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 (622) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 1,319 1,318 2
Proteins 1,317 1,317 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 process2.031e-085.54e-08Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process4.415e-075.216e-07Least InformativeDirect
Biological Process (BP)biosynthetic process6.63e-082.091e-08Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process1.164e-073.952e-06Least InformativeDirect
Biological Process (BP)heterocycle metabolic process1.831e-084.375e-08Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process6.968e-081.457e-07Least InformativeDirect
Biological Process (BP)gene expression5.415e-142.251e-12Moderately InformativeDirect
Biological Process (BP)RNA metabolic process3.152e-156.785e-13Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process8.388e-142.78e-14Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process2.358e-143.114e-14Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process1.784e-146.812e-13Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process5.962e-142.618e-14Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process5.047e-132.518e-13Moderately InformativeDirect
Biological Process (BP)transcription, DNA-dependent00InformativeDirect
Biological Process (BP)transcription from RNA polymerase II promoter00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle4.368e-081.389e-05Least InformativeDirect
Cellular Component (CC)protein complex1.119e-131.082e-10Least InformativeDirect
Cellular Component (CC)intracellular organelle part1.053e-078.36e-07Least InformativeDirect
Cellular Component (CC)nuclear part7.186e-117.46e-09Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen01.689e-14Moderately InformativeDirect
Cellular Component (CC)nucleoplasm part00InformativeDirect
Cellular Component (CC)nuclear DNA-directed RNA polymerase complex6.269e-059.793e-07InformativeDirect
Cellular Component (CC)transcription elongation factor complex5.272e-152.496e-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 5.54e-08 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 5.216e-07 Least Informative Direct
Biological Process (BP) biosynthetic process 2.091e-08 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 3.952e-06 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 4.375e-08 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.457e-07 Least Informative Direct
Biological Process (BP) gene expression 2.251e-12 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 6.785e-13 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 2.78e-14 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 3.114e-14 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 6.812e-13 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 2.618e-14 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 2.518e-13 Moderately Informative Direct
Biological Process (BP) transcription, DNA-dependent 0 Informative Direct
Biological Process (BP) transcription from RNA polymerase II promoter 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1.389e-05 Least Informative Direct
Cellular Component (CC) protein complex 1.082e-10 Least Informative Direct
Cellular Component (CC) intracellular organelle part 8.36e-07 Least Informative Direct
Cellular Component (CC) nuclear part 7.46e-09 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 1.689e-14 Moderately Informative Direct
Cellular Component (CC) nucleoplasm part 0 Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 9.793e-07 Informative Direct
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 6.867e-08 Highly Informative Direct
Cellular Component (CC) transcription elongation factor complex 2.496e-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

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 componentNucleus9.997e-14Least InformativeDirect
Cellular componentChromosome7.409e-14InformativeDirect
Cellular componentCentromere0Highly InformativeDirect
Cellular componentDNA-directed RNA polymerase0Highly InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationTransferase1.58e-05Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationActivator2.655e-10Moderately InformativeDirect
Post-translational modificationRepressor5.952e-10Moderately 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 ]