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Enzyme Commission (EC): Intramolecular oxidoreductases 
(show info)
Biomedical Ontology
Like Gene Ontology (GO), biomedical ontology such as phenotype 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. Biomedical ontologies we have incorporated are as follows:
- Disease Ontology (DO) Ontology DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM.
- Human Phenotype (HP) Ontology 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 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 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 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 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 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 displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
- Xenopus Anatomy (XA) Ontology 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 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 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.
- UniProtKB KeyWords (KW) Ontology 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).
- CTD Diseases (CD) Ontology CD is MEDIC disease vocabulary that is modified by CTD from the "Diseases" [C] branch of Medical Subject Headings (MeSH), combined with genetic disorders from the Online Mendelian Inheritance in OMIM database.
- CTD Chemicals (CC) Ontology CC is chemical vocabulary that is adapted by CTD from the "Chemicals and Drugs" category and Supplementary Concept Records of Medical Subject Headings (MeSH, a hierarchical vocabulary used to index articles for MEDLINE/PubMed).
Jump to [ Top · Hierarchy · Annotations ]
Root: EC Hierarchy (from IntEnz release 70)
Jump to [ Top · Hierarchy ]
Family( show details)
Highlighted in gray are those with FDR_all>0.001
| SCOP term |
FDR (all) |
Annotation (direct or inherited) |
| PA3566-like | 0 | DIRECT |
| AraA N-terminal and middle domain-like | 0 | DIRECT |
| beta-Hydroxydecanol thiol ester dehydrase | 0 | DIRECT |
| KduI-like | 0 | DIRECT |
| Xylose isomerase | 0 | DIRECT |
| Tryptophan biosynthesis enzymes | 0 | DIRECT |
| PDI-like | 0 | DIRECT |
| Uronate isomerase-like | 0 | DIRECT |
| Glucose-6-phosphate isomerase, GPI | 0 | DIRECT |
| mono-SIS domain | 0 | DIRECT |
| Triosephosphate isomerase (TIM) | 0 | DIRECT |
| AraA C-terminal domain-like | 0 | DIRECT |
| Muconalactone isomerase, MLI | 0 | DIRECT |
| FMN-linked oxidoreductases | 0 | DIRECT |
| Phosphoglucose isomerase, PGI | 0 | DIRECT |
| Type I phosphomannose isomerase | 0 | DIRECT |
| Hypothetical protein YgbM (EC1530) | 0 | DIRECT |
| Histidine biosynthesis enzymes | 0 | DIRECT |
| Ketosteroid isomerase-like | 0 | DIRECT |
| PhzC/PhzF-like | 0 | DIRECT |
| Acyl-CoA binding protein | 0 | DIRECT |
| IF2B-like | 0 | DIRECT |
| L-rhamnose isomerase | 0 | DIRECT |
| MIF-related | 0 | DIRECT |
| L-fucose isomerase, C-terminal domain | 0 | DIRECT |
| Allene oxide cyclase-like | 0 | DIRECT |
| IolI-like | 0 | DIRECT |
| L-fucose isomerase, N-terminal and second domains | 0 | DIRECT |
| Ribose/Galactose isomerase RpiB/AlsB | 0 | DIRECT |
| D-ribose-5-phosphate isomerase (RpiA), catalytic domain | 0 | DIRECT |
| Retinol binding protein-like | 0 | DIRECT |
| D-ribose-5-phosphate isomerase (RpiA), lid domain | 0 | DIRECT |
| 4-oxalocrotonate tautomerase-like | 0 | DIRECT |
| ERP29 C domain-like | 0 | DIRECT |
| IPP isomerase-like | 0 | DIRECT |
| Crotonase-like | 3.693e-16 | DIRECT |
| HCDH C-domain-like | 0.0000000000009799 | DIRECT |
| 6-phosphogluconate dehydrogenase-like, N-terminal domain | 0.000000000004343 | DIRECT |
| mannose-1-phosphate guanylyl transferase | 0.0000001715 | DIRECT |
| MAPEG domain | 0.00000556 | DIRECT |
| Co-chaperone p23-like | 0.00005067 | DIRECT |
| FumA C-terminal domain-like | 0.0001846 | DIRECT |
| Growth factor receptor domain | 0.0006891 | DIRECT |
| CBS-domain pair | 0.01664 | INHERITED FROM: Arabinose-5-phosphate isomerase |
| FAH | 0.05164 | INHERITED FROM: Transposing C=C bonds || 5-carboxymethyl-2-hydroxymuconate Delta-isomerase |
| RuBisCo, large subunit, C-terminal domain | 0.05691 | INHERITED FROM: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase || Interconverting keto- and enol-groups |
| Ribulose 1,5-bisphosphate carboxylase-oxygenase | 0.06247 | INHERITED FROM: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase || Interconverting keto- and enol-groups |
| double-SIS domain | 0.1356 | INHERITED FROM: Mannose-6-phosphate isomerase || Glucose-6-phosphate isomerase |
| Glutathione S-transferase (GST), C-terminal domain | 0.1936 | INHERITED FROM: Other intramolecular oxidoreductases |
| Glutathione S-transferase (GST), N-terminal domain | 0.1936 | INHERITED FROM: Other intramolecular oxidoreductases |
| Cytochrome P450 | 0.6855 | INHERITED FROM: Other intramolecular oxidoreductases || Thromboxane-A synthase |
| Class I glutamine amidotransferases (GAT) | 1 | INHERITED FROM: Phosphoribosylanthranilate isomerase |
| Tyrosine-dependent oxidoreductases | 1 | INHERITED FROM: Transposing C=C bonds || Steroid Delta-isomerase |
| SCOP term |
FDR (all) |
Annotation (direct or inherited) |
| PA3566-like | 0 | Direct |
| AraA N-terminal and middle domain-like | 0 | Direct |
| beta-Hydroxydecanol thiol ester dehydrase | 0 | Direct |
| KduI-like | 0 | Direct |
| Xylose isomerase | 0 | Direct |
| Tryptophan biosynthesis enzymes | 0 | Direct |
| PDI-like | 0 | Direct |
| Uronate isomerase-like | 0 | Direct |
| Glucose-6-phosphate isomerase, GPI | 0 | Direct |
| mono-SIS domain | 0 | Direct |
| Triosephosphate isomerase (TIM) | 0 | Direct |
| AraA C-terminal domain-like | 0 | Direct |
| Muconalactone isomerase, MLI | 0 | Direct |
| FMN-linked oxidoreductases | 0 | Direct |
| Phosphoglucose isomerase, PGI | 0 | Direct |
| Type I phosphomannose isomerase | 0 | Direct |
| Hypothetical protein YgbM (EC1530) | 0 | Direct |
| Histidine biosynthesis enzymes | 0 | Direct |
| Ketosteroid isomerase-like | 0 | Direct |
| PhzC/PhzF-like | 0 | Direct |
| Acyl-CoA binding protein | 0 | Direct |
| IF2B-like | 0 | Direct |
| L-rhamnose isomerase | 0 | Direct |
| MIF-related | 0 | Direct |
| L-fucose isomerase, C-terminal domain | 0 | Direct |
| Allene oxide cyclase-like | 0 | Direct |
| IolI-like | 0 | Direct |
| L-fucose isomerase, N-terminal and second domains | 0 | Direct |
| Ribose/Galactose isomerase RpiB/AlsB | 0 | Direct |
| D-ribose-5-phosphate isomerase (RpiA), catalytic domain | 0 | Direct |
| Retinol binding protein-like | 0 | Direct |
| D-ribose-5-phosphate isomerase (RpiA), lid domain | 0 | Direct |
| 4-oxalocrotonate tautomerase-like | 0 | Direct |
| ERP29 C domain-like | 0 | Direct |
| IPP isomerase-like | 0 | Direct |
| Crotonase-like | 3.693e-16 | Direct |
| HCDH C-domain-like | 0.0000000000009799 | Direct |
| 6-phosphogluconate dehydrogenase-like, N-terminal domain | 0.000000000004343 | Direct |
| mannose-1-phosphate guanylyl transferase | 0.0000001715 | Direct |
| MAPEG domain | 0.00000556 | Direct |
| Co-chaperone p23-like | 0.00005067 | Direct |
| FumA C-terminal domain-like | 0.0001846 | Direct |
| Growth factor receptor domain | 0.0006891 | Direct |
| CBS-domain pair | 0.01664 | Inherited |
| FAH | 0.05164 | Inherited |
| RuBisCo, large subunit, C-terminal domain | 0.05691 | Inherited |
| Ribulose 1,5-bisphosphate carboxylase-oxygenase | 0.06247 | Inherited |
| double-SIS domain | 0.1356 | Inherited |
| Glutathione S-transferase (GST), C-terminal domain | 0.1936 | Inherited |
| Glutathione S-transferase (GST), N-terminal domain | 0.1936 | Inherited |
| Cytochrome P450 | 0.6855 | Inherited |
| Class I glutamine amidotransferases (GAT) | 1 | Inherited |
| Tyrosine-dependent oxidoreductases | 1 | Inherited |
LINKTO: Domain2BO Download and Domain2BO Algorithm
Jump to [ Top · Hierarchy ]
Supra-domain (Single)( show details)
Highlighted in gray are those with FDR>0.001
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Jump to [ Top · Hierarchy ]
Supra-domain (Duplex) in N- to C-terminal order( show details)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
52833,47933
52833 - Thioredoxin-like
47933 - ERP29 C domain-like | 0 | DIRECT |
52833,52833
52833 - Thioredoxin-like
52833 - Thioredoxin-like | 0 | DIRECT |
47027,52096
47027 - Acyl-CoA binding protein
52096 - ClpP/crotonase | 0 | DIRECT |
51366,51366
51366 - Ribulose-phoshate binding barrel
51366 - Ribulose-phoshate binding barrel | 0 | DIRECT |
53743,50443
53743 - FucI/AraA N-terminal and middle domains
50443 - FucI/AraA C-terminal domain-like | 0 | DIRECT |
56529,56529
56529 - FAH
56529 - FAH | 0 | DIRECT |
53697,54631
53697 - SIS domain
54631 - CBS-domain pair | 0 | DIRECT |
100950,75445
100950 - NagB/RpiA/CoA transferase-like
75445 - D-ribose-5-phosphate isomerase (RpiA), lid domain | 0 | DIRECT |
52317,51366
52317 - Class I glutamine amidotransferase-like
51366 - Ribulose-phoshate binding barrel | 0 | DIRECT |
48179,48179
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like | 0.0000000000002839 | DIRECT |
52096,51735
52096 - ClpP/crotonase
51735 - NAD(P)-binding Rossmann-fold domains | 0.000000000001562 | DIRECT |
51735,48179
51735 - NAD(P)-binding Rossmann-fold domains
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like | 0.000000000002255 | DIRECT |
53448,51182
53448 - Nucleotide-diphospho-sugar transferases
51182 - RmlC-like cupins | 0.0000001041 | DIRECT |
48179,52096
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like
52096 - ClpP/crotonase | 0.0000003499 | DIRECT |
54966,51649
54966 - RuBisCO, large subunit, small (N-terminal) domain
51649 - RuBisCo, C-terminal domain | 0.009575 | INHERITED FROM: Interconverting keto- and enol-groups || 2,3-diketo-5-methylthiopentyl-1-phosphate enolase |
52833,47616
52833 - Thioredoxin-like
47616 - GST C-terminal domain-like | 0.1828 | INHERITED FROM: Other intramolecular oxidoreductases |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
52833,47933
52833 - Thioredoxin-like
47933 - ERP29 C domain-like | 0 | Direct |
52833,52833
52833 - Thioredoxin-like
52833 - Thioredoxin-like | 0 | Direct |
47027,52096
47027 - Acyl-CoA binding protein
52096 - ClpP/crotonase | 0 | Direct |
51366,51366
51366 - Ribulose-phoshate binding barrel
51366 - Ribulose-phoshate binding barrel | 0 | Direct |
53743,50443
53743 - FucI/AraA N-terminal and middle domains
50443 - FucI/AraA C-terminal domain-like | 0 | Direct |
56529,56529
56529 - FAH
56529 - FAH | 0 | Direct |
53697,54631
53697 - SIS domain
54631 - CBS-domain pair | 0 | Direct |
100950,75445
100950 - NagB/RpiA/CoA transferase-like
75445 - D-ribose-5-phosphate isomerase (RpiA), lid domain | 0 | Direct |
52317,51366
52317 - Class I glutamine amidotransferase-like
51366 - Ribulose-phoshate binding barrel | 0 | Direct |
48179,48179
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like | 0.0000000000002839 | Direct |
52096,51735
52096 - ClpP/crotonase
51735 - NAD(P)-binding Rossmann-fold domains | 0.000000000001562 | Direct |
51735,48179
51735 - NAD(P)-binding Rossmann-fold domains
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like | 0.000000000002255 | Direct |
53448,51182
53448 - Nucleotide-diphospho-sugar transferases
51182 - RmlC-like cupins | 0.0000001041 | Direct |
48179,52096
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like
52096 - ClpP/crotonase | 0.0000003499 | Direct |
54966,51649
54966 - RuBisCO, large subunit, small (N-terminal) domain
51649 - RuBisCo, C-terminal domain | 0.009575 | Inherited |
52833,47616
52833 - Thioredoxin-like
47616 - GST C-terminal domain-like | 0.1828 | Inherited |
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Jump to [ Top · Hierarchy ]
Supra-domain (Triple) in N- to C-terminal order( show details)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
52833,52833,52833
52833 - Thioredoxin-like
52833 - Thioredoxin-like
52833 - Thioredoxin-like | 0 | DIRECT |
52833,52833,47933
52833 - Thioredoxin-like
52833 - Thioredoxin-like
47933 - ERP29 C domain-like | 0 | DIRECT |
52317,51366,51366
52317 - Class I glutamine amidotransferase-like
51366 - Ribulose-phoshate binding barrel
51366 - Ribulose-phoshate binding barrel | 0 | DIRECT |
51735,48179,48179
51735 - NAD(P)-binding Rossmann-fold domains
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like | 0.0000000000002839 | DIRECT |
52096,51735,48179
52096 - ClpP/crotonase
51735 - NAD(P)-binding Rossmann-fold domains
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like | 0.000000000001562 | DIRECT |
48179,48179,52096
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like
52096 - ClpP/crotonase | 0.0000003499 | DIRECT |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
52833,52833,52833
52833 - Thioredoxin-like
52833 - Thioredoxin-like
52833 - Thioredoxin-like | 0 | Direct |
52833,52833,47933
52833 - Thioredoxin-like
52833 - Thioredoxin-like
47933 - ERP29 C domain-like | 0 | Direct |
52317,51366,51366
52317 - Class I glutamine amidotransferase-like
51366 - Ribulose-phoshate binding barrel
51366 - Ribulose-phoshate binding barrel | 0 | Direct |
51735,48179,48179
51735 - NAD(P)-binding Rossmann-fold domains
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like | 0.0000000000002839 | Direct |
52096,51735,48179
52096 - ClpP/crotonase
51735 - NAD(P)-binding Rossmann-fold domains
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like | 0.000000000001562 | Direct |
48179,48179,52096
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like
52096 - ClpP/crotonase | 0.0000003499 | Direct |
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Plot distribution on species Tree Of Life (sTOL) for Superfamily and/or Family domains annotated by this EC term
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Plot tree as:
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Download Newick format tree:
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( show help)
Trees by TreeVector
A presence/absence matrix is generated using protein domain
architecture data for all genomes in SUPERFAMILY. The PAUP
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.
Plot distribution on species Tree Of Life (sTOL) for single supra-domains annotated by this EC term
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Plot tree as:
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Download Newick format tree:
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Browsing in TREE OF LIFE:
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( show help)
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.
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> BO Hierarchy > Intramolecular oxidoreductases
