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Conserved domains on  [gi|371560277|gb|AEX36923|]
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DNA-directed RNA polymerase subunit beta, partial [Sandarakinorhabdus limnophila]

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;
1-360 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: 822.04  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277    1 FFGSSQLSQFMDQTNPLSEVTHKRRVSAPGPGGLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRVNKY 80
Cdd:PRK00405  426 FFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEY 505

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   81 GFIETPYRKVDNGKLTDDVVYLSAMEEARHTIAQANAGIDAGGTYVEELISARQAGEFLMAPASTITLADVSPKQLVSVA 160
Cdd:PRK00405  506 GFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVA 585

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  161 ASLIPFLENDDANRALMGSNMQRQAVPLVKAESPFVGTGMEGTVARDSGAAIAAKRTGIVDQVDATRIVIRAtQEVEPGK 240
Cdd:PRK00405  586 ASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRV-EELDPGE 664

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  241 SGVDIYTLMKFERSNQSTCINQRPLVTVGDLVQKGDIIADGPSTEDGELALGRNVLVAFMPWNGYNYEDSILINEKIVKE 320
Cdd:PRK00405  665 DGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKE 744

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 371560277  321 DVFTSIHIDEFEVMARDTKLGPEDITRDIPNVGEEALKNL 360
Cdd:PRK00405  745 DVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNL 784
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-360 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 822.04  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277    1 FFGSSQLSQFMDQTNPLSEVTHKRRVSAPGPGGLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRVNKY 80
Cdd:PRK00405  426 FFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEY 505

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   81 GFIETPYRKVDNGKLTDDVVYLSAMEEARHTIAQANAGIDAGGTYVEELISARQAGEFLMAPASTITLADVSPKQLVSVA 160
Cdd:PRK00405  506 GFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVA 585

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  161 ASLIPFLENDDANRALMGSNMQRQAVPLVKAESPFVGTGMEGTVARDSGAAIAAKRTGIVDQVDATRIVIRAtQEVEPGK 240
Cdd:PRK00405  586 ASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRV-EELDPGE 664

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  241 SGVDIYTLMKFERSNQSTCINQRPLVTVGDLVQKGDIIADGPSTEDGELALGRNVLVAFMPWNGYNYEDSILINEKIVKE 320
Cdd:PRK00405  665 DGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKE 744

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 371560277  321 DVFTSIHIDEFEVMARDTKLGPEDITRDIPNVGEEALKNL 360
Cdd:PRK00405  745 DVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNL 784
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-360 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: 699.49  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277     1 FFGSSQLSQFMDQTNPLSEVTHKRRVSAPGPGGLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRVNKY 80
Cdd:TIGR02013  381 FFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEY 460

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277    81 GFIETPYRKVDNGKL--TDDVVYLSAMEEARHTIAQANAGIDAGGTYVEELISARQAGEFLMAPASTITLADVSPKQLVS 158
Cdd:TIGR02013  461 GFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVS 540

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   159 VAASLIPFLENDDANRALMGSNMQRQAVPLVKAESPFVGTGMEGTVARDSGAAIAAKRTGIVDQVDATRIVIRATQEVEP 238
Cdd:TIGR02013  541 VAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEE 620

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   239 GKSGVDIYTLMKFERSNQSTCINQRPLVTVGDLVQKGDIIADGPSTEDGELALGRNVLVAFMPWNGYNYEDSILINEKIV 318
Cdd:TIGR02013  621 PDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLV 700

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|..
gi 371560277   319 KEDVFTSIHIDEFEVMARDTKLGPEDITRDIPNVGEEALKNL 360
Cdd:TIGR02013  701 KDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNL 742
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-360 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: 634.84  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277    1 FFGSSQLSQFMDQTNPLSEVTHKRRVSAPGPGGLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRVNKY 80
Cdd:COG0085   365 FFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEY 444

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   81 GFIETPYRKVDNGKLTDDVVYLSAMEEARHTIAQANAGIDAGGTYVEELISARQAGEFLMAPASTITLADVSPKQLVSVA 160
Cdd:COG0085   445 GFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVA 524

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  161 ASLIPFLENDDANRALMGSNMQRQAVPLVKAESPFvgtgmegtvardsgaaiaakrtgivdqvdatriviratqevepgk 240
Cdd:COG0085   525 TSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL--------------------------------------------- 559

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  241 sgvDIYTLMKFERSNQSTCINQRPLVTVGDLVQKGDIIADGPSTEDGELALGRNVLVAFMPWNGYNYEDSILINEKIVKE 320
Cdd:COG0085   560 ---LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKD 636

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 371560277  321 DVFTSIHIDEFEVMARDTKLGPEDITRDIPNVGEEALKNL 360
Cdd:COG0085   637 DVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNL 676
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-360 4.34e-100

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: 314.89  E-value: 4.34e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   1 FFGSSQ------------LSQFMDQTNPLSEVTHKRRVSApgpGGLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLI 68
Cdd:cd00653  295 FLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLV 371

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  69 NSLATFSRVNkyGFIETPYRKVDNgkltddvvylsameearhtiaqanagidaggtyveelisarqageflmapasTITL 148
Cdd:cd00653  372 KNLALMARIS--GRIERPYRIVEK----------------------------------------------------EVTH 397

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277 149 ADVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVP----------------LVKAESPFVGTGMEGTVARdsgaai 212
Cdd:cd00653  398 IEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAF------ 471

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277 213 aakrtgivdqvdatriviratqevepgksgvdiytlmkfersnqstcinqrplvtvgdlvqkgdiiadgpstedGELALG 292
Cdd:cd00653  472 --------------------------------------------------------------------------GELPLG 477

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 371560277 293 RNVLVAFMPWNGYNYEDSILINEKIVKEDVFTSIHIDEFEVMARDTKLGPEDITR-DIPNVGEEALKNL 360
Cdd:cd00653  478 QNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNL 546
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 214-360 2.78e-54

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: 182.73  E-value: 2.78e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  214 AKRTGIVDQVDATRIVIRATQevepGKSGVDIYTLMKFERSNQST---CINQRPLVTVGDlVQKGDiiadgpsteDGELA 290
Cdd:pfam00562   2 ASLIPFVDHNQSPRNTYQCAM----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGG---------FGELP 67

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 371560277  291 LGRNVLVAFMPWNGYNYEDSILINEKIVKEDVFTSIHIDEFEvmARDTKLGP-EDITRDIPNVGEEALKNL 360
Cdd:pfam00562  68 LGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKL 136
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-360 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 822.04  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277    1 FFGSSQLSQFMDQTNPLSEVTHKRRVSAPGPGGLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRVNKY 80
Cdd:PRK00405  426 FFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEY 505

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   81 GFIETPYRKVDNGKLTDDVVYLSAMEEARHTIAQANAGIDAGGTYVEELISARQAGEFLMAPASTITLADVSPKQLVSVA 160
Cdd:PRK00405  506 GFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVA 585

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  161 ASLIPFLENDDANRALMGSNMQRQAVPLVKAESPFVGTGMEGTVARDSGAAIAAKRTGIVDQVDATRIVIRAtQEVEPGK 240
Cdd:PRK00405  586 ASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRV-EELDPGE 664

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  241 SGVDIYTLMKFERSNQSTCINQRPLVTVGDLVQKGDIIADGPSTEDGELALGRNVLVAFMPWNGYNYEDSILINEKIVKE 320
Cdd:PRK00405  665 DGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKE 744

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 371560277  321 DVFTSIHIDEFEVMARDTKLGPEDITRDIPNVGEEALKNL 360
Cdd:PRK00405  745 DVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNL 784
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-360 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: 699.49  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277     1 FFGSSQLSQFMDQTNPLSEVTHKRRVSAPGPGGLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRVNKY 80
Cdd:TIGR02013  381 FFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEY 460

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277    81 GFIETPYRKVDNGKL--TDDVVYLSAMEEARHTIAQANAGIDAGGTYVEELISARQAGEFLMAPASTITLADVSPKQLVS 158
Cdd:TIGR02013  461 GFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVS 540

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   159 VAASLIPFLENDDANRALMGSNMQRQAVPLVKAESPFVGTGMEGTVARDSGAAIAAKRTGIVDQVDATRIVIRATQEVEP 238
Cdd:TIGR02013  541 VAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEE 620

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   239 GKSGVDIYTLMKFERSNQSTCINQRPLVTVGDLVQKGDIIADGPSTEDGELALGRNVLVAFMPWNGYNYEDSILINEKIV 318
Cdd:TIGR02013  621 PDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLV 700

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|..
gi 371560277   319 KEDVFTSIHIDEFEVMARDTKLGPEDITRDIPNVGEEALKNL 360
Cdd:TIGR02013  701 KDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNL 742
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-360 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: 634.84  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277    1 FFGSSQLSQFMDQTNPLSEVTHKRRVSAPGPGGLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRVNKY 80
Cdd:COG0085   365 FFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEY 444

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   81 GFIETPYRKVDNGKLTDDVVYLSAMEEARHTIAQANAGIDAGGTYVEELISARQAGEFLMAPASTITLADVSPKQLVSVA 160
Cdd:COG0085   445 GFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVA 524

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  161 ASLIPFLENDDANRALMGSNMQRQAVPLVKAESPFvgtgmegtvardsgaaiaakrtgivdqvdatriviratqevepgk 240
Cdd:COG0085   525 TSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL--------------------------------------------- 559

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  241 sgvDIYTLMKFERSNQSTCINQRPLVTVGDLVQKGDIIADGPSTEDGELALGRNVLVAFMPWNGYNYEDSILINEKIVKE 320
Cdd:COG0085   560 ---LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKD 636

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 371560277  321 DVFTSIHIDEFEVMARDTKLGPEDITRDIPNVGEEALKNL 360
Cdd:COG0085   637 DVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNL 676
rpoB CHL00001
RNA polymerase beta subunit
 1-360 3.36e-172

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 507.52  E-value: 3.36e-172
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277    1 FFGSSQLSQFMDQTNPLSEVTHKRRVSAPGPGGLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRVNKY 80
Cdd:CHL00001  368 FFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHW 447

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   81 GFIETPYRKVDNGKLTDDVVYLSAMEEARHTIAQANAGIDAGGTYVEELISARQAGEFLMAPASTITLADVSPKQLVSVA 160
Cdd:CHL00001  448 GSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIG 527

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  161 ASLIPFLENDDANRALMGSNMQRQAVPLVKAESPFVGTGMEGTVARDSGAAIAAKRTGIVDQVDATRIVIRatqevepGK 240
Cdd:CHL00001  528 ASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILS-------GN 600

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  241 SGVDIYTLMKFERSNQSTCINQRPLVTVGDLVQKGDIIADGPSTEDGELALGRNVLVAFMPWNGYNYEDSILINEKIVKE 320
Cdd:CHL00001  601 GDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYE 680

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 371560277  321 DVFTSIHIDEFEVMARDTKLGPEDITRDIPNVGEEALKNL 360
Cdd:CHL00001  681 DIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNL 720
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-360 1.64e-170

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 526.88  E-value: 1.64e-170
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277    1 FFGSSQLSQFMDQTNPLSEVTHKRRVSAPGPGGLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRVNKY 80
Cdd:PRK14844  526 FFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKY 605

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   81 GFIETPYRKVDNGKLTDDVVYLSAMEEARHTIAQANAGIDAGGTYVEELISARQAGEFLMAPASTITLADVSPKQLVSVA 160
Cdd:PRK14844  606 GFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVA 685

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  161 ASLIPFLENDDANRALMGSNMQRQAVPLVKAESPFVGTGMEGTVARDSGAAIAAKRTGIVDQVDATRIVIRATQEVEPGK 240
Cdd:PRK14844  686 ASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERVNY 765

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  241 SGVDIYTLMKFERSNQSTCINQRPLVTVGDLVQKGDIIADGPSTEDGELALGRNVLVAFMPWNGYNYEDSILINEKIVKE 320
Cdd:PRK14844  766 LDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKK 845

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 371560277  321 DVFTSIHIDEFEVMARDTKLGPEDITRDIPNVGEEALKNL 360
Cdd:PRK14844  846 DLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHL 885
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-360 2.56e-167

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 517.55  E-value: 2.56e-167
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277    1 FFGSSQLSQFMDQTNPLSEVTHKRRVSAPGPGGLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRVNKY 80
Cdd:PRK09603  519 FFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDL 598

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   81 GFIETPYRKVDNGKLTDDVVYLSAMEEARHTIAQANAGIDAGGTYVEELISARQAGEFLMAPASTITLADVSPKQLVSVA 160
Cdd:PRK09603  599 GFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVA 678

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  161 ASLIPFLENDDANRALMGSNMQRQAVPLVKAESPFVGTGMEGTVARDSGAAIAAKRTGIVDQVDATRIVIRATQEVEpgk 240
Cdd:PRK09603  679 ASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGKEE--- 755

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  241 SGVDIYTLMKFERSNQSTCINQRPLVTVGDLVQKGDIIADGPSTEDGELALGRNVLVAFMPWNGYNYEDSILINEKIVKE 320
Cdd:PRK09603  756 AYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKD 835

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 371560277  321 DVFTSIHIDEFEVMARDTKLGPEDITRDIPNVGEEALKNL 360
Cdd:PRK09603  836 DIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHL 875
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-360 9.97e-160

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 475.35  E-value: 9.97e-160
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277    1 FFGSSQLSQFMDQTNPLSEVTHKRRVSAPGPGGLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRVNKY 80
Cdd:CHL00207  360 FFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKF 439

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   81 GFIETPYRKVDNGKL--TDDVVYLSAMEEARHTIAQANAGIDAGGTYVEELISARQAGEFLMAPASTITLADVSPKQLVS 158
Cdd:CHL00207  440 GFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFS 519

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  159 VAASLIPFLENDDANRALMGSNMQRQAVPLVKAESPFVGTGMEGTVARDSGAAIAAKRTGIVDQVDATRIVIRatqevep 238
Cdd:CHL00207  520 IAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQ------- 592

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  239 GKSGVDI-YTLMKFERSNQSTCINQRPLVTVGDLVQKGDIIADGPSTEDGELALGRNVLVAFMPWNGYNYEDSILINEKI 317
Cdd:CHL00207  593 DDNNRYIhYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRL 672

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|...
gi 371560277  318 VKEDVFTSIHIDEFEVMARDTKLGPEDITRDIPNVGEEALKNL 360
Cdd:CHL00207  673 VYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNL 715
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-360 4.34e-100

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: 314.89  E-value: 4.34e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   1 FFGSSQ------------LSQFMDQTNPLSEVTHKRRVSApgpGGLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLI 68
Cdd:cd00653  295 FLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLV 371

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  69 NSLATFSRVNkyGFIETPYRKVDNgkltddvvylsameearhtiaqanagidaggtyveelisarqageflmapasTITL 148
Cdd:cd00653  372 KNLALMARIS--GRIERPYRIVEK----------------------------------------------------EVTH 397

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277 149 ADVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVP----------------LVKAESPFVGTGMEGTVARdsgaai 212
Cdd:cd00653  398 IEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAF------ 471

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277 213 aakrtgivdqvdatriviratqevepgksgvdiytlmkfersnqstcinqrplvtvgdlvqkgdiiadgpstedGELALG 292
Cdd:cd00653  472 --------------------------------------------------------------------------GELPLG 477

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 371560277 293 RNVLVAFMPWNGYNYEDSILINEKIVKEDVFTSIHIDEFEVMARDTKLGPEDITR-DIPNVGEEALKNL 360
Cdd:cd00653  478 QNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNL 546
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 214-360 2.78e-54

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: 182.73  E-value: 2.78e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  214 AKRTGIVDQVDATRIVIRATQevepGKSGVDIYTLMKFERSNQST---CINQRPLVTVGDlVQKGDiiadgpsteDGELA 290
Cdd:pfam00562   2 ASLIPFVDHNQSPRNTYQCAM----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGG---------FGELP 67

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 371560277  291 LGRNVLVAFMPWNGYNYEDSILINEKIVKEDVFTSIHIDEFEvmARDTKLGP-EDITRDIPNVGEEALKNL 360
Cdd:pfam00562  68 LGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKL 136
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 9-76 5.46e-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: 133.04  E-value: 5.46e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 371560277    9 QFMDQTNPLSEVTHKRRVSAPgPGGLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSR 76
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSP-RGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
 87-152 8.27e-29

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: 106.30  E-value: 8.27e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 371560277   87 YRKVDNGKLTDDVVYLSAMEEARHTIAQANAGIDAGGTYVEELISARQAGEFLMAPASTITLADVS 152
Cdd:pfam10385   1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 8-360 3.87e-24

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 103.88  E-value: 3.87e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277    8 SQFMDQTNPLSEVTHKRRVSAPgpggLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRV---------- 77
Cdd:PRK08565  403 SQLLDRTNYLSTLSHLRRVVSP----LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQIsvgvdeeeve 478

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   78 ----------------NKY-----------------------------------------GFIETPY------------- 87
Cdd:PRK08565  479 eilyelgvvpveeareEEYiswsrvylngrligyhpdgeelaekirelrrsgkisdevnvAYIETGEinevyvncdsgrv 558

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277   88 -------------------RKVDNGKLT-DDVV------YLSAMEEARHTIAQANAGIDAGGTYVEelisarqagefLMA 141
Cdd:PRK08565  559 rrplivvengkpkltrehvEKLKKGELTfDDLVkmgvieYLDAEEEENAYVALDPEDLTPEHTHLE-----------IWP 627

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  142 PAstitladvspkqLVSVAASLIPFLENDDANRALMGSNMQRQAVPLvkaespfvgtgmegtvardsGAAIAAKRTGivd 221
Cdd:PRK08565  628 PA------------ILGITASIIPYPEHNQSPRNTYQAAMAKQSLGL--------------------YAANFRIRTD--- 672

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560277  222 qvdaTRiviratqevepgksgvdiYTLMKFErsnqstcinQRPLVTVGDLvqkgDIIA--DGPStedgelalGRNVLVAF 299
Cdd:PRK08565  673 ----TR------------------GHLLHYP---------QRPLVQTRAL----EIIGynDRPA--------GQNAVVAV 709

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 371560277  300 MPWNGYNYEDSILINEKIVKEDVFTSIHIDEFEVMARDTKLGPED-ITRDIPNV----GEEALKNL 360
Cdd:PRK08565  710 LSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDkIEIPEPNVrgyrGEEYYRKL 775
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 3-79 2.01e-22

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 98.10  E-value: 2.01e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 371560277   3 GSSQLSQFMDQTNPLSEVTHKRRVSAPgpggLTRERPAFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRVNK 79
Cdd:PRK09606 401 GRTGVSQLLDRTDYMATLSHLRRVVSP----LSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEIST 473
 
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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