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

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. [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. [2]. 8858155. Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Malhotra A, Severinova E, Darst SA;. Cell 1996;87:127-136. (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 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:

2024-10-16

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

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this is the primary sigma factor of bacteria

Gene:

rpoD

Date:

2021-07-23

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