SUPERFAMILY 1.75 HMM library and genome assignments server


RBP11-like subunits of RNA polymerase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   DCoH-like [ 55247] (5)
Superfamily:   RBP11-like subunits of RNA polymerase [ 55257] (2)
Families:   RBP11/RpoL [ 64311] (2)
  RNA polymerase alpha subunit dimerisation domain [ 55258] (2)


Superfamily statistics
Genomes (3,232) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,341 0 8
Proteins 5,327 0 8


Functional annotation
General category coiled coil
Detailed category This is a complex coiled arrangement. The details of which will appear on this page shortly (some coiled coil details are being checked before they are included on the site). If you want to see examples of the states please click here here. If you require further details urgently please contact Owen Rackham

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 process8.144e-075.414e-08Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process1.233e-051.512e-06Least InformativeDirect
Biological Process (BP)biosynthetic process2.497e-061.371e-08Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process4.176e-062.986e-05Least InformativeDirect
Biological Process (BP)heterocycle metabolic process7.501e-073.814e-08Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process2.438e-062.289e-07Least InformativeDirect
Biological Process (BP)gene expression1.065e-117.281e-15Moderately InformativeDirect
Biological Process (BP)RNA metabolic process6.001e-130Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process1.347e-110Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process4.356e-120Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process4.182e-120Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process9.957e-120Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process6.411e-110Moderately InformativeDirect
Biological Process (BP)transcription, DNA-dependent00InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups3.344e-111.558e-15Moderately InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity00InformativeDirect
Molecular Function (MF)RNA polymerase activity00Highly InformativeDirect
Cellular Component (CC)protein complex2.915e-150Least InformativeDirect
Cellular Component (CC)intracellular organelle part6.201e-146.138e-08Least InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle0.37210.07544Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle1.242e-080.002351Least InformativeInherited
Cellular Component (CC)nuclear part00Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen01.106e-13Moderately InformativeDirect
Cellular Component (CC)nucleoplasm part6.052e-101.528e-09InformativeDirect
Cellular Component (CC)nuclear DNA-directed RNA polymerase complex00InformativeDirect
Cellular Component (CC)DNA-directed RNA polymerase II, core complex3.687e-050Highly InformativeDirect
Cellular Component (CC)nucleolar part2.662e-051.492e-14Highly 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 5.414e-08 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1.512e-06 Least Informative Direct
Biological Process (BP) biosynthetic process 1.371e-08 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 2.986e-05 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 3.814e-08 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 2.289e-07 Least Informative Direct
Biological Process (BP) gene expression 7.281e-15 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) cellular nitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) transcription, DNA-dependent 0 Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1.558e-15 Moderately Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) RNA polymerase activity 0 Highly Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 6.138e-08 Least Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.07544 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.002351 Least Informative Inherited
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 1.106e-13 Moderately Informative Direct
Cellular Component (CC) plastid 7.749e-05 Informative Direct
Cellular Component (CC) nucleoplasm part 1.528e-09 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
Cellular Component (CC) nucleolar part 1.492e-14 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

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP 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 componentPlastid0Moderately InformativeDirect
Cellular componentDNA-directed RNA polymerase0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009025 SSF55257 Protein matches
Abstract

RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and the prokaryotic RNAP alpha subunit homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/betaż) can interact [PubMed11453250]. These different subunits share regions of homology. Rpb11 contains a domain (Rpb11-like domain) that is required for dimerisation, and binds to a homologous region on Rpb3. The Rpb11-like domain in Rpb11 and archaeal L subunits is contiguous, whereas in Rpb3, archaeal D, and prokaryotic alpha subunits , the Rpb11-like domain is interrupted by an insert domain . In the prokaryotic RNAP alpha subunit, the Rpb11-like domain and the insert domain form two subregions of the N-terminal domain.

The structure of the Rpb11-like domain consists of a two-layer alpha/beta fold consisting of beta(2)-alpha-beta(2)-alpha. Rpb3 and Rpb11 in yeast RNAP [PubMed11313498, PubMed12191485] have been shown to share a high degree of sequence and structural similarity to the alpha subunit of bacterial RNAP [PubMed9657722, PubMed12000971].


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) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 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 RBP11-like subunits of RNA polymerase 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 RBP11-like subunits of RNA polymerase 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) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]