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).
| Shortest distance to current term (+ for parents, - for children) |
EC term [EC ID] <#Children> |
(#SF|#FA) |
#Supra-domain (Single|Duplex|Triple) |
| + + + 3: | root [root] <6> |
| + + 2: | Lyases [4] <7> | (139|176) |
(158|94|34) |
| + 1: | Carbon-oxygen lyases [4.2] <4> | (68|83) |
(76|43|20) |
| 0: | Acting on phosphates [4.2.3] <116> | (11|14) |
(11|7|5) |
| - 1: | (+)-T-muurolol synthase [4.2.3.98] | (0|0) |
(0|0|0) |
| - 1: | (+)-alpha-barbatene synthase [4.2.3.69] | (0|0) |
(0|0|0) |
| - 1: | (+)-alpha-santalene synthase ((2Z,6Z)-farnesyl dip [4.2.3.50] | (0|0) |
(0|0|0) |
| - 1: | (+)-beta-caryophyllene synthase [4.2.3.89] | (0|0) |
(0|0|0) |
| - 1: | (+)-cubenene synthase [4.2.3.63] | (0|0) |
(0|0|0) |
| - 1: | (+)-delta-cadinene synthase [4.2.3.13] | (2|2) |
(2|1|0) |
| - 1: | (+)-delta-selinene synthase [4.2.3.76] | (0|0) |
(0|0|0) |
| - 1: | (+)-epicubenol synthase [4.2.3.64] | (0|0) |
(0|0|0) |
| - 1: | (+)-gamma-cadinene synthase [4.2.3.92] | (0|0) |
(0|0|0) |
| - 1: | (+)-germacrene D synthase [4.2.3.77] | (0|0) |
(0|0|0) |
| - 1: | (-)-alpha-cuprenene synthase [4.2.3.95] | (0|0) |
(0|0|0) |
| - 1: | (-)-alpha-pinene synthase [4.2.3.n7] | (0|0) |
(0|0|0) |
| - 1: | (-)-beta-caryophyllene synthase [4.2.3.57] | (0|0) |
(0|0|0) |
| - 1: | (-)-camphene synthase [4.2.3.n4] | (0|0) |
(0|0|0) |
| - 1: | (-)-delta-cadinene synthase [4.2.3.97] | (0|0) |
(0|0|0) |
| - 1: | (-)-endo-fenchol synthase [4.2.3.10] | (0|0) |
(0|0|0) |
| - 1: | (-)-gamma-cadinene synthase ((2Z,6E)-farnesyl diph [4.2.3.62] | (0|0) |
(0|0|0) |
| - 1: | (-)-germacrene D synthase [4.2.3.75] | (0|0) |
(1|0|0) |
| - 1: | (3R,6E)-nerolidol synthase [4.2.3.49] | (0|0) |
(0|0|0) |
| - 1: | (3S,6E)-nerolidol synthase [4.2.3.48] | (0|0) |
(2|1|0) |
| - 1: | (4S)-beta-phellandrene synthase (geranyl-diphospha [4.2.3.52] | (0|0) |
(0|0|0) |
| - 1: | (4S)-limonene synthase [4.2.3.16] | (0|0) |
(2|1|0) |
| - 1: | (E)-gamma-bisabolene synthase [4.2.3.59] | (0|0) |
(0|0|0) |
| - 1: | (E,E)-germacrene B synthase [4.2.3.71] | (0|0) |
(0|0|0) |
| - 1: | (R)-limonene synthase [4.2.3.20] | (0|0) |
(0|0|0) |
| - 1: | (S)-beta-bisabolene synthase [4.2.3.55] | (0|0) |
(0|0|0) |
| - 1: | (Z)-gamma-bisabolene synthase [4.2.3.40] | (0|0) |
(0|0|0) |
| - 1: | 10-epi-gamma-eudesmol synthase [4.2.3.84] | (0|0) |
(0|0|0) |
| - 1: | 2-methylisoborneol synthase [4.2.3.n14] | (1|0) |
(0|0|0) |
| - 1: | 3-dehydroquinate synthase [4.2.3.4] | (5|6) |
(5|5|4) |
| - 1: | 5-epi-alpha-selinene synthase [4.2.3.90] | (0|0) |
(0|0|0) |
| - 1: | 5-epiaristolochene synthase [4.2.3.61] | (2|2) |
(2|1|0) |
| - 1: | 6-pyruvoyltetrahydropterin synthase [4.2.3.12] | (1|1) |
(1|0|0) |
| - 1: | 7-epi-alpha-selinene synthase [4.2.3.86] | (0|0) |
(0|0|0) |
| - 1: | 7-epi-sesquithujene synthase [4.2.3.101] | (0|0) |
(0|0|0) |
| - 1: | Abietadiene synthase [4.2.3.18] | (0|0) |
(0|0|0) |
| - 1: | Alpha-bisabolene synthase [4.2.3.38] | (0|0) |
(0|0|0) |
| - 1: | Alpha-eudesmol synthase [4.2.3.85] | (0|0) |
(0|0|0) |
| - 1: | Alpha-farnesene synthase [4.2.3.46] | (0|0) |
(2|1|0) |
| - 1: | Alpha-guaiene synthase [4.2.3.87] | (0|0) |
(0|0|0) |
| - 1: | Alpha-gurjunene synthase [4.2.3.72] | (0|0) |
(0|0|0) |
| - 1: | Alpha-longipinene synthase [4.2.3.80] | (0|0) |
(0|0|0) |
| - 1: | Alpha-santalene synthase [4.2.3.82] | (0|0) |
(0|0|0) |
| - 1: | Amorpha-4,11-diene synthase [4.2.3.24] | (0|0) |
(0|0|0) |
| - 1: | Aphidicolan-16-beta-ol synthase [4.2.3.42] | (0|0) |
(0|0|0) |
| - 1: | Aristolochene synthase [4.2.3.9] | (0|0) |
(0|0|0) |
| - 1: | Avermitilol synthase [4.2.3.96] | (0|0) |
(0|0|0) |
| - 1: | Beta-chamigrene synthase [4.2.3.78] | (0|0) |
(0|0|0) |
| - 1: | Beta-eudesmol synthase [4.2.3.68] | (0|0) |
(0|0|0) |
| - 1: | Beta-farnesene synthase [4.2.3.47] | (2|2) |
(2|1|0) |
| - 1: | Beta-phellandrene synthase (neryl-diphosphate-cycl [4.2.3.51] | (0|0) |
(0|0|0) |
| - 1: | Beta-santalene synthase [4.2.3.83] | (0|0) |
(0|0|0) |
| - 1: | Beta-selinene cyclase [4.2.3.66] | (0|0) |
(0|0|0) |
| - 1: | Bicyclogermacrene synthase [4.2.3.100] | (0|0) |
(0|0|0) |
| - 1: | Casbene synthase [4.2.3.8] | (0|0) |
(0|0|0) |
| - 1: | Chorismate synthase [4.2.3.5] | (1|1) |
(1|0|0) |
| - 1: | Cis-muuroladiene synthase [4.2.3.67] | (0|0) |
(0|0|0) |
| - 1: | Cubebol synthase [4.2.3.91] | (0|0) |
(0|0|0) |
| - 1: | Delta-guaiene synthase [4.2.3.93] | (0|0) |
(0|0|0) |
| - 1: | Delta-selinene synthase [4.2.3.n2] | (0|0) |
(0|0|0) |
| - 1: | Elisabethatriene synthase [4.2.3.41] | (0|0) |
(0|0|0) |
| - 1: | Ent-cassa-12,15-diene synthase [4.2.3.28] | (0|0) |
(0|0|0) |
| - 1: | Ent-isokaurene synthase [4.2.3.n8] | (0|0) |
(0|0|0) |
| - 1: | Ent-kaurene synthase [4.2.3.19] | (1|0) |
(1|2|1) |
| - 1: | Ent-pimara-8(14),15-diene synthase [4.2.3.30] | (0|0) |
(0|0|0) |
| - 1: | Ent-pimara-9(11),15-diene synthase [4.2.3.31] | (0|0) |
(0|0|0) |
| - 1: | Ent-sandaracopimaradiene synthase [4.2.3.29] | (0|0) |
(0|0|0) |
| - 1: | Epi-cedrol synthase [4.2.3.39] | (0|0) |
(0|0|0) |
| - 1: | Epi-isozizaene synthase [4.2.3.37] | (0|0) |
(0|0|0) |
| - 1: | Ethanolamine-phosphate phospho-lyase [4.2.3.2] | (0|0) |
(0|0|0) |
| - 1: | Exo-alpha-bergamotene synthase [4.2.3.81] | (0|0) |
(0|0|0) |
| - 1: | Fusicocca-2,10(14)-diene synthase [4.2.3.43] | (0|0) |
(0|0|0) |
| - 1: | Gamma-curcumene synthase [4.2.3.94] | (0|0) |
(0|0|0) |
| - 1: | Gamma-humulene synthase [4.2.3.56] | (0|0) |
(0|0|0) |
| - 1: | Germacradienol synthase [4.2.3.22] | (0|0) |
(0|0|0) |
| - 1: | Germacrene C synthase [4.2.3.60] | (0|0) |
(0|0|0) |
| - 1: | Germacrene-A synthase [4.2.3.23] | (0|0) |
(0|0|0) |
| - 1: | Isopimara-7,15-diene synthase [4.2.3.44] | (0|0) |
(0|0|0) |
| - 1: | Isoprene synthase [4.2.3.27] | (0|0) |
(2|1|0) |
| - 1: | Labdatriene synthase [4.2.3.99] | (0|0) |
(0|0|0) |
| - 1: | Levopimaradiene synthase [4.2.3.32] | (0|0) |
(2|2|1) |
| - 1: | Longifolene synthase [4.2.3.58] | (0|0) |
(0|0|0) |
| - 1: | Methylglyoxal synthase [4.2.3.3] | (1|1) |
(1|0|0) |
| - 1: | Myrcene synthase [4.2.3.15] | (2|2) |
(2|1|0) |
| - 1: | Patchoulol synthase [4.2.3.70] | (0|0) |
(0|0|0) |
| - 1: | Pentalenene synthase [4.2.3.7] | (0|0) |
(0|0|0) |
| - 1: | Phyllocladan-16-alpha-ol synthase [4.2.3.45] | (0|0) |
(0|0|0) |
| - 1: | Pinene synthase [4.2.3.14] | (0|0) |
(2|1|0) |
| - 1: | Presilphiperfolanol synthase [4.2.3.74] | (0|0) |
(0|0|0) |
| - 1: | R-linalool synthase [4.2.3.26] | (0|0) |
(2|1|0) |
| - 1: | S-linalool synthase [4.2.3.25] | (0|0) |
(0|0|0) |
| - 1: | Sabinene-hydrate synthase [4.2.3.11] | (0|0) |
(0|0|0) |
| - 1: | Selinene synthase [4.2.3.n11] | (0|0) |
(0|0|0) |
| - 1: | Sesquithujene synthase [4.2.3.102] | (0|0) |
(0|0|0) |
| - 1: | Stemar-13-ene synthase [4.2.3.33] | (0|0) |
(0|0|0) |
| - 1: | Stemod-13(17)-ene synthase [4.2.3.34] | (0|0) |
(0|0|0) |
| - 1: | Syn-pimara-7,15-diene synthase [4.2.3.35] | (0|0) |
(0|0|0) |
| - 1: | Taxadiene synthase [4.2.3.17] | (0|0) |
(2|2|1) |
| - 1: | Terpentetriene synthase [4.2.3.36] | (0|0) |
(0|0|0) |
| - 1: | Terpinolene synthase [4.2.3.n6] | (0|0) |
(0|0|0) |
| - 1: | Threonine synthase [4.2.3.1] | (1|1) |
(1|0|0) |
| - 1: | Thujopsene synthase [4.2.3.79] | (0|0) |
(0|0|0) |
| - 1: | Transferred entry: 4.2.3.38 [4.2.3.n1] | (0|0) |
(0|0|0) |
| - 1: | Transferred entry: 4.2.3.44 [4.2.3.n9] | (0|0) |
(0|0|0) |
| - 1: | Transferred entry: 4.2.3.52 [4.2.3.n5] | (0|0) |
(0|0|0) |
| - 1: | Transferred entry: 4.2.3.56 [4.2.3.n3] | (0|0) |
(0|0|0) |
| - 1: | Transferred entry: 4.2.3.62 [4.2.3.n10] | (0|0) |
(0|0|0) |
| - 1: | Transferred entry: 4.2.3.65 [4.2.3.n12] | (0|0) |
(0|0|0) |
| - 1: | Transferred entry: 4.2.3.75 [4.2.3.n13] | (0|0) |
(0|0|0) |
| - 1: | Trichodiene synthase [4.2.3.6] | (1|1) |
(1|0|0) |
| - 1: | Valencene synthase [4.2.3.73] | (0|0) |
(0|0|0) |
| - 1: | Vetispiradiene synthase [4.2.3.21] | (0|0) |
(1|0|0) |
| - 1: | Viridiflorene synthase [4.2.3.88] | (0|0) |
(0|0|0) |
| - 1: | Zingiberene synthase [4.2.3.65] | (0|0) |
(0|0|0) |
| - 1: | cyclizing) [4.2.3.54] | (0|0) |
(0|0|0) |
| - 1: | cyclizing) [4.2.3.53] | (0|0) |
(0|0|0) |
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.
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.
