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Conserved domains on  [gi|1334286570|gb|PNT02051|]
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hypothetical protein POPTR_015G138800v4 [Populus trichocarpa]

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
 5-134 3.12e-66

DNA-directed RNA polymerase; Provisional


:

Pssm-ID: 177755  Cd Length: 130  Bit Score: 197.01  E-value: 3.12e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334286570   5 EYNDVDMGYEDEPAEPEIEEGADEDAENNNNEDDTGEPIETEDKEEQAPVERPRKTSKFMTKYERARILGTRALQISMNA 84
Cdd:PLN00152    1 DYNDMDMGYEDEPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQEPVQRPRKTTPYMTKYERARILGTRALQISMNA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1334286570  85 PVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 134
Cdd:PLN00152   81 PVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 130
 
Name Accession Description Interval E-value
PLN00152 PLN00152
DNA-directed RNA polymerase; Provisional
 5-134 3.12e-66

DNA-directed RNA polymerase; Provisional


Pssm-ID: 177755  Cd Length: 130  Bit Score: 197.01  E-value: 3.12e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334286570   5 EYNDVDMGYEDEPAEPEIEEGADEDAENNNNEDDTGEPIETEDKEEQAPVERPRKTSKFMTKYERARILGTRALQISMNA 84
Cdd:PLN00152    1 DYNDMDMGYEDEPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQEPVQRPRKTTPYMTKYERARILGTRALQISMNA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1334286570  85 PVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 134
Cdd:PLN00152   81 PVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 130
RNA_pol_Rpb6 pfam01192
RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and ...
 58-110 1.19e-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: 53.30  E-value: 1.19e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1334286570  58 RKTSKFMTKYERARILGTRALQISMNAPVMVELEGEtDPLEIAMKELRERKIP 110
Cdd:pfam01192   1 DLLKKVDNRYELVVIAAKRARQLSMGAPPIKLDSFD-KPVVIALREIAEGKIP 52
RpoZ COG1758
DNA-directed RNA polymerase, subunit K/omega [Transcription]; DNA-directed RNA polymerase, ...
 66-115 5.09e-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: 36.30  E-value: 5.09e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1334286570  66 KYERARILGTRALQISMNAPVMVELEGEtDPLEIAMKELRERKIPFTIRR 115
Cdd:COG1758    16 RYELVLLAAKRARQLAEGAEPLVEPDSD-KPVVIALREIAEGKITIEILE 64
 
Name Accession Description Interval E-value
PLN00152 PLN00152
DNA-directed RNA polymerase; Provisional
 5-134 3.12e-66

DNA-directed RNA polymerase; Provisional


Pssm-ID: 177755  Cd Length: 130  Bit Score: 197.01  E-value: 3.12e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334286570   5 EYNDVDMGYEDEPAEPEIEEGADEDAENNNNEDDTGEPIETEDKEEQAPVERPRKTSKFMTKYERARILGTRALQISMNA 84
Cdd:PLN00152    1 DYNDMDMGYEDEPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQEPVQRPRKTTPYMTKYERARILGTRALQISMNA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1334286570  85 PVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 134
Cdd:PLN00152   81 PVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 130
rpoK PRK01099
DNA-directed RNA polymerase subunit K; Provisional
 65-119 3.35e-24

DNA-directed RNA polymerase subunit K; Provisional


Pssm-ID: 179220  Cd Length: 62  Bit Score: 88.45  E-value: 3.35e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1334286570  65 TKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPD 119
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 ...
 58-110 1.19e-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: 53.30  E-value: 1.19e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1334286570  58 RKTSKFMTKYERARILGTRALQISMNAPVMVELEGEtDPLEIAMKELRERKIP 110
Cdd:pfam01192   1 DLLKKVDNRYELVVIAAKRARQLSMGAPPIKLDSFD-KPVVIALREIAEGKIP 52
RpoZ COG1758
DNA-directed RNA polymerase, subunit K/omega [Transcription]; DNA-directed RNA polymerase, ...
 66-115 5.09e-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: 36.30  E-value: 5.09e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1334286570  66 KYERARILGTRALQISMNAPVMVELEGEtDPLEIAMKELRERKIPFTIRR 115
Cdd:COG1758    16 RYELVLLAAKRARQLAEGAEPLVEPDSD-KPVVIALREIAEGKITIEILE 64
CobT2 COG4547
Cobalamin biosynthesis cobaltochelatase CobT subunit [Coenzyme transport and metabolism]; ...
 8-55 6.52e-03

Cobalamin biosynthesis cobaltochelatase CobT subunit [Coenzyme transport and metabolism]; Cobalamin biosynthesis cobaltochelatase CobT subunit is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis


Pssm-ID: 443611 [Multi-domain]  Cd Length: 608  Bit Score: 35.54  E-value: 6.52e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1334286570   8 DVDMGYEDEPAEPEIEEGADEDAENNNNEDDTGEPIETEDKEEQAPVE 55
Cdd:COG4547   204 DLDLAEELGEDEDEEDEDDEDDSGEQEEDEEDGEDEDEESDEGAEAED 251
 
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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