SUPERFAMILY 1.75 HMM library and genome assignments server


RPB6/omega subunit-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   RPB6/omega subunit-like [ 63561]
Superfamily:   RPB6/omega subunit-like [ 63562] (2)
Families:   RNA polymerase omega subunit [ 63563]
  RPB6 [ 55294]


Superfamily statistics
Genomes (2,823) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,975 15,978 5
Proteins 2,965 15,971 5


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular aromatic compound metabolic process3.136e-081.491e-06Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process4.484e-078.587e-06Least InformativeDirect
Biological Process (BP)biosynthetic process9.306e-087.367e-07Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process1.544e-074.438e-05Least InformativeDirect
Biological Process (BP)heterocycle metabolic process2.896e-081.245e-06Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process9.105e-083.158e-06Least InformativeDirect
Biological Process (BP)gene expression7.111e-136.322e-10Moderately InformativeDirect
Biological Process (BP)RNA metabolic process4.803e-142.134e-10Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process8.878e-131.826e-11Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process3.072e-131.85e-11Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process2.95e-132.534e-10Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process6.674e-131.723e-11Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process3.851e-129.579e-11Moderately InformativeDirect
Biological Process (BP)transcription, DNA-dependent03.722e-15InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups2.022e-071.053e-05Moderately InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity1.131e-121.493e-11InformativeDirect
Molecular Function (MF)RNA polymerase activity6.754e-160Highly InformativeDirect
Cellular Component (CC)protein complex3.266e-097.405e-07Least InformativeDirect
Cellular Component (CC)intracellular organelle part7.047e-050.000277Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.00074620.02269Least InformativeInherited
Cellular Component (CC)nuclear part1.299e-103.808e-07Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen9.267e-112.06e-07Moderately InformativeDirect
Cellular Component (CC)nucleoplasm part03.968e-12InformativeDirect
Cellular Component (CC)nuclear DNA-directed RNA polymerase complex00InformativeDirect
Cellular Component (CC)DNA-directed RNA polymerase II, core complex00Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 1.491e-06 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 8.587e-06 Least Informative Direct
Biological Process (BP) biosynthetic process 7.367e-07 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 4.438e-05 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1.245e-06 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 3.158e-06 Least Informative Direct
Biological Process (BP) gene expression 6.322e-10 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 2.134e-10 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 1.826e-11 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 1.85e-11 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 2.534e-10 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 1.723e-11 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 9.579e-11 Moderately Informative Direct
Biological Process (BP) transcription, DNA-dependent 3.722e-15 Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1.053e-05 Moderately Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 1.493e-11 Informative Direct
Molecular Function (MF) RNA polymerase activity 0 Highly Informative Direct
Cellular Component (CC) protein complex 7.405e-07 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000277 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.02269 Least Informative Inherited
Cellular Component (CC) nuclear part 3.808e-07 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 2.06e-07 Moderately Informative Direct
Cellular Component (CC) nucleoplasm part 3.968e-12 Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 0 Informative Direct
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 0 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)DNA-directed RNA polymerase0InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed RNA polymerase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentDNA-directed RNA polymerase0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR006110 SSF63562 Protein matches
Abstract

In eukaryotes, there are three different forms of DNA-dependent RNA polymerases transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. A component of 14 to 18 kDa shared by all three forms of eukaryotic RNA polymerases and which has been sequenced in budding yeast (gene RPB6 or RPO26), in fission yeast (gene rpb6 or rpo15), in human and in African swine fever virus is evolutionary related to the archaebacterial subunit K (gene rpoK). The archaebacterial protein is colinear with the C-terminal part of the eukaryotic subunit.

The structures of the omega subunit and RBP6, and the structures of the omega/beta' and RPB6/RPB1 interfaces, suggest a molecular mechanism for the function of omega and RPB6 in promoting RNAP assembly and/or stability. The conserved regions of omega and RPB6 form a compact structural domain that interacts simultaneously with conserved regions of the largest RNAP subunit and with the C-terminal tail following a conserved region of the largest RNAP subunit. The second half of the conserved region of omega and RPB6 forms an arc that projects away from the remainder of the structural domain and wraps over and around the C-terminal tail of the largest RNAP subunit, clamping it in a crevice, and threading the C-terminal tail of the largest RNAP subunit through the narrow gap between omega and RPB6 [PubMed11158566].


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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · 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 4 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 RPB6/omega subunit-like 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 4 hidden Markov models representing the RPB6/omega subunit-like 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]