SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (679) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 1,432 3,915 2
Proteins 1,430 3,911 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 process0.0000034490.000001601Least InformativeDirect
Biological Process (BP)biosynthetic process0.00050420.00007406Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.000011210.000004962Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.000032940.0002088Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.0000035540.000001418Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.0000094130.000003498Least InformativeDirect
Biological Process (BP)primary metabolic process0.0032460.003558Least InformativeInherited
Biological Process (BP)gene expression0.00000000039940.0000000015Moderately InformativeDirect
Biological Process (BP)RNA metabolic process0.000000000014920.0000000002686Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.000012280.00000124Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.0000027450.0000006953Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.00000043420.0000009903Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.000022670.000003142Moderately InformativeDirect
Biological Process (BP)transcription, DNA-templated0.00000002050.0000001464InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.000000000003990.000000006761Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.000017270.0001151Least InformativeDirect
Cellular Component (CC)protein complex0.89510.7898Least InformativeInherited
Cellular Component (CC)nuclear part0.00000015020.000003416Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen0.000000000046910.000000002349Moderately InformativeDirect
Cellular Component (CC)transferase complex0.00000000012960.000000006821Moderately InformativeDirect
Cellular Component (CC)nucleoplasm part00InformativeDirect
Cellular Component (CC)transferase complex, transferring phosphorus-containing groups0.000000000000096840.0000000000029InformativeDirect
Cellular Component (CC)transcription elongation factor complex0.000000000000017710.0000000000002218Highly 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 0.000001601 Least Informative Direct
Biological Process (BP) biosynthetic process 0.00007406 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.000004962 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0002088 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.000001418 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000003498 Least Informative Direct
Biological Process (BP) primary metabolic process 0.003558 Least Informative Inherited
Biological Process (BP) gene expression 0.0000000015 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.0000000002686 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.00000124 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0000006953 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.0000009903 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.000003142 Moderately Informative Direct
Biological Process (BP) transcription, DNA-templated 0.0000001464 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000000006761 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0001151 Least Informative Direct
Cellular Component (CC) protein complex 0.7898 Least Informative Inherited
Cellular Component (CC) nuclear part 0.000003416 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000000002349 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.000000006821 Moderately Informative Direct
Cellular Component (CC) nucleoplasm part 0 Informative Direct
Cellular Component (CC) transferase complex, transferring phosphorus-containing groups 0.0000000000029 Informative Direct
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 0.0000002763 Highly Informative Direct
Cellular Component (CC) transcription elongation factor complex 0.0000000000002218 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processmRNA processing0.000000000002866InformativeDirect
Cellular componentNucleus0.0000000000005653Least InformativeDirect
Cellular componentChromosome0.0000000000001786InformativeDirect
Cellular componentCentromere0Highly InformativeDirect
Cellular componentDNA-directed RNA polymerase0Highly InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationTransferase0.000008741Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationActivator0.0000000005144Moderately InformativeDirect
Post-translational modificationRepressor0.000000001153Moderately 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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]