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DNA-directed DNA polymerase
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Enzyme Commission (EC)
Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed. To navigate hierarchical structure of EC, we display all parental EC terms to the current EC term of interest ordered by their shortest distances to the current term. Also, only direct children EC terms of the current EC term are listed.
Structural Classification of Proteins (SCOP)
SCOP classifies evolutionary-related domains into Superfamily level and Family level. Accordingly, we have generated the domain-centric EC annotations for each of the three concepts at each of the two domain levels.
Structural Domain Enzyme Commission Ontology (SDEO)
As domain-centric ontology, SDEO only refers to those EC terms which are the most informative to annotate SCOP domains.
EC annotations for SCOP domains
For details, please visit Documentation: EC annotations for SCOP domains. Therein, we provide several relevant files ( Data Availability) for the download, including an annotation file (i.e., Domain2EC.txt) and the corresponding ontology (i.e., SDEO.txt).
Supra-domain Enzyme Commission Ontology (SPEO)
As an extension, SPEO includes those EC terms which are the most informative to annotate supra-domains and individual SCOP domains at the Superfamily level.
EC annotations for Supra-domains
For details, please visit Documentation: EC annotations for Supra-domains. Therein, we provide several relevant files ( Data Availability) for the download, including a annotation file (i.e., SP2EC.txt) and an ontology (i.e., SPEO.txt). For the sake of being browsable, listed below are those supra-domains (single, dual, triple, quad).
Jump to [ Top · EC Hierarchy · Superfamily · Family · Supra-domain ]
Root: EC Hierarchy (from IntEnz release 70)
Jump to [ Top · EC Hierarchy · Superfamily · Family · Supra-domain ]
Superfamily(show details)
Jump to [ Top · EC Hierarchy · Superfamily · Family · Supra-domain ]
Family(show details)
Family domains annotated to this (SDEO level: Informative)
Highlighted in gray are those with FDR_all>0.001
SCOP term |
FDR (all) |
Annotation (direct or inherited) |
DnaQ-like 3'-5' exonuclease | 0 | DIRECT |
Ribonuclease H | 0 | DIRECT |
TBP-associated factors, TAFs | 0 | DIRECT |
Retrovirus zinc finger-like domains | 0 | DIRECT |
5' to 3' exonuclease catalytic domain | 0 | DIRECT |
Retrovirus capsid protein C-terminal domain | 0 | DIRECT |
AF1531-like | 0 | DIRECT |
DNA polymerase I | 0 | DIRECT |
N-terminal Zn binding domain of HIV integrase | 0 | DIRECT |
Immunodeficiency virus matrix proteins | 0 | DIRECT |
PHP domain | 0 | DIRECT |
DNA polymerase III clamp loader subunits, C-terminal domain | 0 | DIRECT |
Lesion bypass DNA polymerase (Y-family), catalytic domain | 0 | DIRECT |
HTLV-II matrix protein | 0 | DIRECT |
DNA polymerase III, beta subunit | 0 | DIRECT |
DNA polymerase beta-like | 0 | DIRECT |
Retroviral protease (retropepsin) | 0 | DIRECT |
Reverse transcriptase | 0 | DIRECT |
5' to 3' exonuclease, C-terminal subdomain | 0 | DIRECT |
Lesion bypass DNA polymerase (Y-family), little finger domain | 0 | DIRECT |
Retroviral integrase, catalytic domain | 0 | DIRECT |
Retrovirus capsid protein, N-terminal core domain | 0 | DIRECT |
DNA-binding domain of retroviral integrase | 0 | DIRECT |
DNA polymerase beta, N-terminal domain-like | 0.000000000001565 | DIRECT |
Intein (protein splicing domain) | 0.00000000005581 | DIRECT |
DNA polymerase beta-like, second domain | 0.00000000008333 | DIRECT |
Extended AAA-ATPase domain | 0.0000000001761 | DIRECT |
SCOP term |
FDR (all) |
Annotation (direct or inherited) |
DnaQ-like 3'-5' exonuclease | 0 | Direct |
Ribonuclease H | 0 | Direct |
TBP-associated factors, TAFs | 0 | Direct |
Retrovirus zinc finger-like domains | 0 | Direct |
5' to 3' exonuclease catalytic domain | 0 | Direct |
Retrovirus capsid protein C-terminal domain | 0 | Direct |
AF1531-like | 0 | Direct |
DNA polymerase I | 0 | Direct |
N-terminal Zn binding domain of HIV integrase | 0 | Direct |
Immunodeficiency virus matrix proteins | 0 | Direct |
PHP domain | 0 | Direct |
DNA polymerase III clamp loader subunits, C-terminal domain | 0 | Direct |
Lesion bypass DNA polymerase (Y-family), catalytic domain | 0 | Direct |
HTLV-II matrix protein | 0 | Direct |
DNA polymerase III, beta subunit | 0 | Direct |
DNA polymerase beta-like | 0 | Direct |
Retroviral protease (retropepsin) | 0 | Direct |
Reverse transcriptase | 0 | Direct |
5' to 3' exonuclease, C-terminal subdomain | 0 | Direct |
Lesion bypass DNA polymerase (Y-family), little finger domain | 0 | Direct |
Retroviral integrase, catalytic domain | 0 | Direct |
Retrovirus capsid protein, N-terminal core domain | 0 | Direct |
DNA-binding domain of retroviral integrase | 0 | Direct |
DNA polymerase beta, N-terminal domain-like | 0.000000000001565 | Direct |
Intein (protein splicing domain) | 0.00000000005581 | Direct |
DNA polymerase beta-like, second domain | 0.00000000008333 | Direct |
Extended AAA-ATPase domain | 0.0000000001761 | Direct |
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this EC term
 |
Plot tree as:
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Download Newick format tree:
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(show help)
Trees by TreeVector
A presence/absence matrix is generated using protein domains and supradomains
for all genomes in SUPERFAMILY. The RAxML
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
Jump to [ Top · EC Hierarchy · Superfamily · Family · Supra-domain ]
Supra-domain (including individual superfamily)
(show details)
(show details)
Supra-domains annotated to this EC term (SPEO level: Moderately Informative)
Highlighted in gray are those with FDR>0.001
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
47353,57756 47353 - Retrovirus capsid dimerization domain-like 57756 - Retrovirus zinc finger-like domains | 0 | DIRECT |
56672,90234 56672 - DNA/RNA polymerases 90234 - Zinc finger domain of DNA polymerase-alpha | 0 | DIRECT |
57756,50630 57756 - Retrovirus zinc finger-like domains 50630 - Acid proteases | 0 | DIRECT |
56672,51294 56672 - DNA/RNA polymerases 51294 - Hedgehog/intein (Hint) domain | 0 | DIRECT |
50249,56300 50249 - Nucleic acid-binding proteins 56300 - Metallo-dependent phosphatases | 0 | DIRECT |
55608,56672 55608 - Homing endonucleases 56672 - DNA/RNA polymerases | 0 | DIRECT |
47943,47353 47943 - Retrovirus capsid protein, N-terminal core domain 47353 - Retrovirus capsid dimerization domain-like | 0 | DIRECT |
50249,89550 50249 - Nucleic acid-binding proteins 89550 - PHP domain-like | 0 | DIRECT |
55979,55979 55979 - DNA clamp 55979 - DNA clamp | 0 | DIRECT |
52540,48019 52540 - P-loop containing nucleoside triphosphate hydrolases 48019 - post-AAA+ oligomerization domain-like | 0 | DIRECT |
88723,47807 88723 - PIN domain-like 47807 - 5' to 3' exonuclease, C-terminal subdomain | 0 | DIRECT |
46919,53098 46919 - N-terminal Zn binding domain of HIV integrase 53098 - Ribonuclease H-like | 0 | DIRECT |
53098,46919 53098 - Ribonuclease H-like 46919 - N-terminal Zn binding domain of HIV integrase | 0 | DIRECT |
56672,55608 56672 - DNA/RNA polymerases 55608 - Homing endonucleases | 0 | DIRECT |
56672,100879 56672 - DNA/RNA polymerases 100879 - Lesion bypass DNA polymerase (Y-family), little finger domain | 0 | DIRECT |
47807,56672 47807 - 5' to 3' exonuclease, C-terminal subdomain 56672 - DNA/RNA polymerases | 0 | DIRECT |
53098,56672 53098 - Ribonuclease H-like 56672 - DNA/RNA polymerases | 0 | DIRECT |
47807,53098 47807 - 5' to 3' exonuclease, C-terminal subdomain 53098 - Ribonuclease H-like | 0 | DIRECT |
56672,53098 56672 - DNA/RNA polymerases 53098 - Ribonuclease H-like | 0 | DIRECT |
50630,56672 50630 - Acid proteases 56672 - DNA/RNA polymerases | 0 | DIRECT |
53098,50122 53098 - Ribonuclease H-like 50122 - DNA-binding domain of retroviral integrase | 0 | DIRECT |
51294,56672 51294 - Hedgehog/intein (Hint) domain 56672 - DNA/RNA polymerases | 0 | DIRECT |
89550,53098 89550 - PHP domain-like 53098 - Ribonuclease H-like | 0 | DIRECT |
47836,47943 47836 - Retroviral matrix proteins 47943 - Retrovirus capsid protein, N-terminal core domain | 0 | DIRECT |
53098,53098 53098 - Ribonuclease H-like 53098 - Ribonuclease H-like | 0.0000000001068 | DIRECT |
47802,81585 47802 - DNA polymerase beta, N-terminal domain-like 81585 - PsbU/PolX domain-like | 0.0000000002763 | DIRECT |
81585,81301 81585 - PsbU/PolX domain-like 81301 - Nucleotidyltransferase | 0.0000000002763 | DIRECT |
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
47353,57756 47353 - Retrovirus capsid dimerization domain-like 57756 - Retrovirus zinc finger-like domains | 0 | Direct |
56672,90234 56672 - DNA/RNA polymerases 90234 - Zinc finger domain of DNA polymerase-alpha | 0 | Direct |
57756,50630 57756 - Retrovirus zinc finger-like domains 50630 - Acid proteases | 0 | Direct |
56672,51294 56672 - DNA/RNA polymerases 51294 - Hedgehog/intein (Hint) domain | 0 | Direct |
50249,56300 50249 - Nucleic acid-binding proteins 56300 - Metallo-dependent phosphatases | 0 | Direct |
55608,56672 55608 - Homing endonucleases 56672 - DNA/RNA polymerases | 0 | Direct |
47943,47353 47943 - Retrovirus capsid protein, N-terminal core domain 47353 - Retrovirus capsid dimerization domain-like | 0 | Direct |
50249,89550 50249 - Nucleic acid-binding proteins 89550 - PHP domain-like | 0 | Direct |
55979,55979 55979 - DNA clamp 55979 - DNA clamp | 0 | Direct |
52540,48019 52540 - P-loop containing nucleoside triphosphate hydrolases 48019 - post-AAA+ oligomerization domain-like | 0 | Direct |
88723,47807 88723 - PIN domain-like 47807 - 5' to 3' exonuclease, C-terminal subdomain | 0 | Direct |
46919,53098 46919 - N-terminal Zn binding domain of HIV integrase 53098 - Ribonuclease H-like | 0 | Direct |
53098,46919 53098 - Ribonuclease H-like 46919 - N-terminal Zn binding domain of HIV integrase | 0 | Direct |
56672,55608 56672 - DNA/RNA polymerases 55608 - Homing endonucleases | 0 | Direct |
56672,100879 56672 - DNA/RNA polymerases 100879 - Lesion bypass DNA polymerase (Y-family), little finger domain | 0 | Direct |
47807,56672 47807 - 5' to 3' exonuclease, C-terminal subdomain 56672 - DNA/RNA polymerases | 0 | Direct |
53098,56672 53098 - Ribonuclease H-like 56672 - DNA/RNA polymerases | 0 | Direct |
47807,53098 47807 - 5' to 3' exonuclease, C-terminal subdomain 53098 - Ribonuclease H-like | 0 | Direct |
56672,53098 56672 - DNA/RNA polymerases 53098 - Ribonuclease H-like | 0 | Direct |
50630,56672 50630 - Acid proteases 56672 - DNA/RNA polymerases | 0 | Direct |
53098,50122 53098 - Ribonuclease H-like 50122 - DNA-binding domain of retroviral integrase | 0 | Direct |
51294,56672 51294 - Hedgehog/intein (Hint) domain 56672 - DNA/RNA polymerases | 0 | Direct |
89550,53098 89550 - PHP domain-like 53098 - Ribonuclease H-like | 0 | Direct |
47836,47943 47836 - Retroviral matrix proteins 47943 - Retrovirus capsid protein, N-terminal core domain | 0 | Direct |
53098,53098 53098 - Ribonuclease H-like 53098 - Ribonuclease H-like | 0.0000000001068 | Direct |
47802,81585 47802 - DNA polymerase beta, N-terminal domain-like 81585 - PsbU/PolX domain-like | 0.0000000002763 | Direct |
81585,81301 81585 - PsbU/PolX domain-like 81301 - Nucleotidyltransferase | 0.0000000002763 | Direct |
(show details)
Supra-domains annotated to this EC term (SPEO level: Moderately Informative)
Highlighted in gray are those with FDR>0.001
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
88723,47807,56672 88723 - PIN domain-like 47807 - 5' to 3' exonuclease, C-terminal subdomain 56672 - DNA/RNA polymerases | 0 | DIRECT |
53098,56672,51294 53098 - Ribonuclease H-like 56672 - DNA/RNA polymerases 51294 - Hedgehog/intein (Hint) domain | 0 | DIRECT |
53098,46919,53098 53098 - Ribonuclease H-like 46919 - N-terminal Zn binding domain of HIV integrase 53098 - Ribonuclease H-like | 0 | DIRECT |
57756,50630,56672 57756 - Retrovirus zinc finger-like domains 50630 - Acid proteases 56672 - DNA/RNA polymerases | 0 | DIRECT |
55979,55979,55979 55979 - DNA clamp 55979 - DNA clamp 55979 - DNA clamp | 0 | DIRECT |
51294,56672,55608 51294 - Hedgehog/intein (Hint) domain 56672 - DNA/RNA polymerases 55608 - Homing endonucleases | 0 | DIRECT |
55608,56672,51294 55608 - Homing endonucleases 56672 - DNA/RNA polymerases 51294 - Hedgehog/intein (Hint) domain | 0 | DIRECT |
53098,56672,90234 53098 - Ribonuclease H-like 56672 - DNA/RNA polymerases 90234 - Zinc finger domain of DNA polymerase-alpha | 0 | DIRECT |
47836,47943,47353 47836 - Retroviral matrix proteins 47943 - Retrovirus capsid protein, N-terminal core domain 47353 - Retrovirus capsid dimerization domain-like | 0 | DIRECT |
47943,47353,57756 47943 - Retrovirus capsid protein, N-terminal core domain 47353 - Retrovirus capsid dimerization domain-like 57756 - Retrovirus zinc finger-like domains | 0 | DIRECT |
56672,53098,46919 56672 - DNA/RNA polymerases 53098 - Ribonuclease H-like 46919 - N-terminal Zn binding domain of HIV integrase | 0 | DIRECT |
46919,53098,50122 46919 - N-terminal Zn binding domain of HIV integrase 53098 - Ribonuclease H-like 50122 - DNA-binding domain of retroviral integrase | 0 | DIRECT |
56672,53098,50122 56672 - DNA/RNA polymerases 53098 - Ribonuclease H-like 50122 - DNA-binding domain of retroviral integrase | 0 | DIRECT |
47353,57756,50630 47353 - Retrovirus capsid dimerization domain-like 57756 - Retrovirus zinc finger-like domains 50630 - Acid proteases | 0 | DIRECT |
47807,53098,56672 47807 - 5' to 3' exonuclease, C-terminal subdomain 53098 - Ribonuclease H-like 56672 - DNA/RNA polymerases | 0 | DIRECT |
50249,89550,53098 50249 - Nucleic acid-binding proteins 89550 - PHP domain-like 53098 - Ribonuclease H-like | 0 | DIRECT |
50630,56672,53098 50630 - Acid proteases 56672 - DNA/RNA polymerases 53098 - Ribonuclease H-like | 0 | DIRECT |
88723,47807,53098 88723 - PIN domain-like 47807 - 5' to 3' exonuclease, C-terminal subdomain 53098 - Ribonuclease H-like | 0 | DIRECT |
56672,55608,56672 56672 - DNA/RNA polymerases 55608 - Homing endonucleases 56672 - DNA/RNA polymerases | 0 | DIRECT |
47802,81585,81301 47802 - DNA polymerase beta, N-terminal domain-like 81585 - PsbU/PolX domain-like 81301 - Nucleotidyltransferase | 0.0000000002763 | DIRECT |
56672,53098,53098 56672 - DNA/RNA polymerases 53098 - Ribonuclease H-like 53098 - Ribonuclease H-like | 0.000000001875 | DIRECT |
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
88723,47807,56672 88723 - PIN domain-like 47807 - 5' to 3' exonuclease, C-terminal subdomain 56672 - DNA/RNA polymerases | 0 | Direct |
53098,56672,51294 53098 - Ribonuclease H-like 56672 - DNA/RNA polymerases 51294 - Hedgehog/intein (Hint) domain | 0 | Direct |
53098,46919,53098 53098 - Ribonuclease H-like 46919 - N-terminal Zn binding domain of HIV integrase 53098 - Ribonuclease H-like | 0 | Direct |
57756,50630,56672 57756 - Retrovirus zinc finger-like domains 50630 - Acid proteases 56672 - DNA/RNA polymerases | 0 | Direct |
55979,55979,55979 55979 - DNA clamp 55979 - DNA clamp 55979 - DNA clamp | 0 | Direct |
51294,56672,55608 51294 - Hedgehog/intein (Hint) domain 56672 - DNA/RNA polymerases 55608 - Homing endonucleases | 0 | Direct |
55608,56672,51294 55608 - Homing endonucleases 56672 - DNA/RNA polymerases 51294 - Hedgehog/intein (Hint) domain | 0 | Direct |
53098,56672,90234 53098 - Ribonuclease H-like 56672 - DNA/RNA polymerases 90234 - Zinc finger domain of DNA polymerase-alpha | 0 | Direct |
47836,47943,47353 47836 - Retroviral matrix proteins 47943 - Retrovirus capsid protein, N-terminal core domain 47353 - Retrovirus capsid dimerization domain-like | 0 | Direct |
47943,47353,57756 47943 - Retrovirus capsid protein, N-terminal core domain 47353 - Retrovirus capsid dimerization domain-like 57756 - Retrovirus zinc finger-like domains | 0 | Direct |
56672,53098,46919 56672 - DNA/RNA polymerases 53098 - Ribonuclease H-like 46919 - N-terminal Zn binding domain of HIV integrase | 0 | Direct |
46919,53098,50122 46919 - N-terminal Zn binding domain of HIV integrase 53098 - Ribonuclease H-like 50122 - DNA-binding domain of retroviral integrase | 0 | Direct |
56672,53098,50122 56672 - DNA/RNA polymerases 53098 - Ribonuclease H-like 50122 - DNA-binding domain of retroviral integrase | 0 | Direct |
47353,57756,50630 47353 - Retrovirus capsid dimerization domain-like 57756 - Retrovirus zinc finger-like domains 50630 - Acid proteases | 0 | Direct |
47807,53098,56672 47807 - 5' to 3' exonuclease, C-terminal subdomain 53098 - Ribonuclease H-like 56672 - DNA/RNA polymerases | 0 | Direct |
50249,89550,53098 50249 - Nucleic acid-binding proteins 89550 - PHP domain-like 53098 - Ribonuclease H-like | 0 | Direct |
50630,56672,53098 50630 - Acid proteases 56672 - DNA/RNA polymerases 53098 - Ribonuclease H-like | 0 | Direct |
88723,47807,53098 88723 - PIN domain-like 47807 - 5' to 3' exonuclease, C-terminal subdomain 53098 - Ribonuclease H-like | 0 | Direct |
56672,55608,56672 56672 - DNA/RNA polymerases 55608 - Homing endonucleases 56672 - DNA/RNA polymerases | 0 | Direct |
47802,81585,81301 47802 - DNA polymerase beta, N-terminal domain-like 81585 - PsbU/PolX domain-like 81301 - Nucleotidyltransferase | 0.0000000002763 | Direct |
56672,53098,53098 56672 - DNA/RNA polymerases 53098 - Ribonuclease H-like 53098 - Ribonuclease H-like | 0.000000001875 | Direct |
Plot distribution on phylogenetic tree for Individual Supra-domains annotated by this EC term
 |
Plot tree as:
| |
Download Newick format tree:
|
(show help)
Trees by TreeVector
A presence/absence matrix is generated using protein domains and supradomains
for all genomes in SUPERFAMILY. The RAxML
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
|