Enzyme Commission (EC): Racemases and epimerases

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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).

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

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: Isomerases [5] <7> (128|160) (128|76|32)

0: Racemases and epimerases [5.1] <4> (32|33) (32|15|8)

- 1: Acting on carbohydrates and derivatives [5.1.3] <46> (15|14) (15|3|2)

- 1: Acting on amino acids and derivatives [5.1.1] <25> (10|11) (10|8|4)

- 1: Acting on other compounds [5.1.99] <8> (5|5) (5|1|0)

- 1: Acting on hydroxy acids and derivatives [5.1.2] <7> (3|3) (3|3|2)

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

Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
ClpP/crotonase	0	Direct
PLP-binding barrel	0	Direct
YjeF N-terminal domain-like	0	Direct
Kelch motif	0	Direct
AraD/HMP-PK domain-like	0	Direct
Diaminopimelate epimerase-like	0	Direct
6-phosphogluconate dehydrogenase C-terminal domain-like	0	Direct
Alanine racemase C-terminal domain-like	0	Direct
Aspartate/glutamate racemase	0	Direct
Dimeric alpha+beta barrel	0	Direct
NAD(P)-binding Rossmann-fold domains	0	Direct
Galactose mutarotase-like	5.111e-16	Direct
beta-Roll	0.0000000001399	Direct
Ribokinase-like	0.000000005427	Direct
ACP-like	0.000002253	Direct
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	0.00001939	Direct
Six-hairpin glycosidases	0.00008629	Direct
CoA-transferase family III (CaiB/BaiF)	0.0004619	Direct
Chondroitin AC/alginate lyase	0.001052	Inherited
Pectin lyase-like	0.001388	Inherited
CoA-dependent acyltransferases	0.003381	Inherited
Acetyl-CoA synthetase-like	0.1726	Inherited
Tetrahydrobiopterin biosynthesis enzymes-like	0.24	Inherited
Tryptophan synthase beta subunit-like PLP-dependent enzymes	0.4236	Inherited
Enolase N-terminal domain-like	0.6035	Inherited
Enolase C-terminal domain-like	0.6638	Inherited
Xylose isomerase-like	0.8961	Inherited
UDP-Glycosyltransferase/glycogen phosphorylase	0.9038	Inherited
RbsD-like	1	Inherited
Ribulose-phoshate binding barrel	1	Inherited
SIS domain	1	Inherited
RmlC-like cupins	1	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
HCDH C-domain-like	0	Direct
NanE-like	0	Direct
Methylmalonyl-CoA epimerase	0	Direct
YjeF N-terminal domain-like	0	Direct
D-ribulose-5-phosphate 3-epimerase	0	Direct
6-phosphogluconate dehydrogenase-like, N-terminal domain	0	Direct
Alanine racemase-like, N-terminal domain	0	Direct
Kelch motif	0	Direct
AraD-like aldolase/epimerase	0	Direct
YjeF C-terminal domain-like	0	Direct
UDP-N-acetylglucosamine 2-epimerase	0	Direct
Diaminopimelate epimerase	0	Direct
Tyrosine-dependent oxidoreductases	0	Direct
Aspartate/glutamate racemase	0	Direct
Aldose 1-epimerase (mutarotase)	0	Direct
Proline racemase	0	Direct
Crotonase-like	0	Direct
Hypothetical protein HI1317	0	Direct
Alanine racemase	0	Direct
YiiL-like	0	Direct
Peptidyl carrier domain	0.000000000004538	Direct
DHN aldolase/epimerase	0.00000000001116	Direct
dTDP-sugar isomerase	0.00000000008712	Direct
Serralysin-like metalloprotease, C-terminal domain	0.0000000001558	Direct
NRPS condensation domain (amide synthase)	0.00000003018	Direct
N-acylglucosamine (NAG) epimerase	0.00000003142	Direct
CoA-transferase family III (CaiB/BaiF)	0.0004777	Direct
D-glucarate dehydratase-like	0.001915	Inherited
double-SIS domain	0.1405	Inherited
Acetyl-CoA synthetase-like	0.1806	Inherited
Tryptophan synthase beta subunit-like PLP-dependent enzymes	0.438	Inherited
Enolase N-terminal domain-like	0.748	Inherited
RbsD-like	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)
6-phosphogluconate dehydrogenase C-terminal domain-like	0	Direct
ClpP/crotonase	0	Direct
Aspartate/glutamate racemase	0	Direct
Kelch motif	0	Direct
Dimeric alpha+beta barrel	0	Direct
AraD/HMP-PK domain-like	0	Direct
NAD(P)-binding Rossmann-fold domains	0	Direct
PLP-binding barrel	0	Direct
YjeF N-terminal domain-like	0	Direct
Diaminopimelate epimerase-like	0	Direct
Alanine racemase C-terminal domain-like	0	Direct
Galactose mutarotase-like	3.548e-16	Direct
beta-Roll	0.000000000103	Direct
Ribokinase-like	0.00000000408	Direct
ACP-like	0.000001767	Direct
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	0.00001544	Direct
Six-hairpin glycosidases	0.00006947	Direct
CoA-transferase family III (CaiB/BaiF)	0.0003774	Direct
Chondroitin AC/alginate lyase	0.0008677	Direct
Pectin lyase-like	0.001149	Inherited
CoA-dependent acyltransferases	0.002825	Inherited
Acetyl-CoA synthetase-like	0.1523	Inherited
Tetrahydrobiopterin biosynthesis enzymes-like	0.2139	Inherited
Tryptophan synthase beta subunit-like PLP-dependent enzymes	0.3846	Inherited
Enolase N-terminal domain-like	0.5539	Inherited
Enolase C-terminal domain-like	0.6097	Inherited
Xylose isomerase-like	0.827	Inherited
UDP-Glycosyltransferase/glycogen phosphorylase	0.8343	Inherited
RbsD-like	0.9717	Inherited
RmlC-like cupins	1	Inherited
SIS domain	1	Inherited
Ribulose-phoshate binding barrel	1	Inherited

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
51419,50621 51419 - PLP-binding barrel 50621 - Alanine racemase C-terminal domain-like	0	Direct
48179,48179 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	0	Direct
51735,48179 51735 - NAD(P)-binding Rossmann-fold domains 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	0	Direct
51735,74650 51735 - NAD(P)-binding Rossmann-fold domains 74650 - Galactose mutarotase-like	0	Direct
54506,54506 54506 - Diaminopimelate epimerase-like 54506 - Diaminopimelate epimerase-like	0	Direct
64153,53613 64153 - YjeF N-terminal domain-like 53613 - Ribokinase-like	0	Direct
51126,51120 51126 - Pectin lyase-like 51120 - beta-Roll	0	Direct
52096,51735 52096 - ClpP/crotonase 51735 - NAD(P)-binding Rossmann-fold domains	0	Direct
53681,53681 53681 - Aspartate/glutamate racemase 53681 - Aspartate/glutamate racemase	0	Direct
51120,51120 51120 - beta-Roll 51120 - beta-Roll	0.0000000000001893	Direct
56801,47336 56801 - Acetyl-CoA synthetase-like 47336 - ACP-like	0.000000000002974	Direct
47336,52777 47336 - ACP-like 52777 - CoA-dependent acyltransferases	0.000000000005537	Direct
52777,56801 52777 - CoA-dependent acyltransferases 56801 - Acetyl-CoA synthetase-like	0.0000005052	Direct
52777,52777 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases	0.0000009236	Direct
54826,51604 54826 - Enolase N-terminal domain-like 51604 - Enolase C-terminal domain-like	0.5421	Inherited

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
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	Direct
52096,51735,48179 52096 - ClpP/crotonase 51735 - NAD(P)-binding Rossmann-fold domains 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	0	Direct
51126,51120,51120 51126 - Pectin lyase-like 51120 - beta-Roll 51120 - beta-Roll	0	Direct
56801,47336,52777 56801 - Acetyl-CoA synthetase-like 47336 - ACP-like 52777 - CoA-dependent acyltransferases	0.0000000000001216	Direct
51120,51120,51120 51120 - beta-Roll 51120 - beta-Roll 51120 - beta-Roll	0.0000000000001893	Direct
47336,52777,52777 47336 - ACP-like 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases	0.000000000005537	Direct
52777,52777,56801 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases 56801 - Acetyl-CoA synthetase-like	0.00000002311	Direct
52777,56801,47336 52777 - CoA-dependent acyltransferases 56801 - Acetyl-CoA synthetase-like 47336 - ACP-like	0.0000000455	Direct

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

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Enzyme Commission (EC): Racemases and epimerases

Superfamily

Family

Supra-domain (including individual superfamily)