SUPERFAMILY 1.75 HMM library and genome assignments server

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 (2,673) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 26,066 129,659 9
Proteins 26,053 129,643 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) biosynthetic process 0.000007032 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00001368 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0000175 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00004942 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.00008915 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0001908 Least Informative Direct
Biological Process (BP) response to stimulus 0.0004383 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.3676 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.001428 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.000000000001187 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.000000000001239 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.000000000001247 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.000000000001898 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.00000000001543 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.00000000003446 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00000000004268 Moderately Informative Direct
Biological Process (BP) gene expression 0.0000000001881 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.02242 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-dependent 0 Informative Direct
Biological Process (BP) response to light stimulus 0.000002234 Informative Direct
Biological Process (BP) response to inorganic substance 0.0003839 Informative Direct
Biological Process (BP) pathogenesis 0.000005535 Highly Informative Direct
Biological Process (BP) cellular response to radiation 0.000006025 Highly Informative Direct
Biological Process (BP) response to heat 0.00002564 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.7714 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) plastid 0.0000001717 Informative Direct

Document: GO annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processSporulation0InformativeDirect
Biological processStress response0.000000000000001859InformativeDirect
Cellular componentCytoplasm0.00000000401Least InformativeDirect
Molecular functionDNA-binding0Least 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) · Arabidopsis Plant Ontology (AP) · 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) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]