SUPERFAMILY 1.75 HMM library and genome assignments server


Sigma3 and sigma4 domains of RNA polymerase sigma factors superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   DNA/RNA-binding 3-helical bundle [ 46688] (14)
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)


Superfamily statistics
Genomes (2,804) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 35,422 86,472 20
Proteins 28,402 69,105 15


Functional annotation
General category Regulation
Detailed category Other regulatory 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 2.817e-05 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 6.074e-05 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 7.745e-05 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0002058 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0007208 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.2839 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.004769 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 4.841e-12 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 5.561e-12 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 5.849e-12 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 7.428e-11 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 2.404e-10 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 2.41e-10 Moderately Informative Direct
Biological Process (BP) gene expression 9.841e-10 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 3.159e-06 Moderately Informative Direct
Biological Process (BP) transcription, DNA-dependent 0 Informative Direct
Biological Process (BP) response to light stimulus 4.52e-06 Informative Direct
Biological Process (BP) cellular response to radiation 5.96e-06 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.8955 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) plastid 5.077e-08 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 response6.476e-14InformativeDirect
Cellular componentCytoplasm9.136e-10Least InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect

Document: KW annotation of SCOP domains

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 [PubMed8858155], Sigma28 (FliA), and SigA [PubMed11931761], while region4 is also found in SigmaF [PubMed11955433] 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 · 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 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 · Gene Ontology (high-coverage) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]