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Conserved domains on  [gi|343197580|pdb|3S2D|F]
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Chain F, DNA-directed RNA polymerases I, II, and III subunit RPABC2

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
 70-154 9.62e-43

DNA-directed RNA polymerase; Provisional


:

Pssm-ID: 177755  Cd Length: 130  Bit Score: 138.08  E-value: 9.62e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3S2D_F        70 KEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVE 149
Cdd:PLN00152  45 EEQEPVQRPRKTTPYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVD 124


                 ....*
3S2D_F       150 ELIVD 154
Cdd:PLN00152 125 ELIVE 129
 
Name Accession Description Interval E-value
PLN00152 PLN00152
DNA-directed RNA polymerase; Provisional
 70-154 9.62e-43

DNA-directed RNA polymerase; Provisional


Pssm-ID: 177755  Cd Length: 130  Bit Score: 138.08  E-value: 9.62e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3S2D_F        70 KEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVE 149
Cdd:PLN00152  45 EEQEPVQRPRKTTPYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVD 124


                 ....*
3S2D_F       150 ELIVD 154
Cdd:PLN00152 125 ELIVE 129
RNA_pol_Rpb6 pfam01192
RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and ...
 79-131 6.85e-12

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: 56.76  E-value: 6.85e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
3S2D_F         79 RATTPYMTKYERARILGTRALQISMNAPVFVDLEGEtDPLRIAMKELAEKKIP 131
Cdd:pfam01192   1 DLLKKVDNRYELVVIAAKRARQLSMGAPPIKLDSFD-KPVVIALREIAEGKIP 52
RpoZ COG1758
DNA-directed RNA polymerase, subunit K/omega [Transcription]; DNA-directed RNA polymerase, ...
 87-136 1.48e-04

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: 37.85  E-value: 1.48e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
3S2D_F       87 KYERARILGTRALQISMNAPVFVDLEGEtDPLRIAMKELAEKKIPLVIRR 136
Cdd:COG1758  16 RYELVLLAAKRARQLAEGAEPLVEPDSD-KPVVIALREIAEGKITIEILE 64
 
Name Accession Description Interval E-value
PLN00152 PLN00152
DNA-directed RNA polymerase; Provisional
 70-154 9.62e-43

DNA-directed RNA polymerase; Provisional


Pssm-ID: 177755  Cd Length: 130  Bit Score: 138.08  E-value: 9.62e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3S2D_F        70 KEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVE 149
Cdd:PLN00152  45 EEQEPVQRPRKTTPYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVD 124


                 ....*
3S2D_F       150 ELIVD 154
Cdd:PLN00152 125 ELIVE 129
rpoK PRK01099
DNA-directed RNA polymerase subunit K; Provisional
 82-140 3.92e-24

DNA-directed RNA polymerase subunit K; Provisional


Pssm-ID: 179220  Cd Length: 62  Bit Score: 88.45  E-value: 3.92e-24
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
3S2D_F        82 TPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPD 140
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 ...
 79-131 6.85e-12

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: 56.76  E-value: 6.85e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
3S2D_F         79 RATTPYMTKYERARILGTRALQISMNAPVFVDLEGEtDPLRIAMKELAEKKIP 131
Cdd:pfam01192   1 DLLKKVDNRYELVVIAAKRARQLSMGAPPIKLDSFD-KPVVIALREIAEGKIP 52
RpoZ COG1758
DNA-directed RNA polymerase, subunit K/omega [Transcription]; DNA-directed RNA polymerase, ...
 87-136 1.48e-04

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: 37.85  E-value: 1.48e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
3S2D_F       87 KYERARILGTRALQISMNAPVFVDLEGEtDPLRIAMKELAEKKIPLVIRR 136
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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