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Conserved domains on  [gi|446624137|ref|WP_000701483|]
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MULTISPECIES: DNA-directed RNA polymerase subunit delta [Staphylococcus]

Protein Classification

DNA-directed RNA polymerase subunit delta( domain architecture ID 10007243)

DNA-directed RNA polymerase subunit delta participates in both the initiation and recycling phases of transcription

EC:  2.7.7.6
Gene Ontology:  GO:0003899|GO:0006351|GO:0003677|GO:0000428|GO:0006355
PubMed:  24211837|18468900|12361249
SCOP:  4005291

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE COG3343
DNA-directed RNA polymerase, delta subunit [Transcription]; DNA-directed RNA polymerase, delta ...
 3-92 1.05e-36

DNA-directed RNA polymerase, delta subunit [Transcription]; DNA-directed RNA polymerase, delta subunit is part of the Pathway/BioSystem: RNA polymerase


:

Pssm-ID: 442572  Cd Length: 90  Bit Score: 122.31  E-value: 1.05e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446624137   3 IQDYTKQMVDEKSFIDMAYTLLNDKGETMNLYDIIDEFRALGDYEYEEIENRVVQFYTDLNTDGRFLNVGENLWGLRDWY 82
Cdd:COG3343    1 LKELSKEQLKELSMIELAYEILEEKGEPMSFRDLIKEVAELKGLSDEELKERIAQFYTDLNIDGRFVSLGENRWGLREWY 80

                         90
                 ....*....|
gi 446624137  83 SVDDIEEKIA 92
Cdd:COG3343   81 PVDQIDEEIA 90
 
Name Accession Description Interval E-value
RpoE COG3343
DNA-directed RNA polymerase, delta subunit [Transcription]; DNA-directed RNA polymerase, delta ...
 3-92 1.05e-36

DNA-directed RNA polymerase, delta subunit [Transcription]; DNA-directed RNA polymerase, delta subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 442572  Cd Length: 90  Bit Score: 122.31  E-value: 1.05e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446624137   3 IQDYTKQMVDEKSFIDMAYTLLNDKGETMNLYDIIDEFRALGDYEYEEIENRVVQFYTDLNTDGRFLNVGENLWGLRDWY 82
Cdd:COG3343    1 LKELSKEQLKELSMIELAYEILEEKGEPMSFRDLIKEVAELKGLSDEELKERIAQFYTDLNIDGRFVSLGENRWGLREWY 80

                         90
                 ....*....|
gi 446624137  83 SVDDIEEKIA 92
Cdd:COG3343   81 PVDQIDEEIA 90
RNAP_delt_lowGC TIGR04567
DNA-directed RNA polymerase delta subunit; Members of this family are the RNA polymerase delta ...
 12-94 8.22e-32

DNA-directed RNA polymerase delta subunit; Members of this family are the RNA polymerase delta subunit, as found in the Firmicutes and the Mollicutes. All members of the seed alignment have an extended C-terminal low-complexity region, consisting largely of Asp and Glu, that is not included in the model. Proteins giving borderline scores should be checked to confirm a similar acidic C-terminal domain. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 275360  Cd Length: 83  Bit Score: 109.58  E-value: 8.22e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446624137   12 DEKSFIDMAYTLLNDKGETMNLYDIIDEFRALGDYEYEEIENRVVQFYTDLNTDGRFLNVGENLWGLRDWYSVDDIEEKI 91
Cdd:TIGR04567   1 NELSMVDLAYEILKEKKEPMSFYDLWNEVAKLKGLSDEEIEERIAQFYTDLNLDGRFISLGENKWGLRSWYPFEEIDEET 80


                  ...
gi 446624137   92 APT 94
Cdd:TIGR04567  81 API 83
HARE-HTH pfam05066
HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in ...
 15-81 1.67e-09

HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in the plant HB1, vertebrate ASXL, the H. pylori restriction endonuclease HpyAIII(HgrA), the RNA polymerase delta subunit(RpoE) of Gram positive bacteria and several restriction endonucleases. The domain is distinguished by the presence of a conserved one-turn helix between helix-3 and the preceding conserved turn. Its diverse architectures in eukaryotic species with extensive gene body methylation is suggestive of a chromatin function. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as hmC. Bacterial versions include fusions to diverse restriction endonucleases, and a DNA glycosylase where it may play a similar role in detecting modified DNA. Certain bacterial version of the HARE-HTH domain show fusions to the helix-hairpin-helix domain of the RNA polymerase alpha subunit and the HTH domains found in regions 3 and 4 of the sigma factors. These versions are predicted to function as a novel inhibitor of the binding of RNA polymerase to transcription start sites, similar to the Bacillus delta protein.


Pssm-ID: 461541  Cd Length: 71  Bit Score: 51.54  E-value: 1.67e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446624137   15 SFIDMAYTLLNDKGETMNLYDIIDEF--RALGDYEYEEIENRV-VQFYTDLNTDGRFLNVGENLWGLRDW 81
Cdd:pfam05066   2 TLKEAAFQVLEEEGRPLHFKEIAEEIqeKGLISLSGKTPEATLaAQLYTDIKEDSLFVRVGPGTFGLRSW 71
 
Name Accession Description Interval E-value
RpoE COG3343
DNA-directed RNA polymerase, delta subunit [Transcription]; DNA-directed RNA polymerase, delta ...
 3-92 1.05e-36

DNA-directed RNA polymerase, delta subunit [Transcription]; DNA-directed RNA polymerase, delta subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 442572  Cd Length: 90  Bit Score: 122.31  E-value: 1.05e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446624137   3 IQDYTKQMVDEKSFIDMAYTLLNDKGETMNLYDIIDEFRALGDYEYEEIENRVVQFYTDLNTDGRFLNVGENLWGLRDWY 82
Cdd:COG3343    1 LKELSKEQLKELSMIELAYEILEEKGEPMSFRDLIKEVAELKGLSDEELKERIAQFYTDLNIDGRFVSLGENRWGLREWY 80

                         90
                 ....*....|
gi 446624137  83 SVDDIEEKIA 92
Cdd:COG3343   81 PVDQIDEEIA 90
RNAP_delt_lowGC TIGR04567
DNA-directed RNA polymerase delta subunit; Members of this family are the RNA polymerase delta ...
 12-94 8.22e-32

DNA-directed RNA polymerase delta subunit; Members of this family are the RNA polymerase delta subunit, as found in the Firmicutes and the Mollicutes. All members of the seed alignment have an extended C-terminal low-complexity region, consisting largely of Asp and Glu, that is not included in the model. Proteins giving borderline scores should be checked to confirm a similar acidic C-terminal domain. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 275360  Cd Length: 83  Bit Score: 109.58  E-value: 8.22e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446624137   12 DEKSFIDMAYTLLNDKGETMNLYDIIDEFRALGDYEYEEIENRVVQFYTDLNTDGRFLNVGENLWGLRDWYSVDDIEEKI 91
Cdd:TIGR04567   1 NELSMVDLAYEILKEKKEPMSFYDLWNEVAKLKGLSDEEIEERIAQFYTDLNLDGRFISLGENKWGLRSWYPFEEIDEET 80


                  ...
gi 446624137   92 APT 94
Cdd:TIGR04567  81 API 83
HARE-HTH pfam05066
HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in ...
 15-81 1.67e-09

HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in the plant HB1, vertebrate ASXL, the H. pylori restriction endonuclease HpyAIII(HgrA), the RNA polymerase delta subunit(RpoE) of Gram positive bacteria and several restriction endonucleases. The domain is distinguished by the presence of a conserved one-turn helix between helix-3 and the preceding conserved turn. Its diverse architectures in eukaryotic species with extensive gene body methylation is suggestive of a chromatin function. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as hmC. Bacterial versions include fusions to diverse restriction endonucleases, and a DNA glycosylase where it may play a similar role in detecting modified DNA. Certain bacterial version of the HARE-HTH domain show fusions to the helix-hairpin-helix domain of the RNA polymerase alpha subunit and the HTH domains found in regions 3 and 4 of the sigma factors. These versions are predicted to function as a novel inhibitor of the binding of RNA polymerase to transcription start sites, similar to the Bacillus delta protein.


Pssm-ID: 461541  Cd Length: 71  Bit Score: 51.54  E-value: 1.67e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446624137   15 SFIDMAYTLLNDKGETMNLYDIIDEF--RALGDYEYEEIENRV-VQFYTDLNTDGRFLNVGENLWGLRDW 81
Cdd:pfam05066   2 TLKEAAFQVLEEEGRPLHFKEIAEEIqeKGLISLSGKTPEATLaAQLYTDIKEDSLFVRVGPGTFGLRSW 71
 
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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