SUPERFAMILY 1.75 HMM library and genome assignments server

RNA polymerase subunits superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Rubredoxin-like [ 57769] (17)
Superfamily:   RNA polymerase subunits [ 63393] (2)
Families:   RBP12 subunit of RNA polymerase II [ 64576]
  RpoE2-like [ 111454]


Superfamily statistics
Genomes (672) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,418 1,820 2
Proteins 1,416 1,819 2


Functional annotation
General category Information
Detailed category DNA replication/repair

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 process0.0000000084320.000000001978Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.00000022590.00000002744Least InformativeDirect
Biological Process (BP)biosynthetic process0.000000026120.0000000006205Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.000000040510.0000002508Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.0000000077960.000000001516Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.00000003190.000000006025Least InformativeDirect
Biological Process (BP)gene expression0.00000000000001550.00000000000003082Moderately InformativeDirect
Biological Process (BP)RNA metabolic process00.000000000000003707Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.000000000000017020Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.0000000000000048440Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.0000000000000032510.000000000000003707Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process0.000000000000012480Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.00000000000010390.000000000000001913Moderately InformativeDirect
Biological Process (BP)transcription, DNA-templated00InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.000000003770.000002105Least InformativeDirect
Cellular Component (CC)protein complex0.00000000000073360.0000000004753Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0000085090.00005155Least InformativeDirect
Cellular Component (CC)nuclear part0.000000039130.0000008616Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen00.0000000000002486Moderately InformativeDirect
Cellular Component (CC)transferase complex0.00000000059690.00000002102Moderately InformativeDirect
Cellular Component (CC)DNA-directed RNA polymerase complex0.00000000000001210.00000000000005851InformativeDirect
Cellular Component (CC)nucleoplasm part00InformativeDirect

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 0.000000001978 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.00000002744 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0000000006205 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0000002508 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.000000001516 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000006025 Least Informative Direct
Biological Process (BP) gene expression 0.00000000000003082 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000000000000003707 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 0.000000000000003707 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.000000000000001913 Moderately Informative Direct
Biological Process (BP) transcription, DNA-templated 0 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000002105 Least Informative Direct
Cellular Component (CC) protein complex 0.0000000004753 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00005155 Least Informative Direct
Cellular Component (CC) nuclear part 0.0000008616 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000000000002486 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.00000002102 Moderately Informative Direct
Cellular Component (CC) DNA-directed RNA polymerase complex 0.00000000000005851 Informative Direct
Cellular Component (CC) nucleoplasm part 0 Informative Direct
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 0.000001431 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)collective phyllome structure0Least 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 componentNucleus0.0000000000001131Least InformativeDirect
Cellular componentChromosome0.00000000000007955InformativeDirect
Cellular componentCentromere0Highly InformativeDirect
Cellular componentDNA-directed RNA polymerase0Highly InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationTransferase0.00001535Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationActivator0.0000000002678Moderately InformativeDirect
Post-translational modificationRepressor0.0000000007212Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · 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 2 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 RNA polymerase subunits 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 2 hidden Markov models representing the RNA polymerase subunits 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 · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]