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.
