Home > SCOP hierarchy > Sigma3 and sigma4 domains of RNA polymerase sigma factors superfamily

Sigma3 and sigma4 domains of RNA polymerase sigma factors superfamily

Root:	SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:	All alpha proteins [ 46456] (258)
Fold:	DNA/RNA-binding 3-helical bundle [ 46688] (14)
	core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down
Superfamily:	Sigma3 and sigma4 domains of RNA polymerase sigma factors [ 88659] (3)
Families:	Sigma3 domain [ 88660] (3)
	Sigma4 domain [ 88665] (4)
	YlxM/p13-like [ 109706] (2)
	Pfam 04297; UPF0122 structural and detectable sequence similarity to Sigma4 domain; contains extra C-terminal all-alpha oligomerization subdomain; forms different, helix-swapped dimers

Superfamily statistics

	Genomes (975)	UniProt 15.0	PDB chains (SCOP 1.73)
Domains	11,643	17,021	19
Proteins	9,353	13,574	14

Functional annotation

General category	Regulation
Detailed category	Other regulatory function

Function annotation of SCOP domain superfamilies

InterPro annotation

Cross references

IPR013324 SSF88659 Protein matches

Abstract

This entry represents regions 3 and 4 (or sigma3 and sigma4 domains) found in several sigma factors, often in conjunction with the sigma2 domain . Both regions are present in Sigma70 [ PubMed 8858155], Sigma28 (FliA), and SigA [ PubMed 11931761], while region4 is also found in SigmaF [ PubMed 11955433] and RpoE. Both regions 3 and 4 have a nucleotide-binding 3-helical core structure, consisting of a closed or partly open bundle with a right-handed twist. Some other nucleotide-binding proteins are thought to contain domains with a similar topology.

InterPro database

PDBeMotif information about ligands, sequence and structure motifs

Cross references

PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.

Alignments of sequences to 10 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.

Browse and view proteins in genomes which have different domain combinations including a Sigma3 and sigma4 domains of RNA polymerase sigma factors domain.

Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.

Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 10 hidden Markov models representing the Sigma3 and sigma4 domains of RNA polymerase sigma factors superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Internal database links ]

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Sigma3 and sigma4 domains of RNA polymerase sigma factors superfamily