Enzyme Commission (EC): Acting on the CH-NH group of donors

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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: Oxidoreductases [1] <26> (213|314) (212|187|94)

0: Acting on the CH-NH group of donors [1.5] <8> (28|35) (28|14|4)

- 1: With NAD(+) or NADP(+) as acceptor [1.5.1] <52> (17|21) (17|8|2)

- 1: With oxygen as acceptor [1.5.3] <33> (4|5) (4|2|0)

- 1: With other acceptors [1.5.99] <15> (2|2) (2|1|0)

- 1: With a flavin as acceptor [1.5.8] <4> (4|4) (4|2|0)

- 1: With a quinone or similar compound as acceptor [1.5.5] <3> (7|7) (7|4|2)

- 1: With other, known, acceptors [1.5.98] <3> (2|2) (2|0|0)

- 1: With an iron-sulfur protein as acceptor [1.5.7] <2> (0|0) (0|0|0)

- 1: With a disulfide as acceptor [1.5.4] <1> (0|0) (0|0|0)

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
Ribbon-helix-helix	0	Direct
FAD-linked oxidoreductase	0	Direct
FAD-linked oxidases, C-terminal domain	0	Direct
N-terminal domain of bifunctional PutA protein	0	Direct
Aminoacid dehydrogenase-like, N-terminal domain	0	Direct
Dihydrofolate reductase-like	0	Direct
F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	0	Direct
NAD(P)-binding Rossmann-fold domains	0	Direct
FMN-binding split barrel	0	Direct
Thymidylate synthase/dCMP hydroxymethylase	0.000000000009549	Direct
FAD-linked reductases, C-terminal domain	0.00000000005478	Direct
Folate-binding domain	0.00000001278	Direct
Aminomethyltransferase beta-barrel domain	0.0000006266	Direct
Electron transport accessory proteins	0.000001979	Direct
ACP-like	0.0001535	Direct
L-sulfolactate dehydrogenase-like	0.0003949	Direct
FMN-dependent nitroreductase-like	0.03445	Inherited
FMT C-terminal domain-like	0.03704	Inherited
Formyltransferase	0.04377	Inherited
4Fe-4S ferredoxins	0.05825	Inherited
Formate/glycerate dehydrogenase catalytic domain-like	0.2363	Inherited
Bacterial luciferase-like	0.4403	Inherited
FAD-binding/transporter-associated domain-like	0.9719	Inherited
ALDH-like	1	Inherited
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	1	Inherited
Flavoproteins	1	Inherited
FAD/NAD(P)-binding domain	1	Inherited
6-phosphogluconate dehydrogenase C-terminal domain-like	1	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
Ornithine cyclodeaminase-like	0	Direct
Proline dehydrohenase domain of bifunctional PutA protein	0	Direct
Dihydrofolate reductases	0	Direct
Tetrahydrofolate dehydrogenase/cyclohydrolase	0	Direct
ETF-QO domain-like	0	Direct
N-(1-D-carboxylethyl)-L-norvaline dehydrogenase	0	Direct
NADH:FMN oxidoreductase-like	0	Direct
PutA pre-N-terminal region-like	0	Direct
Aminoacid dehydrogenase-like, C-terminal domain	0	Direct
Electron transfer flavoprotein-ubiquinone oxidoreductase-like	0	Direct
Cytokinin dehydrogenase 1	0	Direct
Methylenetetrahydrofolate reductase	0	Direct
R67 dihydrofolate reductase	0	Direct
N-terminal domain of bifunctional PutA protein	0	Direct
ProC C-terminal domain-like	0	Direct
F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	0	Direct
L-alanine dehydrogenase-like	0.000000000001762	Direct
FAD-linked reductases, N-terminal domain	0.00000000000874	Direct
FAD-linked oxidases, N-terminal domain	0.00000000001829	Direct
Thymidylate synthase/dCMP hydroxymethylase	0.00000000001863	Direct
Aminomethyltransferase beta-barrel domain	0.0000008934	Direct
Aminomethyltransferase folate-binding domain	0.0000009275	Direct
F420 dependent oxidoreductases	0.000001906	Direct
D-aminoacid oxidase-like	0.000003217	Direct
L-aminoacid/polyamine oxidase	0.000005194	Direct
Homoserine dehydrogenase-like	0.00001539	Direct
NADPH-dependent FMN reductase	0.00005015	Direct
L-sulfolactate dehydrogenase-like	0.001652	Inherited
Post formyltransferase domain	0.04092	Inherited
Formyltransferase	0.05093	Inherited
NADH oxidase/flavin reductase	0.1076	Inherited
ALDH-like	1	Inherited
6-phosphogluconate dehydrogenase-like, N-terminal domain	1	Inherited
Tyrosine-dependent oxidoreductases	1	Inherited
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	1	Inherited

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Supra-domain (including individual superfamily)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Dihydrofolate reductase-like	0	Direct
FMN-binding split barrel	0	Direct
NAD(P)-binding Rossmann-fold domains	0	Direct
FAD-linked oxidoreductase	0	Direct
Ribbon-helix-helix	0	Direct
FAD-linked oxidases, C-terminal domain	0	Direct
F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	0	Direct
N-terminal domain of bifunctional PutA protein	0	Direct
Aminoacid dehydrogenase-like, N-terminal domain	0	Direct
Thymidylate synthase/dCMP hydroxymethylase	0.000000000006906	Direct
FAD-linked reductases, C-terminal domain	0.00000000004001	Direct
Folate-binding domain	0.000000009663	Direct
Aminomethyltransferase beta-barrel domain	0.0000004861	Direct
Electron transport accessory proteins	0.000001551	Direct
ACP-like	0.0001243	Direct
L-sulfolactate dehydrogenase-like	0.000322	Direct
FMN-dependent nitroreductase-like	0.0296	Inherited
FMT C-terminal domain-like	0.03185	Inherited
Formyltransferase	0.03769	Inherited
4Fe-4S ferredoxins	0.05048	Inherited
Formate/glycerate dehydrogenase catalytic domain-like	0.2104	Inherited
Bacterial luciferase-like	0.4004	Inherited
FAD-binding/transporter-associated domain-like	0.8993	Inherited
6-phosphogluconate dehydrogenase C-terminal domain-like	1	Inherited
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	1	Inherited
Flavoproteins	1	Inherited
ALDH-like	1	Inherited
FAD/NAD(P)-binding domain	1	Inherited

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
47336,53720 47336 - ACP-like 53720 - ALDH-like	0	Direct
56176,55103 56176 - FAD-binding/transporter-associated domain-like 55103 - FAD-linked oxidases, C-terminal domain	0	Direct
51730,53720 51730 - FAD-linked oxidoreductase 53720 - ALDH-like	0	Direct
53223,51735 53223 - Aminoacid dehydrogenase-like, N-terminal domain 51735 - NAD(P)-binding Rossmann-fold domains	0	Direct
47598,81935 47598 - Ribbon-helix-helix 81935 - N-terminal domain of bifunctional PutA protein	0	Direct
50486,47336 50486 - FMT C-terminal domain-like 47336 - ACP-like	0	Direct
53597,55831 53597 - Dihydrofolate reductase-like 55831 - Thymidylate synthase/dCMP hydroxymethylase	0	Direct
81935,51730 81935 - N-terminal domain of bifunctional PutA protein 51730 - FAD-linked oxidoreductase	0	Direct
51905,54373 51905 - FAD/NAD(P)-binding domain 54373 - FAD-linked reductases, C-terminal domain	0.000000000002776	Direct
103025,101790 103025 - Folate-binding domain 101790 - Aminomethyltransferase beta-barrel domain	0.0000004861	Direct
53328,50486 53328 - Formyltransferase 50486 - FMT C-terminal domain-like	0.02855	Inherited
52283,51735 52283 - Formate/glycerate dehydrogenase catalytic domain-like 51735 - NAD(P)-binding Rossmann-fold domains	0.7198	Inherited
51735,55347 51735 - NAD(P)-binding Rossmann-fold domains 55347 - Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	1	Inherited
51735,48179 51735 - NAD(P)-binding Rossmann-fold domains 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	1	Inherited

(show details)

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
81935,51730,53720 81935 - N-terminal domain of bifunctional PutA protein 51730 - FAD-linked oxidoreductase 53720 - ALDH-like	0	Direct
47598,81935,51730 47598 - Ribbon-helix-helix 81935 - N-terminal domain of bifunctional PutA protein 51730 - FAD-linked oxidoreductase	0	Direct
50486,47336,53720 50486 - FMT C-terminal domain-like 47336 - ACP-like 53720 - ALDH-like	0	Direct
53328,50486,47336 53328 - Formyltransferase 50486 - FMT C-terminal domain-like 47336 - ACP-like	0	Direct

Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term

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Enzyme Commission (EC): Acting on the CH-NH group of donors

Superfamily

Family

Supra-domain (including individual superfamily)