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Conserved domains on  [gi|822606443|dbj|BAR79848|]
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RNA polymerase beta subunit, partial [Klebsiella variicola]

Protein Classification

DNA-directed RNA polymerase subunit beta( domain architecture ID 1000195)

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

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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;
1-329 0e+00

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member PRK00405:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1112  Bit Score: 753.09  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443    1 RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGR 80
Cdd:PRK00405  399 RMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGR 478

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   81 VCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCR 160
Cdd:PRK00405  479 ICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTAR 558

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  161 SKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAV 240
Cdd:PRK00405  559 YKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVV 638

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  241 AKRGGTVQYVDASRIVIKVneDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALG 320
Cdd:PRK00405  639 AKRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALG 716


                  ....*....
gi 822606443  321 QNMRVAFMP 329
Cdd:PRK00405  717 QNVLVAFMP 725
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-329 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 753.09  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443    1 RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGR 80
Cdd:PRK00405  399 RMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGR 478

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   81 VCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCR 160
Cdd:PRK00405  479 ICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTAR 558

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  161 SKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAV 240
Cdd:PRK00405  559 YKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVV 638

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  241 AKRGGTVQYVDASRIVIKVneDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALG 320
Cdd:PRK00405  639 AKRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALG 716


                  ....*....
gi 822606443  321 QNMRVAFMP 329
Cdd:PRK00405  717 QNVLVAFMP 725
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-329 0e+00

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: 668.68  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443     1 RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGR 80
Cdd:TIGR02013  354 RMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGR 433

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443    81 VCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVV--TDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVT 158
Cdd:TIGR02013  434 ICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVV 513

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   159 CRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVT 238
Cdd:TIGR02013  514 ARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAV 593

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   239 AVAKRGGTVQYVDASRIVIKVNEDEMYPgEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELA 318
Cdd:TIGR02013  594 IVAKRGGVVEYVDAKRIVIRYDEDEEEP-DGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELA 672

                          330
                   ....*....|.
gi 822606443   319 LGQNMRVAFMP 329
Cdd:TIGR02013  673 LGRNVLVAFMP 683
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-329 0e+00

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: 540.08  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443    1 RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGR 80
Cdd:COG0085   338 RMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGR 417

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   81 VCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCR 160
Cdd:COG0085   418 MCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVR 497

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  161 SKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLvgtgmeravavdsgvtav 240
Cdd:COG0085   498 YRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL------------------ 559

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  241 akrggtvqyvdasrivikvnedemypgeagiDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALG 320
Cdd:COG0085   560 -------------------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALG 608


                  ....*....
gi 822606443  321 QNMRVAFMP 329
Cdd:COG0085   609 QNLLVAFMP 617
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 8-234 7.69e-79

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: 257.11  E-value: 7.69e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   8 DTLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISAlgpGGLTRERAGFEVRDVHP 75
Cdd:cd00653  275 KDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHP 351

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  76 THYGRVCPIETPEGPNIGLINSLSVYAQTNeyGFLETPYRKVtdgvvtdeihylsaieegnyviaqansnldenghfved 155
Cdd:cd00653  352 SHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIV-------------------------------------- 391

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443 156 lvtcrskgesslfsRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPT----------------LRAD 219
Cdd:cd00653  392 --------------EKEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTpalnqqyrmdtklyllLYPQ 457

                        250
                 ....*....|....*
gi 822606443 220 KPLVGTGMERAVAVD 234
Cdd:cd00653  458 KPLVGTGIEEYIAFG 472
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 36-103 1.05e-38

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: 131.49  E-value: 1.05e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 822606443   36 QFMDQNNPLSEITHKRRISAlGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 103
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-329 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 753.09  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443    1 RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGR 80
Cdd:PRK00405  399 RMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGR 478

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   81 VCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCR 160
Cdd:PRK00405  479 ICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTAR 558

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  161 SKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAV 240
Cdd:PRK00405  559 YKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVV 638

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  241 AKRGGTVQYVDASRIVIKVneDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALG 320
Cdd:PRK00405  639 AKRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALG 716


                  ....*....
gi 822606443  321 QNMRVAFMP 329
Cdd:PRK00405  717 QNVLVAFMP 725
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-329 0e+00

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: 668.68  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443     1 RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGR 80
Cdd:TIGR02013  354 RMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGR 433

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443    81 VCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVV--TDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVT 158
Cdd:TIGR02013  434 ICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVV 513

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   159 CRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVT 238
Cdd:TIGR02013  514 ARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAV 593

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   239 AVAKRGGTVQYVDASRIVIKVNEDEMYPgEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELA 318
Cdd:TIGR02013  594 IVAKRGGVVEYVDAKRIVIRYDEDEEEP-DGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELA 672

                          330
                   ....*....|.
gi 822606443   319 LGQNMRVAFMP 329
Cdd:TIGR02013  673 LGRNVLVAFMP 683
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-329 0e+00

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: 540.08  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443    1 RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGR 80
Cdd:COG0085   338 RMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGR 417

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   81 VCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCR 160
Cdd:COG0085   418 MCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVR 497

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  161 SKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLvgtgmeravavdsgvtav 240
Cdd:COG0085   498 YRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL------------------ 559

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  241 akrggtvqyvdasrivikvnedemypgeagiDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALG 320
Cdd:COG0085   560 -------------------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALG 608


                  ....*....
gi 822606443  321 QNMRVAFMP 329
Cdd:COG0085   609 QNLLVAFMP 617
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
5-329 4.20e-148

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 460.93  E-value: 4.20e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443    5 GDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPI 84
Cdd:PRK09603  496 GAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPI 575

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   85 ETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGE 164
Cdd:PRK09603  576 ETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGE 655

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  165 SSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRG 244
Cdd:PRK09603  656 IVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRA 735

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  245 GTVQYVDASRIVIkVNEDEmypGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALGQNMR 324
Cdd:PRK09603  736 GVVEKIDSKNIYI-LGEGK---EEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVR 811


                  ....*
gi 822606443  325 VAFMP 329
Cdd:PRK09603  812 VAFMP 816
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
2-328 2.91e-146

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 455.62  E-value: 2.91e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443    2 LSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRV 81
Cdd:PRK14844  500 MSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRI 579

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   82 CPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRS 161
Cdd:PRK14844  580 CPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRY 659

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  162 KGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVA 241
Cdd:PRK14844  660 AGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLA 739

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  242 KRGGTVQYVDASRIVIKVNEDEMYpGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALGQ 321
Cdd:PRK14844  740 KRDGIVDSSDSNSIVIRAFDKERV-NYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQ 818


                  ....*..
gi 822606443  322 NMRVAFM 328
Cdd:PRK14844  819 NLLVAFM 825
rpoB CHL00001
RNA polymerase beta subunit
 12-329 4.39e-144

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 433.17  E-value: 4.39e-144
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   12 PQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 91
Cdd:CHL00001  352 PQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGIN 431

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   92 IGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRD 171
Cdd:CHL00001  432 AGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWE 511

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  172 QVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGTVQYVD 251
Cdd:CHL00001  512 QIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTD 591

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 822606443  252 ASRIVIKVNEDEMYpgeagidiYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALGQNMRVAFMP 329
Cdd:CHL00001  592 TDKIILSGNGDTLS--------IPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMP 661
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-329 1.30e-133

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 406.01  E-value: 1.30e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443    1 RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGR 80
Cdd:CHL00207  333 RMTICDIDSLSKFNLINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGR 412

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   81 VCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVV--TDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVT 158
Cdd:CHL00207  413 ICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIP 492

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  159 CRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVT 238
Cdd:CHL00207  493 VRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMT 572

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  239 AVAKRGGTVQYVDASRIVIKVNEDEMYpgeagidIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELA 318
Cdd:CHL00207  573 IISLTEGIVVSVSAYKIIIQDDNNRYI-------HYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELA 645

                         330
                  ....*....|.
gi 822606443  319 LGQNMRVAFMP 329
Cdd:CHL00207  646 LGQNVLVAYMP 656
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 8-234 7.69e-79

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: 257.11  E-value: 7.69e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443   8 DTLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISAlgpGGLTRERAGFEVRDVHP 75
Cdd:cd00653  275 KDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHP 351

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  76 THYGRVCPIETPEGPNIGLINSLSVYAQTNeyGFLETPYRKVtdgvvtdeihylsaieegnyviaqansnldenghfved 155
Cdd:cd00653  352 SHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIV-------------------------------------- 391

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443 156 lvtcrskgesslfsRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPT----------------LRAD 219
Cdd:cd00653  392 --------------EKEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTpalnqqyrmdtklyllLYPQ 457

                        250
                 ....*....|....*
gi 822606443 220 KPLVGTGMERAVAVD 234
Cdd:cd00653  458 KPLVGTGIEEYIAFG 472
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 36-103 1.05e-38

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: 131.49  E-value: 1.05e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 822606443   36 QFMDQNNPLSEITHKRRISAlGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 103
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
 114-179 3.23e-38

RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region.


Pssm-ID: 463067 [Multi-domain]  Cd Length: 66  Bit Score: 130.18  E-value: 3.23e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 822606443  114 YRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVS 179
Cdd:pfam10385   1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 35-103 2.65e-19

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 88.86  E-value: 2.65e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 822606443   35 SQFMDQNNPLSEITHKRRIsaLGPggLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 103
Cdd:PRK08565  403 SQLLDRTNYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQ 467
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 30-103 7.46e-18

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 83.85  E-value: 7.46e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 822606443  30 GSSQLSQFMDQNNPLSEITHKRRISAlgPggLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 103
Cdd:PRK09606 401 GRTGVSQLLDRTDYMATLSHLRRVVS--P--LSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVE 470
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 240-329 3.77e-16

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: 78.34  E-value: 3.77e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443  240 VAKRGGTVQYVDASRIVIKVNEdemypGEAGIDIYNLTKYTRSNQNT---CINQMPCVSLGEpIERGDvladgpstdLGE 316
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAM-----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGG---------FGE 65

                          90
                  ....*....|...
gi 822606443  317 LALGQNMRVAFMP 329
Cdd:pfam00562  66 LPLGQNAIVAVMS 78
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 126-225 1.79e-04

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 43.03  E-value: 1.79e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822606443 126 IHYLSAIEEGNYVIAQANSNLDENgHfvedlvtcrskgesslfsrdqvDYMDVSTQQVVSVGASLIPFLEHDDANRALMG 205
Cdd:PRK07225  98 IEYLDAEEEENAYIAVYEEDLTEE-H----------------------THLEIDPSLILGIGAGMIPYPEHNASPRITMG 154

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 822606443 206 ANMQRQA--VPT----LRAD----------KPLVGT 225
Cdd:PRK07225 155 AGMIKQSlgLPAanykLRPDtrghllhypqVPLVKT 190
 
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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