Enzyme Commission (EC): Acting on the CH-NH(2) 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(2) group of donors [1.4] <9> (23|27) (23|14|4)

- 1: With NAD(+) or NADP(+) as acceptor [1.4.1] <25> (11|11) (11|5|0)

- 1: With oxygen as acceptor [1.4.3] <25> (11|13) (11|8|4)

- 1: With other acceptors [1.4.99] <6> (1|0) (1|0|0)

- 1: With a copper protein as acceptor [1.4.9] <2> (2|2) (2|0|0)

- 1: With a disulfide as acceptor [1.4.4] <2> (1|1) (1|1|0)

- 1: With a cytochrome as acceptor [1.4.2] <1> (0|0) (0|0|0)

- 1: With a quinone or similar compound as acceptor [1.4.5] <1> (1|0) (1|0|0)

- 1: With an iron-sulfur protein as acceptor [1.4.7] <1> (3|3) (3|0|0)

- 1: With other, known, acceptors [1.4.98] <1> (0|0) (0|0|0)

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
Methylamine dehydrogenase, L chain	0	Direct
Copper amine oxidase, domain N	0	Direct
Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	0	Direct
Amine oxidase catalytic domain	0	Direct
FAD-linked reductases, C-terminal domain	0	Direct
PLP-dependent transferases	0	Direct
Alpha subunit of glutamate synthase, C-terminal domain	0	Direct
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	0	Direct
Amine oxidase N-terminal region	0	Direct
Nucleotide-binding domain	0	Direct
SRCR-like	0	Direct
FMN-binding split barrel	0	Direct
YVTN repeat-like/Quinoprotein amine dehydrogenase	0.000000001064	Direct
FAD/NAD(P)-binding domain	0.0000001826	Direct
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.000001257	Direct
Aminoacid dehydrogenase-like, N-terminal domain	0.00001116	Direct
alpha-helical ferredoxin	0.006777	Inherited
Formate/glycerate dehydrogenase catalytic domain-like	0.01026	Inherited
ThiG-like	0.2159	Inherited
FMN-linked oxidoreductases	0.685	Inherited
4Fe-4S ferredoxins	1	Inherited
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	1	Inherited
NAD(P)-binding Rossmann-fold domains	1	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
D-aminoacid oxidase, N-terminal domain	0	Direct
Aminoacid dehydrogenases	0	Direct
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	0	Direct
L-alanine dehydrogenase-like	0	Direct
Glycine dehydrogenase subunits (GDC-P)	0	Direct
Amine oxidase catalytic domain	0	Direct
Class II glutamine amidotransferases	0	Direct
Methylamine dehydrogenase, L chain	0	Direct
Copper amine oxidase, domain N	0	Direct
Amine oxidase N-terminal region	0	Direct
FAD-linked reductases, N-terminal domain	0	Direct
Methylamine dehydrogenase, H-chain	0	Direct
Alpha subunit of glutamate synthase, C-terminal domain	0	Direct
L-aminoacid/polyamine oxidase	0	Direct
Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain	0	Direct
PNP-oxidase like	0	Direct
Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	0	Direct
Scavenger receptor cysteine-rich (SRCR) domain	0	Direct
D-aminoacid oxidase-like	0	Direct
N-terminal domain of adrenodoxin reductase-like	0.0002291	Direct
Dihydropyrimidine dehydrogenase, N-terminal domain	0.002046	Inherited
Formate/glycerate dehydrogenases, NAD-domain	0.03698	Inherited
Dihydrodipicolinate reductase-like	0.1379	Inherited
ThiG-like	0.2268	Inherited
Aminoacid dehydrogenase-like, C-terminal domain	0.2646	Inherited
FMN-linked oxidoreductases	0.8153	Inherited
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	1	Inherited

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Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]

Supra-domain (including individual superfamily)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
PLP-dependent transferases	0	Direct
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	0	Direct
Methylamine dehydrogenase, L chain	0	Direct
Nucleotide-binding domain	0	Direct
Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	0	Direct
Copper amine oxidase, domain N	0	Direct
FMN-binding split barrel	0	Direct
Alpha subunit of glutamate synthase, C-terminal domain	0	Direct
Amine oxidase catalytic domain	0	Direct
Amine oxidase N-terminal region	0	Direct
FAD-linked reductases, C-terminal domain	0	Direct
SRCR-like	0	Direct
YVTN repeat-like/Quinoprotein amine dehydrogenase	0.0000000007925	Direct
FAD/NAD(P)-binding domain	0.0000001401	Direct
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.0000009802	Direct
Aminoacid dehydrogenase-like, N-terminal domain	0.000008834	Direct
alpha-helical ferredoxin	0.005709	Inherited
Formate/glycerate dehydrogenase catalytic domain-like	0.008693	Inherited
ThiG-like	0.1916	Inherited
FMN-linked oxidoreductases	0.6294	Inherited
4Fe-4S ferredoxins	1	Inherited
NAD(P)-binding Rossmann-fold domains	1	Inherited
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	1	Inherited

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
55383,54416 55383 - Copper amine oxidase, domain N 54416 - Amine oxidase N-terminal region	0	Direct
51971,54373 51971 - Nucleotide-binding domain 54373 - FAD-linked reductases, C-terminal domain	0	Direct
54416,49998 54416 - Amine oxidase N-terminal region 49998 - Amine oxidase catalytic domain	0	Direct
56487,56487 56487 - SRCR-like 56487 - SRCR-like	0	Direct
54862,51395 54862 - 4Fe-4S ferredoxins 51395 - FMN-linked oxidoreductases	0	Direct
56425,46977 56425 - Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain 46977 - Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	0	Direct
53383,53383 53383 - PLP-dependent transferases 53383 - PLP-dependent transferases	0	Direct
54416,54416 54416 - Amine oxidase N-terminal region 54416 - Amine oxidase N-terminal region	0	Direct
51905,54373 51905 - FAD/NAD(P)-binding domain 54373 - FAD-linked reductases, C-terminal domain	0	Direct
51905,56425 51905 - FAD/NAD(P)-binding domain 56425 - Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	0	Direct
46548,51971 46548 - alpha-helical ferredoxin 51971 - Nucleotide-binding domain	0.00000005272	Direct
53223,51735 53223 - Aminoacid dehydrogenase-like, N-terminal domain 51735 - NAD(P)-binding Rossmann-fold domains	0.000005469	Direct
52283,51735 52283 - Formate/glycerate dehydrogenase catalytic domain-like 51735 - NAD(P)-binding Rossmann-fold domains	0.007049	Inherited
51735,55347 51735 - NAD(P)-binding Rossmann-fold domains 55347 - Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	1	Inherited

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
51905,56425,46977 51905 - FAD/NAD(P)-binding domain 56425 - Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain 46977 - Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	0	Direct
55383,54416,54416 55383 - Copper amine oxidase, domain N 54416 - Amine oxidase N-terminal region 54416 - Amine oxidase N-terminal region	0	Direct
56487,56487,56487 56487 - SRCR-like 56487 - SRCR-like 56487 - SRCR-like	0	Direct
54416,54416,49998 54416 - Amine oxidase N-terminal region 54416 - Amine oxidase N-terminal region 49998 - Amine oxidase catalytic domain	0	Direct

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Enzyme Commission (EC): Acting on the CH-NH(2) group of donors

Superfamily

Family

Supra-domain (including individual superfamily)