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Conserved domains on  [gi|78101161|pdb|1ZYR|E]
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Chain E, DNA-directed RNA polymerase omega chain

Protein Classification

DNA-directed RNA polymerase subunit omega( domain architecture ID 10011409)

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:0003677|GO:0003899|GO:0000428|GO:0006351
PubMed:  32920946|33238579|16908155

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rpoZ PRK00392
DNA-directed RNA polymerase subunit omega; Reviewed
 1-84 3.03e-09

DNA-directed RNA polymerase subunit omega; Reviewed


:

Pssm-ID: 234744  Cd Length: 69  Bit Score: 48.76  E-value: 3.03e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1ZYR_E        1 MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFkntvlEPEERPKMqtleglfddpNAETWAMKELLTGRLVFGENLV 80
Cdd:PRK00392  1 MARPTIEDLLEKVDNRYELVLLAAKRARQLRAGAK-----PPVDKSSD----------KPVVIALREIAEGKVTYEILEE 65


                ....
1ZYR_E       81 PEDR 84
Cdd:PRK00392 66 VEIE 69
 
Name Accession Description Interval E-value
rpoZ PRK00392
DNA-directed RNA polymerase subunit omega; Reviewed
 1-84 3.03e-09

DNA-directed RNA polymerase subunit omega; Reviewed


Pssm-ID: 234744  Cd Length: 69  Bit Score: 48.76  E-value: 3.03e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1ZYR_E        1 MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFkntvlEPEERPKMqtleglfddpNAETWAMKELLTGRLVFGENLV 80
Cdd:PRK00392  1 MARPTIEDLLEKVDNRYELVLLAAKRARQLRAGAK-----PPVDKSSD----------KPVVIALREIAEGKVTYEILEE 65


                ....
1ZYR_E       81 PEDR 84
Cdd:PRK00392 66 VEIE 69
RpoZ COG1758
DNA-directed RNA polymerase, subunit K/omega [Transcription]; DNA-directed RNA polymerase, ...
 1-46 1.08e-08

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: 47.09  E-value: 1.08e-08
                       10        20        30        40
               ....*....|....*....|....*....|....*....|....*.
1ZYR_E       1 MAEPGIDKLFGMVDSKYRLTVVVAKRAQQlLRHGFKNTVLEPEERP 46
Cdd:COG1758  1 MARPTVEDLLEKVDNRYELVLLAAKRARQ-LAEGAEPLVEPDSDKP 45
rpoZ TIGR00690
DNA-directed RNA polymerase, omega subunit; This small component of highly purified E. coli ...
 1-47 2.01e-05

DNA-directed RNA polymerase, omega subunit; This small component of highly purified E. coli RNA polymerase is not required for transcription, but acts in assembly and is present in stochiometric amounts. The trusted cutoff excludes archaeal homologs but captures some organellar sequences. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 188073  Cd Length: 60  Bit Score: 38.99  E-value: 2.01e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
1ZYR_E         1 MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGfkNTVLEPEERPK 47
Cdd:TIGR00690  1 MARPTIEDAMKKIGSRYDLVLVAARRARQLQLEG--GDPIVPEENDK 45
RNA_pol_Rpb6 pfam01192
RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and ...
 13-57 3.81e-05

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: 37.89  E-value: 3.81e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
1ZYR_E        13 VDSKYRLTVVVAKRAQQlLRHGFKNTVLEPEERPKMQTLEGLFDD 57
Cdd:pfam01192  6 VDNRYELVVIAAKRARQ-LSMGAPPIKLDSFDKPVVIALREIAEG 49
 
Name Accession Description Interval E-value
rpoZ PRK00392
DNA-directed RNA polymerase subunit omega; Reviewed
 1-84 3.03e-09

DNA-directed RNA polymerase subunit omega; Reviewed


Pssm-ID: 234744  Cd Length: 69  Bit Score: 48.76  E-value: 3.03e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1ZYR_E        1 MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFkntvlEPEERPKMqtleglfddpNAETWAMKELLTGRLVFGENLV 80
Cdd:PRK00392  1 MARPTIEDLLEKVDNRYELVLLAAKRARQLRAGAK-----PPVDKSSD----------KPVVIALREIAEGKVTYEILEE 65


                ....
1ZYR_E       81 PEDR 84
Cdd:PRK00392 66 VEIE 69
RpoZ COG1758
DNA-directed RNA polymerase, subunit K/omega [Transcription]; DNA-directed RNA polymerase, ...
 1-46 1.08e-08

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: 47.09  E-value: 1.08e-08
                       10        20        30        40
               ....*....|....*....|....*....|....*....|....*.
1ZYR_E       1 MAEPGIDKLFGMVDSKYRLTVVVAKRAQQlLRHGFKNTVLEPEERP 46
Cdd:COG1758  1 MARPTVEDLLEKVDNRYELVLLAAKRARQ-LAEGAEPLVEPDSDKP 45
rpoZ TIGR00690
DNA-directed RNA polymerase, omega subunit; This small component of highly purified E. coli ...
 1-47 2.01e-05

DNA-directed RNA polymerase, omega subunit; This small component of highly purified E. coli RNA polymerase is not required for transcription, but acts in assembly and is present in stochiometric amounts. The trusted cutoff excludes archaeal homologs but captures some organellar sequences. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 188073  Cd Length: 60  Bit Score: 38.99  E-value: 2.01e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
1ZYR_E         1 MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGfkNTVLEPEERPK 47
Cdd:TIGR00690  1 MARPTIEDAMKKIGSRYDLVLVAARRARQLQLEG--GDPIVPEENDK 45
RNA_pol_Rpb6 pfam01192
RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and ...
 13-57 3.81e-05

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: 37.89  E-value: 3.81e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
1ZYR_E        13 VDSKYRLTVVVAKRAQQlLRHGFKNTVLEPEERPKMQTLEGLFDD 57
Cdd:pfam01192  6 VDNRYELVVIAAKRARQ-LSMGAPPIKLDSFDKPVVIALREIAEG 49
 
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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