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Conserved domains on  [gi|255082354|ref|XP_002504163|]
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predicted protein [Micromonas commoda]

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
 18-131 2.22e-53

DNA-directed RNA polymerase; Provisional


:

Pssm-ID: 177755  Cd Length: 130  Bit Score: 164.27  E-value: 2.22e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255082354  18 EPAGGDDEPEAEDAEMPEGGVEVLEHAPQQGGGAVTE-----RTTTPYMTKYERARILGTRALQISMNAPVLVQLDGETD 92
Cdd:PLN00152  12 EPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQEpvqrpRKTTPYMTKYERARILGTRALQISMNAPVMVELEGETD 91

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 255082354  93 PLEIAGKELREKRIPFTVRRYLPDGSWEDWGVDELIVED 131
Cdd:PLN00152  92 PLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 130
 
Name Accession Description Interval E-value
PLN00152 PLN00152
DNA-directed RNA polymerase; Provisional
 18-131 2.22e-53

DNA-directed RNA polymerase; Provisional


Pssm-ID: 177755  Cd Length: 130  Bit Score: 164.27  E-value: 2.22e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255082354  18 EPAGGDDEPEAEDAEMPEGGVEVLEHAPQQGGGAVTE-----RTTTPYMTKYERARILGTRALQISMNAPVLVQLDGETD 92
Cdd:PLN00152  12 EPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQEpvqrpRKTTPYMTKYERARILGTRALQISMNAPVMVELEGETD 91

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 255082354  93 PLEIAGKELREKRIPFTVRRYLPDGSWEDWGVDELIVED 131
Cdd:PLN00152  92 PLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 130
RNA_pol_Rpb6 pfam01192
RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and ...
 57-107 1.02e-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: 50.99  E-value: 1.02e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 255082354   57 TTPYMTKYERARILGTRALQISMNAPVLVqLDGETDPLEIAGKELREKRIP 107
Cdd:pfam01192   3 LKKVDNRYELVVIAAKRARQLSMGAPPIK-LDSFDKPVVIALREIAEGKIP 52
 
Name Accession Description Interval E-value
PLN00152 PLN00152
DNA-directed RNA polymerase; Provisional
 18-131 2.22e-53

DNA-directed RNA polymerase; Provisional


Pssm-ID: 177755  Cd Length: 130  Bit Score: 164.27  E-value: 2.22e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255082354  18 EPAGGDDEPEAEDAEMPEGGVEVLEHAPQQGGGAVTE-----RTTTPYMTKYERARILGTRALQISMNAPVLVQLDGETD 92
Cdd:PLN00152  12 EPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQEpvqrpRKTTPYMTKYERARILGTRALQISMNAPVMVELEGETD 91

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 255082354  93 PLEIAGKELREKRIPFTVRRYLPDGSWEDWGVDELIVED 131
Cdd:PLN00152  92 PLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 130
rpoK PRK01099
DNA-directed RNA polymerase subunit K; Provisional
 58-116 2.75e-24

DNA-directed RNA polymerase subunit K; Provisional


Pssm-ID: 179220  Cd Length: 62  Bit Score: 88.45  E-value: 2.75e-24
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 255082354  58 TPYMTKYERARILGTRALQISMNAPVLVQLDGETDPLEIAGKELREKRIPFTVRRYLPD 116
Cdd:PRK01099   4 PMKLTRFERARIIGARALQISMGAPVLIDIPESTDPLDIAEEEFKRGVLPITVKRPLPN 62
RNA_pol_Rpb6 pfam01192
RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and ...
 57-107 1.02e-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: 50.99  E-value: 1.02e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 255082354   57 TTPYMTKYERARILGTRALQISMNAPVLVqLDGETDPLEIAGKELREKRIP 107
Cdd:pfam01192   3 LKKVDNRYELVVIAAKRARQLSMGAPPIK-LDSFDKPVVIALREIAEGKIP 52
 
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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