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Conserved domains on  [gi|157879780]
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Chain A, DNA-DIRECTED RNA POLYMERASE II 14.4 KD POLYPEPTIDE

Protein Classification

RpoK/RPB6 RNA polymerase subunit family protein( domain architecture ID 10010664)

RpoK/RPB6 RNA polymerase subunit family protein similar to DNA-directed RNA polymerases I, II, and III subunit RPABC2 is a common component of RNA polymerases I, II, and III, which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN00152 PLN00152
DNA-directed RNA polymerase; Provisional
 26-127 1.19e-45

DNA-directed RNA polymerase; Provisional


:

Pssm-ID: 177755  Cd Length: 130  Bit Score: 144.24  E-value: 1.19e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157879780  26 ENAEEEGQENVEILPSGERPQANQkRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPII 105
Cdd:PLN00152  30 NNDEVKGSIGENEDKEEQEPVQRP-RKTTPYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFT 108

                         90       100
                 ....*....|....*....|..
gi 157879780 106 IRRYLPDGSYEDWGVDELIITD 127
Cdd:PLN00152 109 IRRYLPDGSYEDWGVDELIVED 130
 
Name Accession Description Interval E-value
PLN00152 PLN00152
DNA-directed RNA polymerase; Provisional
 26-127 1.19e-45

DNA-directed RNA polymerase; Provisional


Pssm-ID: 177755  Cd Length: 130  Bit Score: 144.24  E-value: 1.19e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157879780  26 ENAEEEGQENVEILPSGERPQANQkRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPII 105
Cdd:PLN00152  30 NNDEVKGSIGENEDKEEQEPVQRP-RKTTPYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFT 108

                         90       100
                 ....*....|....*....|..
gi 157879780 106 IRRYLPDGSYEDWGVDELIITD 127
Cdd:PLN00152 109 IRRYLPDGSYEDWGVDELIVED 130
RNA_pol_Rpb6 pfam01192
RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and ...
 51-103 5.89e-10

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: 50.99  E-value: 5.89e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 157879780   51 RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGEtDPLLIAMKELKARKIP 103
Cdd:pfam01192   1 DLLKKVDNRYELVVIAAKRARQLSMGAPPIKLDSFD-KPVVIALREIAEGKIP 52
RpoZ COG1758
DNA-directed RNA polymerase, subunit K/omega [Transcription]; DNA-directed RNA polymerase, ...
 59-108 5.71e-03

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: 33.22  E-value: 5.71e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 157879780  59 KYERARVLGTRALQIAMCAPVMVELEGEtDPLLIAMKELKARKIPIIIRR 108
Cdd:COG1758   16 RYELVLLAAKRARQLAEGAEPLVEPDSD-KPVVIALREIAEGKITIEILE 64
 
Name Accession Description Interval E-value
PLN00152 PLN00152
DNA-directed RNA polymerase; Provisional
 26-127 1.19e-45

DNA-directed RNA polymerase; Provisional


Pssm-ID: 177755  Cd Length: 130  Bit Score: 144.24  E-value: 1.19e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157879780  26 ENAEEEGQENVEILPSGERPQANQkRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPII 105
Cdd:PLN00152  30 NNDEVKGSIGENEDKEEQEPVQRP-RKTTPYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFT 108

                         90       100
                 ....*....|....*....|..
gi 157879780 106 IRRYLPDGSYEDWGVDELIITD 127
Cdd:PLN00152 109 IRRYLPDGSYEDWGVDELIVED 130
rpoK PRK01099
DNA-directed RNA polymerase subunit K; Provisional
 52-112 1.07e-23

DNA-directed RNA polymerase subunit K; Provisional


Pssm-ID: 179220  Cd Length: 62  Bit Score: 86.52  E-value: 1.07e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 157879780  52 ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPD 112
Cdd:PRK01099   2 MGPMKLTRFERARIIGARALQISMGAPVLIDIPESTDPLDIAEEEFKRGVLPITVKRPLPN 62
RNA_pol_Rpb6 pfam01192
RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and ...
 51-103 5.89e-10

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: 50.99  E-value: 5.89e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 157879780   51 RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGEtDPLLIAMKELKARKIP 103
Cdd:pfam01192   1 DLLKKVDNRYELVVIAAKRARQLSMGAPPIKLDSFD-KPVVIALREIAEGKIP 52
RpoZ COG1758
DNA-directed RNA polymerase, subunit K/omega [Transcription]; DNA-directed RNA polymerase, ...
 59-108 5.71e-03

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: 33.22  E-value: 5.71e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 157879780  59 KYERARVLGTRALQIAMCAPVMVELEGEtDPLLIAMKELKARKIPIIIRR 108
Cdd:COG1758   16 RYELVLLAAKRARQLAEGAEPLVEPDSD-KPVVIALREIAEGKITIEILE 64
 
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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