NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2449376709|ref|WP_274595411|]
View 

DNA-directed RNA polymerase subunit RpoH/Rpb5 C-terminal domain-containing protein, partial [Halorubrum sp. SS7]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RPB5 super family cl43584
DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]; DNA-directed RNA polymerase, ...
 1-37 6.97e-13

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


The actual alignment was detected with superfamily member COG2012:

Pssm-ID: 441615 [Multi-domain]  Cd Length: 80  Bit Score: 55.58  E-value: 6.97e-13
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 2449376709  1 MVDVSQHELVPDHVLLDADEIEEVLAEYDVKKTNLPK 37
Cdd:COG2012    4 KFNVLDHELVPKHEILSEEEAEEVLKEYGIKPEQLPK 40
 
Name Accession Description Interval E-value
RPB5 COG2012
DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]; DNA-directed RNA polymerase, ...
 1-37 6.97e-13

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: 55.58  E-value: 6.97e-13
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 2449376709  1 MVDVSQHELVPDHVLLDADEIEEVLAEYDVKKTNLPK 37
Cdd:COG2012    4 KFNVLDHELVPKHEILSEEEAEEVLKEYGIKPEQLPK 40
rpoH PRK09570
DNA-directed RNA polymerase subunit H; Reviewed
 1-37 1.41e-12

DNA-directed RNA polymerase subunit H; Reviewed


Pssm-ID: 236575 [Multi-domain]  Cd Length: 79  Bit Score: 54.84  E-value: 1.41e-12
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 2449376709  1 MVDVSQHELVPDHVLLDADEIEEVLAEYDVKKTNLPK 37
Cdd:PRK09570   3 KFDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPK 39
RNA_pol_Rpb5_C pfam01191
RNA polymerase Rpb5, C-terminal domain; The assembly domain of Rpb5. The archaeal equivalent ...
 2-37 1.03e-11

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: 52.43  E-value: 1.03e-11
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 2449376709  2 VDVSQHELVPDHVLLDADEIEEVLAEYDVKKTNLPK 37
Cdd:pfam01191  1 VNITKHELVPKHEVLSEEEKEELLKKYKIKEEQLPK 36
 
Name Accession Description Interval E-value
RPB5 COG2012
DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]; DNA-directed RNA polymerase, ...
 1-37 6.97e-13

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: 55.58  E-value: 6.97e-13
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 2449376709  1 MVDVSQHELVPDHVLLDADEIEEVLAEYDVKKTNLPK 37
Cdd:COG2012    4 KFNVLDHELVPKHEILSEEEAEEVLKEYGIKPEQLPK 40
rpoH PRK09570
DNA-directed RNA polymerase subunit H; Reviewed
 1-37 1.41e-12

DNA-directed RNA polymerase subunit H; Reviewed


Pssm-ID: 236575 [Multi-domain]  Cd Length: 79  Bit Score: 54.84  E-value: 1.41e-12
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 2449376709  1 MVDVSQHELVPDHVLLDADEIEEVLAEYDVKKTNLPK 37
Cdd:PRK09570   3 KFDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPK 39
RNA_pol_Rpb5_C pfam01191
RNA polymerase Rpb5, C-terminal domain; The assembly domain of Rpb5. The archaeal equivalent ...
 2-37 1.03e-11

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: 52.43  E-value: 1.03e-11
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 2449376709  2 VDVSQHELVPDHVLLDADEIEEVLAEYDVKKTNLPK 37
Cdd:pfam01191  1 VNITKHELVPKHEVLSEEEKEELLKKYKIKEEQLPK 36
PTZ00061 PTZ00061
DNA-directed RNA polymerase; Provisional
 1-37 2.25e-07

DNA-directed RNA polymerase; Provisional


Pssm-ID: 173356  Cd Length: 205  Bit Score: 43.67  E-value: 2.25e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2449376709   1 MVDVSQHELVPDHVLLDADEIEEVLAEYDVKKTNLPK 37
Cdd:PTZ00061  131 LVNITKHELVPKHIPLTDDEKLNLLQRYKVKESQLPR 167
PLN03111 PLN03111
DNA-directed RNA polymerase II subunit family protein; Provisional
 2-37 1.10e-05

DNA-directed RNA polymerase II subunit family protein; Provisional


Pssm-ID: 215582 [Multi-domain]  Cd Length: 206  Bit Score: 39.11  E-value: 1.10e-05
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2449376709   2 VDVSQHELVPDHVLLDADEIEEVLAEYDVKKTNLPK 37
Cdd:PLN03111  133 VNITKHVLVPKHQVLTDEEKKTLLKRYTVKETQLPR 168
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH