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Conserved domains on  [gi|667477985|ref|NP_001288059|]
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DNA-directed RNA polymerases I, II, and III subunit RPABC2 isoform 3 [Homo sapiens]

Protein Classification

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 ...
 26-100 1.95e-27

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 PLN00152:

Pssm-ID: 449344  Cd Length: 130  Bit Score: 99.17  E-value: 1.95e-27
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 667477985  26 ENAEEEGQENVEILPSGERPQANQkRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELNAR 100
Cdd:PLN00152  30 NNDEVKGSIGENEDKEEQEPVQRP-RKTTPYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRER 103
 
Name Accession Description Interval E-value
PLN00152 PLN00152
DNA-directed RNA polymerase; Provisional
 26-100 1.95e-27

DNA-directed RNA polymerase; Provisional


Pssm-ID: 177755  Cd Length: 130  Bit Score: 99.17  E-value: 1.95e-27
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 667477985  26 ENAEEEGQENVEILPSGERPQANQkRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELNAR 100
Cdd:PLN00152  30 NNDEVKGSIGENEDKEEQEPVQRP-RKTTPYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRER 103
RNA_pol_Rpb6 pfam01192
RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and ...
 51-99 1.03e-09

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: 51.37  E-value: 1.03e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 667477985   51 RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGEtDPLLIAMKELNA 99
Cdd:pfam01192   1 DLLKKVDNRYELVVIAAKRARQLSMGAPPIKLDSFD-KPVVIALREIAE 48
 
Name Accession Description Interval E-value
PLN00152 PLN00152
DNA-directed RNA polymerase; Provisional
 26-100 1.95e-27

DNA-directed RNA polymerase; Provisional


Pssm-ID: 177755  Cd Length: 130  Bit Score: 99.17  E-value: 1.95e-27
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 667477985  26 ENAEEEGQENVEILPSGERPQANQkRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELNAR 100
Cdd:PLN00152  30 NNDEVKGSIGENEDKEEQEPVQRP-RKTTPYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRER 103
rpoK PRK01099
DNA-directed RNA polymerase subunit K; Provisional
 52-99 4.10e-18

DNA-directed RNA polymerase subunit K; Provisional


Pssm-ID: 179220  Cd Length: 62  Bit Score: 73.42  E-value: 4.10e-18
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 667477985  52 ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELNA 99
Cdd:PRK01099   2 MGPMKLTRFERARIIGARALQISMGAPVLIDIPESTDPLDIAEEEFKR 49
RNA_pol_Rpb6 pfam01192
RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and ...
 51-99 1.03e-09

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: 51.37  E-value: 1.03e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 667477985   51 RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGEtDPLLIAMKELNA 99
Cdd:pfam01192   1 DLLKKVDNRYELVVIAAKRARQLSMGAPPIKLDSFD-KPVVIALREIAE 48
 
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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