Protein Family Models

This is the N-terminal domain of response regulator PhyR and related proteins. It consists of three alpha-helices and together with sigma4 constitutes the PhyR receiver domain. This domain was shown to bind to anti-sigma factor NepR [1]. Paper describing PDB structure 2lfw. [1]. 22550171. Structural basis for sigma factor mimicry in the general stress response of Alphaproteobacteria. Campagne S, Damberger FF, Kaczmarczyk A, Francez-Charlot A, Allain FH, Vorholt JA;. Proc Natl Acad Sci U S A. 2012;109:E1405-E1414. Paper describing PDB structure 3n0r. [2]. 20735776. A structural model of anti-anti-sigma inhibition by a two-component receiver domain: the PhyR stress response regulator. Herrou J, Foreman R, Fiebig A, Crosson S;. Mol Microbiol. 2010;78:290-304. Paper describing PDB structure 3t0y. [3]. 22550172. Structural basis of a protein partner switch that regulates the general stress response of alpha-proteobacteria. Herrou J, Rotskoff G, Luo Y, Roux B, Crosson S;. Proc Natl Acad Sci U S A. 2012;109:E1415-E1423. (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]. [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

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:

2024-10-16

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

RNA polymerase sigma factor plays a role in bacterial signal transduction and is regulated by anti-sigma factors. May belong to the ECF-type subfamily. Generally, sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

Date:

2024-04-06

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