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Conserved domains on  [gi|1823964775|gb|KAF3502837|]
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hypothetical protein F2Q69_00039614 [Brassica cretica]

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
 81-207 1.25e-63

DNA-directed RNA polymerase; Provisional


:

Pssm-ID: 177755  Cd Length: 130  Bit Score: 193.55  E-value: 1.25e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1823964775  81 DGDKKYEDEPAEPEIEEGVEDDAEMKENDDVDGEPIEAEDKVEEEAVPRPRKTSKFMTKYERARILGTRALQISMNAPVM 160
Cdd:PLN00152    4 DMDMGYEDEPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQEPVQRPRKTTPYMTKYERARILGTRALQISMNAPVM 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1823964775 161 VELEGETDPLEIAMKELRQRKIPFTIRRYLPDGSFEEWGVDELIVED 207
Cdd:PLN00152   84 VELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 130
 
Name Accession Description Interval E-value
PLN00152 PLN00152
DNA-directed RNA polymerase; Provisional
 81-207 1.25e-63

DNA-directed RNA polymerase; Provisional


Pssm-ID: 177755  Cd Length: 130  Bit Score: 193.55  E-value: 1.25e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1823964775  81 DGDKKYEDEPAEPEIEEGVEDDAEMKENDDVDGEPIEAEDKVEEEAVPRPRKTSKFMTKYERARILGTRALQISMNAPVM 160
Cdd:PLN00152    4 DMDMGYEDEPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQEPVQRPRKTTPYMTKYERARILGTRALQISMNAPVM 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1823964775 161 VELEGETDPLEIAMKELRQRKIPFTIRRYLPDGSFEEWGVDELIVED 207
Cdd:PLN00152   84 VELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 130
RNA_pol_Rpb6 pfam01192
RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and ...
 131-183 5.07e-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: 50.60  E-value: 5.07e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1823964775 131 RKTSKFMTKYERARILGTRALQISMNAPVMVELEGEtDPLEIAMKELRQRKIP 183
Cdd:pfam01192   1 DLLKKVDNRYELVVIAAKRARQLSMGAPPIKLDSFD-KPVVIALREIAEGKIP 52
RpoZ COG1758
DNA-directed RNA polymerase, subunit K/omega [Transcription]; DNA-directed RNA polymerase, ...
 139-188 6.19e-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: 33.99  E-value: 6.19e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1823964775 139 KYERARILGTRALQISMNAPVMVELEGEtDPLEIAMKELRQRKIPFTIRR 188
Cdd:COG1758    16 RYELVLLAAKRARQLAEGAEPLVEPDSD-KPVVIALREIAEGKITIEILE 64
 
Name Accession Description Interval E-value
PLN00152 PLN00152
DNA-directed RNA polymerase; Provisional
 81-207 1.25e-63

DNA-directed RNA polymerase; Provisional


Pssm-ID: 177755  Cd Length: 130  Bit Score: 193.55  E-value: 1.25e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1823964775  81 DGDKKYEDEPAEPEIEEGVEDDAEMKENDDVDGEPIEAEDKVEEEAVPRPRKTSKFMTKYERARILGTRALQISMNAPVM 160
Cdd:PLN00152    4 DMDMGYEDEPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQEPVQRPRKTTPYMTKYERARILGTRALQISMNAPVM 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1823964775 161 VELEGETDPLEIAMKELRQRKIPFTIRRYLPDGSFEEWGVDELIVED 207
Cdd:PLN00152   84 VELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 130
rpoK PRK01099
DNA-directed RNA polymerase subunit K; Provisional
 138-192 2.77e-23

DNA-directed RNA polymerase subunit K; Provisional


Pssm-ID: 179220  Cd Length: 62  Bit Score: 88.45  E-value: 2.77e-23
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1823964775 138 TKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRQRKIPFTIRRYLPD 192
Cdd:PRK01099    8 TRFERARIIGARALQISMGAPVLIDIPESTDPLDIAEEEFKRGVLPITVKRPLPN 62
RNA_pol_Rpb6 pfam01192
RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and ...
 131-183 5.07e-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: 50.60  E-value: 5.07e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1823964775 131 RKTSKFMTKYERARILGTRALQISMNAPVMVELEGEtDPLEIAMKELRQRKIP 183
Cdd:pfam01192   1 DLLKKVDNRYELVVIAAKRARQLSMGAPPIKLDSFD-KPVVIALREIAEGKIP 52
RpoZ COG1758
DNA-directed RNA polymerase, subunit K/omega [Transcription]; DNA-directed RNA polymerase, ...
 139-188 6.19e-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: 33.99  E-value: 6.19e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1823964775 139 KYERARILGTRALQISMNAPVMVELEGEtDPLEIAMKELRQRKIPFTIRR 188
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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