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 (671) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,416 1,820 2
Proteins 1,414 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 process0.0000000066230.000000001662Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.00000018950.00000002322Least InformativeDirect
Biological Process (BP)biosynthetic process0.000000026940.0000000006283Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.000000039740.0000002444Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.0000000061360.000000001275Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.000000025970.000000005154Least InformativeDirect
Biological Process (BP)gene expression0.0000000000000079780.0000000000000161Moderately InformativeDirect
Biological Process (BP)RNA metabolic process00.000000000000003755Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.00000000000001560Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.0000000000000032610Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.0000000000000032610.000000000000003755Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process0.000000000000012530Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.000000000000096170Moderately InformativeDirect
Biological Process (BP)transcription, DNA-dependent00InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.000000005890.00000332Least InformativeDirect
Cellular Component (CC)protein complex0.00000000000077760.0000000005258Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0000082990.00006052Least InformativeDirect
Cellular Component (CC)nuclear part0.000000063940.000002666Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen00.000000000001043Moderately InformativeDirect
Cellular Component (CC)nucleoplasm part00InformativeDirect
Cellular Component (CC)nuclear DNA-directed RNA polymerase complex0.000014510.0000003132InformativeDirect

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 0.000000001662 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.00000002322 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0000000006283 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0000002444 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.000000001275 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000005154 Least Informative Direct
Biological Process (BP) gene expression 0.0000000000000161 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000000000000003755 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 0.000000000000003755 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) transcription, DNA-dependent 0 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000332 Least Informative Direct
Cellular Component (CC) protein complex 0.0000000005258 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00006052 Least Informative Direct
Cellular Component (CC) nuclear part 0.000002666 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000000000001043 Moderately Informative Direct
Cellular Component (CC) nucleoplasm part 0 Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 0.0000003132 Informative Direct
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 0.00000008603 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 ]