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Sigma2 domain of RNA polymerase sigma factors superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Sigma2 domain of RNA polymerase sigma factors [ 88945]
Superfamily:   Sigma2 domain of RNA polymerase sigma factors [ 88946]
Families:   Sigma2 domain of RNA polymerase sigma factors [ 88947] (5)


Superfamily statistics
Genomes (2,674) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 26,067 213,421 9
Proteins 26,054 213,381 9


Functional annotation
General category Other
Detailed category Unknown function

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00000000000005058 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.000000194 Least Informative Direct
Biological Process (BP) primary metabolic process 0.00001192 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00000000000002436 Least Informative Direct
Biological Process (BP) biological regulation 0.002904 Least Informative Inherited
Biological Process (BP) response to stimulus 0.01174 Least Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.0000002376 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.0006051 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.01685 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.4 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.004147 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.3693 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.005769 Moderately Informative Inherited
Biological Process (BP) reproduction 0.3048 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-templated 0 Informative Direct
Biological Process (BP) regulation of ion transport 0.00006203 Informative Direct
Biological Process (BP) interspecies interaction between organisms 0.00003379 Informative Direct
Biological Process (BP) cellular response to inorganic substance 0.00002194 Informative Direct
Biological Process (BP) response to metal ion 0.824 Informative Inherited
Biological Process (BP) response to radiation 0.5485 Informative Inherited
Biological Process (BP) response to temperature stimulus 0.004105 Informative Inherited
Biological Process (BP) pathogenesis 0.0001705 Highly Informative Direct
Biological Process (BP) response to heat 0.00001101 Highly Informative Direct
Biological Process (BP) response to iron ion 0.0000000004329 Highly Informative Direct
Biological Process (BP) cellular response to abiotic stimulus 0.001217 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.3458 Least Informative Inherited
Cellular Component (CC) plastid 0.00002209 Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processStress response0InformativeDirect
Biological processSporulation2.442e-16InformativeDirect
Cellular componentCytoplasm0.000000000007424Least InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR013325 SSF88946 Protein matches
Abstract

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme [PubMed3052291]. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, Sigma70 (gene rpoD; major sigma factor) and Sigma54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

This entry represents region 2 (sigma2 domain) found in several sigma factors, often in conjunction with sigma3 and sigma4 domains . This region is present in Sigma70 [PubMed8858155], Sigma28 (FliA), SigA [PubMed11931761], SigR and RpoE. The sigma2 domain has a conserved 4-helical core, and often a variable insert subdomain.


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 · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) ]

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 6 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 Sigma2 domain 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 6 hidden Markov models representing the Sigma2 domain 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 · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]