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Conserved domains on  [gi|464680|sp|P35018|]
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RecName: Full=DNA-directed RNA polymerase subunit beta''; AltName: Full=PEP; AltName: Full=Plastid-encoded RNA polymerase subunit beta''; Short=RNA polymerase subunit beta''

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
rpoC2 super family cl35188
DNA-directed RNA polymerase subunit beta'; Provisional
1-66 6.86e-24

DNA-directed RNA polymerase subunit beta'; Provisional


The actual alignment was detected with superfamily member PRK02597:

Pssm-ID: 235052 [Multi-domain]  Cd Length: 1331  Bit Score: 93.14  E-value: 6.86e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 464680       1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTGFKQFYLYEYTKKNCEENIISLDPYNFE 66
Cdd:PRK02597 1184 SFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSGFEEELSAEAGPHPDILAEDPAGYR 1249
 
Name Accession Description Interval E-value
rpoC2 PRK02597
DNA-directed RNA polymerase subunit beta'; Provisional
1-66 6.86e-24

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 235052 [Multi-domain]  Cd Length: 1331  Bit Score: 93.14  E-value: 6.86e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 464680       1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTGFKQFYLYEYTKKNCEENIISLDPYNFE 66
Cdd:PRK02597 1184 SFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSGFEEELSAEAGPHPDILAEDPAGYR 1249
RNAP_beta'_C cd02655
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ...
1-40 2.24e-23

Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.


Pssm-ID: 132721 [Multi-domain]  Cd Length: 204  Bit Score: 87.97  E-value: 2.24e-23
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 464680     1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTGF 40
Cdd:cd02655 165 SFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204
rpoC2_cyan TIGR02388
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ...
1-43 1.20e-20

DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274104 [Multi-domain]  Cd Length: 1227  Bit Score: 84.13  E-value: 1.20e-20
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 464680        1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTGFKQF 43
Cdd:TIGR02388 1183 SFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSSY 1225
 
Name Accession Description Interval E-value
rpoC2 PRK02597
DNA-directed RNA polymerase subunit beta'; Provisional
1-66 6.86e-24

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 235052 [Multi-domain]  Cd Length: 1331  Bit Score: 93.14  E-value: 6.86e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 464680       1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTGFKQFYLYEYTKKNCEENIISLDPYNFE 66
Cdd:PRK02597 1184 SFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSGFEEELSAEAGPHPDILAEDPAGYR 1249
RNAP_beta'_C cd02655
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ...
1-40 2.24e-23

Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.


Pssm-ID: 132721 [Multi-domain]  Cd Length: 204  Bit Score: 87.97  E-value: 2.24e-23
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 464680     1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTGF 40
Cdd:cd02655 165 SFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204
rpoC2 CHL00117
RNA polymerase beta'' subunit; Reviewed
1-72 3.92e-23

RNA polymerase beta'' subunit; Reviewed


Pssm-ID: 214368 [Multi-domain]  Cd Length: 1364  Bit Score: 91.15  E-value: 3.92e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 464680       1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTGFKQFY--LYEYTKKNCEENIISLDPYNFEDNIIYK 72
Cdd:CHL00117 1278 SFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKGLVhrSKQHKNKNLEIKKKNLFEGEMRDILFHH 1351
PRK00566 PRK00566
DNA-directed RNA polymerase subunit beta'; Provisional
1-43 1.46e-21

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 234794 [Multi-domain]  Cd Length: 1156  Bit Score: 86.66  E-value: 1.46e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 464680       1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTGFKQF 43
Cdd:PRK00566 1098 SFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARY 1140
rpoC2_cyan TIGR02388
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ...
1-43 1.20e-20

DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274104 [Multi-domain]  Cd Length: 1227  Bit Score: 84.13  E-value: 1.20e-20
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 464680        1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTGFKQF 43
Cdd:TIGR02388 1183 SFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSSY 1225
rpoC_TIGR TIGR02386
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
1-41 4.76e-18

DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274103 [Multi-domain]  Cd Length: 1140  Bit Score: 76.63  E-value: 4.76e-18
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 464680        1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTGFK 41
Cdd:TIGR02386 1096 SFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLK 1136
PRK14906 PRK14906
DNA-directed RNA polymerase subunit beta';
1-51 7.01e-14

DNA-directed RNA polymerase subunit beta';


Pssm-ID: 184899 [Multi-domain]  Cd Length: 1460  Bit Score: 64.89  E-value: 7.01e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 464680       1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTGFKQFYLYEYTKK 51
Cdd:PRK14906 1197 SFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTGLSRYRDVGLTYH 1247
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-40 9.53e-13

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 61.56  E-value: 9.53e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 464680       1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTGF 40
Cdd:PRK14844 2745 SFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTGL 2784
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-50 8.15e-12

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 59.17  E-value: 8.15e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 464680       1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTGF---KQFYLYEYTK 50
Cdd:PRK09603 2834 SFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTGMyknKKIVLRTLED 2886
RNAP_largest_subunit_C cd00630
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
1-39 1.71e-09

Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.


Pssm-ID: 132719 [Multi-domain]  Cd Length: 158  Bit Score: 50.88  E-value: 1.71e-09
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 464680     1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTG 39
Cdd:cd00630 119 SFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTG 157
RNAP_A'' cd06528
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ...
1-39 1.32e-06

A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.


Pssm-ID: 132725 [Multi-domain]  Cd Length: 363  Bit Score: 44.16  E-value: 1.32e-06
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 464680     1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTG 39
Cdd:cd06528 317 AFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTG 355
PRK04309 PRK04309
DNA-directed RNA polymerase subunit A''; Validated
2-39 1.68e-06

DNA-directed RNA polymerase subunit A''; Validated


Pssm-ID: 235277 [Multi-domain]  Cd Length: 383  Bit Score: 43.68  E-value: 1.68e-06
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 464680      2 FQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTG 39
Cdd:PRK04309 335 FEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTG 372
PRK14898 PRK14898
DNA-directed RNA polymerase subunit A''; Provisional
1-39 4.15e-05

DNA-directed RNA polymerase subunit A''; Provisional


Pssm-ID: 237854 [Multi-domain]  Cd Length: 858  Bit Score: 39.88  E-value: 4.15e-05
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 464680      1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTG 39
Cdd:PRK14898 804 AFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTG 842
PRK14897 PRK14897
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
1-39 1.09e-04

unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional


Pssm-ID: 237853 [Multi-domain]  Cd Length: 509  Bit Score: 38.64  E-value: 1.09e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 464680      1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTG 39
Cdd:PRK14897 458 AFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTG 496
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
1-51 1.62e-03

bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 35.39  E-value: 1.62e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 464680       1 SFQETRRVLTKAAFENHIDWLKGLKENVIIGRLIPAGTGfKQFYLYEYTKK 51
Cdd:PRK14977 1271 AFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSG-KVDLLMDFSGK 1320
 
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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