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Conserved domains on  [gi|270161157|gb|ACZ63456|]
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RpoB, partial [Rahnella sp. 73-Celery]

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;
1-306 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: 690.69  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157    1 RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRD 80
Cdd:PRK00405  391 RMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRD 470

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157   81 VHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDEEGRF 160
Cdd:PRK00405  471 VHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRF 550

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157  161 IEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240
Cdd:PRK00405  551 VDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVA 630

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 270161157  241 VDSGVTAVAKRGGIVQYVDASRIVIRVneEEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVNLGE 306
Cdd:PRK00405  631 RDSGAVVVAKRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGD 694
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-306 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 690.69  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157    1 RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRD 80
Cdd:PRK00405  391 RMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRD 470

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157   81 VHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDEEGRF 160
Cdd:PRK00405  471 VHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRF 550

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157  161 IEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240
Cdd:PRK00405  551 VDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVA 630

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 270161157  241 VDSGVTAVAKRGGIVQYVDASRIVIRVneEEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVNLGE 306
Cdd:PRK00405  631 RDSGAVVVAKRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGD 694
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-307 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: 611.28  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157     1 RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRD 80
Cdd:TIGR02013  346 RMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRD 425

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157    81 VHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDG--LVTDEINYLSAIEEGNFVIAQANSNLDEEG 158
Cdd:TIGR02013  426 VHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGkvVVTDEIDYLTADEEDNYVIAQANAPLDENG 505

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157   159 RFIEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERA 238
Cdd:TIGR02013  506 RFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAK 585

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 270161157   239 VAVDSGVTAVAKRGGIVQYVDASRIVIRVNEEEMYPgEAGIDIYNLTKYTRSNQNTCINQMPCVNLGEP 307
Cdd:TIGR02013  586 VARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEP-DGGIDIYRLLKYQRSNQDTCINQRPIVSVGDR 653
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-306 1.27e-164

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: 483.46  E-value: 1.27e-164
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157    1 RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRD 80
Cdd:COG0085   330 RMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRD 409

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157   81 VHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDEEGRF 160
Cdd:COG0085   410 VHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNF 489

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157  161 IEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLvgtgmerava 240
Cdd:COG0085   490 LEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL---------- 559

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 270161157  241 vdsgvtavakrggivqyvdasrivirvneeemypgeagiDIYNLTKYTRSNQNTCINQMPCVNLGE 306
Cdd:COG0085   560 ---------------------------------------LHYPLQKFQRSNQGTCINQRPIVRVGD 586
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-242 1.59e-80

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: 260.96  E-value: 1.59e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157   1 RVERAVKERLS--LGDLDTLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISAlgp 66
Cdd:cd00653  258 RLEREVKEKLQkqLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS--- 334

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157  67 GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNeyGFLETPYRRVrdglvtdeinylsaieegnfv 146
Cdd:cd00653  335 LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIV--------------------- 391

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157 147 iaqansnldeegrfiedlvtcrskgesslfsRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPT--- 223
Cdd:cd00653  392 -------------------------------EKEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTpal 440

                        250       260       270
                 ....*....|....*....|....*....|..
gi 270161157 224 -------------LRADKPLVGTGMERAVAVD 242
Cdd:cd00653  441 nqqyrmdtklyllLYPQKPLVGTGIEEYIAFG 472
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 44-111 6.13e-39

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: 6.13e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 270161157   44 QFMDQNNPLSEITHKRRISAlGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 111
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-306 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 690.69  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157    1 RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRD 80
Cdd:PRK00405  391 RMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRD 470

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157   81 VHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDEEGRF 160
Cdd:PRK00405  471 VHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRF 550

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157  161 IEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240
Cdd:PRK00405  551 VDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVA 630

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 270161157  241 VDSGVTAVAKRGGIVQYVDASRIVIRVneEEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVNLGE 306
Cdd:PRK00405  631 RDSGAVVVAKRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGD 694
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-307 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: 611.28  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157     1 RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRD 80
Cdd:TIGR02013  346 RMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRD 425

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157    81 VHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDG--LVTDEINYLSAIEEGNFVIAQANSNLDEEG 158
Cdd:TIGR02013  426 VHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGkvVVTDEIDYLTADEEDNYVIAQANAPLDENG 505

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157   159 RFIEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERA 238
Cdd:TIGR02013  506 RFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAK 585

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 270161157   239 VAVDSGVTAVAKRGGIVQYVDASRIVIRVNEEEMYPgEAGIDIYNLTKYTRSNQNTCINQMPCVNLGEP 307
Cdd:TIGR02013  586 VARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEP-DGGIDIYRLLKYQRSNQDTCINQRPIVSVGDR 653
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-306 1.27e-164

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: 483.46  E-value: 1.27e-164
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157    1 RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRD 80
Cdd:COG0085   330 RMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRD 409

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157   81 VHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDEEGRF 160
Cdd:COG0085   410 VHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNF 489

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157  161 IEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLvgtgmerava 240
Cdd:COG0085   490 LEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL---------- 559

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 270161157  241 vdsgvtavakrggivqyvdasrivirvneeemypgeagiDIYNLTKYTRSNQNTCINQMPCVNLGE 306
Cdd:COG0085   560 ---------------------------------------LHYPLQKFQRSNQGTCINQRPIVRVGD 586
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-306 1.12e-133

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 418.64  E-value: 1.12e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157    1 RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRD 80
Cdd:PRK14844  491 KLERAVVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRD 570

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157   81 VHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDEEGRF 160
Cdd:PRK14844  571 VHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCF 650

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157  161 IEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240
Cdd:PRK14844  651 VDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVA 730

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 270161157  241 VDSGVTAVAKRGGIVQYVDASRIVIRVNEEEMYpGEAGIDIYNLTKYTRSNQNTCINQMPCVNLGE 306
Cdd:PRK14844  731 SGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERV-NYLDVDIYHLRKFQRSNHNTCINQKPLVCVGD 795
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-306 1.26e-129

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 407.00  E-value: 1.26e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157    1 RVERAVKERLSL--GDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEV 78
Cdd:PRK09603  482 KMQKTIKDKLTTmsGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEA 561

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157   79 RDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDEEG 158
Cdd:PRK09603  562 RDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEG 641

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157  159 RFIEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERA 238
Cdd:PRK09603  642 NILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKI 721

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 270161157  239 VAVDSGVTAVAKRGGIVQYVDASRIVIRVNEEEmypgEAGIDIYNLTKYTRSNQNTCINQMPCVNLGE 306
Cdd:PRK09603  722 IARDSWGAIKANRAGVVEKIDSKNIYILGEGKE----EAYIDAYSLQKNLRTNQNTSFNQVPIVKVGD 785
rpoB CHL00001
RNA polymerase beta subunit
 1-306 3.91e-126

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 385.41  E-value: 3.91e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157    1 RVERAVKERLSLGDLDTLM--PQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEV 78
Cdd:CHL00001  331 RLENAVRGTICGAIRRKLIptPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRV 410

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157   79 RDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDEEG 158
Cdd:CHL00001  411 RDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQG 490

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157  159 RFIEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERA 238
Cdd:CHL00001  491 IQEEQVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQ 570

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 270161157  239 VAVDSGVTAVAKRGGIVQYVDASRIVIRVNEEEMYpgeagidiYNLTKYTRSNQNTCINQMPCVNLGE 306
Cdd:CHL00001  571 VALDSGVVAIAEHEGKIIYTDTDKIILSGNGDTLS--------IPLVMYQRSNKNTCMHQKPQVRRGK 630
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-306 1.61e-121

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 373.27  E-value: 1.61e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157    1 RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRD 80
Cdd:CHL00207  325 RLERILRNRMTICDIDSLSKFNLINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRD 404

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157   81 VHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGLV--TDEINYLSAIEEGNFVIAQANSNLDEEG 158
Cdd:CHL00207  405 IHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNN 484

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157  159 RFIEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERA 238
Cdd:CHL00207  485 YFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQ 564

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 270161157  239 VAVDSGVTAVAKRGGIVQYVDASRIVIRVNEEEMYpgeagidIYNLTKYTRSNQNTCINQMPCVNLGE 306
Cdd:CHL00207  565 IALDSGMTIISLTEGIVVSVSAYKIIIQDDNNRYI-------HYYLQKYQRSNQNTCINYRPIVWVGE 625
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-242 1.59e-80

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: 260.96  E-value: 1.59e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157   1 RVERAVKERLS--LGDLDTLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISAlgp 66
Cdd:cd00653  258 RLEREVKEKLQkqLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS--- 334

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157  67 GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNeyGFLETPYRRVrdglvtdeinylsaieegnfv 146
Cdd:cd00653  335 LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIV--------------------- 391

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157 147 iaqansnldeegrfiedlvtcrskgesslfsRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPT--- 223
Cdd:cd00653  392 -------------------------------EKEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTpal 440

                        250       260       270
                 ....*....|....*....|....*....|..
gi 270161157 224 -------------LRADKPLVGTGMERAVAVD 242
Cdd:cd00653  441 nqqyrmdtklyllLYPQKPLVGTGIEEYIAFG 472
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 44-111 6.13e-39

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: 6.13e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 270161157   44 QFMDQNNPLSEITHKRRISAlGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 111
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
 122-187 2.35e-35

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: 122.09  E-value: 2.35e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 270161157  122 YRRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDEEGRFIEDLVTCRSKGESSLFSRDQVDYMDVS 187
Cdd:pfam10385   1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 43-236 2.80e-20

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 91.17  E-value: 2.80e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157   43 SQFMDQNNPLSEITHKRRIsaLGPggLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ----TNEYGFL 118
Cdd:PRK08565  403 SQLLDRTNYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQisvgVDEEEVE 478

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157  119 ETPYR------------------RV------------------------RDGLVTDEINyLSAIEEGNF----------- 145
Cdd:PRK08565  479 EILYElgvvpveeareeeyiswsRVylngrligyhpdgeelaekirelrRSGKISDEVN-VAYIETGEInevyvncdsgr 557

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157  146 ----VIAQANSNLDEEGRFIEDLvtcrSKGE---SSLFSRDQVDYMDVSTQQ------------------------VVSV 194
Cdd:PRK08565  558 vrrpLIVVENGKPKLTREHVEKL----KKGEltfDDLVKMGVIEYLDAEEEEnayvaldpedltpehthleiwppaILGI 633

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 270161157  195 GASLIPFLEHDDANRALMGANMQRQA--VPT----LRAD----------KPLVGT-GME 236
Cdd:PRK08565  634 TASIIPYPEHNQSPRNTYQAAMAKQSlgLYAanfrIRTDtrghllhypqRPLVQTrALE 692
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 38-111 1.32e-17

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 82.69  E-value: 1.32e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 270161157  38 GSSQLSQFMDQNNPLSEITHKRRISAlgpgGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 111
Cdd:PRK09606 401 GRTGVSQLLDRTDYMATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVE 470
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 125-233 1.33e-04

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 43.41  E-value: 1.33e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270161157 125 VRDGLvtdeINYLSAIEEGNFVIAQANSNLDEEGRFIEdlvtcrskgesslfsrdqvdymdVSTQQVVSVGASLIPFLEH 204
Cdd:PRK07225  93 VKQGV----IEYLDAEEEENAYIAVYEEDLTEEHTHLE-----------------------IDPSLILGIGAGMIPYPEH 145

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 270161157 205 DDANRALMGANMQRQA--VPT----LRAD----------KPLVGT 233
Cdd:PRK07225 146 NASPRITMGAGMIKQSlgLPAanykLRPDtrghllhypqVPLVKT 190
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-31 7.23e-04

RNA polymerase beta subunit; 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 forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.


Pssm-ID: 367994 [Multi-domain]  Cd Length: 396  Bit Score: 40.83  E-value: 7.23e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 270161157    1 RVERAVKERL--SLGDLDTLMPQDMINAKPISA 31
Cdd:pfam04563 364 KLVRDVRERLqkVLGSPDDLMLQLLVNAKPITS 396
 
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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