Protein Family Models

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)

Date:

2024-10-16

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.

Date:

2024-10-16

Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [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)

Date:

2024-10-16

Date:

2024-08-14

RNA polymerase sigma factor RpoS is the master transcriptional regulator of the stationary phase and the general stress response; it controls, positively or negatively, the expression of several hundred genes, which are mainly involved in metabolism, transport, regulation and stress management

Date:

2023-03-16

Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this sigma factor controls a regulon of genes required for protection against external stresses

Gene:

rpoS

Date:

2021-08-25

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.

Date:

2024-06-27

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).

Gene:

rpoS

Date:

2024-05-16