Enzyme Commission (EC): Acting on other nitrogenous compounds as 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 other nitrogenous compounds as donors [1.7] <8> (22|24) (22|13|6)

- 1: With NAD(+) or NADP(+) as acceptor [1.7.1] <17> (12|11) (12|7|4)

- 1: With a cytochrome as acceptor [1.7.2] <8> (7|8) (7|4|0)

- 1: With other acceptors [1.7.99] <8> (3|3) (3|1|0)

- 1: With oxygen as acceptor [1.7.3] <6> (1|1) (1|1|0)

- 1: With a quinone or similar compound as acceptor [1.7.5] <2> (4|4) (4|1|0)

- 1: With an iron-sulfur protein as acceptor [1.7.7] <2> (2|2) (2|2|2)

- 1: With a nitrogenous group as acceptor [1.7.6] <1> (0|0) (0|0|0)

- 1: With a copper protein as acceptor [1.7.9] (0|0) (0|0|0)

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

Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
Inosine monophosphate dehydrogenase (IMPDH)	0	Direct
Flavoproteins	0	Direct
Prismane protein-like	0	Direct
Multiheme cytochromes	0	Direct
E set domains	0	Direct
Cytochrome b5-like heme/steroid binding domain	0	Direct
Tetrahydrobiopterin biosynthesis enzymes-like	0	Direct
Nitrous oxide reductase, N-terminal domain	0	Direct
Oxidoreductase molybdopterin-binding domain	0	Direct
ADC-like	0.000000000251	Direct
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	0.0000000007292	Direct
Formate dehydrogenase/DMSO reductase, domains 1-3	0.00000000275	Direct
Ferredoxin reductase-like, C-terminal NADP-linked domain	0.00003275	Direct
Riboflavin synthase domain-like	0.00005699	Direct
Respiratory nitrate reductase 1 gamma chain	0.0001801	Direct
Cupredoxins	0.001192	Inherited
Cytochrome c	0.002472	Inherited
Nitrite/Sulfite reductase N-terminal domain-like	0.038	Inherited
ISP domain	0.0616	Inherited
4Fe-4S ferredoxins	0.9953	Inherited
Nitrite and sulphite reductase 4Fe-4S domain-like	1	Inherited
FAD/NAD(P)-binding domain	1	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
Quinone reductase	0	Direct
Urate oxidase (uricase)	0	Direct
Di-heme elbow motif	0	Direct
Inosine monophosphate dehydrogenase (IMPDH)	0	Direct
Nitrosocyanin	0	Direct
NirD-like	0	Direct
Hybrid cluster protein (prismane protein)	0	Direct
N-terminal (heme c) domain of cytochrome cd1-nitrite reductase	0	Direct
Oxidoreductase molybdopterin-binding domain	0	Direct
Cytochrome b5	0	Direct
Nitrous oxide reductase, N-terminal domain	0	Direct
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	0	Direct
Molybdenum-containing oxidoreductases-like dimerisation domain	0	Direct
Reductases	0	Direct
GTP cyclohydrolase I	0.000000000000003997	Direct
Formate dehydrogenase/DMSO reductase, C-terminal domain	0.0000000000002151	Direct
Ferredoxin reductase FAD-binding domain-like	0.000000000000666	Direct
Formate dehydrogenase/DMSO reductase, domains 1-3	0.000000000004747	Direct
Respiratory nitrate reductase 1 gamma chain	0.000008426	Direct
Multidomain cupredoxins	0.0001899	Direct
Ferredoxin domains from multidomain proteins	0.005917	Inherited
Duplicated SiR/NiR-like domains 1 and 3	0.0728	Inherited
Nitrite and sulphite reductase 4Fe-4S domain-like	0.7076	Inherited
FAD/NAD-linked reductases, N-terminal and central domains	1	Inherited

Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term

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Supra-domain (including individual superfamily)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Nitrous oxide reductase, N-terminal domain	0	Direct
E set domains	0	Direct
Inosine monophosphate dehydrogenase (IMPDH)	0	Direct
Oxidoreductase molybdopterin-binding domain	0	Direct
Cytochrome b5-like heme/steroid binding domain	0	Direct
Multiheme cytochromes	0	Direct
Prismane protein-like	0	Direct
Flavoproteins	0	Direct
Tetrahydrobiopterin biosynthesis enzymes-like	0	Direct
ADC-like	0.0000000001854	Direct
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	0.0000000005416	Direct
Formate dehydrogenase/DMSO reductase, domains 1-3	0.00000000206	Direct
Ferredoxin reductase-like, C-terminal NADP-linked domain	0.00002614	Direct
Riboflavin synthase domain-like	0.00004569	Direct
Respiratory nitrate reductase 1 gamma chain	0.0001459	Direct
Cupredoxins	0.0009842	Direct
Cytochrome c	0.00206	Inherited
Nitrite/Sulfite reductase N-terminal domain-like	0.03268	Inherited
ISP domain	0.0534	Inherited
4Fe-4S ferredoxins	0.922	Inherited
Nitrite and sulphite reductase 4Fe-4S domain-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)
56524,81296 56524 - Oxidoreductase molybdopterin-binding domain 81296 - E set domains	0	Direct
55620,55620 55620 - Tetrahydrobiopterin biosynthesis enzymes-like 55620 - Tetrahydrobiopterin biosynthesis enzymes-like	0	Direct
46626,51004 46626 - Cytochrome c 51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	0	Direct
56014,50022 56014 - Nitrite and sulphite reductase 4Fe-4S domain-like 50022 - ISP domain	0	Direct
81296,55856 81296 - E set domains 55856 - Cytochrome b5-like heme/steroid binding domain	0	Direct
55856,63380 55856 - Cytochrome b5-like heme/steroid binding domain 63380 - Riboflavin synthase domain-like	0	Direct
50974,49503 50974 - Nitrous oxide reductase, N-terminal domain 49503 - Cupredoxins	0	Direct
53706,50692 53706 - Formate dehydrogenase/DMSO reductase, domains 1-3 50692 - ADC-like	0.000000007575	Direct
63380,52343 63380 - Riboflavin synthase domain-like 52343 - Ferredoxin reductase-like, C-terminal NADP-linked domain	0.0000006079	Direct
49503,49503 49503 - Cupredoxins 49503 - Cupredoxins	0.001788	Inherited
55124,56014 55124 - Nitrite/Sulfite reductase N-terminal domain-like 56014 - Nitrite and sulphite reductase 4Fe-4S domain-like	0.02542	Inherited
56014,55124 56014 - Nitrite and sulphite reductase 4Fe-4S domain-like 55124 - Nitrite/Sulfite reductase N-terminal domain-like	0.3508	Inherited
51905,51905 51905 - FAD/NAD(P)-binding domain 51905 - FAD/NAD(P)-binding domain	0.6831	Inherited

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
81296,55856,63380 81296 - E set domains 55856 - Cytochrome b5-like heme/steroid binding domain 63380 - Riboflavin synthase domain-like	0	Direct
55124,56014,50022 55124 - Nitrite/Sulfite reductase N-terminal domain-like 56014 - Nitrite and sulphite reductase 4Fe-4S domain-like 50022 - ISP domain	0	Direct
56524,81296,55856 56524 - Oxidoreductase molybdopterin-binding domain 81296 - E set domains 55856 - Cytochrome b5-like heme/steroid binding domain	0	Direct
55856,63380,52343 55856 - Cytochrome b5-like heme/steroid binding domain 63380 - Riboflavin synthase domain-like 52343 - Ferredoxin reductase-like, C-terminal NADP-linked domain	0	Direct
55124,56014,55124 55124 - Nitrite/Sulfite reductase N-terminal domain-like 56014 - Nitrite and sulphite reductase 4Fe-4S domain-like 55124 - Nitrite/Sulfite reductase N-terminal domain-like	0.3508	Inherited
56014,55124,56014 56014 - Nitrite and sulphite reductase 4Fe-4S domain-like 55124 - Nitrite/Sulfite reductase N-terminal domain-like 56014 - Nitrite and sulphite reductase 4Fe-4S domain-like	0.3508	Inherited

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

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Enzyme Commission (EC): Acting on other nitrogenous compounds as donors

Superfamily

Family

Supra-domain (including individual superfamily)