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Conserved domains on  [gi|938148816|ref|NP_001303253|]
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DNA-directed RNA polymerases I, II, and III subunit RPABC1 isoform b [Homo sapiens]

Protein Classification

Rpo5/RPB5 family RNA polymerase subunit( domain architecture ID 1903945)

Rpo5/RPB5 family RNA polymerase subunit similar to yeast DNA-directed RNA polymerases I, II, and III subunit RPABC1, a common component of RNAPs I, II, and III

Gene Ontology:  GO:0000428|GO:0003899|GO:0003677|GO:0006351
PubMed:  10841537|17179178

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03111 super family cl42850
DNA-directed RNA polymerase II subunit family protein; Provisional
 1-116 2.55e-59

DNA-directed RNA polymerase II subunit family protein; Provisional


The actual alignment was detected with superfamily member PTZ00061:

Pssm-ID: 456195  Cd Length: 205  Bit Score: 181.18  E-value: 2.55e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938148816   1 MQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRI 80
Cdd:PTZ00061  89 MEEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVKESQLPRI 168

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 938148816  81 QAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLV 116
Cdd:PTZ00061 169 QSADPVARYFGLSKGQVVKIIRPSETAGRYVTYRLV 204
 
Name Accession Description Interval E-value
PTZ00061 PTZ00061
DNA-directed RNA polymerase; Provisional
 1-116 2.55e-59

DNA-directed RNA polymerase; Provisional


Pssm-ID: 173356  Cd Length: 205  Bit Score: 181.18  E-value: 2.55e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938148816   1 MQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRI 80
Cdd:PTZ00061  89 MEEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVKESQLPRI 168

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 938148816  81 QAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLV 116
Cdd:PTZ00061 169 QSADPVARYFGLSKGQVVKIIRPSETAGRYVTYRLV 204
RNA_pol_Rpb5_C pfam01191
RNA polymerase Rpb5, C-terminal domain; The assembly domain of Rpb5. The archaeal equivalent ...
 44-116 3.25e-44

RNA polymerase Rpb5, C-terminal domain; The assembly domain of Rpb5. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain.


Pssm-ID: 426111 [Multi-domain]  Cd Length: 73  Bit Score: 138.33  E-value: 3.25e-44
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 938148816   44 INITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLV 116
Cdd:pfam01191   1 VNITKHELVPKHEVLSEEEKEELLKKYKIKEEQLPKILKTDPVARYLGAKPGDVVKITRKSETAGEYVTYRLV 73
RPB5 COG2012
DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]; DNA-directed RNA polymerase, ...
 44-116 7.55e-31

DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]; DNA-directed RNA polymerase, subunit H, RpoH/RPB5 is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441615 [Multi-domain]  Cd Length: 80  Bit Score: 104.89  E-value: 7.55e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 938148816  44 INITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLV 116
Cdd:COG2012    5 FNVLDHELVPKHEILSEEEAEEVLKEYGIKPEQLPKIKASDPAVKAIGAKPGDVIKIIRKSPTAGEAVYYRLV 77
 
Name Accession Description Interval E-value
PTZ00061 PTZ00061
DNA-directed RNA polymerase; Provisional
 1-116 2.55e-59

DNA-directed RNA polymerase; Provisional


Pssm-ID: 173356  Cd Length: 205  Bit Score: 181.18  E-value: 2.55e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938148816   1 MQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRI 80
Cdd:PTZ00061  89 MEEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVKESQLPRI 168

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 938148816  81 QAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLV 116
Cdd:PTZ00061 169 QSADPVARYFGLSKGQVVKIIRPSETAGRYVTYRLV 204
PLN03111 PLN03111
DNA-directed RNA polymerase II subunit family protein; Provisional
 1-116 2.48e-57

DNA-directed RNA polymerase II subunit family protein; Provisional


Pssm-ID: 215582 [Multi-domain]  Cd Length: 206  Bit Score: 175.86  E-value: 2.48e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938148816   1 MQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRI 80
Cdd:PLN03111  90 MKDENVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRYTVKETQLPRI 169

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 938148816  81 QAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLV 116
Cdd:PLN03111 170 QVSDPIARYYGLKRGQVVKIIRPSETAGRYVTYRCV 205
RNA_pol_Rpb5_C pfam01191
RNA polymerase Rpb5, C-terminal domain; The assembly domain of Rpb5. The archaeal equivalent ...
 44-116 3.25e-44

RNA polymerase Rpb5, C-terminal domain; The assembly domain of Rpb5. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain.


Pssm-ID: 426111 [Multi-domain]  Cd Length: 73  Bit Score: 138.33  E-value: 3.25e-44
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 938148816   44 INITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLV 116
Cdd:pfam01191   1 VNITKHELVPKHEVLSEEEKEELLKKYKIKEEQLPKILKTDPVARYLGAKPGDVVKITRKSETAGEYVTYRLV 73
RPB5 COG2012
DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]; DNA-directed RNA polymerase, ...
 44-116 7.55e-31

DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]; DNA-directed RNA polymerase, subunit H, RpoH/RPB5 is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441615 [Multi-domain]  Cd Length: 80  Bit Score: 104.89  E-value: 7.55e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 938148816  44 INITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLV 116
Cdd:COG2012    5 FNVLDHELVPKHEILSEEEAEEVLKEYGIKPEQLPKIKASDPAVKAIGAKPGDVIKIIRKSPTAGEAVYYRLV 77
rpoH PRK09570
DNA-directed RNA polymerase subunit H; Reviewed
 44-116 1.05e-30

DNA-directed RNA polymerase subunit H; Reviewed


Pssm-ID: 236575 [Multi-domain]  Cd Length: 79  Bit Score: 104.15  E-value: 1.05e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 938148816  44 INITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLV 116
Cdd:PRK09570   4 FDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPKIKASDPVVKAIGAKPGDVIKIVRKSPTAGEAVYYRLV 76
 
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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