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DNA/RNA polymerases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   DNA/RNA polymerases [ 56671]
Superfamily:   DNA/RNA polymerases [ 56672] (6)
Families:   DNA polymerase I [ 56673] (4)
  Lesion bypass DNA polymerase (Y-family), catalytic domain [ 100888] (4)
  Reverse transcriptase [ 56686] (2)
  T7 RNA polymerase [ 56691]
  RNA-dependent RNA-polymerase [ 56694] (2)
  dsRNA phage RNA-dependent RNA-polymerase [ 64480]


Superfamily statistics
Genomes (3,191) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 58,500 570,102 164
Proteins 57,724 568,105 164


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 process0.36330Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.48440Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.61010Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.36610Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.46510Least InformativeInherited
Biological Process (BP)biosynthetic process0.53340Least InformativeInherited
Biological Process (BP)response to stimulus0.35730.1048Least InformativeInherited
Biological Process (BP)primary metabolic process10.00000003608Least InformativeInherited
Biological Process (BP)cellular response to stress0.0001020Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.025520Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.014480Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.0091640Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.038240.0000000000001403Moderately InformativeInherited
Biological Process (BP)response to external stimulus0.0019080.8389Moderately InformativeInherited
Biological Process (BP)cell communication0.0093681Moderately InformativeInherited
Biological Process (BP)DNA metabolic process0.00028590InformativeDirect
Biological Process (BP)cellular response to DNA damage stimulus0.00000030960InformativeDirect
Biological Process (BP)response to extracellular stimulus0.00014930.0007906InformativeDirect
Biological Process (BP)cellular response to extracellular stimulus0.000000085610.0002297Highly InformativeDirect
Molecular Function (MF)transferase activity0.14920Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.00033430Moderately InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.0000000064240InformativeDirect
Molecular Function (MF)RNA polymerase activity0.10391Highly InformativeInherited

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 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.00000003608 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.1048 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.00000000001462 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.000000006312 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) regulation of localization 0.000000002798 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.000405 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.0000000000001602 Moderately Informative Direct
Biological Process (BP) multi-organism process 0 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0000000000001403 Moderately Informative Direct
Biological Process (BP) response to external stimulus 0.8389 Moderately Informative Inherited
Biological Process (BP) response to biotic stimulus 0.577 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.003483 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.1968 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.1945 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.03682 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.9691 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) immune system process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) mitochondrion organization 0.0000000916 Informative Direct
Biological Process (BP) response to radiation 0.0003372 Informative Direct
Biological Process (BP) regulation of catabolic process 0 Informative Direct
Biological Process (BP) response to extracellular stimulus 0.0007906 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.000000000000007296 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0 Informative Direct
Biological Process (BP) negative regulation of molecular function 0 Informative Direct
Biological Process (BP) interspecies interaction between organisms 0 Informative Direct
Biological Process (BP) chromosome organization 0.0007072 Informative Direct
Biological Process (BP) regulation of cellular localization 0 Informative Direct
Biological Process (BP) system process 1 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.9169 Informative Inherited
Biological Process (BP) regulation of immune response 0.2716 Informative Inherited
Biological Process (BP) regulation of defense response 0.2415 Informative Inherited
Biological Process (BP) cell development 1 Informative Inherited
Biological Process (BP) hemopoiesis 0.2797 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.4807 Informative Inherited
Biological Process (BP) cell cycle process 0.8881 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.2834 Informative Inherited
Biological Process (BP) myeloid cell homeostasis 0.00002823 Highly Informative Direct
Biological Process (BP) DNA replication 0 Highly Informative Direct
Biological Process (BP) aging 0.0001003 Highly Informative Direct
Biological Process (BP) digestion 0.0000006036 Highly Informative Direct
Biological Process (BP) response to UV 0.00000001345 Highly Informative Direct
Biological Process (BP) regulation of autophagy 0 Highly Informative Direct
Biological Process (BP) viral process 0 Highly Informative Direct
Biological Process (BP) positive regulation of cellular catabolic process 0 Highly Informative Direct
Biological Process (BP) negative regulation of defense response 0.000006408 Highly Informative Direct
Biological Process (BP) cellular response to extracellular stimulus 0.0002297 Highly Informative Direct
Biological Process (BP) modification of morphology or physiology of other organism involved in symbiotic interaction 0.000000000000003734 Highly Informative Direct
Biological Process (BP) anatomical structure homeostasis 0.000000002549 Highly Informative Direct
Biological Process (BP) anatomical structure maturation 0.00006181 Highly Informative Direct
Biological Process (BP) negative regulation of immune system process 0.05009 Highly Informative Inherited
Biological Process (BP) myeloid cell differentiation 0.001782 Highly Informative Inherited
Biological Process (BP) cell maturation 0.002654 Highly Informative Inherited
Biological Process (BP) multicellular organismal homeostasis 0.002831 Highly Informative Inherited
Biological Process (BP) double-strand break repair 1 Highly Informative Inherited
Biological Process (BP) regulation of DNA metabolic process 0.4574 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to stress 0.1451 Highly Informative Inherited
Molecular Function (MF) transferase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.2082 Least Informative Inherited
Molecular Function (MF) hydrolase activity 0.01663 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0000000002287 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0 Moderately Informative Direct
Molecular Function (MF) RNA binding 0.000001034 Informative Direct
Molecular Function (MF) nuclease activity 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 1 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) chromatin binding 0.000000001204 Highly Informative Direct
Molecular Function (MF) S-adenosylmethionine-dependent methyltransferase activity 0.09893 Highly Informative Inherited
Molecular Function (MF) RNA polymerase activity 1 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000004494 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000000002012 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.05299 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000000001837 Moderately Informative Direct
Cellular Component (CC) transferase complex 0 Moderately Informative Direct
Cellular Component (CC) chromosome 0.0000000000155 Informative Direct
Cellular Component (CC) protein-DNA complex 0 Informative Direct
Cellular Component (CC) transferase complex, transferring phosphorus-containing groups 0 Informative Direct
Cellular Component (CC) replisome 0 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.0000001713 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)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups1Least InformativeInherited
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0Moderately InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0Moderately InformativeDirect
Enzyme Commission (EC)Cysteine endopeptidases0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0Moderately InformativeDirect
Enzyme Commission (EC)Serine endopeptidases1Moderately InformativeInherited
Enzyme Commission (EC)Omega peptidases0.587Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases1Moderately InformativeInherited
Enzyme Commission (EC)Methyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)mRNA (nucleoside-2'-O-)-methyltransferase0InformativeDirect
Enzyme Commission (EC)mRNA (guanine-N(7)-)-methyltransferase0InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0InformativeDirect
Enzyme Commission (EC)Flavivirin0InformativeDirect
Enzyme Commission (EC)RNA-directed DNA polymerase0InformativeDirect
Enzyme Commission (EC)Nucleoside-triphosphatase0InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0InformativeDirect
Enzyme Commission (EC)Aspartic endopeptidases0InformativeDirect
Enzyme Commission (EC)RNA-directed RNA polymerase0InformativeDirect
Enzyme Commission (EC)Hepacivirin0Highly InformativeDirect
Enzyme Commission (EC)Picornain 3C0Highly InformativeDirect
Enzyme Commission (EC)Polynucleotide 5'-phosphatase0Highly InformativeDirect
Enzyme Commission (EC)Ribonuclease H0.00000000000002098Highly InformativeDirect
Enzyme Commission (EC)Picornain 2A0.0000000002396Highly InformativeDirect
Enzyme Commission (EC)Nuclear-inclusion-a endopeptidase0.000000001069Highly InformativeDirect
Enzyme Commission (EC)Pestivirus NS3 polyprotein peptidase0.0000001803Highly InformativeDirect
Enzyme Commission (EC)Calicivirin0.000002573Highly InformativeDirect
Enzyme Commission (EC)Helper-component proteinase0.000003673Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processDNA damage0Moderately InformativeDirect
Biological processIon transport0Moderately InformativeDirect
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processApoptosis0.000000002702Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processDNA repair0InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processmRNA processing0InformativeDirect
Biological processViral RNA replication0InformativeDirect
Biological processViral immunoevasion0InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Biological processEukaryotic host gene expression shutoff by virus0InformativeDirect
Biological processDNA integration0Highly InformativeDirect
Biological processmRNA capping0Highly InformativeDirect
Biological processActivation of host autophagy by virus0Highly InformativeDirect
Biological processModulation of host ubiquitin pathway by viral deubiquitinase0Highly InformativeDirect
Biological processFusion of virus membrane with host endosomal membrane0Highly InformativeDirect
Biological processViral genome integration0Highly InformativeDirect
Biological processVirus exit from host cell0Highly InformativeDirect
Biological processDNA synthesis0.00000000000007185Highly InformativeDirect
Biological processIntron homing0.0000000001537Highly InformativeDirect
Biological processInhibition of host NF-kappa-B by virus0.0000000001869Highly InformativeDirect
Biological processInhibition of host STAT2 by virus0.0000005745Highly InformativeDirect
Biological processModulation of host cell apoptosis by virus0.00007398Highly InformativeDirect
Biological processSOS response1Highly InformativeInherited
Cellular componentMembrane6.573e-16Least InformativeDirect
Cellular componentVirion0Moderately InformativeDirect
Cellular componentMitochondrion0.03743Moderately InformativeInherited
Cellular componentCapsid protein0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Cellular componentChromosome0.07353InformativeInherited
Cellular componentHost cytoplasmic vesicle0Highly InformativeDirect
Cellular componentHost endoplasmic reticulum0Highly InformativeDirect
Cellular componentHost endosome0Highly InformativeDirect
Cellular componentTelomere0.000000002513Highly InformativeDirect
Cellular componentDNA-directed RNA polymerase0.0004661Highly InformativeDirect
Coding sequence diversityRibosomal frameshifting0Moderately InformativeDirect
Coding sequence diversityRNA suppression of termination0InformativeDirect
Developmental stageEarly protein0.0000003726Least InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DiseaseOncogene0Moderately InformativeDirect
DomainTransmembrane0.7721Least InformativeInherited
DomainZinc-finger0Moderately InformativeDirect
DomainSH3-binding0InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionNucleotide-binding0.00000000000001312Least InformativeDirect
Molecular functionLipid-binding0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationHelicase0InformativeDirect
Post-translational modificationIon channel0InformativeDirect
Post-translational modificationThiol protease0InformativeDirect
Post-translational modificationEndonuclease0.00000000001897InformativeDirect
Post-translational modificationAspartyl protease0Highly InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationViral nucleoprotein0Highly InformativeDirect
Post-translational modificationRNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationRNA-directed RNA polymerase0Highly InformativeDirect
Post-translational modificationViral ion channel0Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0Moderately InformativeDirect
Post-translational modificationUbl conjugation0.000000000002468Moderately InformativeDirect
Post-translational modificationMyristate0InformativeDirect
Post-translational modificationAutocatalytic cleavage0.2323InformativeInherited
Post-translational modificationCovalent protein-RNA linkage0Highly InformativeDirect
Post-translational modificationProtein splicing0.00000000000002772Highly 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 34 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 DNA/RNA polymerases 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 34 hidden Markov models representing the DNA/RNA polymerases 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 ]