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Conserved domains on  [gi|124028625|sp|Q3AZJ0|]
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RecName: Full=DNA-directed RNA polymerase subunit omega; Short=RNAP omega subunit; AltName: Full=RNA polymerase omega subunit; AltName: Full=Transcriptase subunit omega

Protein Classification

DNA-directed RNA polymerase subunit omega( domain architecture ID 52380)

DNA-directed RNA polymerase subunit omega promotes RNA polymerase assembly by latching the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits

EC:  2.7.7.6
Gene Ontology:  GO:0000428|GO:0003677|GO:0003899|GO:0006351
PubMed:  32920946|33238579|16908155

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNA_pol_Rpb6 super family cl14651
RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and ...
 13-82 2.57e-17

RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit. Rpb6 and omega are structurally conserved and both function in polymerase assembly.


The actual alignment was detected with superfamily member CHL00191:

Pssm-ID: 449344  Cd Length: 76  Bit Score: 69.04  E-value: 2.57e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124028625 13 VDSSDLAKRGESLIRQSSNRYLTTVRIAFRAKQRRFDDFDgLLEESSVKPVQRAIVELSDEQDQPDLLPG 82
Cdd:CHL00191  8 YDSNEILYKTEELLNAASNRYKITIQVANRAKRRRYEDID-IINDPSIKPIIRAILEMVDEINQPEIISD 76
 
Name Accession Description Interval E-value
ycf61 CHL00191
DNA-directed RNA polymerase subunit omega; Provisional
 13-82 2.57e-17

DNA-directed RNA polymerase subunit omega; Provisional


Pssm-ID: 214390  Cd Length: 76  Bit Score: 69.04  E-value: 2.57e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124028625 13 VDSSDLAKRGESLIRQSSNRYLTTVRIAFRAKQRRFDDFDgLLEESSVKPVQRAIVELSDEQDQPDLLPG 82
Cdd:CHL00191  8 YDSNEILYKTEELLNAASNRYKITIQVANRAKRRRYEDID-IINDPSIKPIIRAILEMVDEINQPEIISD 76
RNA_pol_Rpb6 pfam01192
RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and ...
 25-73 7.91e-07

RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit. Rpb6 and omega are structurally conserved and both function in polymerase assembly.


Pssm-ID: 426112  Cd Length: 52  Bit Score: 41.74  E-value: 7.91e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 124028625  25 LIRQSSNRYLTTVRIAFRAKQRRFDDFDgLLEESSVKPVQRAIVELSDE 73
Cdd:pfam01192  2 LLKKVDNRYELVVIAAKRARQLSMGAPP-IKLDSFDKPVVIALREIAEG 49
RpoZ COG1758
DNA-directed RNA polymerase, subunit K/omega [Transcription]; DNA-directed RNA polymerase, ...
 23-80 3.41e-06

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


Pssm-ID: 441364  Cd Length: 64  Bit Score: 40.16  E-value: 3.41e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 124028625 23 ESLIRQSSNRYLTTVRIAFRAKQRRfDDFDGLLEESSVKPVQRAIVELSDEQDQPDLL 80
Cdd:COG1758   7 EDLLEKVDNRYELVLLAAKRARQLA-EGAEPLVEPDSDKPVVIALREIAEGKITIEIL 63
 
Name Accession Description Interval E-value
ycf61 CHL00191
DNA-directed RNA polymerase subunit omega; Provisional
 13-82 2.57e-17

DNA-directed RNA polymerase subunit omega; Provisional


Pssm-ID: 214390  Cd Length: 76  Bit Score: 69.04  E-value: 2.57e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124028625 13 VDSSDLAKRGESLIRQSSNRYLTTVRIAFRAKQRRFDDFDgLLEESSVKPVQRAIVELSDEQDQPDLLPG 82
Cdd:CHL00191  8 YDSNEILYKTEELLNAASNRYKITIQVANRAKRRRYEDID-IINDPSIKPIIRAILEMVDEINQPEIISD 76
rpoZ PRK00392
DNA-directed RNA polymerase subunit omega; Reviewed
 23-81 3.65e-11

DNA-directed RNA polymerase subunit omega; Reviewed


Pssm-ID: 234744  Cd Length: 69  Bit Score: 53.00  E-value: 3.65e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 124028625 23 ESLIRQSSNRYLTTVRIAFRAKQRRFDDFDgLLEESSVKPVQRAIVELSDEQDQPDLLP 81
Cdd:PRK00392  7 EDLLEKVDNRYELVLLAAKRARQLRAGAKP-PVDKSSDKPVVIALREIAEGKVTYEILE 64
RNA_pol_Rpb6 pfam01192
RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and ...
 25-73 7.91e-07

RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit. Rpb6 and omega are structurally conserved and both function in polymerase assembly.


Pssm-ID: 426112  Cd Length: 52  Bit Score: 41.74  E-value: 7.91e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 124028625  25 LIRQSSNRYLTTVRIAFRAKQRRFDDFDgLLEESSVKPVQRAIVELSDE 73
Cdd:pfam01192  2 LLKKVDNRYELVVIAAKRARQLSMGAPP-IKLDSFDKPVVIALREIAEG 49
RpoZ COG1758
DNA-directed RNA polymerase, subunit K/omega [Transcription]; DNA-directed RNA polymerase, ...
 23-80 3.41e-06

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


Pssm-ID: 441364  Cd Length: 64  Bit Score: 40.16  E-value: 3.41e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 124028625 23 ESLIRQSSNRYLTTVRIAFRAKQRRfDDFDGLLEESSVKPVQRAIVELSDEQDQPDLL 80
Cdd:COG1758   7 EDLLEKVDNRYELVLLAAKRARQLA-EGAEPLVEPDSDKPVVIALREIAEGKITIEIL 63
 
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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