Enzyme Commission (EC): Catalysing the translocation of inorganic cations

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Phenotype Ontology
Like Gene Ontology (GO), phenotypy ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Phenotype ontologies we have incorporated are as follows:

Disease Ontology (DO) Ontology (DO)
DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
Human Phenotype (HP) Ontology (HP)
HP captures phenotypic abnormalities that are described in OMIM, along with the corresponding disease-causing genes. It includes three complementary biological concepts: Mode_of_Inheritance (MI), ONset_and_clinical_course (ON), and Phenotypic_Abnormality (PA).
Mouse Phenotype (MP) Ontology (MP)
MP describes phenotypes of the mouse after a specific gene is genetically disrupted. Using it, Mouse Genome Informatics (MGI) provides high-coverate gene-level phenotypes for the mouse.
Worm Phenotype (WP) Ontology (WP)
WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
Yeast Phenotype (YP) Ontology (YP)
Based on YP which is the major contributor to the Ascomycete phenotype ontology, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
Fly Phenotype (FP) Ontology (FP)
FP refers to FlyBase controlled vocabulary. Specifically, a structured controlled vocabulary is used for the annotation of alleles (for their mutagen etc) in FlyBase.
Fly Anatomy (FA) Ontology (FA)
FA is a structured controlled vocabulary of the anatomy of Drosophila melanogaster, used for the description of phenotypes and where a gene is expressed.
Zebrafish Anatomy (ZA) Ontology (ZA)
ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
Xenopus Anatomy (XA) Ontology (XA)
XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
Arabidopsis Plant Ontology (AP) Ontology (AP)
As a major contributor to Plant Ontology which describes plant anatomical and morphological structures (AN) and growth and developmental stages (DE), the Arabidopsis Information Resource (TAIR) provides arabidopsis plant ontology annotations for the model higher plant Arabidopsis thaliana.
Enzyme Commission (EC) Ontology (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.
DrugBank ATC (DB) Ontology (DB)
In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
UniProtKB KeyWords (KW) Ontology (KW)
Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
UniProtKB UniPathway (UP) Ontology (UP)
UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.

Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).

Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).

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Root: EC Hierarchy (from IntEnz release 70)

Shortest distance to current term (+ for parents, - for children) EC term [EC ID] <#Children> (#SF|#FA) #Supra-domain
(Single|Duplex|Triple)

+ + 2: root [root] <7>

+ 1: Translocases [7] <6> (41|40) (40|34|19)

0: Catalysing the translocation of inorganic cations [7.2] <4> (15|13) (15|13|8)

- 1: Linked to the hydrolysis of a nucleoside triphosphate [7.2.2] <20> (9|9) (9|10|7)

- 1: Linked to decarboxylation [7.2.4] <5> (3|3) (3|1|0)

- 1: Linked to oxidoreductase reactions [7.2.1] <3> (3|1) (3|2|1)

- 1: Linked to the hydrolysis of diphosphate [7.2.3] (0|0) (0|0|0)

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
HMA, heavy metal-associated domain	0	Direct
Calcium ATPase, transduction domain A	0	Direct
Calcium ATPase, transmembrane domain M	0	Direct
HAD-like	0	Direct
Riboflavin synthase domain-like	0	Direct
2Fe-2S ferredoxin-like	0	Direct
Ferredoxin reductase-like, C-terminal NADP-linked domain	0	Direct
Metal cation-transporting ATPase, ATP-binding domain N	0	Direct
Single hybrid motif	0.0000003093	Direct
post-HMGL domain-like	0.005039	Inherited
MOP-like	0.957	Inherited
C-terminal domain of alpha and beta subunits of F1 ATP synthase	1	Inherited
N-terminal domain of alpha and beta subunits of F1 ATP synthase	1	Inherited
Aldolase	1	Inherited
P-loop containing nucleoside triphosphate hydrolases	1	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
Metal cation-transporting ATPase, ATP-binding domain N	0	Direct
Ferredoxin reductase FAD-binding domain-like	0	Direct
Calcium ATPase, transduction domain A	0	Direct
Meta-cation ATPase, catalytic domain P	0	Direct
Calcium ATPase, transmembrane domain M	0	Direct
HMA, heavy metal-associated domain	0	Direct
Biotinyl/lipoyl-carrier proteins and domains	0.0000003428	Direct
Conserved carboxylase domain	0.0000004715	Direct
HMGL-like	0.08608	Inherited
RecA protein-like (ATPase-domain)	1	Inherited
C-terminal domain of alpha and beta subunits of F1 ATP synthase	1	Inherited
ABC transporter ATPase domain-like	1	Inherited
N-terminal domain of alpha and beta subunits of F1 ATP synthase	1	Inherited

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Supra-domain (including individual superfamily)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Calcium ATPase, transmembrane domain M	0	Direct
2Fe-2S ferredoxin-like	0	Direct
Metal cation-transporting ATPase, ATP-binding domain N	0	Direct
Ferredoxin reductase-like, C-terminal NADP-linked domain	0	Direct
Riboflavin synthase domain-like	0	Direct
HAD-like	0	Direct
HMA, heavy metal-associated domain	0	Direct
Calcium ATPase, transduction domain A	0	Direct
Single hybrid motif	0.0000002384	Direct
post-HMGL domain-like	0.004227	Inherited
MOP-like	0.8853	Inherited
Aldolase	0.9428	Inherited
P-loop containing nucleoside triphosphate hydrolases	1	Inherited
C-terminal domain of alpha and beta subunits of F1 ATP synthase	1	Inherited
N-terminal domain of alpha and beta subunits of F1 ATP synthase	1	Inherited

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
63380,52343 63380 - Riboflavin synthase domain-like 52343 - Ferredoxin reductase-like, C-terminal NADP-linked domain	0	Direct
56784,81665 56784 - HAD-like 81665 - Calcium ATPase, transmembrane domain M	0	Direct
81660,56784 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like	0	Direct
81665,81660 81665 - Calcium ATPase, transmembrane domain M 81660 - Metal cation-transporting ATPase, ATP-binding domain N	0	Direct
56784,81660 56784 - HAD-like 81660 - Metal cation-transporting ATPase, ATP-binding domain N	0	Direct
81665,56784 81665 - Calcium ATPase, transmembrane domain M 56784 - HAD-like	0	Direct
81653,81665 81653 - Calcium ATPase, transduction domain A 81665 - Calcium ATPase, transmembrane domain M	0	Direct
55008,55008 55008 - HMA, heavy metal-associated domain 55008 - HMA, heavy metal-associated domain	0	Direct
54292,63380 54292 - 2Fe-2S ferredoxin-like 63380 - Riboflavin synthase domain-like	0	Direct
51569,89000 51569 - Aldolase 89000 - post-HMGL domain-like	0.004227	Inherited
52540,50331 52540 - P-loop containing nucleoside triphosphate hydrolases 50331 - MOP-like	0.8853	Inherited
52540,47917 52540 - P-loop containing nucleoside triphosphate hydrolases 47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase	1	Inherited
50615,52540 50615 - N-terminal domain of alpha and beta subunits of F1 ATP synthase 52540 - P-loop containing nucleoside triphosphate hydrolases	1	Inherited

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
55008,55008,55008 55008 - HMA, heavy metal-associated domain 55008 - HMA, heavy metal-associated domain 55008 - HMA, heavy metal-associated domain	0	Direct
54292,63380,52343 54292 - 2Fe-2S ferredoxin-like 63380 - Riboflavin synthase domain-like 52343 - Ferredoxin reductase-like, C-terminal NADP-linked domain	0	Direct
81665,81660,56784 81665 - Calcium ATPase, transmembrane domain M 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like	0	Direct
56784,81660,56784 56784 - HAD-like 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like	0	Direct
81653,81665,81660 81653 - Calcium ATPase, transduction domain A 81665 - Calcium ATPase, transmembrane domain M 81660 - Metal cation-transporting ATPase, ATP-binding domain N	0	Direct
81660,56784,81665 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like 81665 - Calcium ATPase, transmembrane domain M	0	Direct
81653,81665,56784 81653 - Calcium ATPase, transduction domain A 81665 - Calcium ATPase, transmembrane domain M 56784 - HAD-like	0	Direct
50615,52540,47917 50615 - N-terminal domain of alpha and beta subunits of F1 ATP synthase 52540 - P-loop containing nucleoside triphosphate hydrolases 47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase	1	Inherited

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Enzyme Commission (EC): Catalysing the translocation of inorganic cations

Superfamily

Family

Supra-domain (including individual superfamily)