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.
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.
