RecName: Full=DNA-directed RNA polymerase subunit beta''; AltName: Full=PEP; AltName: Full=Plastid-encoded RNA polymerase subunit beta''; Short=RNA polymerase subunit beta''
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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Blast search parameters | ||||
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