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Conserved domains on  [gi|494650927|ref|WP_007408871|]
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MULTISPECIES: TFIIB-type zinc ribbon-containing protein [Bacillus]

Protein Classification

TFIIB-type zinc ribbon-containing protein( domain architecture ID 10550151)

TFIIB-type zinc ribbon-containing protein similar to transcription factors TFIIB and Brf which have conserved functional surfaces but different roles in transcription initiation.

Gene Ontology:  GO:0008270
PubMed:  18631123

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 5-40 1.08e-04

TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.


:

Pssm-ID: 400527 [Multi-domain]  Cd Length: 43  Bit Score: 39.21  E-value: 1.08e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 494650927    5 YKCPNCG-DDMVFDSSSGMLTCHSCGRQDQIESLPKE 40
Cdd:pfam08271   1 YKCPNCGsTNLVEDYERGELVCTDCGLVLEDNSIDEG 37
 
Name Accession Description Interval E-value
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 5-40 1.08e-04

TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.


Pssm-ID: 400527 [Multi-domain]  Cd Length: 43  Bit Score: 39.21  E-value: 1.08e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 494650927    5 YKCPNCG-DDMVFDSSSGMLTCHSCGRQDQIESLPKE 40
Cdd:pfam08271   1 YKCPNCGsTNLVEDYERGELVCTDCGLVLEDNSIDEG 37
RPC10 COG1996
DNA-directed RNA polymerase, subunit RPC12/RpoP, contains C4-type Zn-finger [Transcription]; ...
 1-29 7.10e-04

DNA-directed RNA polymerase, subunit RPC12/RpoP, contains C4-type Zn-finger [Transcription]; DNA-directed RNA polymerase, subunit RPC12/RpoP, contains C4-type Zn-finger is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441599  Cd Length: 48  Bit Score: 36.99  E-value: 7.10e-04
                         10        20
                 ....*....|....*....|....*....
gi 494650927   1 MIISYKCPNCGDDMVFDSSSGMLTCHSCG 29
Cdd:COG1996    2 AMVEYKCPRCGAEVELDEGTPAIRCPYCG 30
SF2_C_priA cd18804
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ...
 6-31 2.04e-03

C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350191 [Multi-domain]  Cd Length: 238  Bit Score: 39.15  E-value: 2.04e-03
                         10        20
                 ....*....|....*....|....*.
gi 494650927   6 KCPNCGDDMVFDSSSGMLTCHSCGRQ 31
Cdd:cd18804   56 ECPNCDVSMTYHKSTNKLKCHYCGYQ 81
rps27e PRK00415
30S ribosomal protein S27e; Reviewed
 6-31 9.87e-03

30S ribosomal protein S27e; Reviewed


Pssm-ID: 179013  Cd Length: 59  Bit Score: 34.11  E-value: 9.87e-03
                         10        20
                 ....*....|....*....|....*..
gi 494650927   6 KCPNCGDD-MVFDSSSGMLTCHSCGRQ 31
Cdd:PRK00415  13 KCPDCGNEqVVFSHASTVVRCLVCGKT 39
 
Name Accession Description Interval E-value
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 5-40 1.08e-04

TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.


Pssm-ID: 400527 [Multi-domain]  Cd Length: 43  Bit Score: 39.21  E-value: 1.08e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 494650927    5 YKCPNCG-DDMVFDSSSGMLTCHSCGRQDQIESLPKE 40
Cdd:pfam08271   1 YKCPNCGsTNLVEDYERGELVCTDCGLVLEDNSIDEG 37
RPC10 COG1996
DNA-directed RNA polymerase, subunit RPC12/RpoP, contains C4-type Zn-finger [Transcription]; ...
 1-29 7.10e-04

DNA-directed RNA polymerase, subunit RPC12/RpoP, contains C4-type Zn-finger [Transcription]; DNA-directed RNA polymerase, subunit RPC12/RpoP, contains C4-type Zn-finger is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441599  Cd Length: 48  Bit Score: 36.99  E-value: 7.10e-04
                         10        20
                 ....*....|....*....|....*....
gi 494650927   1 MIISYKCPNCGDDMVFDSSSGMLTCHSCG 29
Cdd:COG1996    2 AMVEYKCPRCGAEVELDEGTPAIRCPYCG 30
SF2_C_priA cd18804
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ...
 6-31 2.04e-03

C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350191 [Multi-domain]  Cd Length: 238  Bit Score: 39.15  E-value: 2.04e-03
                         10        20
                 ....*....|....*....|....*.
gi 494650927   6 KCPNCGDDMVFDSSSGMLTCHSCGRQ 31
Cdd:cd18804   56 ECPNCDVSMTYHKSTNKLKCHYCGYQ 81
rps27e PRK00415
30S ribosomal protein S27e; Reviewed
 6-31 9.87e-03

30S ribosomal protein S27e; Reviewed


Pssm-ID: 179013  Cd Length: 59  Bit Score: 34.11  E-value: 9.87e-03
                         10        20
                 ....*....|....*....|....*..
gi 494650927   6 KCPNCGDD-MVFDSSSGMLTCHSCGRQ 31
Cdd:PRK00415  13 KCPDCGNEqVVFSHASTVVRCLVCGKT 39
 
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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