SUPERFAMILY 1.75 HMM library and genome assignments server


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 (2,444) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 56,047 293,130 164
Proteins 55,383 292,598 164


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)heterocycle metabolic process4.304e-080Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process5.228e-080Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process1.985e-070Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process6.987e-070Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process1.63e-060Least InformativeDirect
Biological Process (BP)response to stimulus0.036920.0003767Least InformativeInherited
Biological Process (BP)single-organism cellular process0.0091140Least InformativeInherited
Biological Process (BP)biosynthetic process0.13631.158e-14Least InformativeInherited
Biological Process (BP)cellular response to stress1.442e-070Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.0023990Moderately InformativeInherited
Biological Process (BP)DNA metabolic process00InformativeDirect
Biological Process (BP)response to DNA damage stimulus7.067e-110InformativeDirect
Biological Process (BP)DNA replication7.549e-050Highly InformativeDirect
Molecular Function (MF)transferase activity1.756e-050Least InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups1.073e-090Moderately InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity00InformativeDirect
Molecular Function (MF)DNA polymerase activity00Highly 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) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0.0003767 Least Informative Direct
Biological Process (BP) biosynthetic process 1.158e-14 Least Informative Direct
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
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) homeostatic process 0.1741 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.9646 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.004562 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.005334 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.007932 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.03191 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) mitochondrion organization 5.062e-08 Informative Direct
Biological Process (BP) anatomical structure homeostasis 6.906e-08 Informative Direct
Biological Process (BP) cell cycle process 0.7823 Informative Inherited
Biological Process (BP) chromosome organization 0.08543 Informative Inherited
Biological Process (BP) DNA replication 0 Highly Informative Direct
Biological Process (BP) DNA repair 9.852e-13 Highly Informative Direct
Biological Process (BP) cell cycle phase 1.972e-07 Highly Informative Direct
Biological Process (BP) mitotic cell cycle 1.599e-05 Highly Informative Direct
Biological Process (BP) aging 0.0005045 Highly Informative Direct
Molecular Function (MF) transferase activity 0 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.1137 Least Informative Inherited
Molecular Function (MF) binding 0.008194 Least Informative Inherited
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) heterocyclic compound binding 3.94e-14 Moderately Informative Direct
Molecular Function (MF) organic cyclic compound binding 1.043e-13 Moderately Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) nuclease activity 0 Informative Direct
Molecular Function (MF) peptidase activity 2.272e-11 Informative Direct
Molecular Function (MF) RNA binding 2.283e-08 Informative Direct
Molecular Function (MF) DNA polymerase activity 0 Highly Informative Direct
Molecular Function (MF) chromatin binding 4.602e-06 Highly Informative Direct
Molecular Function (MF) RNA polymerase activity 1 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0003672 Least Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.2938 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.0349 Least Informative Inherited
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.07653 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.05692 Moderately Informative Inherited
Cellular Component (CC) chromosome 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 4.897e-10 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 H2.098e-14Highly InformativeDirect
Enzyme Commission (EC)Picornain 2A2.396e-10Highly InformativeDirect
Enzyme Commission (EC)Nuclear-inclusion-a endopeptidase1.069e-09Highly InformativeDirect
Enzyme Commission (EC)Pestivirus NS3 polyprotein peptidase1.803e-07Highly InformativeDirect
Enzyme Commission (EC)Calicivirin2.573e-06Highly InformativeDirect
Enzyme Commission (EC)Helper-component proteinase3.673e-06Highly InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)immune system phenotype0.0008647Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.08773Least InformativeInherited
Mammalian Phenotype (MP)tumorigenesis0.0005702Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal leukopoiesis0.1695Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte morphology0.1727Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.2146Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell differentiation0.3003Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal bone marrow cell morphology/development0.7398Moderately InformativeInherited
Mammalian Phenotype (MP)malignant tumors7.437e-05InformativeDirect
Mammalian Phenotype (MP)abnormal B cell differentiation0.01702InformativeInherited
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.2876InformativeInherited
Mammalian Phenotype (MP)T cell derived lymphoma0.0001832Highly InformativeDirect
Mammalian Phenotype (MP)chromosomal instability0.0002169Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.0006634Least InformativeDirect
Worm Phenotype (WP)cell organization biogenesis variant0.02369Moderately InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.02455Moderately InformativeInherited
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.001572InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)UV resistance0.0009877Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)radiation sensitive3.66e-08InformativeDirect
Fly Phenotype (FP)stress response defective0.0006542InformativeDirect
Fly Phenotype (FP)DNA repair defective1.625e-07Highly InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)multi-tissue structure0Least InformativeDirect
Zebrafish Anatomy (ZA)cavitated compound organ0Least InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)0 seed germination stage4.733e-08InformativeDirect

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)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases1Moderately InformativeInherited
Enzyme Commission (EC)RNA-directed RNA polymerase0InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)Cysteine endopeptidases0InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides0InformativeDirect
Enzyme Commission (EC)RNA helicase0InformativeDirect
Enzyme Commission (EC)Omega peptidases0.7159InformativeInherited
Enzyme Commission (EC)Serine endopeptidases1InformativeInherited
Enzyme Commission (EC)mRNA (guanine-N(7)-)-methyltransferase0Highly InformativeDirect
Enzyme Commission (EC)mRNA (nucleoside-2'-O)-methyltransferase0Highly InformativeDirect
Enzyme Commission (EC)RNA-directed DNA polymerase0Highly InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0Highly InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0Highly InformativeDirect
Enzyme Commission (EC)Polynucleotide 5'-phosphatase0Highly InformativeDirect
Enzyme Commission (EC)Flavivirin0Highly InformativeDirect
Enzyme Commission (EC)Picornain 3C0Highly InformativeDirect
Enzyme Commission (EC)HIV-1 retropepsin0Highly InformativeDirect
Enzyme Commission (EC)Nucleoside-triphosphate phosphatase0Highly InformativeDirect
Enzyme Commission (EC)Picornain 2A2.096e-10Highly InformativeDirect
Enzyme Commission (EC)HIV-2 retropepsin2.954e-05Highly InformativeDirect

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)antiinfectives for systemic use1.109e-05Moderately InformativeDirect
Drugbank ATC_code (DB)dermatologicals0.0259Moderately InformativeInherited
Drugbank ATC_code (DB)antibiotics and chemotherapeutics for dermatological use4.239e-05InformativeDirect
Drugbank ATC_code (DB)antiinfectives0.0002132InformativeDirect

Document: DB 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 processApoptosis4.36e-10Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processViral RNA replication0InformativeDirect
Biological processViral immunoevasion0InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Biological processViral attachment to host cell4.755e-10InformativeDirect
Biological processmRNA capping0Highly InformativeDirect
Biological processCapsid maturation0Highly 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 processViral ion channel0Highly InformativeDirect
Biological processModulation of host cell apoptosis by virus1.826e-15Highly InformativeDirect
Biological processDNA synthesis5.745e-13Highly InformativeDirect
Biological processInhibition of host TYK2 by virus6.638e-10Highly InformativeDirect
Biological processModulation of host cell cycle by virus5.423e-07Highly InformativeDirect
Biological processSOS response1Highly InformativeInherited
Biological processHost gene expression shutoff by virus1Highly InformativeInherited
Cellular componentMembrane0Least InformativeDirect
Cellular componentMitochondrion0.08137Moderately InformativeInherited
Cellular componentVirion0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Cellular componentChromosome0.3316InformativeInherited
Cellular componentHost cytoplasmic vesicle0Highly InformativeDirect
Cellular componentHost endoplasmic reticulum0Highly InformativeDirect
Cellular componentHost endosome0Highly InformativeDirect
Cellular componentViral nucleoprotein8.146e-12Highly InformativeDirect
Cellular componentTelomere1.85e-07Highly InformativeDirect
Coding sequence diversityRibosomal frameshifting0Moderately InformativeDirect
Coding sequence diversityAlternative promoter usage0.0004105Moderately InformativeDirect
Coding sequence diversityRNA suppression of termination0InformativeDirect
Developmental stageEarly protein2.743e-05Least InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DiseaseOncogene0Moderately InformativeDirect
DomainTransmembrane0.0002162Least InformativeDirect
DomainSH3-binding0InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionNucleotide-binding7.266e-15Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionZinc-finger0Moderately InformativeDirect
Molecular functionHelicase0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationCapsid protein0InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationIon channel0InformativeDirect
Post-translational modificationThiol protease0InformativeDirect
Post-translational modificationEndonuclease3.166e-14InformativeDirect
Post-translational modificationAspartyl protease0Highly InformativeDirect
Post-translational modificationRNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationRNA-directed RNA polymerase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0Moderately InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationMyristate0InformativeDirect
Post-translational modificationAutocatalytic cleavage0.2706InformativeInherited
Post-translational modificationCovalent protein-RNA linkage0Highly InformativeDirect
Post-translational modificationProtein splicing2.282e-14Highly 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · Internal database links ]