHhc
Confidence            4999999999999999999999999999999999999999765 6789999999999999997654 5678999999999


Q ss_pred             CCccCceEEEEEEEEECCCccceeeEEeEEEEeeeccccccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCceeEEeee
Q 001532          110 DMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQ  189 (1058)
Q Consensus       110 ~lTYsa~l~v~v~~~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~ls~~elv~~gE~~~d~GGYFIING~EKVI~~q  189 (1058)
                      ++||+|+|+|++++..++    ..+++++|++|+|||||+|++|||++++|+||++.||||.|+||||||||+|||||+|
T Consensus        80 ~lTYsa~l~v~i~~~~~~----~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~p~D~GGYFIING~ERVI~~q  155 (1103)
T PRK08565         80 NLTYAAPLYLTMIPVENG----IEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQ  155 (1103)
T ss_pred             CCCcceEEEEEEEEEECC----eeeEEEEEEeccCCeEeCCCcccCCCCCHHHHHhcCCCccCCCCeEEECCcEEEEEEE
Confidence            999999999999998654    4455668999999999999999999999999999999999999999999999999999


Q ss_pred             ecccCCEEEEEeCCCC---cEEEEEEecCCCc-ceEEEEEeeCCEEEEEEcceeccccHhhHHHHhCCCCHHHHHHHhCC
Q 001532          190 EQLSKNRVIIDTDKKG---NINASVTSSTETV-KSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGR  265 (1058)
Q Consensus       190 ~~~~~N~i~~~~~~~g---~~~~~v~s~~~~~-~s~~~~~~~~g~i~~~~~~~~~~IPl~ilLkALg~~sd~eI~~~i~~  265 (1058)
                      |++++|+++++.+.++   .+.|.++|..... .+..+++..+|.++++++++.++||+++||||||..||+||++.++.
T Consensus       156 ~~~s~n~~~~~~~~~~~~~~~~a~i~s~~~~~~~~~~l~~~~~g~i~~~~~~~~~~IPi~illkALG~~sD~eI~~~i~~  235 (1103)
T PRK08565        156 EDLAPNRVLVDKGEAGSSITHTAKVISSRAGYRAQVTVERRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSL  235 (1103)
T ss_pred             EecCCCEEEEEEecCCCcceEEEEEEeccCCCcceEEEEEecCCeEEEEEcCcccEeeHHHHHHHcCCCCHHHHHHHhcc
Confidence            9999999998765443   3678888877644 34444455678999999987678999999999999999999999976


Q ss_pred             chhHHhhhhhhHHHHHhcCC-cCHHHHHHHHhhcccccCCCCCCCChHHHHHHHHHhhhccCCCCCCCCCCCcchhHHHH
Q 001532          266 DPRYSALLLPSIEECANLDI-YTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVM  344 (1058)
Q Consensus       266 ~~~~~~~l~~~l~~~~~~~i-~t~~~al~yig~~~~~~~~~~~~~~~~e~~~~~L~~~llpHl~~~~~~~~~K~~~L~~M  344 (1058)
                      +..+.+.+..+++++.  .+ .|+++|+.|||++|++.  .++.. ..+.|+++|++++|||++.+..++.+|+.+|++|
T Consensus       236 ~~~~~~~l~~~l~~~~--~~~~t~~~al~~ig~~~~~~--~~~~~-~~e~~~~~L~~~ll~Hig~~~~~~~~K~~~L~~M  310 (1103)
T PRK08565        236 DPEIQQELLPSLEQAS--SIAATVEDALDYIGKRVAIG--QPREY-RIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQM  310 (1103)
T ss_pred             cHHHHHHHHHHHHHhh--ccccCHHHHHHHHHHhccCC--CCCcc-HHHHHHHHHHhhCcccCCCcccchhHHHHHHHHH
Confidence            6666777777777653  25 79999999999999875  33444 6789999999999999998765567899999999


Q ss_pred             HHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCCccccccccccchhhhh
Q 001532          345 LRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLE  424 (1058)
Q Consensus       345 i~kLl~~~~G~~~~DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~  424 (1058)
                      ++||++++.|.+.+||+|||+||||+++|+||+.+||++|+++++.+|+++.+.+.+.   ..+++..+++++.||++|+
T Consensus       311 i~kLl~l~~g~~~~DD~D~l~NKRv~l~G~Ll~~~fr~~l~~~~~~ik~~l~~~~~~~---~~~~~~~~i~~~~It~~i~  387 (1103)
T PRK08565        311 ASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARG---RKLDLRAIVRPDIITERIR  387 (1103)
T ss_pred             HHHHHhhhcCCCCCCCccccCCcEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc---ccCCHHHhcccchhhHHHH
Confidence            9999999999999999999999999999999999999999999999999998765432   2456667778889999999


Q ss_pred             hhhccCCCcccccccccccceEEcccccccccccccccccccccccccccCCCcCCCCCccccccCCCCCCCcccccccc
Q 001532          425 RTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNL  504 (1058)
Q Consensus       425 ~~~sTGn~~~~~~~~q~sG~sq~l~rln~ls~lshlRrv~~~~~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~L  504 (1058)
                      +|||||||..     |++|+||+|+|+||+|+||||||+++++.+++|.++||+||||||||+||||||||++|||++||
T Consensus       388 ~~~sTGnw~~-----~~sGvSq~ldr~N~l~~lSh~Rrv~s~~~r~~~~~~vR~Lhps~wG~iCPveTPEG~~cGLv~~L  462 (1103)
T PRK08565        388 HALATGNWVG-----GRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNL  462 (1103)
T ss_pred             HHHhcCcccc-----CCcceEEecccCCHHHHHHHHhhccCCcccCCCCccccccChhhccccCCCCCCCccccchhhhh
Confidence            9999999984     67999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cceeeeecCCCChhHHHHHhhcCCeeccccCccccCCCCcEEEEECCeEEeeccChhhHHHHHHHHhhcCCcCceeEEEe
Q 001532          505 ALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFV  584 (1058)
Q Consensus       505 A~~a~Is~~~~~~~i~~~l~~~g~~~l~~~~~~~~~~~~~~~V~lnG~~vG~~~~~~~~~~~lr~~rr~~~i~~~v~i~~  584 (1058)
                      |++|+|+++.+.+++.++|.++|+.++..+++...  ...++|||||+|||++++|..|++.||.+||.|.++.+++|++
T Consensus       463 A~~a~It~~~~~~~i~~~l~~~G~~~~~~~~~~~~--~~~~~V~lnG~~iG~~~~~~~l~~~lR~~Rr~g~i~~~v~I~~  540 (1103)
T PRK08565        463 ALMAQISVGVDEEEVEEILYELGVVPVEEAREEEY--ISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAY  540 (1103)
T ss_pred             hcccccccCCChHHHHHHHHHcCCCchhhcCcccC--CCceEEEECCEEEEEECCHHHHHHHHHHHhhcCCCCCeEEEEE
Confidence            99999999888899999999999998765544332  2568999999999999999999999999999999999999999


Q ss_pred             cc--ccceEEEecCCCeeeeeEEEEecCcccchhhhHHHhhcCCccchhhhccCceeEeccccccceEEEeecCCCCCCc
Q 001532          585 NE--KQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDT  662 (1058)
Q Consensus       585 ~~--~~~~i~I~sd~GRl~RPll~v~~~~~~~~~~~~~~l~~~~~s~~~~~~~~~iE~id~~e~~~~~Ia~~~~~~~~~~  662 (1058)
                      +.  ..++|+|+||+||++|||++|++|++.+++++++.++.+..+|+||+++|.+||||++||++++||+.++++...+
T Consensus       541 ~~~~~~~~i~I~sd~GRl~RP~~~v~~g~~~~~~~~~~~l~~~~~~~~~l~~~g~iEyid~~Ee~~~~Ia~~~~~l~~~~  620 (1103)
T PRK08565        541 IETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEH  620 (1103)
T ss_pred             ccccccceEEEecCCceeeeeEEEEecCceeccHHHHHHhhccccchhhHhhcCcEEeeCHHHhcCcEEeccccccCcce
Confidence            98  8899999999999999999999999999999999988788899999999999999999999999999999987778


Q ss_pred             eeeeecCccccccccccCCCCCCCCCCccccccccccCCccceeEeeeeccccceeeeeCCCcceeechhhhhhcCCCCC
Q 001532          663 THIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLG  742 (1058)
Q Consensus       663 th~Ei~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaiG~~~~n~~~R~D~~~y~l~ypQ~Plv~t~~~~~~~~~~~~  742 (1058)
                      ||+||+|+++||++||+|||+||||||||||||||+|||||++++|+..|+|++.|+|+|||+|||+|+.++.++++++|
T Consensus       621 th~Ei~p~~ilsv~asliPF~~hNqspRn~yq~~M~KQa~g~~~~n~~~r~d~~~~~l~~pQ~Plv~t~~~~~~~~~~~p  700 (1103)
T PRK08565        621 THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRP  700 (1103)
T ss_pred             eccccCCccccceeeeccCCcccCcccchhhhhhhhhcccccccccceEeecCCcceeecCceeEEEeccccccccccCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcceEEEEeecCCCCCCCcEEEecceeeccceEEEEEEEEEEEeecccCCccceecCCCCCC---CcccccccCCCCcc
Q 001532          743 AGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTG---PGAERMQILDDDGL  819 (1058)
Q Consensus       743 ~G~N~~Vav~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~---~~~~~~~~ld~dGi  819 (1058)
                      +|+||+||||||+||||||||||||+|+|||+|||+||++|++++++...+..|.++.|..+.   +....|++||+|||
T Consensus       701 ~G~N~iVAv~sy~GYn~EDaiIink~s~~rG~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ld~dGi  780 (1103)
T PRK08565        701 AGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGI  780 (1103)
T ss_pred             CCeeEEEEEEcccCcchHHhhhhhhhhhhcCCceEEEEEEEEEEeeecCCCCceEEecCCCcccccCchhhhhcCCCCCC
Confidence            999999999999999999999999999999999999999999998876556556777653321   12246899999999


Q ss_pred             ccCCcEeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceEEeeCCCCCceEEEEEEEeeCCCCCEEEEEEEeecCCCc
Q 001532          820 AAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPE  899 (1058)
Q Consensus       820 ~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~vd~v~~~~~~~~~~~v~v~i~~~R~p~  899 (1058)
                      |++|++|++|||||||++|..+..+.... +......+|.|++++.+|  +|+||+|.++.++++.+.|||++|+.|+|+
T Consensus       781 ~~~G~~v~~gdili~k~~p~~~~~~~~~~-~~~~~~~~~~s~~~~~~e--~g~V~~V~~~~~~~~~~~vkv~ir~~R~p~  857 (1103)
T PRK08565        781 VSPEVEVKGGDVLIGKTSPPRFLEELEEL-SLGLQERRDTSVTVRHGE--KGIVDTVLITESPEGNKLVKVRVRDLRIPE  857 (1103)
T ss_pred             cCCCcEEcCCCEEEEEecCCCCCcchhhc-cccCCccccceEEecCCC--ceEEEEEEEEecCCCcEEEEEEEEEEecCc
Confidence            99999999999999999986533221110 111134789999999999  999999999988889999999999999999


Q ss_pred             ccceecccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCcccHHHHHHHhhccchhcCCceeeeecccCCCCCCC
Q 001532          900 LGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHAD  979 (1058)
Q Consensus       900 iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNP~~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpf~~~~~~~~  979 (1058)
                      ||||||||||||||||++||+||||||+||++|||||||||||||||||||+|+++||++++.|.+.|+|||+     ..
T Consensus       858 iGDKfssRhGqKGv~s~i~~~edmPf~~~G~~pDiI~NPh~~PSRMtiG~l~E~~~gk~~~~~g~~~d~t~F~-----~~  932 (1103)
T PRK08565        858 LGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFY-----GE  932 (1103)
T ss_pred             hhhhhhhhccCcceeeeecccccCCcCCCCCCccEEECCCCCcccccHHHHHHHHHHHHHHhcCceeeecCcC-----Cc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999     56


Q ss_pred             CHHHHHHHHHHcCCCCCCceEEEeCCCCcEeeeeEeeeeeeeeccccccCcceEEeccCCccccccCCcCcccCCCCC
Q 001532          980 TVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGF 1057 (1058)
Q Consensus       980 ~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~ 1057 (1058)
                      ..+++++.|+++||+++|+|+||||+||++|+++||+|++|||||+|||.||+|||++||++.|||||++||+|+|||
T Consensus       933 ~~~~~~~~L~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV~DK~~~R~~Gp~~~lt~QP~~Gr~~~GG~ 1010 (1103)
T PRK08565        933 PEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGL 1010 (1103)
T ss_pred             hHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhheechhhhchhhhhccCCCcchhhhCCccccccCCCe
Confidence            789999999999999999999999999999999999999999999999999999999999999999999999999997

>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription] Back     alignment and domain information
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription] Back     alignment and domain information
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription] Back     alignment and domain information
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] Back     alignment and domain information
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit Back     alignment and domain information
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit Back     alignment and domain information
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed Back     alignment and domain information
>CHL00001 rpoB RNA polymerase beta subunit Back     alignment and domain information
>CHL00207 rpoB RNA polymerase beta subunit; 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
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated Back     alignment and domain information
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B Back     alignment and domain information
>PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 DNA-directed RNA polymerases 2 Back     alignment and domain information
>PRK09606 DNA-directed RNA polymerase subunit B''; Validated Back     alignment and domain information
>PF04563 RNA_pol_Rpb2_1: RNA polymerase beta subunit; InterPro: IPR007644 RNA polymerases catalyse the DNA dependent polymerisation of RNA Back     alignment and domain information
>PF04565 RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; InterPro: IPR007645 RNA polymerases catalyse the DNA dependent polymerisation of RNA Back     alignment and domain information
>PF04561 RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; InterPro: IPR007642 RNA polymerases catalyse the DNA-dependent polymerisation of RNA Back     alignment and domain information
>PF04566 RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; InterPro: IPR007646 RNA polymerases catalyse the DNA dependent polymerisation of RNA Back     alignment and domain information
>PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 RNA polymerases catalyse the DNA dependent polymerisation of RNA Back     alignment and domain information
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription] Back     alignment and domain information
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] Back     alignment and domain information
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription] Back     alignment and domain information
>PF06883 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific domain ; InterPro: IPR009674 This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2 Back     alignment and domain information
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query1058
2waq_B 1131 The Complete Structure Of The Archaeal 13-Subunit D 0.0
2pmz_B1124 Archaeal Rna Polymerase From Sulfolobus Solfataricu 0.0
1i3q_B1224 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 1e-180
3h0g_B1210 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 1e-179
1i6v_C1118 Thermus Aquaticus Core Rna Polymerase-Rifampicin Co 4e-33
1l9u_C1118 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 4e-33
1hqm_C1119 Crystal Structure Of Thermus Aquaticus Core Rna Pol 4e-33
1ynj_C1119 Taq Rna Polymerase-Sorangicin Complex Length = 1119 4e-33
1iw7_C1119 Crystal Structure Of The Rna Polymerase Holoenzyme 6e-33
3iyd_C1342 Three-Dimensional Em Structure Of An Intact Activat 1e-17
3lu0_C1342 Molecular Model Of Escherichia Coli Core Rna Polyme 1e-17
>pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 1131 Back     alignment and structure 
Iteration: 1

 Score =  652 bits (1681), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/1052 (35%), Positives = 586/1052 (55%), Gaps = 52/1052 (4%)
Query: 27   SVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVR 86
            S+ ++++++  + K +GLV+QHLDS+N FV   +++I+     I + I P + +R   +R
Sbjct: 9    SIDERWKVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPTEI-PGLKVRLGKIR 67
Query: 87   IGQPSMTVDGVSEK-LNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIP 145
            IG+P +      E+ ++P   RL ++TYAAP+ + +  V+ +       E  +V IG +P
Sbjct: 68   IGKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIPVENN----IEAEPEEVYIGDLP 123
Query: 146  IMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKG 205
            IML+S    +      +L  +GE P DPGGYFI+ G+E+V++ QE L+ NRV++DT K G
Sbjct: 124  IMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVLVDTGKTG 183
Query: 206  -NINAXXXXXXXXXXXXXXIQMEK---GKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQ 261
             NI                + +E+   G  ++       KIP +++M+A+G+ +D+++V 
Sbjct: 184  SNITHTAKIISSTAGYRVPVTIERLKDGTFHVSFPAVPGKIPFVILMRALGILTDRDIVY 243
Query: 262  MVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRD 321
             V  DP     L PS+E+ ++  I   + AL+++  +V     G    +R  +A  I+  
Sbjct: 244  AVSLDPEIQNELFPSLEQASS--IANVDDALDFIGSRV---AIGQKRENRIEKAQQIIDK 298
Query: 322  VFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFE 381
             FL ++    ++ R K +Y+A  + +++E  L +   DDKD+  NKRL L+G L + LF 
Sbjct: 299  YFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFASLFR 358
Query: 382  DLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHR 441
              FK  + ++   ++       R  +  L   +  D +T  +   L+TGN+        R
Sbjct: 359  VAFKAFVKDLTYQLE---KSKVRGRKLALKALVRPDIVTERIRHALATGNW-----VGGR 410
Query: 442  KGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLV 501
             G++Q+L R +++  L H+ RV     + +     R L  +QWG +CP +TPEG   GLV
Sbjct: 411  TGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLV 470
Query: 502  KNLALMTHVTTDEEEGPLISLCYCLGVEDLELL---SGEELHNPNSFL----VIFNGLIL 554
            KNLALM  +     E  +    Y +GV  +E +     E   + N +L    VI NG ++
Sbjct: 471  KNLALMAQIAVGINEKIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILNGRLV 530
Query: 555  GKHRRPKCFADVMRKLRRAGKI------GEFVSVFVNEKQRCVYIASDGGRVCRPLVIAD 608
            G +R  +  A  +R+ RR G+I      G  V+ F+NE    V++  D GRV RPL+I  
Sbjct: 531  GYYRDGEELAKKIRERRRKGEISDEVNVGHIVTDFINE----VHVNCDSGRVRRPLIIVS 586
Query: 609  KGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIE 668
             G   +    +++L  G  +FDD +R+G IEYLD  EE NA +AL   D TP+ TH+EI 
Sbjct: 587  NGNPLVTREDIEKLDSGSITFDDLVRQGKIEYLDAEEEENAYVALEPSDLTPEHTHLEIW 646
Query: 669  PFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLL 728
               ILG+ A +IPYP HNQSPRNTYQ AM KQA+G  A N   R D+  +LL YPQRPL+
Sbjct: 647  SPAILGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLV 706
Query: 729  TTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQ 788
             TR ++++GY    AG NA +AV+S++GY++ED+I+MN+SS++RG  R    + Y+    
Sbjct: 707  QTRALDIIGYTNRPAGNNAILAVISFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEV 766
Query: 789  KYANSTSDRILRPD---RTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSI 845
            KY     D+I+ P+   R   G E  ++L+D+G+ +P   +K  DV I K SP       
Sbjct: 767  KYPGGQEDKIVMPEPGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEF 826
Query: 846  MSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFS 905
               + +   R  S    +    GE  +VD V +     G+  +K  +R  R P +GDKF+
Sbjct: 827  KELSPEQAKRDTSIVTRH----GEMGIVDLVLITETAEGNKLVKVRVRDLRIPSIGDKFA 882
Query: 906  SRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRF 965
            SRHGQKGV G ++ Q D P++ +G+ PD+I+NPH  PSRMT+G+++E + GK     G  
Sbjct: 883  SRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGKYAALSGNI 942
Query: 966  HYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLK 1025
               + F     +   +E +   ++K+G+  +  ++ Y G TG  +++ I+ G +YYQKL 
Sbjct: 943  VDATPF-----YKTPIEQLQNEILKYGYLPDATEVTYDGRTGQKIKSRIYFGVVYYQKLH 997
Query: 1026 HMVLDKMHARGSGPRVMLTRQPTEGRARNGGF 1057
            HMV DK+HAR  GP  +LTRQPTEGRAR GG 
Sbjct: 998  HMVADKIHARARGPVQILTRQPTEGRAREGGL 1029
>pdb|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 1124 Back     alignment and structure
>pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1224 Back     alignment and structure
>pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1210 Back     alignment and structure
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1118 Back     alignment and structure
>pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1118 Back     alignment and structure
>pdb|1HQM|C Chain C, 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 = 1119 Back     alignment and structure
>pdb|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex Length = 1119 Back     alignment and structure
>pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 1119 Back     alignment and structure
>pdb|3IYD|C Chain C, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 1342 Back     alignment and structure
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1342 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query1058
3h0g_B1210 DNA-directed RNA polymerase II subunit RPB2; trans 0.0
1twf_B1224 DNA-directed RNA polymerase II 140 kDa polypeptid; 0.0
4ayb_B 1131 DNA-directed RNA polymerase; transferase, multi-su 0.0
2a6h_C1119 DNA-directed RNA polymerase beta chain; RNA polyme 1e-32
2a6h_C 1119 DNA-directed RNA polymerase beta chain; RNA polyme 1e-15
3lu0_C1342 DNA-directed RNA polymerase subunit beta; E. coli 2e-18
3lu0_C 1342 DNA-directed RNA polymerase subunit beta; E. coli 8e-09
3lu0_C 1342 DNA-directed RNA polymerase subunit beta; E. coli 5e-05
3lu0_C 1342 DNA-directed RNA polymerase subunit beta; E. coli 4e-04
1vt4_I1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-10
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-09
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-08
1vt4_I1221 APAF-1 related killer DARK; drosophila apoptosome, 8e-04
3mlq_A188 DNA-directed RNA polymerase subunit beta; tudor, t 6e-06
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1210 Back     alignment and structure
 Score = 1245 bits (3222), Expect = 0.0
 Identities = 382/1124 (33%), Positives = 584/1124 (51%), Gaps = 108/1124 (9%)

Query: 24   PVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIV-----------S 72
               +  D + ++  F +   L +Q L SF+ FV   +++IV  +  +             
Sbjct: 10   ETLTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQG 69

Query: 73   GIDPSIFLRFKDVRIGQPSMT-VDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHT-- 129
             +     + F  + + +P+MT  DG +  + P   RL ++TY++P+ V++          
Sbjct: 70   DVTRRYEINFGQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADS 129

Query: 130  -----------EKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFI 178
                       E+   E + V IG+IPIMLRS  C+L G  ++EL  L ECP D GGYFI
Sbjct: 130  NVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFI 189

Query: 179  IKGTEKVLLIQEQLSKNRVIIDTDKKGNINA--SVTSSTETVKSKTVIQMEK-------- 228
            I G+EKV++ QE+ + N V +      +  A  +   S     S+ +  M+         
Sbjct: 190  INGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTE 249

Query: 229  ---GKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDP---RYSALLLPSIEECAN 282
                 +   L      IPI++V +A+G+  D+++++ +  DP   +   ++ P IEE   
Sbjct: 250  NSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFV 309

Query: 283  LDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVA 342
              I  ++ AL+Y+  +    T G     R   A  IL+   L ++         K F++ 
Sbjct: 310  --IQDKDIALDYIGKRGS--TTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLG 365

Query: 343  VMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKP 402
             M+ RM+   L +   DD+D+ G KRL+L+G L++ LF  LF+ M  +V K +   +   
Sbjct: 366  YMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETN 425

Query: 403  SRSSRFDLSQFIVRDSITVGLERTLSTGNF-DVKRFKMHRKGMTQVLARLSFIGTLGHMT 461
                 F+L+  +  + IT GL  +L+TGN+ D KR  ++R G++QVL R +F  TL H+ 
Sbjct: 426  RE---FNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLR 482

Query: 462  RVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLIS 521
            R +    +  K++ PR L  + WGM+CP +TPEG+ACGLVKNL+LM++V+      P+I 
Sbjct: 483  RTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIE 542

Query: 522  LCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVS 581
                 G+E LE  +     +PN+  V  NG+ LG HR P    + +R LRR   I   VS
Sbjct: 543  FLEEWGLETLEDYNPS--ASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVS 600

Query: 582  VFVNEKQRCVYIASDGGRVCRPLVIAD-------KGISRIKEHHMKELLDGVR------- 627
            +  + +++ + + +D GR+CRPL I D       +G   I++ H+++L++          
Sbjct: 601  IVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDPE 660

Query: 628  ---SFDDFLREGLIEYLDVNEENNALIALYEGDATPDT---------------------- 662
                +   +  GLIEYLD  EE   +IA+   D                           
Sbjct: 661  QRFGWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAP 720

Query: 663  -------THIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDS 715
                   TH EI P  ILG++A +IP+P HNQSPRNTYQ AMGKQAMG    N   RMD+
Sbjct: 721  NPHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDT 780

Query: 716  LLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFG 775
            +  +L YPQ+PL TTR++E + + +L AGQNA VA++ YSGY+ ED+I+MN++S+DRG  
Sbjct: 781  MANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLF 840

Query: 776  RCIVVKKYTAINQKYANSTSDRILRPDR---TGPGAERMQILDDDGLAAPGEIIKPNDVY 832
            R I  + YT   +K   +  +   RP R             L+DDGL APG  +   D+ 
Sbjct: 841  RSIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDII 900

Query: 833  INKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLI 892
            I K +P+      +          R      +    E+ +VD+V + +++ G   +K  +
Sbjct: 901  IGKTAPIPLDHEELGQ-RTQLHAKRDVSTPLRST--ESGIVDQVMVTTNQEGLKFVKVRM 957

Query: 893  RHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIE 952
            R TR P++GDKF+SRHGQKG  G   + ED PFS +GI PD+I+NPH  PSRMTV  ++E
Sbjct: 958  RSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVE 1017

Query: 953  LLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQA 1012
                K     G     + F +      TVE++S+ L  HGF   G +++Y G TG  L A
Sbjct: 1018 CQLSKVSALSGFEGDATPFTD-----VTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVA 1072

Query: 1013 YIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGG 1056
             +F+GP YYQ+LKH+V DK+HAR  GP  +LTRQP EGR+R+GG
Sbjct: 1073 QVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGG 1116
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ... Length = 1224 Back     alignment and structure
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B 2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B Length = 1131 Back     alignment and structure
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... Length = 1119 Back     alignment and structure
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... Length = 1119 Back     alignment and structure
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342 Back     alignment and structure
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342 Back     alignment and structure
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342 Back     alignment and structure
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus} Length = 188 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 1058
d1twfb_1207 e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces c 0.0
d1smyc_1119 e.29.1.1 (C:) RNA-polymerase beta {Thermus thermop 1e-167
>d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1207 Back     information, alignment and structure

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
domain: RBP2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  747 bits (1928), Expect = 0.0
 Identities = 378/1127 (33%), Positives = 587/1127 (52%), Gaps = 107/1127 (9%)

Query: 19   QKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIV------- 71
            +  +AP+ +  D + ++  F + +GLV Q LDSFN FV+  ++ I+  +  ++       
Sbjct: 2    EDESAPI-TAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQH 60

Query: 72   ----SGIDPSIFLRFKDVRIGQPSMTV-DGVSEKLNPHMCRLSDMTYAAPILVNIEYVQG 126
                  I     + F  + + +P +   DGV+  L P   RL ++TY++ + V+++    
Sbjct: 61   TTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTY 120

Query: 127  SHTEKTT---------------MEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPL 171
               +                   E   V IGR+PIMLRS  C L    E++L +L ECP 
Sbjct: 121  EAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPF 180

Query: 172  DPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASVTS--STETVKSKTVIQME-- 227
            D GGYFII G+EKVL+ QE+ + N V +      +  + V    S     S+ +  ++  
Sbjct: 181  DMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVK 240

Query: 228  --------KGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSA---LLLPS 276
                       +   L    + IPI+++ +A+G+  D E+++ +  D        +L P 
Sbjct: 241  LYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPC 300

Query: 277  IEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRP 336
            +E+     I  +E AL+++    + +  G     R   A  IL+  FL ++         
Sbjct: 301  VEDG--FVIQDRETALDFIG--RRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESR 356

Query: 337  KCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVD 396
            K F++  M+ R++   L++   DD+D+ G KRL+L+G L++ LF+ LFK +  ++ + + 
Sbjct: 357  KAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQ 416

Query: 397  IILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRK-GMTQVLARLSFIG 455
                    +  F++   I   +IT GL+  L+TGN+  ++  M  + G++QVL R ++  
Sbjct: 417  RT---VEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSS 473

Query: 456  TLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEE 515
            TL H+ R +    +  K++ PR L  + WG++CP +TPEG+ACGLVKNL+LM+ ++   +
Sbjct: 474  TLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTD 533

Query: 516  EGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGK 575
              P+I+     G+E LE        +P++  V  NG+  G HR P    + +R LRR G 
Sbjct: 534  PMPIITFLSEWGMEPLEDY--VPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGD 591

Query: 576  IGEFVSVFVNEKQRCVYIASDGGRVCRPLVIAD------KGISRIKEHHMKELLDG---- 625
            I   VS+  + +++ + I +D GRV RPL I +          ++++ H+ +L+      
Sbjct: 592  INPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQD 651

Query: 626  ---------VRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTT------------- 663
                       ++   L EGL+EY+D  EE + LIA+   D  P                
Sbjct: 652  IEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKR 711

Query: 664  -----------HIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCR 712
                       H EI P  ILGV A +IP+P HNQSPRNTYQ AMGKQAMG    N   R
Sbjct: 712  IRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVR 771

Query: 713  MDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDR 772
            MD++  +L YPQ+PL TTR +E + + +L AGQNA VA+  YSGY+ ED+++MN+SS+DR
Sbjct: 772  MDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDR 831

Query: 773  GFGRCIVVKKYTAINQKYANS---TSDRILRPDRTGPGAERMQILDDDGLAAPGEIIKPN 829
            G  R +  + Y    +KY  S   T ++  R +           LDDDGL APG  +   
Sbjct: 832  GLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGE 891

Query: 830  DVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIK 889
            DV I K +P+          GQ  + +     +      E  +VD+V + ++++G   +K
Sbjct: 892  DVIIGKTTPI---SPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVK 948

Query: 890  FLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGK 949
              +R T+ P++GDKF+SRHGQKG  G   ++ED PF+  GI PDLI+NPH  PSRMTV  
Sbjct: 949  VRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAH 1008

Query: 950  MIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCP 1009
            +IE L  K     G     S F +      TVE IS+ L +HG+   G +++Y+G TG  
Sbjct: 1009 LIECLLSKVAALSGNEGDASPFTD-----ITVEGISKLLREHGYQSRGFEVMYNGHTGKK 1063

Query: 1010 LQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGG 1056
            L A IF GP YYQ+L+HMV DK+HAR  GP  +LTRQP EGR+R+GG
Sbjct: 1064 LMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGG 1110
>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Length = 1119 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query1058
d1twfb_1207 RBP2 {Baker's yeast (Saccharomyces cerevisiae) [Ta 100.0
d1smyc_1119 RNA-polymerase beta {Thermus thermophilus [TaxId: 100.0
d1smyc_ 1119 RNA-polymerase beta {Thermus thermophilus [TaxId: 93.18
>d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
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
domain: RBP2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=0  Score=2127.01  Aligned_cols=1019  Identities=37%  Similarity=0.628  Sum_probs=904.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHCCCCEECC-----------CCCEEEEEEEEEECCCC
Q ss_conf             8776400122246211144351799999999999847799987047611058-----------99499999489992870
Q 001532           23 APVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGI-----------DPSIFLRFKDVRIGQPS   91 (1058)
Q Consensus        23 ~~~~~~~~~~~~i~~~f~~~~lv~~qi~SFn~Fi~~gl~~ii~~~~~i~~~~-----------~~~~~l~f~~i~i~~P~   91 (1058)
                      +..++++|.|.++++||+.++||+|||||||+|+++||++|+++..||....           ...+.|+|+++++++|+
T Consensus         5 ~~~~~~~d~w~~i~~~f~~~~Lv~~qidSFn~Fi~~gi~~Ii~~~~pi~~~~~~~~~~~~~~~~~~~~l~f~~i~i~kP~   84 (1207)
T d1twfb_           5 SAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPM   84 (1207)
T ss_dssp             TCCCCTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHTHHHHHHHTTCBCC------------------CCEECCCEEEEEE
T ss_pred             CCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCHHHHHHHCCCEEEECCCCCCCCCCCCCCEEEEEEEEEEECCCE
T ss_conf             79888788898799986899860898999999998787999985097576315555554467885699999899983883


Q ss_pred             CCCCC-CCCCCCHHHHHHCCCCCCCEEEEEEEEEECCCC---------------CCEEEEEEEEEEEEECCCCCCCCCCC
Q ss_conf             13588-667899144763299547409999999999875---------------42024786899965202013565227
Q 001532           92 MTVDG-VSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHT---------------EKTTMEKNDVVIGRIPIMLRSCRCVL  155 (1058)
Q Consensus        92 ~~~~~-~~~~l~P~eaR~r~lTYsa~l~v~i~~~~~~~~---------------~~~~~~~~~v~iG~iPIMv~S~~C~L  155 (1058)
                      +.+.+ ..+++||+|||+|++||+|+|+|++++...+..               .......++|+||+|||||+|++|||
T Consensus        85 ~~e~~g~~~~l~P~EcR~r~lTYs~~l~v~i~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~v~iG~IPIMv~S~~C~L  164 (1207)
T d1twfb_          85 VNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYL  164 (1207)
T ss_dssp             ECCSSSCCEECCHHHHHHTTCCCEEEEECCEECCCCC-------------------------CCEEEEEECCTTSTTSGG
T ss_pred             EECCCCCCCCCCHHHHHHCCCCCCEEEEEEEEEEEEECCCCCCCCCCEEECCCCCCCCEEEEEEEEEECCEEECCCCCCC
T ss_conf             77078862656989998409951317999999999740356654111000234555531562089977887808885448


Q ss_pred             CCCCHHHHHHCCCCCCCCCCEEEECCCEEEEEEEECCCCCEEEEEECCCC---CEEEEEEECCCCCC----EEEEEEE-E
Q ss_conf             99998889762999899994899919134786420035987999957997---57999982589950----0899995-5
Q 001532          156 YGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKG---NINASVTSSTETVK----SKTVIQM-E  227 (1058)
Q Consensus       156 ~~~s~~el~~~gE~~~d~GGYFIInG~EKVIi~q~~~~~N~i~~~~~~~g---~~~~~v~s~~~~~~----~~~~~~~-~  227 (1058)
                      ++++++++++.||||+|+||||||||+||||++|++.++|++++++++..   .+.+.++|...+..    +..+.++ +
T Consensus       165 ~~~~~~~l~~~gEc~~D~GGYFIING~EKVIi~Q~r~~~n~~~v~~~~~~~~~~~~~~irS~~~~~~~~~~~~~~~~~~~  244 (1207)
T d1twfb_         165 SEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGR  244 (1207)
T ss_dssp             GTCCHHHHHHTTCCTTCCCCSEEETTEEEEECEEEEECSSCCEEEECCTTSSEEEEEEEECCCSSSCCCCCEEEEEEESC
T ss_pred             CCCCHHHHHHCCCCCCCCCCEEEECCEEEEEEEEEECCCCEEEEEECCCCCCEEEEEEEEEEECCCCCEEEEEEEEEEEC
T ss_conf             99698999872899778981799899999999997469976999974799936999999999279973437999999871


Q ss_pred             CC----EEEEEECCEECCCCHHHHHHHHCCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC
Q ss_conf             88----99999811001323856899828998889998817---944678635661999884287688999999850033
Q 001532          228 KG----KMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVG---RDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVK  300 (1058)
Q Consensus       228 ~g----~i~~~~~~~~~~IPi~illrALg~~sD~eI~~~i~---~~~~~~~~l~~~l~~~~~~~~~t~~~al~yig~~~~  300 (1058)
                      ++    .+.+.++++..+||++++|||||..+|+||++.+.   .+..+.+.+..++++.  ..+.++++|+.|||++++
T Consensus       245 ~~~~~~~i~~~~~~~~~~IPl~illrALG~~sD~eI~~~i~~~~~~~~~~~~l~~~~~~~--~~~~t~e~al~yig~~~~  322 (1207)
T d1twfb_         245 EGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDG--FVIQDRETALDFIGRRGT  322 (1207)
T ss_dssp             SSCSSCCEEEECTTCSSCEEHHHHHHHTTCCSHHHHHHHHCCCTTCHHHHHHHHHHHHHT--TTCCSHHHHHHHHHHTTS
T ss_pred             CCCCCEEEEEEEEHHCCCCHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHCC
T ss_conf             886536999995101045318888987388510434644046730167899988887630--104668899999876312


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEECCHHHHHHHHH
Q ss_conf             46789999981789999987643168787888889730248899999998623987778846434608711278899999
Q 001532          301 RSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLF  380 (1058)
Q Consensus       301 ~~~~~~~~~~~~e~~~~~L~~~llpHl~~~~~~~~~K~~~L~~Mv~kLl~l~~g~~~~Dd~D~l~NKRv~l~G~Ll~~lf  380 (1058)
                      .. ..+..+ ..+.++++|.+.+|||++....++..|+.+|++|++||+.+..|.+.+||+|||+||||+++|+||+.+|
T Consensus       323 ~~-~~~~~~-~~~~~~~iL~~~llpHl~~~~~~~~~K~~~L~~mi~kll~~~~g~~~~dd~D~~~nkrv~~~G~Ll~~~f  400 (1207)
T d1twfb_         323 AL-GIKKEK-RIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLF  400 (1207)
T ss_dssp             CT-TSCHHH-HHHHHHHHHHHTSSTTTCCSSSCHHHHHHHHHHHHHHHHHHHTTSSCCCCTTCGGGEEEECHHHHHHHHH
T ss_pred             CC-CCCCCC-HHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCHHHHHHHHHHHHH
T ss_conf             55-887442-6899999987530123465432025678889999988777651446776345541004542789999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC-CCCCCCCCEEECCCCCCCCCCCC
Q ss_conf             99999999999999876723999888775223433344206454530248775101-13433454287133340000235
Q 001532          381 EDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKR-FKMHRKGMTQVLARLSFIGTLGH  459 (1058)
Q Consensus       381 r~~l~~~~~~i~~~l~k~~~~~~~~~~~~~~~~i~~~~It~~l~~~lsTGnw~~~~-~~~q~sG~sq~l~Rln~ls~LSh  459 (1058)
                      |+.|+++.+.+++.+.+...+.   ..+++...++++.||++|++|||||||+... ...|++|+||+|+|+||+++|||
T Consensus       401 r~~~~~~~~~i~~~~~~~~~~~---~~~~~~~~~~~~~it~~i~~~~~TGn~~~~~~~~~~~~G~sq~l~r~n~l~~lSh  477 (1207)
T d1twfb_         401 KTLFKKLTKDIFRYMQRTVEEA---HDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSH  477 (1207)
T ss_dssp             HHHHHHHHHHHHHHHHSCCC-----------CCCCTHHHHHHHHHHHHHCCCC---------CCCEEECCCSSHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCCCC---CCCCHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHCCHHHHHHH
T ss_conf             9999998888876400111223---3567345332670779999987507644344554434302223330479899886


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHCCCEECCCCCCCCC
Q ss_conf             44236532345433589867999764433477999876322223551155414899705999986419744124685456
Q 001532          460 MTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEEL  539 (1058)
Q Consensus       460 lRrv~~~~~~~~k~t~~R~Lhps~wGfICPveTPEG~~cGLi~~LA~~a~Is~~~~~~~i~~~l~~~G~~~l~~~~~~~~  539 (1058)
                      +||+++++++++|+++||+|||||||||||+|||||+||||+||||++|+|+.+.++.++.++|..+|+..+........
T Consensus       478 ~Rrv~~~~~~~~k~~~~R~Lhps~~G~iCPveTPEG~~~GLv~~La~~a~i~~~~~~~~~~~~l~~~g~~~~~~~~~~~~  557 (1207)
T d1twfb_         478 LRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQS  557 (1207)
T ss_dssp             HTEEECCC------CCTTSCCGGGTTTBCSSCCCSGGGBTTEEEBCTTCEECCCCCCHHHHHHHHHTTCEEGGGCCGGGC
T ss_pred             HHCCCCCCCCCCCCCHHHHCCHHHCCCEEEEECCCCCCCCCEECCCEEEEECCCCCCCEEEEEEECCCCCCCEEEEECCC
T ss_conf             44146776555555315333664454210024789875343213421465303664202567751358632024420105


Q ss_pred             CCCCCEEEEECCEEEEECCCHHHHHHHHHHHHHCCCCCCEEEEEECCCCCEEEEECCCCEEEEEEEEEECCCC------C
Q ss_conf             7998079999794876326924489999987643876731599861456349995399823443999724831------2
Q 001532          540 HNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGIS------R  613 (1058)
Q Consensus       540 ~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~lrr~~~i~~~v~i~~~~~~~~i~I~td~gRl~RPll~v~~~~~------~  613 (1058)
                        .+..+||+||.|+|+++++..|++.+|.+||.|.++.++++.++....+++|++|+||++|||++++|+..      .
T Consensus       558 --~~~~~V~~nG~~~G~~~~~~~l~~~lr~~R~~g~i~~~~s~~~~~~~~~i~i~td~Gr~~rPlfi~~nd~~~~~~~~~  635 (1207)
T d1twfb_         558 --PDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELK  635 (1207)
T ss_dssp             --TTCEEEEETTEEEEEESCHHHHHHHHHHHHHHTSSCTTCEEEEETTTTEEEEECCSCCEEEEEEEEECCCTTSSCEES
T ss_pred             --CCCCEEEEEEEEEEEECCHHEEEHHEEEEEECCCCCCEEEEEEECCCCCEEEEECCCCCCCCCEEECCHHHHCCCCEE
T ss_conf             --653103320127899700101100035645416766234443203455328994476556773444052230454435


Q ss_pred             CHHHHHHHHHC-------------CCCCCHHHHCCCCEEEECCCCCCCEEEEEECCCCC---------------------
Q ss_conf             10656887631-------------77650121015815576044332258995139999---------------------
Q 001532          614 IKEHHMKELLD-------------GVRSFDDFLREGLIEYLDVNEENNALIALYEGDAT---------------------  659 (1058)
Q Consensus       614 ~~~~~~~~~~~-------------~~~~~~~ll~~g~iE~id~~Eq~~~~Ia~~~~~~~---------------------  659 (1058)
                      +.+.++..+..             ...+|.+++..|.+||||++|+.++.||+.++++.                     
T Consensus       636 mqrq~v~~l~~~e~~~v~~~~e~~~~~~~~~~~~~g~ieyid~~E~~~~~Ia~~~~~i~~~~~~~~~~~~~~~~~~~~~~  715 (1207)
T d1twfb_         636 VRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVS  715 (1207)
T ss_dssp             CCHHHHHHHHHHHHCC---------CCCHHHHHHTTSEEEEEHHHHTTCCEESSGGGGCC---------CCCTTSCCCCC
T ss_pred             EEHHHHHHHHCCCCCCCCCCCCCHHHCCCCCCCCCCCEEEECCHHCCEEEEEECCCCCCCCCCCCCCCCCCCCHHHEEEE
T ss_conf             56766765413201125566311121254100457713554000046389996233244223554455445521320110


Q ss_pred             ---CCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCEEEEECCCCCEEECHHHHHH
Q ss_conf             ---97301442376000322366778899999864101112457765315753100135205520799531323023221
Q 001532          660 ---PDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELV  736 (1058)
Q Consensus       660 ---~~~th~Ei~p~~ilsv~AsliPF~~hNqspRn~yq~~M~KQaiG~~~~n~~~r~d~~~y~L~ypQ~PlV~t~~~~~~  736 (1058)
                         ..+||+||+|+++||++|++|||+||||||||+|||||+|||||++++|+..|.|+++|+|+|||+|||+|+.++.+
T Consensus       716 ~~~~~~th~Ei~p~~ilg~~as~iPf~~hNqSpRn~yq~qm~KQa~G~~~~~~~~r~D~~~~~l~~pQ~Plv~t~~~~~~  795 (1207)
T d1twfb_         716 HHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYL  795 (1207)
T ss_dssp             CCCSCCCEECSCGGGGSCTTGGGSSSGGGSCHHHHHHHHHHGGGBCBCSCTTTTTCCCSEEEEESSCBCCSEECTTHHHH
T ss_pred             CCCCCCCCCCCCCCEEEEEECCEEEECCCCCCCCEEECCCCCCCCCCCCCCCCCEECCCCCEEEECCCCCEEECCCHHHH
T ss_conf             24554322223661277531206873123445640110347745677211344233035540674178722500200111


Q ss_pred             CCCCCCCCCCEEEEEEECCCCCCCCCEEEECCEEECCCEEEEEEEEEEEEEECCCCCCCCEECCCCCC---CCCCCCCCC
Q ss_conf             68988898403799961478887771998543110143479999999999620369863123199999---995100114
Q 001532          737 GYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRT---GPGAERMQI  813 (1058)
Q Consensus       737 ~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~p~~~---~~~~~~~~~  813 (1058)
                      +++++|+|+||+||||||+|||||||||+||+|++||+|||+||++|++++++...+..+.+..|...   ..+...|++
T Consensus       796 ~~~e~p~G~N~iVAvmsy~GYN~EDAiIiNk~si~rG~f~s~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  875 (1207)
T d1twfb_         796 KFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDK  875 (1207)
T ss_dssp             TTTTSCCCEEEEEEECBSSSTTTTTEEEEEHHHHHTTTTCEEEEEEEEECCCCSCTTCCCEESCCCCSSSCBCCSSCGGG
T ss_pred             HHHCCCCHHCEEEEEEECCCCCCCCCCCCCHHHHHHCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHC
T ss_conf             22115200052899980457655544323566632031212235789988213666322114565445543332111210


Q ss_pred             CCCCCCCCCCCEECCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEEEEECCCCCEEEEEEEE
Q ss_conf             99983006893768999899973589887887899998786532231772079997139999998518999779999983
Q 001532          814 LDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIR  893 (1058)
Q Consensus       814 ld~~Gl~~~g~~v~~gdili~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~e~~~g~v~~v~~~~~~~~~~~v~v~ir  893 (1058)
                      ||+||+|++|++|++||+|+||++|....+..... ......++|.|++++.++  .|+||+|..+.+.++.+.++|++|
T Consensus       876 Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~-~~~~~~~~~~s~~~~~~~--~g~V~~v~~~~~~~~~~~~kv~i~  952 (1207)
T d1twfb_         876 LDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQ-RTAYHSKRDASTPLRSTE--NGIVDQVLVTTNQDGLKFVKVRVR  952 (1207)
T ss_dssp             CCTTSBCCTTCEECTTCEEECEECCCC--------------CCBBCCEECCTTC--CEEEEEEEEEECSSSCEEEEEEEE
T ss_pred             CCCCCCCCCCCCCCCCCEEEEEEECCCCCHHHHHH-CCCCCCCCCEEEECCCCC--CEEEEEEEEEECCCCCCEEEEEEE
T ss_conf             65212013321146895313454104786012100-111223452568823799--737899997202564201249999


Q ss_pred             ECCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHCCCHHCCCCEEEEECCCC
Q ss_conf             22799644300023798227975414678899899998828708999988653889999841000002794034300147
Q 001532          894 HTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGE  973 (1058)
Q Consensus       894 ~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpF~~  973 (1058)
                      +.|+|+||||||||||||||||++||+||||||+||++|||||||||||||||||||+|+++||+|+++|.+.|+|||+ 
T Consensus       953 ~~R~p~iGDKfasRhGqKGv~s~i~p~eDMPf~~dG~~pDiI~NP~g~PSRMtiGql~E~~~gk~~~~~g~~~d~t~F~- 1031 (1207)
T d1twfb_         953 TTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFT- 1031 (1207)
T ss_dssp             EEECCCTTCEEECTTSCEEEEEEEECTTTSCEETTSCCCSEEECGGGSTTTTCHHHHHHHHHHHHHHHHCSCEECCSSS-
T ss_pred             EEECCCHHHHHHHCCCCCCEEEEEECHHHCCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC-
T ss_conf             8731621556642257751344341366399488999861887898676667199999998778887349855558879-


Q ss_pred             CCCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCCEEEEEEEEEEEEEECCCCCCCCCEEEECCCCCCCCCCCCCCCCCC
Q ss_conf             99999989999999998399999945998288894765569663421220356348610784127843332378674349
Q 001532          974 PSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRAR 1053 (1058)
Q Consensus       974 ~~~~~~~~~~~~~~l~~~g~~~~G~e~l~~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~ 1053 (1058)
                          +..++++++.|.++||+++|+|.||||+||++|+++||+||+|||||+|||+||+|||++|||+.|||||++||||
T Consensus      1032 ----~~~~~~~~~~L~~~g~~~~G~e~ly~G~tG~~~~~~i~~G~~yy~rL~HmV~DK~~~Rs~Gp~~~lT~QP~~Gr~~ 1107 (1207)
T d1twfb_        1032 ----DITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSR 1107 (1207)
T ss_dssp             ----SCCHHHHHHHHHTTTSCTTSEECEECTTTCCBCSSCEEEEEEEEEEBSSCGGGTCEEECCCC--------------
T ss_pred             ----CCCHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCEEEEEHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCC
T ss_conf             ----9658999999998699989998988899998814608986547543133525265764428997625699986546


Q ss_pred             CCCCC
Q ss_conf             89999
Q 001532         1054 NGGFP 1058 (1058)
Q Consensus      1054 ~GG~~ 1058 (1058)
                      +|||-
T Consensus      1108 ~GG~R 1112 (1207)
T d1twfb_        1108 DGGLR 1112 (1207)
T ss_dssp             --CCC
T ss_pred             CCCCC
T ss_conf             78842
>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure