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) |
52949,52949 52949 - Macro domain-like 52949 - Macro domain-like | 0 | Direct |
52418,54680 52418 - Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain 54680 - Pyrimidine nucleoside phosphorylase C-terminal domain | 0 | Direct |
48452,48452 48452 - TPR-like 48452 - TPR-like | 0 | Direct |
54675,51690 54675 - Nicotinate/Quinolinate PRTase N-terminal domain-like 51690 - Nicotinate/Quinolinate PRTase C-terminal domain-like | 0 | Direct |
47648,52418 47648 - Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain 52418 - Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 0 | Direct |
50692,47648 50692 - ADC-like 47648 - Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | 0 | Direct |
53448,50370 53448 - Nucleotide-diphospho-sugar transferases 50370 - Ricin B-like lectins | 0 | Direct |
81296,49452 81296 - E set domains 49452 - Starch-binding domain-like | 0 | Direct |
117839,56399 117839 - WWE domain 56399 - ADP-ribosylation | 0 | Direct |
52540,47648 52540 - P-loop containing nucleoside triphosphate hydrolases 47648 - Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | 0 | Direct |
69360,51445 69360 - Cell wall binding repeat 51445 - (Trans)glycosidases | 0 | Direct |
56037,53271 56037 - PheT/TilS domain 53271 - PRTase-like | 0 | Direct |
56235,53271 56235 - N-terminal nucleophile aminohydrolases (Ntn hydrolases) 53271 - PRTase-like | 0 | Direct |
51445,51011 51445 - (Trans)glycosidases 51011 - Glycosyl hydrolase domain | 0 | Direct |
53850,54913 53850 - Periplasmic binding protein-like II 54913 - GlnB-like | 0 | Direct |
47769,56399 47769 - SAM/Pointed domain 56399 - ADP-ribosylation | 0 | Direct |
53756,53756 53756 - UDP-Glycosyltransferase/glycogen phosphorylase 53756 - UDP-Glycosyltransferase/glycogen phosphorylase | 0 | Direct |
53756,56784 53756 - UDP-Glycosyltransferase/glycogen phosphorylase 56784 - HAD-like | 0 | Direct |
81296,81296 81296 - E set domains 81296 - E set domains | 0 | Direct |
52317,47648 52317 - Class I glutamine amidotransferase-like 47648 - Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | 0 | Direct |
52113,142921 52113 - BRCT domain 142921 - WGR domain-like | 0 | Direct |
51011,81296 51011 - Glycosyl hydrolase domain 81296 - E set domains | 0 | Direct |
53271,51366 53271 - PRTase-like 51366 - Ribulose-phoshate binding barrel | 0 | Direct |
56519,56601 56519 - Penicillin binding protein dimerisation domain 56601 - beta-lactamase/transpeptidase-like | 0 | Direct |
47587,56399 47587 - Domain of poly(ADP-ribose) polymerase 56399 - ADP-ribosylation | 0 | Direct |
142921,47587 142921 - WGR domain-like 47587 - Domain of poly(ADP-ribose) polymerase | 0 | Direct |
81296,51445 81296 - E set domains 51445 - (Trans)glycosidases | 0 | Direct |
53955,56601 53955 - Lysozyme-like 56601 - beta-lactamase/transpeptidase-like | 0 | Direct |
51445,69360 51445 - (Trans)glycosidases 69360 - Cell wall binding repeat | 0.00000000109 | Direct |
69360,69360 69360 - Cell wall binding repeat 69360 - Cell wall binding repeat | 0.00000000109 | Direct |
48403,48403 48403 - Ankyrin repeat 48403 - Ankyrin repeat | 0.000001514 | Direct |
74650,48208 74650 - Galactose mutarotase-like 48208 - Six-hairpin glycosidases | 0.00003472 | Direct |
52540,53271 52540 - P-loop containing nucleoside triphosphate hydrolases 53271 - PRTase-like | 0.00009211 | Direct |
53448,53448 53448 - Nucleotide-diphospho-sugar transferases 53448 - Nucleotide-diphospho-sugar transferases | 0.0001376 | Direct |
48403,47769 48403 - Ankyrin repeat 47769 - SAM/Pointed domain | 0.0002451 | Direct |
88713,88688 88713 - Glycoside hydrolase/deacetylase 88688 - Families 57/38 glycoside transferase middle domain | 0.01226 | Inherited |
82829,56037 82829 - MesJ substrate recognition domain-like 56037 - PheT/TilS domain | 0.6278 | Inherited |
52402,82829 52402 - Adenine nucleotide alpha hydrolases-like 82829 - MesJ substrate recognition domain-like | 0.9132 | 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.