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:

2024-08-14

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:

2024-08-14

Region 1.1 modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [1,2]. Region 1.1 is also involved in promoter binding [1] [1]. 9927430. A mutation in region 1.1 of sigma70 affects promoter DNA binding. by Escherichia coli RNA polymerase holoenzyme.. Bowers CW, Dombroski AJ;. EMBO J 1999;18:709-716.. [2]. 10613885. Effects of amino acid substitutions at conserved and acidic. residues within region 1.1 of Escherichia coli sigma(70).. Bowers CW, McCracken A, Dombroski AJ;. J Bacteriol 2000;182:221-224. (from Pfam)

Date:

2024-08-14

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:

2024-08-14

Date:

2024-08-14

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 is the primary sigma factor of bacteria

Gene:

rpoD

Date:

2021-08-26

RNA polymerase sigma factor RpoD/SigA is the primary sigma factor during exponential growth

Date:

2017-11-20

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

This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.

Gene:

rpoD

Date:

2024-05-30