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Links from Protein

Items: 7

1.

sigma factor-like helix-turn-helix DNA-binding protein

Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. [1]. 11931761. Structure of the bacterial RNA polymerase promoter specificity. sigma subunit.. Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O,. Trester-Zedlitz ML, Darst SA;. Mol Cell 2002;9:527-539. (from Pfam)

GO Terms:
Molecular Function:
DNA binding (GO:0003677)
Molecular Function:
DNA-binding transcription factor activity (GO:0003700)
Biological Process:
DNA-templated transcription initiation (GO:0006352)
Biological Process:
regulation of DNA-templated transcription (GO:0006355)
Molecular Function:
sigma factor activity (GO:0016987)
Date:
2024-08-14
Family Accession:
NF019886.5
Method:
HMM
2.

sigma factor-like helix-turn-helix DNA-binding protein

Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives. [1]. 11931761. Structure of the bacterial RNA polymerase promoter specificity. sigma subunit.. Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O,. Trester-Zedlitz ML, Darst SA;. Mol Cell 2002;9:527-539. (from Pfam)

GO Terms:
Molecular Function:
DNA-binding transcription factor activity (GO:0003700)
Biological Process:
DNA-templated transcription initiation (GO:0006352)
Biological Process:
regulation of DNA-templated transcription (GO:0006355)
Date:
2024-08-14
Family Accession:
NF016432.5
Method:
HMM
3.

sigma factor

This HMM hits a core region shared by multiple sigma factors, interchangeable subunits that complete the RNA polymerase holoenzyme and allow transcription to start. In E. coli K-12 alone, this HMM hits RpoD (sigma-70), RpoH (sigma-32), FliA (sigma-28), FecI (sigma-19), RpoS, and RpoE.

GO Terms:
Molecular Function:
DNA-binding transcription factor activity (GO:0003700)
Biological Process:
DNA-templated transcription initiation (GO:0006352)
Biological Process:
regulation of DNA-templated transcription (GO:0006355)
Date:
2024-08-14
Family Accession:
NF016430.5
Method:
HMM
4.
new record, indexing in progress
Family Accession:
5.
new record, indexing in progress
Family Accession:
6.
new record, indexing in progress
Family Accession:
7.

sigma-70 family RNA polymerase sigma factor

This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (PF04542) and Sigma-70, region 4 (PF04545), but not always above their respective trusted cutoffs.

GO Terms:
Molecular Function:
DNA-binding transcription factor activity (GO:0003700)
Biological Process:
DNA-templated transcription initiation (GO:0006352)
Biological Process:
regulation of DNA-templated transcription (GO:0006355)
Molecular Function:
sigma factor activity (GO:0016987)
Date:
2024-06-27
Family Accession:
TIGR02937.1
Method:
HMM
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