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Conserved domains on  [gi|1833819269|gb|QJD07199|]
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RNA polymerase subunit beta [Apicomplexa sp. corallicolid ex Leiopathes glaberrima]

Protein Classification

DNA-directed RNA polymerase subunit beta( domain architecture ID 1002928)

DNA-directed RNA polymerase subunit beta catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

CATH:  3.90.1110.10
EC:  2.7.7.6
Gene Ontology:  GO:0000428|GO:0003899|GO:0006351
PubMed:  6266829
SCOP:  4003708

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
39-1067 0e+00

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member CHL00207:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1077  Bit Score: 806.24  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269   39 FSIITK-NNFIKFKLLPEYLKFKLSKLNdSTINAVEEKTPKIQVIVPLKIIFKTLNKYILIYCPLIELPYTDLQGNFILN 117
Cdd:CHL00207    33 FSKIFDyTGNLELLLFGKNYKLKYPKYN-LLSAKSYDSNYSIQIYLPLKFINLKTNKIKFINYLIGNLPKMTQRGTFIIN 111

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  118 GMKRGLVSKMVRQNGVYFNL-RRKYGEDIYSAQLILNeRSKYFIELFKEGIFIYNKFNK--KINLINFLHFIGLNNSTIS 194
Cdd:CHL00207   112 GLERVIVSQIIRSPGIYFKKeIKKNSNKIYSATLIPN-RGSWIKFELDKNKEIWIRIDKnrKKPLIIFLKALGLTDQDIY 190

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  195 SISRYgtteIFKNFYYFNSKEDIQELEKIKTLLNMLN---PELNLKY-LKNKLNFSRHLTSlKNSLISRTGNFL------ 264
Cdd:CHL00207   191 SRLTK----SEFLKKLKPILLNSNSYTNEEILLEIYKnlsPIEPATVnDANQNLFSRFFDP-KNYDLGKVGRYKinnkln 265

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  265 ----ESSFAILGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLIS-------AHLEYILPNKLFKilnllFKSK 333
Cdd:CHL00207   266 lnipERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQnqfriglKRLERILRNRMTI-----CDID 340

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  334 FITSSLLIENlkesfNKNKISIKELLTVNPLIQYLEEVNSVSELMHKVRISSIGPGSLTQNQAGVAVREVRPSQLGKICI 413
Cdd:CHL00207   341 SLSKFNLINP-----KPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICP 415

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  414 LDTNEGPSSGLVVALASNARINKEGSIETLIHPNKKLRSYSK----FLNSFEQESFLVSFENLIPRKQSFLNKYSTSItF 489
Cdd:CHL00207   416 IETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVKKFgnpiYLTADSEDLYRIAPNDINLNKNNYFKKNIIPV-R 494

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  490 EKGEIKSKTNISDTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAVPLIYRNKPYILTGFESIIASKTSNLLR 569
Cdd:CHL00207   495 YKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTII 574

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  570 AYQEGVITKVTSYKIVLIDLFNREITYYLQKYKKTNQGTFIHQLPIVWPGERVLSGQLLTENQDISDSEFNIGNNLNVLY 649
Cdd:CHL00207   575 SLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAY 654

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  650 GSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSkYPIDTPEYSTLDLPKRTSYQKRHLDKLGIITEGSKVLDGDIL 729
Cdd:CHL00207   655 MPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELR-QTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDIL 733

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  730 ISKISVSNlTLEDSPFSELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELFAVTNKATSTYGQnYLTLRVFVAKQRMLQ 809
Cdd:CHL00207   734 VGKITPKG-ESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGY-YLKIRVFIAQIRKIQ 811

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  810 IGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLKDKRlLINSLLNNNLNNN 889
Cdd:CHL00207   812 VGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKR-FKILPFDEMYGSE 890

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  890 YTKTYLYTSLQSLKYYTGNKSLLNPYIPGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPI 969
Cdd:CHL00207   891 YSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPL 970

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  970 KGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSDDLISRNNLQEYLLNNTPLEPNYLPEALKLLIRELHGLSLNLEG 1049
Cdd:CHL00207   971 GGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEA 1050

                         1050
                   ....*....|....*...
gi 1833819269 1050 FMVTDLLDGKLLPLNINY 1067
Cdd:CHL00207  1051 YKIENFLEGQRLEIEINL 1068
 
Name Accession Description Interval E-value
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 39-1067 0e+00

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 806.24  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269   39 FSIITK-NNFIKFKLLPEYLKFKLSKLNdSTINAVEEKTPKIQVIVPLKIIFKTLNKYILIYCPLIELPYTDLQGNFILN 117
Cdd:CHL00207    33 FSKIFDyTGNLELLLFGKNYKLKYPKYN-LLSAKSYDSNYSIQIYLPLKFINLKTNKIKFINYLIGNLPKMTQRGTFIIN 111

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  118 GMKRGLVSKMVRQNGVYFNL-RRKYGEDIYSAQLILNeRSKYFIELFKEGIFIYNKFNK--KINLINFLHFIGLNNSTIS 194
Cdd:CHL00207   112 GLERVIVSQIIRSPGIYFKKeIKKNSNKIYSATLIPN-RGSWIKFELDKNKEIWIRIDKnrKKPLIIFLKALGLTDQDIY 190

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  195 SISRYgtteIFKNFYYFNSKEDIQELEKIKTLLNMLN---PELNLKY-LKNKLNFSRHLTSlKNSLISRTGNFL------ 264
Cdd:CHL00207   191 SRLTK----SEFLKKLKPILLNSNSYTNEEILLEIYKnlsPIEPATVnDANQNLFSRFFDP-KNYDLGKVGRYKinnkln 265

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  265 ----ESSFAILGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLIS-------AHLEYILPNKLFKilnllFKSK 333
Cdd:CHL00207   266 lnipERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQnqfriglKRLERILRNRMTI-----CDID 340

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  334 FITSSLLIENlkesfNKNKISIKELLTVNPLIQYLEEVNSVSELMHKVRISSIGPGSLTQNQAGVAVREVRPSQLGKICI 413
Cdd:CHL00207   341 SLSKFNLINP-----KPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICP 415

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  414 LDTNEGPSSGLVVALASNARINKEGSIETLIHPNKKLRSYSK----FLNSFEQESFLVSFENLIPRKQSFLNKYSTSItF 489
Cdd:CHL00207   416 IETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVKKFgnpiYLTADSEDLYRIAPNDINLNKNNYFKKNIIPV-R 494

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  490 EKGEIKSKTNISDTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAVPLIYRNKPYILTGFESIIASKTSNLLR 569
Cdd:CHL00207   495 YKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTII 574

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  570 AYQEGVITKVTSYKIVLIDLFNREITYYLQKYKKTNQGTFIHQLPIVWPGERVLSGQLLTENQDISDSEFNIGNNLNVLY 649
Cdd:CHL00207   575 SLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAY 654

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  650 GSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSkYPIDTPEYSTLDLPKRTSYQKRHLDKLGIITEGSKVLDGDIL 729
Cdd:CHL00207   655 MPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELR-QTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDIL 733

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  730 ISKISVSNlTLEDSPFSELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELFAVTNKATSTYGQnYLTLRVFVAKQRMLQ 809
Cdd:CHL00207   734 VGKITPKG-ESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGY-YLKIRVFIAQIRKIQ 811

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  810 IGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLKDKRlLINSLLNNNLNNN 889
Cdd:CHL00207   812 VGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKR-FKILPFDEMYGSE 890

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  890 YTKTYLYTSLQSLKYYTGNKSLLNPYIPGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPI 969
Cdd:CHL00207   891 YSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPL 970

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  970 KGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSDDLISRNNLQEYLLNNTPLEPNYLPEALKLLIRELHGLSLNLEG 1049
Cdd:CHL00207   971 GGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEA 1050

                         1050
                   ....*....|....*...
gi 1833819269 1050 FMVTDLLDGKLLPLNINY 1067
Cdd:CHL00207  1051 YKIENFLEGQRLEIEINL 1068
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 55-1048 2.83e-178

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273928 [Multi-domain]  Cd Length: 1065  Bit Score: 549.27  E-value: 2.83e-178
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269   55 EYLKFKLSKLNDStinaVEE-----KTPKIQVIVPLKIIFK--TLNKYI---LIYcpLIELPYTDLQGNFILNGMKRGLV 124
Cdd:TIGR02013   66 EYLSYRLGEPKYS----VEEckergLTYSAPLKVKLRLINKeeDGTKEIkeqDVY--MGDIPLMTDRGTFIINGAERVVV 139

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  125 SKMVRQNGVYFN---LRRKYGEDIYSAQLILNERS-KYFIELFKEGIFIYNKFNKKINLINFLHFIGLNNSTISsISRYG 200
Cdd:TIGR02013  140 SQLHRSPGVFFSsekDTTKSGKVLFSARIIPYRGSwLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLI-LNRLG 218

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  201 TTEifknfYYFNS----KEDIQElEKIKTLLNMLNP-----ELNLKYLKNKLNFS--RH-LTSLKNSLISRTGNFLESSF 268
Cdd:TIGR02013  219 SGE-----YIRNTlrkdPTNSEE-EALVEIYRKLRPgepptVEAARSLLENLFFDpkRYdLGRVGRYKLNKKLGLDVPES 292

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  269 AIL--GQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLISAHLEYILpNKLFKI---------LNLLFKSKFITS 337
Cdd:TIGR02013  293 IGVltKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGL-ARMERIvrermstqdTDTLTPQDLINA 371

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  338 SLLIENLKESFNKNKISikelltvnpliQYLEEVNSVSELMHKVRISSIGPGSLTQNQAGVAVREVRPSQLGKICILDTN 417
Cdd:TIGR02013  372 KPISAAIKEFFGSSQLS-----------QFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETP 440

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  418 EGPSSGLVVALASNARINKEGSIETlihPNKKLRS-------YSKFLNSFEQESFLVSF------ENLIPRKQSFLNKYs 484
Cdd:TIGR02013  441 EGPNIGLINSLSTYARVNEYGFIET---PYRKVKDgkvvvtdEIDYLTADEEDNYVIAQanapldENGRFVEDLVVARY- 516

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  485 tsitfeKGEIKSKTNISDTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAVPLIYRNKPYILTGFESIIASKT 564
Cdd:TIGR02013  517 ------RGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDS 590

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  565 SNLLRAYQEGVITKVTSYKIVL------IDLFNREITYYLQKYKKTNQGTFIHQLPIVWPGERVLSGQLLTENQDISDSE 638
Cdd:TIGR02013  591 GAVIVAKRGGVVEYVDAKRIVIrydedeEEPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGE 670

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  639 FNIGNNLNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSkypiDT---PEYSTLDLPKRTSYQKRHLDKLG 715
Cdd:TIGR02013  671 LALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEAR----DTklgPEEITRDIPNVSEEALRNLDENG 746

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  716 IITEGSKVLDGDILISKI---SVSNLTLEDspfsELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELFAVTNKATSTYG 792
Cdd:TIGR02013  747 IVRIGAEVKAGDILVGKVtpkGETELTPEE----KLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPG 822

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  793 QNYLtLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLK 872
Cdd:TIGR02013  823 VNKL-VKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRL 901

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  873 DKRLLINSllnnnlnnnyTKTYLYTSLQSLKYYTgNKSLLNPyiPGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDK 952
Cdd:TIGR02013  902 GRKGVPIA----------TPVFDGASEEEIKEYL-EKAGLPR--DGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDK 968

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  953 VHYRTFGPYTEITQQPIKGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSDDLISRNNLQEYLLNNTPLEPNYLPEA 1032
Cdd:TIGR02013  969 MHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPES 1048

                         1050
                   ....*....|....*.
gi 1833819269 1033 LKLLIRELHGLSLNLE 1048
Cdd:TIGR02013 1049 FNVLIKELQSLGLDIE 1064
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 112-1048 2.02e-153

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 482.30  E-value: 2.02e-153
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  112 GNFILNGMKRGLVSKMVRQNGVYFN-LRRKYGEDIYSAQLILNeRSKYF-IELFKEGIfIYNKFN--KKINLINFLHFIG 187
Cdd:COG0085    110 GTFIINGTERVIVSQLVRSPGVYFVeEEDKSGKDLYSAKVIPS-RGAWLeFETDKDGT-IYVRIDrkRKIPVTVLLRALG 187

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  188 L-NNSTIssISRYGTTEIFKNFYY------FNSKED-IQEL------------EKIKTLL-NML-NPE-----------L 234
Cdd:COG0085    188 LeTDEEI--LEAFGDDPIQEYILAtlekdnTKTQEEaLLEIyrklrpgepptiERAEQLLdNLFfDPKrydlahvgrykI 265

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  235 NLKYLKNKLNFSRHLTslknslisrtgnflessfailGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLISAH- 313
Cdd:COG0085    266 NKKLGLDVPPEDRVLT---------------------AEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQf 324

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  314 ------LEYILPNKLFKIlnllfKSKFITSSLLIenlkesfNKNKI--SIKELLTVNPLIQYLEEVNSVSELMHKVRISS 385
Cdd:COG0085    325 rvglsrMERVVRERMTTQ-----DVEAITPQSLI-------NIRPVvaAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSA 392

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  386 IGPGSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARINKEGSIETlihP-----NKKLRSYSKFLNSF 460
Cdd:COG0085    393 LGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIET---PyrkveNGKVTDEIEYLTAD 469

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  461 EQESFLVSFENL-IPRKQSFLNKYSTSITFEKGEIKSKTNIsdTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGARMQT 539
Cdd:COG0085    470 EEENYYIAQANApLDEDGNFLEERVLVRYRGEEVLVPPEEV--DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQR 547

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  540 QAVPLIYRNKPYIltgfesiiasktsnllrayqegvitkvtsykivlidlfnreiTYYLQKYKKTNQGTFIHQLPIVWPG 619
Cdd:COG0085    548 QAVPLLRPEAPLL------------------------------------------HYPLQKFQRSNQGTCINQRPIVRVG 585

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  620 ERVLSGQLLTENQDISDSEFNIGNNLNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSKYPIDtPEYSTLD 699
Cdd:COG0085    586 DRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLG-PEEITRD 664

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  700 LPKRTSYQKRHLDKLGIITEGSKVLDGDILISKIS---VSNLTLEDspfsELIFSLFGTKLRQLQDKSISVPIGNSGRVI 776
Cdd:COG0085    665 IPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTpkgETELTPEE----RLLRAIFGEKAREVRDTSLRVPHGEKGKVI 740

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  777 KTELFAVTNKATSTYGQNYLtLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYnvMSQ--YPDIITGPLGVPSR 854
Cdd:COG0085    741 DVKVFSREEGDELPPGVNKL-VRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPF--LEDgtPVDIVLNPLGVPSR 817

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  855 MNLGQLFESLFGYNCVLKDKRLLinsllnnnlnnnyTKTYLYTSLQSLKYYTGnKSLLNPyiPGKLLLRDGRTGYRLKGG 934
Cdd:COG0085    818 MNVGQVLETHLGWAAALLGRRVA-------------TPVFDGAPEEEIRELLE-KAGLPP--DGKEVLYDGRTGEPFDNP 881

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  935 AFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPikgrgkgggqrfgEMEVWALEAFGASYTLRELLTSKSDDLISRNNL 1014
Cdd:COG0085    882 VTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPlggkaqfggqrfgEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKV 961

                          970       980       990
                   ....*....|....*....|....*....|....*
gi 1833819269 1015 QEYLLNNTPL-EPNyLPEALKLLIRELHGLSLNLE 1048
Cdd:COG0085    962 YEAIVKGENIpEPG-IPESFKVLLKELQSLGLDVE 995
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 21-1048 7.68e-130

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 415.81  E-value: 7.68e-130
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269   21 YDTLLKVSILQAIKSLVPFSIITKNNFIKFKllpeYLKFKLSKLNDSTINAVEEKTP----------------KIQVIVP 84
Cdd:cd00653      9 FNYFLNVGLQEIVKSIPPITDTDDDGRLKLK----FGDIYLGKPKVEEGGVTRKLTPnecrlrdltysaplyvDIRLTVN 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269   85 LKIIFKTLNKYI--------LIYCPLIELPYTDL----------QGNFILNGMKRGLVSKMVRQNGVYFNLRRKyGEDIY 146
Cdd:cd00653     85 DKGKIKEQEVFIgeipimlrSKLCNLNGLTPEELiklgecpldpGGYFIINGTEKVIINQEQRSPNVIIVEDSK-GKRIY 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  147 SAQLILNERSKYfielfkeGIFIYNKFNKKINLINFLHfiglnnstissisrygtteifknfYYFNSKEDIQELEKiktl 226
Cdd:cd00653    164 TKTSIPSYSPYR-------GSWLEVKSDKKKDRIYVRI------------------------DLKRQEEALKYIGK---- 208

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  227 lnmlnpelnlkylknklnfsrhltslknslisrtgnflessfaiLGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESL 306
Cdd:cd00653    209 --------------------------------------------RFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLA 244

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  307 GHLIS-------AHLEYILPNKLFKIL---NLLFKSKFITSSLLIENLKESFNK-NKISIKELLTVNPLIQYLEEVNSVS 375
Cdd:cd00653    245 GELLQnlfrsglKRLEREVKEKLQKQLskkKDLTPQLLINSKPITSGIKEFLATgNWGSKRFLMQRSGLSQVLDRLNPLS 324

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  376 ELMHKVRISSigpGSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARINkeGSIEtlihpnkklRSYSK 455
Cdd:cd00653    325 ELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIE---------RPYRI 390

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  456 flnsfeqesflvsfenliprkqsflnkystsitfekgeIKSKTnisdTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGA 535
Cdd:cd00653    391 --------------------------------------VEKEV----THIEISPSQILSVAASLIPFPEHNQSPRNLYQS 428

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  536 RMQTQAVPLIYRNKPYIltgfesiIASKTSNLLRAYQEGVITKvtsykivLIDLFNREityylqkykktnqgtfihQLPi 615
Cdd:cd00653    429 NMQKQAVGTPALNQQYR-------MDTKLYLLLYPQKPLVGTG-------IEEYIAFG------------------ELP- 475

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  616 vwpgervlSGQlltenqdisdsefNI--------GNNLNvlygsyygyeyeDSLIISQKVLYKNIFTSIHFDIYEIKYSK 687
Cdd:cd00653    476 --------LGQ-------------NAivavmsysGYNFE------------DAIIINKSSVDRGFFRSIHYKKYEIELRK 522

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  688 YPIDTPEYSTLDLPKRTSYQKRHLDKLGIITEGSKVLDGDILISKISVSNLTLEDSPFselifslfGTKLRQLQDKSISV 767
Cdd:cd00653    523 TKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIF--------GEKARDVRDTSLKY 594

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  768 PIGNSGRVIKTELFAVTNKAtstygQNYLTLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITG 847
Cdd:cd00653    595 PGGEKGIVDDVKIFSRELND-----GGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILN 669

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  848 PLGVPSRMNLGQLFESLFGYNCVLKDKRllinsllnnNLNNNYTKTYLYTSLQSLKyytgnKSLLNPYipGKLLLRDGRT 927
Cdd:cd00653    670 PHGFPSRMTIGQLLESLLGKAGALLGKF---------GDATPFDGAEEEDISELLG-----EAGLNYY--GKEVLYDGRT 733

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  928 GYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPIkgrgkgggqrfgEMEVWALEAFGASYTLRELLTSKSDD 1007
Cdd:cd00653    734 GEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLkgrsrgggqrfgEMERDALIAHGAAYLLQERLTIKSDD 813

                         1050      1060      1070      1080      1090
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1833819269 1008 LISRNNLQEYLL----------NNTPLEPNYLPEALKLLIRELHGLSLNLE 1048
Cdd:cd00653    814 VVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPR 864
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 570-969 2.21e-82

RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 272.48  E-value: 2.21e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  570 AYQEGVITKVTSYKIVLIDLFNREI--TYYLQKYKKTNQGTF---IHQLPIVWPGeRVLSGQLltenqdisdSEFNIGNN 644
Cdd:pfam00562    2 ASLIPFVDHNQSPRNTYQCAMGKQAmgIYTLNKFYRSDQNTYvlcYPQKPLVKTG-AVEAGGF---------GELPLGQN 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  645 LNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKysKYPIDTPEYSTLDLPKRTSYQKRHLDKLGIITEGSKVL 724
Cdd:pfam00562   72 AIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIEAR--KTKLGPIEEITRDIPNVSEEALKKLDEDGIVRVGAEVK 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  725 DGDILISKISvsnltleDSPFSELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELFAVTNKatstygqNYLTLRVFVAK 804
Cdd:pfam00562  150 PGDILVGKVG-------PTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFELPPG-------GIKMVKVYIRQ 215

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  805 QRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLKDKRLLINSLLNN 884
Cdd:pfam00562  216 KRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGA 295

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  885 NLNNNYTKTYLYtslqslkyytgnKSLLNPYipGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEI 964
Cdd:pfam00562  296 STEVEDIGELLE------------KAGYNYY--GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLL 361


                   ....*
gi 1833819269  965 TQQPI 969
Cdd:pfam00562  362 TRQPL 366
 
Name Accession Description Interval E-value
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 39-1067 0e+00

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 806.24  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269   39 FSIITK-NNFIKFKLLPEYLKFKLSKLNdSTINAVEEKTPKIQVIVPLKIIFKTLNKYILIYCPLIELPYTDLQGNFILN 117
Cdd:CHL00207    33 FSKIFDyTGNLELLLFGKNYKLKYPKYN-LLSAKSYDSNYSIQIYLPLKFINLKTNKIKFINYLIGNLPKMTQRGTFIIN 111

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  118 GMKRGLVSKMVRQNGVYFNL-RRKYGEDIYSAQLILNeRSKYFIELFKEGIFIYNKFNK--KINLINFLHFIGLNNSTIS 194
Cdd:CHL00207   112 GLERVIVSQIIRSPGIYFKKeIKKNSNKIYSATLIPN-RGSWIKFELDKNKEIWIRIDKnrKKPLIIFLKALGLTDQDIY 190

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  195 SISRYgtteIFKNFYYFNSKEDIQELEKIKTLLNMLN---PELNLKY-LKNKLNFSRHLTSlKNSLISRTGNFL------ 264
Cdd:CHL00207   191 SRLTK----SEFLKKLKPILLNSNSYTNEEILLEIYKnlsPIEPATVnDANQNLFSRFFDP-KNYDLGKVGRYKinnkln 265

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  265 ----ESSFAILGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLIS-------AHLEYILPNKLFKilnllFKSK 333
Cdd:CHL00207   266 lnipERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQnqfriglKRLERILRNRMTI-----CDID 340

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  334 FITSSLLIENlkesfNKNKISIKELLTVNPLIQYLEEVNSVSELMHKVRISSIGPGSLTQNQAGVAVREVRPSQLGKICI 413
Cdd:CHL00207   341 SLSKFNLINP-----KPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICP 415

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  414 LDTNEGPSSGLVVALASNARINKEGSIETLIHPNKKLRSYSK----FLNSFEQESFLVSFENLIPRKQSFLNKYSTSItF 489
Cdd:CHL00207   416 IETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVKKFgnpiYLTADSEDLYRIAPNDINLNKNNYFKKNIIPV-R 494

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  490 EKGEIKSKTNISDTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAVPLIYRNKPYILTGFESIIASKTSNLLR 569
Cdd:CHL00207   495 YKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTII 574

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  570 AYQEGVITKVTSYKIVLIDLFNREITYYLQKYKKTNQGTFIHQLPIVWPGERVLSGQLLTENQDISDSEFNIGNNLNVLY 649
Cdd:CHL00207   575 SLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAY 654

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  650 GSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSkYPIDTPEYSTLDLPKRTSYQKRHLDKLGIITEGSKVLDGDIL 729
Cdd:CHL00207   655 MPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELR-QTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDIL 733

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  730 ISKISVSNlTLEDSPFSELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELFAVTNKATSTYGQnYLTLRVFVAKQRMLQ 809
Cdd:CHL00207   734 VGKITPKG-ESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGY-YLKIRVFIAQIRKIQ 811

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  810 IGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLKDKRlLINSLLNNNLNNN 889
Cdd:CHL00207   812 VGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKR-FKILPFDEMYGSE 890

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  890 YTKTYLYTSLQSLKYYTGNKSLLNPYIPGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPI 969
Cdd:CHL00207   891 YSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPL 970

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  970 KGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSDDLISRNNLQEYLLNNTPLEPNYLPEALKLLIRELHGLSLNLEG 1049
Cdd:CHL00207   971 GGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEA 1050

                         1050
                   ....*....|....*...
gi 1833819269 1050 FMVTDLLDGKLLPLNINY 1067
Cdd:CHL00207  1051 YKIENFLEGQRLEIEINL 1068
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 55-1048 2.83e-178

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273928 [Multi-domain]  Cd Length: 1065  Bit Score: 549.27  E-value: 2.83e-178
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269   55 EYLKFKLSKLNDStinaVEE-----KTPKIQVIVPLKIIFK--TLNKYI---LIYcpLIELPYTDLQGNFILNGMKRGLV 124
Cdd:TIGR02013   66 EYLSYRLGEPKYS----VEEckergLTYSAPLKVKLRLINKeeDGTKEIkeqDVY--MGDIPLMTDRGTFIINGAERVVV 139

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  125 SKMVRQNGVYFN---LRRKYGEDIYSAQLILNERS-KYFIELFKEGIFIYNKFNKKINLINFLHFIGLNNSTISsISRYG 200
Cdd:TIGR02013  140 SQLHRSPGVFFSsekDTTKSGKVLFSARIIPYRGSwLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLI-LNRLG 218

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  201 TTEifknfYYFNS----KEDIQElEKIKTLLNMLNP-----ELNLKYLKNKLNFS--RH-LTSLKNSLISRTGNFLESSF 268
Cdd:TIGR02013  219 SGE-----YIRNTlrkdPTNSEE-EALVEIYRKLRPgepptVEAARSLLENLFFDpkRYdLGRVGRYKLNKKLGLDVPES 292

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  269 AIL--GQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLISAHLEYILpNKLFKI---------LNLLFKSKFITS 337
Cdd:TIGR02013  293 IGVltKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGL-ARMERIvrermstqdTDTLTPQDLINA 371

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  338 SLLIENLKESFNKNKISikelltvnpliQYLEEVNSVSELMHKVRISSIGPGSLTQNQAGVAVREVRPSQLGKICILDTN 417
Cdd:TIGR02013  372 KPISAAIKEFFGSSQLS-----------QFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETP 440

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  418 EGPSSGLVVALASNARINKEGSIETlihPNKKLRS-------YSKFLNSFEQESFLVSF------ENLIPRKQSFLNKYs 484
Cdd:TIGR02013  441 EGPNIGLINSLSTYARVNEYGFIET---PYRKVKDgkvvvtdEIDYLTADEEDNYVIAQanapldENGRFVEDLVVARY- 516

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  485 tsitfeKGEIKSKTNISDTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAVPLIYRNKPYILTGFESIIASKT 564
Cdd:TIGR02013  517 ------RGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDS 590

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  565 SNLLRAYQEGVITKVTSYKIVL------IDLFNREITYYLQKYKKTNQGTFIHQLPIVWPGERVLSGQLLTENQDISDSE 638
Cdd:TIGR02013  591 GAVIVAKRGGVVEYVDAKRIVIrydedeEEPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGE 670

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  639 FNIGNNLNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSkypiDT---PEYSTLDLPKRTSYQKRHLDKLG 715
Cdd:TIGR02013  671 LALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEAR----DTklgPEEITRDIPNVSEEALRNLDENG 746

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  716 IITEGSKVLDGDILISKI---SVSNLTLEDspfsELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELFAVTNKATSTYG 792
Cdd:TIGR02013  747 IVRIGAEVKAGDILVGKVtpkGETELTPEE----KLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPG 822

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  793 QNYLtLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLK 872
Cdd:TIGR02013  823 VNKL-VKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRL 901

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  873 DKRLLINSllnnnlnnnyTKTYLYTSLQSLKYYTgNKSLLNPyiPGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDK 952
Cdd:TIGR02013  902 GRKGVPIA----------TPVFDGASEEEIKEYL-EKAGLPR--DGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDK 968

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  953 VHYRTFGPYTEITQQPIKGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSDDLISRNNLQEYLLNNTPLEPNYLPEA 1032
Cdd:TIGR02013  969 MHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPES 1048

                         1050
                   ....*....|....*.
gi 1833819269 1033 LKLLIRELHGLSLNLE 1048
Cdd:TIGR02013 1049 FNVLIKELQSLGLDIE 1064
rpoB CHL00001
RNA polymerase beta subunit
 33-1052 3.05e-169

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 525.62  E-value: 3.05e-169
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269   33 IKSLVPFSIITK-NNFIKFKLLPEYLKFKLSKLNDStiNAVEEK-TPKIQVIVPLKIIFKTLN---KYILIYCpliELPY 107
Cdd:CHL00001    32 TEELSKFPKIEDtDQEIEFQLFVETYQLVEPLIKER--DAVYESlTYSSELYVPAGLIWKKSRdmqEQTVFIG---NIPL 106

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  108 TDLQGNFILNGMKRGLVSKMVRQNGVYFNLRRKY-GEDIYSAQLILN--ERSKYFIELfKEGIFIYNKFNKKINLINFLH 184
Cdd:CHL00001   107 MNSLGTFIINGIYRVVINQILRSPGIYYRSELDHnGISVYTGTIISDwgGRLELEIDR-KARIWARVSRKQKISILVLLS 185

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  185 FIGLNNSTISSISRYgtTEIFKNFYYFNSKEDIQELEKIktllnMLNPELNLKYLKNKLNFSRHLTS-LKNSL------I 257
Cdd:CHL00001   186 AMGLNLREILDNVCY--PEIFLSFLNDKEKKKIGSKENA-----ILEFYQQFACVGGDPVFSESLCKeLQKKFfqqrceL 258

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  258 SRTG----------NFLESSFAILGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLISAHLEYILpNKL----F 323
Cdd:CHL00001   259 GRIGrrnmnrklnlDIPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLAL-NRLenavR 337

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  324 KILNLLFKSKFI-------TSSLLIENLKESFNknkisikelltVNPLIQYLEEVNSVSELMHKVRISSIGPGSLTQNQA 396
Cdd:CHL00001   338 GTICGAIRRKLIptpqnlvTSTPLTTTYESFFG-----------SHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTA 406

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  397 GVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARINKEGSIETlihPNKKLRSYSK-----FLNSFEQESFLVSFEN 471
Cdd:CHL00001   407 SFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLES---PFYEISERSKeermvYLSPSEDEYYMIAAGN 483

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  472 L------IPRKQSFLNKYS---TSITFEKGEIKSktnisdtyykINPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAV 542
Cdd:CHL00001   484 SlalnqgIQEEQVVPARYRqefLTIAWEQIHLRS----------IFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAV 553

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  543 PLIYRNKPYILTGFESIIASKTSNLLRAYQEGVITKVTSYKIVLIDLFNrEITYYLQKYKKTNQGTFIHQLPIVWPGERV 622
Cdd:CHL00001   554 PLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNGD-TLSIPLVMYQRSNKNTCMHQKPQVRRGKCV 632

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  623 LSGQLLTENQDISDSEFNIGNNLNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKySKYPIDTPEYSTLDLPK 702
Cdd:CHL00001   633 KKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQ-THVTSQGPERITKEIPH 711

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  703 RTSYQKRHLDKLGIITEGSKVLDGDILISKIsvSNLTLEDS---PFSELIFSLFGTKLRQLQDKSISVPIGNSGRVIktE 779
Cdd:CHL00001   712 LEAHLLRNLDKNGIVMLGSWVETGDILVGKL--TPQEAEESsyaPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVI--D 787

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  780 LFAVTNKATSTYgqNYLTLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYnVMSQYP-DIITGPLGVPSRMNLG 858
Cdd:CHL00001   788 VRWIQKKGGSSY--NPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPY-LQDGTPvDMVLNPLGVPSRMNVG 864

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  859 QLFESLFG---------YNCVLKDKRllinsllnnnlnnnYTK--------TYLY-TSLQslkyyTGNKSLLNPYIPGKL 920
Cdd:CHL00001   865 QIFECLLGlagdllnrhYRIAPFDER--------------YEQeasrklvfSELYeASKQ-----TANPWVFEPEYPGKS 925

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  921 LLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPIKGRGKGGGQRFGEMEVWALEAFGASYTLREL 1000
Cdd:CHL00001   926 RLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEM 1005

                         1050      1060      1070      1080      1090
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1833819269 1001 LTSKSDDLISRNNLQEYLLNNTPL-EPNYLPEALKLLIRELHGLSLNLEGFMV 1052
Cdd:CHL00001  1006 LTYKSDHIRARQEVLGAIITGGTIpKPEDAPESFRLLVRELRSLALELNHFLV 1058
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 83-1048 1.08e-155

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 491.15  E-value: 1.08e-155
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269   83 VPLKIIFKTLNKYI------LIYcpLIELPY-TDlQGNFILNGMKRGLVSKMVRQNGVYFNL---RRKYGEDIYSAQLIL 152
Cdd:PRK00405    95 APLRVKLRLINKETgeikeqEVY--MGDIPLmTE-NGTFIINGTERVIVSQLHRSPGVYFDHdkdKTSSGKLLYSARIIP 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  153 NERSkyFIELF---KEGIFIYNKFNKKINLINFLHFIGLNNSTIssISRYGTTEIFKNF-----------YYFNSKEDIQ 218
Cdd:PRK00405   172 YRGS--WLEFEfdpKDILYVRIDRRRKLPVTVLLRALGYSDEEI--LDLFYEKEEFGKEievpveyllgkVLAEDIVDEE 247

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  219 ELEKIKTLLNMLNPELNLKYLKNKLNfSRHLTSLKNSLIS-----RTG---------NFLESSF---------------- 268
Cdd:PRK00405   248 TGEVLAEANDEITEELDGPYIRNTLE-KDPTSSREEALVEiyrrlRPGepptveaarSLLENLFfdpkrydlskvgrykl 326

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  269 -------------AILGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLI--------------------SAHLE 315
Cdd:PRK00405   327 nkklgldededvrVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLqnqfriglsrmeravrermsLQDLD 406

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  316 YILPNKLfkiLNllfkSKFITSSllienlkesfnknkisIKELLTVNPLIQYLEEVNSVSELMHKVRISSIGPGSLTQNQ 395
Cdd:PRK00405   407 TLTPQDL---IN----AKPVVAA----------------IKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRER 463

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  396 AGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARINKEGSIETlihP-----NKKLRSYSKFLNSFEQESFLV--- 467
Cdd:PRK00405   464 AGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIET---PyrkvvDGKVTDEIVYLTADEEDNYVIaqa 540

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  468 --------SF-ENLIP--RKQSFlnkystsITFEKGEIksktnisdTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGAR 536
Cdd:PRK00405   541 napldedgRFvDELVTarYKGEF-------VLVPPEEV--------DYMDVSPKQVVSVAASLIPFLEHDDANRALMGSN 605

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  537 MQTQAVPLIYRNKPYILTGFESIIASKTSNLLRAYQEGVITKVTSYKIV-----LIDLFNREITYYLQKYKKTNQGTFIH 611
Cdd:PRK00405   606 MQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVvrveeLDPGEDGVDIYNLIKFQRSNQNTCIN 685

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  612 QLPIVWPGERVLSGQLLTENQDISDSEFNIGNNL----------NvlygsyygyeYEDSLIISQKVLYKNIFTSIHFDIY 681
Cdd:PRK00405   686 QRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVlvafmpwngyN----------FEDAILISERLVKEDVFTSIHIEEY 755

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  682 EIKYSkypiDT---PEYSTLDLPKRTSYQKRHLDKLGIITEGSKVLDGDILISKIS---VSNLTLEDspfsELIFSLFGT 755
Cdd:PRK00405   756 EIEAR----DTklgPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTpkgETELTPEE----KLLRAIFGE 827

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  756 KLRQLQDKSISVPIGNSGRVIKTELFA-VTNKATSTYGQNYLtLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELP 834
Cdd:PRK00405   828 KARDVKDTSLRVPHGEEGTVIDVKVFTrIEQGDELPPGVNKL-VKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMP 906

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  835 Y-----NVmsqypDIITGPLGVPSRMNLGQLFESLFGYNCVLKDKRllinsllnnnlnnnyTKTYLY--TSLQSLKYYTg 907
Cdd:PRK00405   907 YledgtPV-----DIVLNPLGVPSRMNIGQILETHLGWAAKGLGIK---------------FATPVFdgAKEEEIKELL- 965

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  908 NKSLLNPYipGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPikgrgkgggqrfgEMEVWA 987
Cdd:PRK00405   966 EEAGLPED--GKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPlggkaqfggqrfgEMEVWA 1043

                         1050      1060      1070      1080      1090      1100
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1833819269  988 LEAFGASYTLRELLTSKSDDLISRNNLQEYLL--NNTPlEPNyLPEALKLLIRELHGLSLNLE 1048
Cdd:PRK00405  1044 LEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVkgENIP-EPG-IPESFNVLVKELQSLGLDVE 1104
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 112-1048 2.02e-153

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 482.30  E-value: 2.02e-153
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  112 GNFILNGMKRGLVSKMVRQNGVYFN-LRRKYGEDIYSAQLILNeRSKYF-IELFKEGIfIYNKFN--KKINLINFLHFIG 187
Cdd:COG0085    110 GTFIINGTERVIVSQLVRSPGVYFVeEEDKSGKDLYSAKVIPS-RGAWLeFETDKDGT-IYVRIDrkRKIPVTVLLRALG 187

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  188 L-NNSTIssISRYGTTEIFKNFYY------FNSKED-IQEL------------EKIKTLL-NML-NPE-----------L 234
Cdd:COG0085    188 LeTDEEI--LEAFGDDPIQEYILAtlekdnTKTQEEaLLEIyrklrpgepptiERAEQLLdNLFfDPKrydlahvgrykI 265

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  235 NLKYLKNKLNFSRHLTslknslisrtgnflessfailGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLISAH- 313
Cdd:COG0085    266 NKKLGLDVPPEDRVLT---------------------AEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQf 324

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  314 ------LEYILPNKLFKIlnllfKSKFITSSLLIenlkesfNKNKI--SIKELLTVNPLIQYLEEVNSVSELMHKVRISS 385
Cdd:COG0085    325 rvglsrMERVVRERMTTQ-----DVEAITPQSLI-------NIRPVvaAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSA 392

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  386 IGPGSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARINKEGSIETlihP-----NKKLRSYSKFLNSF 460
Cdd:COG0085    393 LGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIET---PyrkveNGKVTDEIEYLTAD 469

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  461 EQESFLVSFENL-IPRKQSFLNKYSTSITFEKGEIKSKTNIsdTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGARMQT 539
Cdd:COG0085    470 EEENYYIAQANApLDEDGNFLEERVLVRYRGEEVLVPPEEV--DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQR 547

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  540 QAVPLIYRNKPYIltgfesiiasktsnllrayqegvitkvtsykivlidlfnreiTYYLQKYKKTNQGTFIHQLPIVWPG 619
Cdd:COG0085    548 QAVPLLRPEAPLL------------------------------------------HYPLQKFQRSNQGTCINQRPIVRVG 585

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  620 ERVLSGQLLTENQDISDSEFNIGNNLNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSKYPIDtPEYSTLD 699
Cdd:COG0085    586 DRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLG-PEEITRD 664

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  700 LPKRTSYQKRHLDKLGIITEGSKVLDGDILISKIS---VSNLTLEDspfsELIFSLFGTKLRQLQDKSISVPIGNSGRVI 776
Cdd:COG0085    665 IPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTpkgETELTPEE----RLLRAIFGEKAREVRDTSLRVPHGEKGKVI 740

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  777 KTELFAVTNKATSTYGQNYLtLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYnvMSQ--YPDIITGPLGVPSR 854
Cdd:COG0085    741 DVKVFSREEGDELPPGVNKL-VRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPF--LEDgtPVDIVLNPLGVPSR 817

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  855 MNLGQLFESLFGYNCVLKDKRLLinsllnnnlnnnyTKTYLYTSLQSLKYYTGnKSLLNPyiPGKLLLRDGRTGYRLKGG 934
Cdd:COG0085    818 MNVGQVLETHLGWAAALLGRRVA-------------TPVFDGAPEEEIRELLE-KAGLPP--DGKEVLYDGRTGEPFDNP 881

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  935 AFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPikgrgkgggqrfgEMEVWALEAFGASYTLRELLTSKSDDLISRNNL 1014
Cdd:COG0085    882 VTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPlggkaqfggqrfgEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKV 961

                          970       980       990
                   ....*....|....*....|....*....|....*
gi 1833819269 1015 QEYLLNNTPL-EPNyLPEALKLLIRELHGLSLNLE 1048
Cdd:COG0085    962 YEAIVKGENIpEPG-IPESFKVLLKELQSLGLDVE 995
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 21-1048 7.68e-130

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 415.81  E-value: 7.68e-130
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269   21 YDTLLKVSILQAIKSLVPFSIITKNNFIKFKllpeYLKFKLSKLNDSTINAVEEKTP----------------KIQVIVP 84
Cdd:cd00653      9 FNYFLNVGLQEIVKSIPPITDTDDDGRLKLK----FGDIYLGKPKVEEGGVTRKLTPnecrlrdltysaplyvDIRLTVN 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269   85 LKIIFKTLNKYI--------LIYCPLIELPYTDL----------QGNFILNGMKRGLVSKMVRQNGVYFNLRRKyGEDIY 146
Cdd:cd00653     85 DKGKIKEQEVFIgeipimlrSKLCNLNGLTPEELiklgecpldpGGYFIINGTEKVIINQEQRSPNVIIVEDSK-GKRIY 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  147 SAQLILNERSKYfielfkeGIFIYNKFNKKINLINFLHfiglnnstissisrygtteifknfYYFNSKEDIQELEKiktl 226
Cdd:cd00653    164 TKTSIPSYSPYR-------GSWLEVKSDKKKDRIYVRI------------------------DLKRQEEALKYIGK---- 208

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  227 lnmlnpelnlkylknklnfsrhltslknslisrtgnflessfaiLGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESL 306
Cdd:cd00653    209 --------------------------------------------RFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLA 244

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  307 GHLIS-------AHLEYILPNKLFKIL---NLLFKSKFITSSLLIENLKESFNK-NKISIKELLTVNPLIQYLEEVNSVS 375
Cdd:cd00653    245 GELLQnlfrsglKRLEREVKEKLQKQLskkKDLTPQLLINSKPITSGIKEFLATgNWGSKRFLMQRSGLSQVLDRLNPLS 324

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  376 ELMHKVRISSigpGSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARINkeGSIEtlihpnkklRSYSK 455
Cdd:cd00653    325 ELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIE---------RPYRI 390

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  456 flnsfeqesflvsfenliprkqsflnkystsitfekgeIKSKTnisdTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGA 535
Cdd:cd00653    391 --------------------------------------VEKEV----THIEISPSQILSVAASLIPFPEHNQSPRNLYQS 428

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  536 RMQTQAVPLIYRNKPYIltgfesiIASKTSNLLRAYQEGVITKvtsykivLIDLFNREityylqkykktnqgtfihQLPi 615
Cdd:cd00653    429 NMQKQAVGTPALNQQYR-------MDTKLYLLLYPQKPLVGTG-------IEEYIAFG------------------ELP- 475

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  616 vwpgervlSGQlltenqdisdsefNI--------GNNLNvlygsyygyeyeDSLIISQKVLYKNIFTSIHFDIYEIKYSK 687
Cdd:cd00653    476 --------LGQ-------------NAivavmsysGYNFE------------DAIIINKSSVDRGFFRSIHYKKYEIELRK 522

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  688 YPIDTPEYSTLDLPKRTSYQKRHLDKLGIITEGSKVLDGDILISKISVSNLTLEDSPFselifslfGTKLRQLQDKSISV 767
Cdd:cd00653    523 TKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIF--------GEKARDVRDTSLKY 594

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  768 PIGNSGRVIKTELFAVTNKAtstygQNYLTLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITG 847
Cdd:cd00653    595 PGGEKGIVDDVKIFSRELND-----GGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILN 669

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  848 PLGVPSRMNLGQLFESLFGYNCVLKDKRllinsllnnNLNNNYTKTYLYTSLQSLKyytgnKSLLNPYipGKLLLRDGRT 927
Cdd:cd00653    670 PHGFPSRMTIGQLLESLLGKAGALLGKF---------GDATPFDGAEEEDISELLG-----EAGLNYY--GKEVLYDGRT 733

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  928 GYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPIkgrgkgggqrfgEMEVWALEAFGASYTLRELLTSKSDD 1007
Cdd:cd00653    734 GEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLkgrsrgggqrfgEMERDALIAHGAAYLLQERLTIKSDD 813

                         1050      1060      1070      1080      1090
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1833819269 1008 LISRNNLQEYLL----------NNTPLEPNYLPEALKLLIRELHGLSLNLE 1048
Cdd:cd00653    814 VVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPR 864
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
273-1065 2.56e-101

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 352.30  E-value: 2.56e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  273 QDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLISAHLEYILPnKLFKILnllfKSKFITSSLLIENL--KESFNK 350
Cdd:PRK09603   435 EDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLV-KMQKTI----KDKLTTMSGAFDSLmpHDLVNS 509

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  351 NKIS--IKELLTVNPLIQYLEEVNSVSELMHKVRISSIGPGSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVAL 428
Cdd:PRK09603   510 KMITstIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTL 589

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  429 ASNARINKEGSIETlihPNKKL-----RSYSKFLNSFEQESFLVS------------FENLIPrkqsflnkystsiTFEK 491
Cdd:PRK09603   590 STFTRVNDLGFIEA---PYKKVvdgkvVGETIYLTAIQEDSHIIApastpideegniLGDLIE-------------TRVE 653

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  492 GEI----KSKTNISDtyykINPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAVPLIYRNKPYILTGFESIIASKTSNL 567
Cdd:PRK09603   654 GEIvlneKSKVTLMD----LSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGA 729

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  568 LRAYQEGVITKVTSYKIVLIDLFNREI---TYYLQKYKKTNQGTFIHQLPIVWPGERVLSGQLLTENQDISDSEFNIGNN 644
Cdd:PRK09603   730 IKANRAGVVEKIDSKNIYILGEGKEEAyidAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKN 809

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  645 LNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSKYPIDTPEYsTLDLPKRTSYQKRHLDKLGIITEGSKVL 724
Cdd:PRK09603   810 VRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEF-TADIPDVKEEALAHLDESGIVKVGTYVS 888

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  725 DGDILISKISVSNlTLEDSPFSELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELF----------------------- 781
Cdd:PRK09603   889 AGMILVGKTSPKG-EIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFtkkgyekdarvlsayeeekakld 967

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  782 -------------------------------------------------AVTNKAT-------------STYGQ---NYL 796
Cdd:PRK09603   968 mehfdrltmlnreellrvssllsqaileepfshngkdykegdqipkeeiASINRFTlaslvkkyskevqNHYEItknNFL 1047

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  797 T-----------------------------LRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITG 847
Cdd:PRK09603  1048 EqkkvlgeeheeklsilekddilpngvikkVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLN 1127

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  848 PLGVPSRMNLGQLFESLFGY---------NCVLKDK--------RLLINSLLNNNLNNNYTKTYLYTSLQS---LKYYTG 907
Cdd:PRK09603  1128 PLGVPSRMNIGQILEMHLGLvgkefgkqiASMLEDKtkdfakelRAKMLEIANAINEKDPLTIHALENCSDeelLEYAKD 1207

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  908 NKSLLNPYIP----------------------GKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEIT 965
Cdd:PRK09603  1208 WSKGVKMAIPvfegisqekfyklfelakiamdGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVT 1287

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  966 QQPIKGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSDDLISRNNLQEYLLNNTPLEPNYLPEALKLLIRELHGLSL 1045
Cdd:PRK09603  1288 HQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLAL 1367

                          970       980
                   ....*....|....*....|
gi 1833819269 1046 NLEGFMVTDLLDGKLLPLNI 1065
Cdd:PRK09603  1368 DINIFGDDVDEDGAPKPIVI 1387
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
203-1048 9.45e-95

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 332.74  E-value: 9.45e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  203 EIFKNFYYFNSKEDIQELEKIKtllnmLNPELNLKYLKNklnfsrhLTSLKNslisrtgnflessfailgQDLISILDFL 282
Cdd:PRK14844   404 EFFRNLFFSPEYYDLSNIGRLK-----LNSYLGLNYDED-------LTVLTH------------------EDIIEIVRKI 453

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  283 LDLKFKKRTLNDLDHFGNRKVESLGHLISAHLEY--------ILPNKLFKILNLLFKSKFITSSLLIENLKESFNKNKIS 354
Cdd:PRK14844   454 VLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTgllkleraVVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLS 533

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  355 ikelltvnpliQYLEEVNSVSELMHKVRISSIGPGSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARI 434
Cdd:PRK14844   534 -----------QFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARI 602

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  435 NKEGSIETLIHP--NKKLRSYSKFLNSFEQESFLVSFENL-IPRKQSFLN-----KYSTSITfekgeIKSKTNISdtYYK 506
Cdd:PRK14844   603 NKYGFIESPYRKvvNRVVTDQIEYLSAIDEGLYYIADTSAkLDENNCFVDdmlycRYAGSFV-----MVSSDQVS--YID 675

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  507 INPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAVPLIYRNKPYILTGFESIIASKTSNLLRAYQEGVITKVTSYKIVl 586
Cdd:PRK14844   676 VSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIV- 754

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  587 IDLFNREIT-------YYLQKYKKTNQGTFIHQLPIVWPGERVLSGQLLTENQDISDSEFNIGNNLNVLYGSYYGYEYED 659
Cdd:PRK14844   755 IRAFDKERVnyldvdiYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFED 834

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  660 SLIISQKVLYKNIFTSIHFDIYEIKYSKYPIDTpEYSTLDLPKRTSYQKRHLDKLGIITEGSKVLDGDILISKISVSNlT 739
Cdd:PRK14844   835 SIIISSEVVKKDLFTSIHIEEFECVVHDTPLGS-EKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTPKP-S 912

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  740 LEDSPFSELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELF-------------------------------------- 781
Cdd:PRK14844   913 LSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFtrrgveenerallikqkeindfekerdyiinvtseyfy 992

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  782 -----------------------------AVTNKATSTYGQNY---------------------------------LTLR 799
Cdd:PRK14844   993 delkkllinsgsqdrekfdsiereqwwgiGLKNQSISEQVKSLkkdfdekvshaiaqfkrkveklhegydlpqgvsMSVK 1072

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  800 VFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNC---------- 869
Cdd:PRK14844  1073 VFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACkklgekvgni 1152

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  870 -----------------------------VLKDKRLLINSLLNNNLNNNYT--------------KTYL------YTSLQ 900
Cdd:PRK14844  1153 ldeinkiksafckgirslnddnftkfaaaYLDNKKIENIDDDEITASVLNTpnknalndelnelvENYLnscksaYSNLR 1232

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  901 S----LKYYTGNKSLLNPY------------------IP--------------------------GKLLLRDGRTGYRLK 932
Cdd:PRK14844  1233 NflieVYSCGSNVSICNNIrdisdnnliefarklrdgIPvaapvfegpkdeqiaklfelagldnsGQAVLYDGCSGEKFD 1312

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  933 GGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPIKGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSDDLISRN 1012
Cdd:PRK14844  1313 RKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRV 1392

                         1050      1060      1070
                   ....*....|....*....|....*....|....*.
gi 1833819269 1013 NLQEYLLNNTPLEPNYLPEALKLLIRELHGLSLNLE 1048
Cdd:PRK14844  1393 KIYESIIKGDSNFECGIPESFNVMIKELRSLCLNVD 1428
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 570-969 2.21e-82

RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 272.48  E-value: 2.21e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  570 AYQEGVITKVTSYKIVLIDLFNREI--TYYLQKYKKTNQGTF---IHQLPIVWPGeRVLSGQLltenqdisdSEFNIGNN 644
Cdd:pfam00562    2 ASLIPFVDHNQSPRNTYQCAMGKQAmgIYTLNKFYRSDQNTYvlcYPQKPLVKTG-AVEAGGF---------GELPLGQN 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  645 LNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKysKYPIDTPEYSTLDLPKRTSYQKRHLDKLGIITEGSKVL 724
Cdd:pfam00562   72 AIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIEAR--KTKLGPIEEITRDIPNVSEEALKKLDEDGIVRVGAEVK 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  725 DGDILISKISvsnltleDSPFSELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELFAVTNKatstygqNYLTLRVFVAK 804
Cdd:pfam00562  150 PGDILVGKVG-------PTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFELPPG-------GIKMVKVYIRQ 215

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  805 QRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLKDKRLLINSLLNN 884
Cdd:pfam00562  216 KRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGA 295

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  885 NLNNNYTKTYLYtslqslkyytgnKSLLNPYipGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEI 964
Cdd:pfam00562  296 STEVEDIGELLE------------KAGYNYY--GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLL 361


                   ....*
gi 1833819269  965 TQQPI 969
Cdd:pfam00562  362 TRQPL 366
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 659-1006 8.89e-41

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.


Pssm-ID: 274713 [Multi-domain]  Cd Length: 599  Bit Score: 159.81  E-value: 8.89e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  659 DSLIISQKVLYKNIFTSIHFDIYEIKYSKYP------IDTPEYSTLDLPKRTSYqkRHLDKLGIITEGSKVLDGDILISK 732
Cdd:TIGR03670  215 DALIMNKASIERGLARSTFFRTYEAEERRYPggqedrFEIPEPDVRGYRGEEAY--KHLDEDGIVYPEVEVKGGDVLIGK 292

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  733 ISVSNLtLEDspfseliFSLFGTKLRQLQDKSISVPIGNSG---RVIKTElfavtnkatstYGQNYLTLRVFVAKQRMLQ 809
Cdd:TIGR03670  293 TSPPRF-LEE-------LREFGLVTERRRDTSVTVRHGEKGivdKVIITE-----------TEEGNKLVKVRVRDLRIPE 353

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  810 IGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLKDKRLLINSllnnnlnnn 889
Cdd:TIGR03670  354 LGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTP--------- 424

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  890 ytktYLYTSLQSLKyytgnKSLL-NPYIP-GKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQ 967
Cdd:TIGR03670  425 ----FEGEPEEELR-----KELLkLGFKPdGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQ 495

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 1833819269  968 PIKGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSD 1006
Cdd:TIGR03670  496 PTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESD 534
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 282-1006 1.28e-39

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 159.74  E-value: 1.28e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  282 LLDLKFKKRTLNDLDHFGNRKVESLGHLISAhleyilpnklfkilnlLFKSKFITsslLIENLKESFNKNKISiKELLTV 361
Cdd:PRK08565   314 LLELYLGRREPDDKDHYANKRLRLAGDLLAE----------------LFRVAFKQ---LVKDLKYQLEKSYAR-GRKLDL 373

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  362 NPLI--------------------------QYLEEVNSVSELMHKVRISSigpgSLTQNQAGVAVREVRPSQLGKICILD 415
Cdd:PRK08565   374 RAIVrpdiiterirhalatgnwvggrtgvsQLLDRTNYLSTLSHLRRVVS----PLSRGQPHFEARDLHGTQWGRICPFE 449

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  416 TNEGPSSGLVVALASNARIN---KEGSIETLI-------------------------------HPN--------KKLRSY 453
Cdd:PRK08565   450 TPEGPNCGLVKNLALMAQISvgvDEEEVEEILyelgvvpveeareeeyiswsrvylngrligyHPDgeelaekiRELRRS 529

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  454 SK--------FLNSFEQESFLV----------------------------------SFENLIPR-KQSFL------NKYs 484
Cdd:PRK08565   530 GKisdevnvaYIETGEINEVYVncdsgrvrrplivvengkpkltrehveklkkgelTFDDLVKMgVIEYLdaeeeeNAY- 608

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  485 tsITFEKGEIKSKTnisdTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAVPLIYRNkpyiltgfesiiaskt 564
Cdd:PRK08565   609 --VALDPEDLTPEH----THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAAN---------------- 666

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  565 snllraYQegvitkvtsykivlidlfnreityylqkYKKTNQGTFIH--QLPIVwpGERVLSGqlltenqdISDSEFNIG 642
Cdd:PRK08565   667 ------FR----------------------------IRTDTRGHLLHypQRPLV--QTRALEI--------IGYNDRPAG 702

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  643 NNLNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSKYP------IDTPEYSTLDLPKRTSYqkRHLDKLGI 716
Cdd:PRK08565   703 QNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPggqedkIEIPEPNVRGYRGEEYY--RKLDEDGI 780

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  717 ITEGSKVLDGDILISKISvsnltledsP--FSELiFSLFGTKLRQLQDKSISVPIGNSG---RVIKTElfavtnkatsTY 791
Cdd:PRK08565   781 VSPEVEVKGGDVLIGKTS---------PprFLEE-LEELSLGLQERRDTSVTVRHGEKGivdTVLITE----------SP 840

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  792 GQNYLtLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVL 871
Cdd:PRK08565   841 EGNKL-VKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAAL 919

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  872 KDKRLlinsllnnnlnnnyTKTYLY-TSLQSLKyytgnKSLL-NPYIP-GKLLLRDGRTGYRLKGGAFMGTLYYSKLIHM 948
Cdd:PRK08565   920 EGRFV--------------DATPFYgEPEEELR-----KELLkLGYKPdGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHM 980

                          810       820       830       840       850
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1833819269  949 VKDKVHYRTFGPYTEITQQPIKGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSD 1006
Cdd:PRK08565   981 VADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSD 1038
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 659-1006 8.24e-32

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 132.39  E-value: 8.24e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  659 DSLIISQKVLYKNIFTSIHFDIYEIKYSKYP------IDTPEYSTLDLPKRTSYqkRHLDKLGIITEGSKVLDGDILISK 732
Cdd:PRK07225   221 DALIMNKASIERGLGRSHFFRTYEGEERRYPggqedrFEIPDKDVRGYRGEEAY--RHLDEDGLVNPETEVKEGDVLIGK 298

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  733 ISVSNLtLEDspfseliFSLFGTKLRQLQDKSISVPIGNSGRVIKTELfavtnkaTSTYGQNYLTlRVFVAKQRMLQIGD 812
Cdd:PRK07225   299 TSPPRF-LEE-------PDDFGISPEKRRETSVTMRSGEEGIVDTVIL-------TETEEGSRLV-KVRVRDLRIPELGD 362

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  813 KLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLKDKRllinsllnnNLNNNYTK 892
Cdd:PRK07225   363 KFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRR---------VDGTAFSG 433

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  893 TyLYTSLQ-SLKYYtGNKSllnpyiPGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPIKG 971
Cdd:PRK07225   434 E-DEEDLReALEKL-GFEH------TGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEG 505

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 1833819269  972 RGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSD 1006
Cdd:PRK07225   506 RAREGGLRFGEMERDVLIGHGAAMLLKERLLDESD 540
RNA_pol_Rpb2_7 pfam04560
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
 982-1048 6.49e-17

RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.


Pssm-ID: 461355 [Multi-domain]  Cd Length: 87  Bit Score: 76.47  E-value: 6.49e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1833819269  982 EMEVWALEAFGASYTLRELLTSKSD----DLISRNNLQEYLL------NNTPLEPNYLPEALKLLIRELHGLSLNLE 1048
Cdd:pfam04560    7 EMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAYNkcpickGETDISPGYIPESFKLLFQELQSLGIDPR 83
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 366-433 1.91e-14

RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.


Pssm-ID: 428011 [Multi-domain]  Cd Length: 67  Bit Score: 68.71  E-value: 1.91e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1833819269  366 QYLEEVNSVSELMHKVRISSiGPGSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNAR 433
Cdd:pfam04565    1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 109-444 9.59e-07

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 52.64  E-value: 9.59e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  109 DLQGNFILNGMKRGLVS-KMVRQNGVYFNLRRKYGEDIYSAQlILNERSKY----FIELFKEGIFiYNKF---NKKINLI 180
Cdd:PRK09606   143 DPGGYFIVNGSERVLMTlEDLAPNKILVEKDERYGDRIEVAK-VFSQRRGYralvTVERNRDGLL-EVSFpsvPGSIPFV 220

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  181 NFLHFIGL--NNSTISSISRYgtTEIFKNFYyfnskEDIQELEkIKTllnmlnPELNLKYLKNKL--------NFSRHLT 250
Cdd:PRK09606   221 ILMRALGLetDEEIVEAVSDD--PEIVKFML-----ENLEEAE-VDT------QEEALEYIGKRVapgqtkeyRIKRAEY 286

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  251 SLKNSLISRTGNflESSfailgqDLISILDFL-------LDLKFKKRTLNDLDHFGNRKVESLGHLISAhleyilpnklf 323
Cdd:PRK09606   287 VIDRYLLPHLGV--EPE------VRRAKAHYLgrmaeacFELALGRREEDDKDHYANKRLKLAGDLMED----------- 347

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  324 kilnlLFKSKFitsSLLIENLKESFNKNKISIKEL----------LTVN---PLI------------QYLEEVNSVSELM 378
Cdd:PRK09606   348 -----LFRVAF---NRLARDVKYQLERANMRNRELsiktavrsdvLTERlehAMAtgnwvggrtgvsQLLDRTDYMATLS 419

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1833819269  379 HKVRISSigpgSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARINKEGSIETLI 444
Cdd:PRK09606   420 HLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVK 481
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 129-304 4.74e-05

RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).


Pssm-ID: 398318 [Multi-domain]  Cd Length: 185  Bit Score: 45.42  E-value: 4.74e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  129 RQNGVYFNlRRKYGEDI---YSAQLILNeRSKYFIELFKEGIFIYNKFNK--KINLINFLHFIGLNNST--ISSISRYGT 201
Cdd:pfam04561    1 RSNGIYVE-KELDKNGIiatYTSSLISN-RGSWLKLEIDGKTLIWSRPSKkrKIPIVIFLKALGLVSDReiLDRLCYDFN 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269  202 T---------EIFKNFYYFNSKEDIQELEKIKTLLNMLNPEL----NLKYLKN-KLNFSRHLTSlknslisrtgNFLESS 267
Cdd:pfam04561   79 DpqmlellkpELEEAENIYTQEEALDYIGKGFALRRGEEPRLqrarEILYSRDpKYNLNKHLGL----------NEPFEN 148

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1833819269  268 FAILGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVE 304
Cdd:pfam04561  149 ERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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