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]. [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

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

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 directs late flagellar biosynthesis genes

Gene:

fliA

Date:

2020-10-26

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

Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.

Date:

2024-05-30