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) |
100939,68906 100939 - SPOC domain-like 68906 - SAP domain | 0 | Direct |
56672,52540 56672 - DNA/RNA polymerases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
50249,52540 50249 - Nucleic acid-binding proteins 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
52540,46785 52540 - P-loop containing nucleoside triphosphate hydrolases 46785 - "Winged helix" DNA-binding domain | 0 | Direct |
160481,160481 160481 - BRK domain-like 160481 - BRK domain-like | 0 | Direct |
50916,46785 50916 - Rap30/74 interaction domains 46785 - "Winged helix" DNA-binding domain | 0 | Direct |
52540,56712 52540 - P-loop containing nucleoside triphosphate hydrolases 56712 - Prokaryotic type I DNA topoisomerase | 0 | Direct |
52540,142877 52540 - P-loop containing nucleoside triphosphate hydrolases 142877 - EndoU-like | 0 | Direct |
100939,101420 100939 - SPOC domain-like 101420 - C-terminal domain of Ku80 | 0 | Direct |
46785,47819 46785 - "Winged helix" DNA-binding domain 47819 - HRDC-like | 0 | Direct |
56731,52540 56731 - DNA primase core 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
48024,52540 48024 - N-terminal domain of DnaB helicase 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
52540,47819 52540 - P-loop containing nucleoside triphosphate hydrolases 47819 - HRDC-like | 0 | Direct |
140367,143076 140367 - Coronavirus NSP7-like 143076 - Coronavirus NSP8-like | 0 | Direct |
47781,46929 47781 - RuvA domain 2-like 46929 - DNA helicase RuvA subunit, C-terminal domain | 0 | Direct |
54160,52540 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
53300,100939 53300 - vWA-like 100939 - SPOC domain-like | 0 | Direct |
53335,142877 53335 - S-adenosyl-L-methionine-dependent methyltransferases 142877 - EndoU-like | 0 | Direct |
55464,52540 55464 - Origin of replication-binding domain, RBD-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
50249,47781 50249 - Nucleic acid-binding proteins 47781 - RuvA domain 2-like | 0 | Direct |
101816,144246 101816 - Replicase NSP9 144246 - Coronavirus NSP10-like | 0 | Direct |
55608,56712 55608 - Homing endonucleases 56712 - Prokaryotic type I DNA topoisomerase | 0 | Direct |
54160,54160 54160 - Chromo domain-like 54160 - Chromo domain-like | 0 | Direct |
143076,101816 143076 - Coronavirus NSP8-like 101816 - Replicase NSP9 | 0 | Direct |
52540,51294 52540 - P-loop containing nucleoside triphosphate hydrolases 51294 - Hedgehog/intein (Hint) domain | 0.000000000000001222 | Direct |
51294,55608 51294 - Hedgehog/intein (Hint) domain 55608 - Homing endonucleases | 0.00000000003703 | Direct |
159936,52949 159936 - NSP3A-like 52949 - Macro domain-like | 0.00000002407 | Direct |
56712,51294 56712 - Prokaryotic type I DNA topoisomerase 51294 - Hedgehog/intein (Hint) domain | 0.00000003502 | Direct |
159936,53335 159936 - NSP3A-like 53335 - S-adenosyl-L-methionine-dependent methyltransferases | 0.0000005024 | Direct |
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.