NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|661918392|pdb|4NC8|B]
View 

Chain B, DNA-directed RNA polymerase subunit delta

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RpoE COG3343
DNA-directed RNA polymerase, delta subunit [Transcription]; DNA-directed RNA polymerase, delta ...
 2-91 1.23e-43

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: 136.56  E-value: 1.23e-43
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NC8_B       2 IKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSWY 81
Cdd:COG3343  1 LKELSKEQLKELSMIELAYEILEEKGEPMSFRDLIKEVAELKGLSDEELKERIAQFYTDLNIDGRFVSLGENRWGLREWY 80

                       90
               ....*....|
4NC8_B      82 PYDQLDEETQ 91
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 ...
 2-91 1.23e-43

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: 136.56  E-value: 1.23e-43
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NC8_B       2 IKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSWY 81
Cdd:COG3343  1 LKELSKEQLKELSMIELAYEILEEKGEPMSFRDLIKEVAELKGLSDEELKERIAQFYTDLNIDGRFVSLGENRWGLREWY 80

                       90
               ....*....|
4NC8_B      82 PYDQLDEETQ 91
Cdd:COG3343 81 PVDQIDEEIA 90
RNAP_delt_lowGC TIGR04567
DNA-directed RNA polymerase delta subunit; Members of this family are the RNA polymerase delta ...
 11-91 7.00e-38

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: 121.91  E-value: 7.00e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NC8_B        11 KEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSWYPYDQLDEET 90
Cdd:TIGR04567  1 NELSMVDLAYEILKEKKEPMSFYDLWNEVAKLKGLSDEEIEERIAQFYTDLNLDGRFISLGENKWGLRSWYPFEEIDEET 80


                 .
4NC8_B        91 Q 91
Cdd:TIGR04567 81 A 81
HARE-HTH pfam05066
HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in ...
 13-80 2.86e-16

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: 66.95  E-value: 2.86e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
4NC8_B        13 MALVEIAHELFEEHKKPVPFQELLNEIASLLGVKK--EELGDRI-AQFYTDLNIDGRFLALSDQTWGLRSW 80
Cdd:pfam05066  1 GTLKEAAFQVLEEEGRPLHFKEIAEEIQEKGLISLsgKTPEATLaAQLYTDIKEDSLFVRVGPGTFGLRSW 71
 
Name Accession Description Interval E-value
RpoE COG3343
DNA-directed RNA polymerase, delta subunit [Transcription]; DNA-directed RNA polymerase, delta ...
 2-91 1.23e-43

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: 136.56  E-value: 1.23e-43
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NC8_B       2 IKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSWY 81
Cdd:COG3343  1 LKELSKEQLKELSMIELAYEILEEKGEPMSFRDLIKEVAELKGLSDEELKERIAQFYTDLNIDGRFVSLGENRWGLREWY 80

                       90
               ....*....|
4NC8_B      82 PYDQLDEETQ 91
Cdd:COG3343 81 PVDQIDEEIA 90
RNAP_delt_lowGC TIGR04567
DNA-directed RNA polymerase delta subunit; Members of this family are the RNA polymerase delta ...
 11-91 7.00e-38

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: 121.91  E-value: 7.00e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NC8_B        11 KEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSWYPYDQLDEET 90
Cdd:TIGR04567  1 NELSMVDLAYEILKEKKEPMSFYDLWNEVAKLKGLSDEEIEERIAQFYTDLNLDGRFISLGENKWGLRSWYPFEEIDEET 80


                 .
4NC8_B        91 Q 91
Cdd:TIGR04567 81 A 81
HARE-HTH pfam05066
HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in ...
 13-80 2.86e-16

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: 66.95  E-value: 2.86e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
4NC8_B        13 MALVEIAHELFEEHKKPVPFQELLNEIASLLGVKK--EELGDRI-AQFYTDLNIDGRFLALSDQTWGLRSW 80
Cdd:pfam05066  1 GTLKEAAFQVLEEEGRPLHFKEIAEEIQEKGLISLsgKTPEATLaAQLYTDIKEDSLFVRVGPGTFGLRSW 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH