SUPERFAMILY 1.75 HMM library and genome assignments server

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 (3,237) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,075 20,660 6
Proteins 4,055 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 0.0001205 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0002209 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0002644 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0005544 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.001493 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.005968 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.000000001645 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.000000001698 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.000000001709 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.00000001031 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.00000001891 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00000002098 Moderately Informative Direct
Biological Process (BP) gene expression 0.00000009693 Moderately Informative Direct
Biological Process (BP) transcription, DNA-templated 0.00000000000004551 Informative Direct
Molecular Function (MF) transferase activity 0.00001452 Least Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.000000006177 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 0.0000000002444 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.004244 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01175 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.0264 Least Informative Inherited
Cellular Component (CC) transferase complex 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.000000003678 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00000002757 Moderately Informative Direct
Cellular Component (CC) DNA-directed RNA polymerase complex 0 Informative Direct
Cellular Component (CC) plastid 0.000001807 Informative Direct
Cellular Component (CC) nucleoplasm part 0.00001531 Informative Direct
Cellular Component (CC) nucleolar part 0.00000000007552 Highly Informative Direct
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 0.00000003227 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 ]