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).
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.
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
47005,52777 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases | 0 | Direct |
52777,52777 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases | 0 | Direct |
69593,47473 69593 - Glycerol-3-phosphate (1)-acyltransferase 47473 - EF-hand | 0 | Direct |
53901,53901 53901 - Thiolase-like 53901 - Thiolase-like | 0 | Direct |
53448,51161 53448 - Nucleotide-diphospho-sugar transferases 51161 - Trimeric LpxA-like enzymes | 0 | Direct |
51735,47336 51735 - NAD(P)-binding Rossmann-fold domains 47336 - ACP-like | 0 | Direct |
57850,57933 57850 - RING/U-box 57933 - TAZ domain | 0 | Direct |
51230,47005 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 0 | Direct |
46785,57903 46785 - "Winged helix" DNA-binding domain 57903 - FYVE/PHD zinc finger | 0 | Direct |
52540,75138 52540 - P-loop containing nucleoside triphosphate hydrolases 75138 - HprK N-terminal domain-like | 0 | Direct |
51230,52777 51230 - Single hybrid motif 52777 - CoA-dependent acyltransferases | 0 | Direct |
52540,55729 52540 - P-loop containing nucleoside triphosphate hydrolases 55729 - Acyl-CoA N-acyltransferases (Nat) | 0 | Direct |
102114,55729 102114 - Radical SAM enzymes 55729 - Acyl-CoA N-acyltransferases (Nat) | 0 | Direct |
54637,52151 54637 - Thioesterase/thiol ester dehydrase-isomerase 52151 - FabD/lysophospholipase-like | 0 | Direct |
55729,47370 55729 - Acyl-CoA N-acyltransferases (Nat) 47370 - Bromodomain | 0 | Direct |
57850,57850 57850 - RING/U-box 57850 - RING/U-box | 0 | Direct |
52151,55048 52151 - FabD/lysophospholipase-like 55048 - Probable ACP-binding domain of malonyl-CoA ACP transacylase | 0 | Direct |
69593,56801 69593 - Glycerol-3-phosphate (1)-acyltransferase 56801 - Acetyl-CoA synthetase-like | 0 | Direct |
53633,55729 53633 - Carbamate kinase-like 55729 - Acyl-CoA N-acyltransferases (Nat) | 0 | Direct |
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain) | 0 | Direct |
54160,55729 54160 - Chromo domain-like 55729 - Acyl-CoA N-acyltransferases (Nat) | 0 | Direct |
51735,51735 51735 - NAD(P)-binding Rossmann-fold domains 51735 - NAD(P)-binding Rossmann-fold domains | 0 | Direct |
51230,51230 51230 - Single hybrid motif 51230 - Single hybrid motif | 0 | Direct |
75138,53659 75138 - HprK N-terminal domain-like 53659 - Isocitrate/Isopropylmalate dehydrogenase-like | 0 | Direct |
55112,55112 55112 - Formylmethanofuran:tetrahydromethanopterin formyltransferase 55112 - Formylmethanofuran:tetrahydromethanopterin formyltransferase | 0 | Direct |
53901,55718 53901 - Thiolase-like 55718 - SCP-like | 0 | Direct |
47336,53474 47336 - ACP-like 53474 - alpha/beta-Hydrolases | 0.00000000001965 | Direct |
55785,55785 55785 - PYP-like sensor domain (PAS domain) 55785 - PYP-like sensor domain (PAS domain) | 0.000005391 | Direct |
47336,52777 47336 - ACP-like 52777 - CoA-dependent acyltransferases | 0.00007321 | Direct |
57903,57903 57903 - FYVE/PHD zinc finger 57903 - FYVE/PHD zinc finger | 0.0006035 | Direct |
51735,50129 51735 - NAD(P)-binding Rossmann-fold domains 50129 - GroES-like | 0.1469 | Inherited |
50129,51735 50129 - GroES-like 51735 - NAD(P)-binding Rossmann-fold domains | 0.5416 | Inherited |
55729,55729 55729 - Acyl-CoA N-acyltransferases (Nat) 55729 - Acyl-CoA N-acyltransferases (Nat) | 0.7956 | Inherited |
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.