SUPERFAMILY 1.75 HMM library and genome assignments server

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Insert subdomain of RNA polymerase alpha subunit superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Insert subdomain of RNA polymerase alpha subunit [ 56552]
Superfamily:   Insert subdomain of RNA polymerase alpha subunit [ 56553]
Families:   Insert subdomain of RNA polymerase alpha subunit [ 56554] (2)


Superfamily statistics
Genomes (3,236) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,073 20,660 6
Proteins 4,053 20,645 6


Functional annotation
General category Regulation
Detailed category DNA-binding

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 0.0001207 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0001955 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0002339 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0004975 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.001334 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.005853 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.000000001581 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.000000001633 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.00000000164 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.000000009946 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.0000000177 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00000002067 Moderately Informative Direct
Biological Process (BP) gene expression 0.0000000601 Moderately Informative Direct
Biological Process (BP) transcription, DNA-dependent 0.00000000000004773 Informative Direct
Molecular Function (MF) transferase activity 0.000004663 Least Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.000000006015 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 0.0000000002746 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.004988 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.02142 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.02495 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00000001679 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000001378 Moderately Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 0 Informative Direct
Cellular Component (CC) plastid 0.000001531 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0005726 Informative Direct
Cellular Component (CC) nucleolar part 0.0000000000381 Highly Informative Direct
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 0.0000000009276 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

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least 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 IPR011262 SSF56553 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 to the prokaryotic RNAP alpha (RpoA) 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/beta') can interact [PubMed11453250].

The dimerisation domains differ between the different subunit families. In eukaryotic Rpb3, archaeal D and bacterial RpoA subunits , the dimerisation domain is comprised of a central insert domain, which interrupts an Rpb11-like domain , dividing it into two halves [PubMed9657722]. In eukaryotic Rpb11 and archaeal L subunits, the insert domain is lacking, leaving the Rpb11-like domain intact and contiguous.


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) · Enzyme Commission (EC) · 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 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 Insert subdomain of RNA polymerase alpha subunit 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 Insert subdomain of RNA polymerase alpha subunit 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) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]