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Links from Protein

Items: 18

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.

ECF-type sigma factor

These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily [1] and show sequence similarity to Pfam:PF04542 and Pfam:PF04545. [1]. 12073657. The extracytoplasmic function (ECF) sigma factors.. Helmann JD;. Adv Microb Physiol 2002;46:47-110. (from Pfam)

Date:
2024-08-14
Family Accession:
NF019265.5
Method:
HMM
3.

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
4.

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
5.

LuxR C-terminal-related transcriptional regulator

GO Terms:
Biological Process:
regulation of DNA-templated transcription (GO:0006355)
Date:
2024-08-14
Family Accession:
NF012422.5
Method:
HMM
6.
new record, indexing in progress
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7.
new record, indexing in progress
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8.
new record, indexing in progress
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9.
new record, indexing in progress
Family Accession:
10.
new record, indexing in progress
Family Accession:
11.
new record, indexing in progress
Family Accession:
12.
new record, indexing in progress
Family Accession:
13.
new record, indexing in progress
Family Accession:
14.
new record, indexing in progress
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15.
new record, indexing in progress
Family Accession:
16.

RNA polymerase sigma-70 factor

RNA polymerase sigma-70 factor; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released

Date:
2018-05-14
Family Accession:
11496275
Method:
Sparcle
17.

RNA polymerase sigma-70 factor

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.

GO Terms:
Molecular Function:
DNA-binding transcription factor activity (GO:0003700)
Biological Process:
regulation of DNA-templated transcription (GO:0006355)
Molecular Function:
sigma factor activity (GO:0016987)
Date:
2021-07-30
Family Accession:
TIGR02985.1
Method:
HMM
18.

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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