|
|
Enzyme Commission (EC): Acting on carbon-nitrogen bonds, other than peptide bonds
(show info)
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)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Superfamily(show details)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Family(show details)
Family domains annotated to this EC term (SDEC level: Moderately Informative)
Highlighted in gray are those with FDR_all>0.001
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| Methylesterase CheB, C-terminal domain | 0 | DIRECT |
| 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB | 0 | DIRECT |
| Peptidylarginine deiminase Pad4, catalytic C-terminal domain | 0 | DIRECT |
| alpha-Subunit of urease | 0 | DIRECT |
| Arginine deiminase | 0 | DIRECT |
| Dihydroorotase | 0 | DIRECT |
| LmbE-like | 0 | DIRECT |
| Zn metallo-beta-lactamase | 0 | DIRECT |
| CinA-like | 0 | DIRECT |
| UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC | 0 | DIRECT |
| Cytidine deaminase | 0 | DIRECT |
| Glutaminase | 0 | DIRECT |
| Tetrahydrofolate dehydrogenase/cyclohydrolase | 0 | DIRECT |
| N-acetylmuramoyl-L-alanine amidase-like | 0 | DIRECT |
| Peptide deformylase | 0 | DIRECT |
| Glutaminase/Asparaginase | 0 | DIRECT |
| Penicillin acylase, catalytic domain | 0 | DIRECT |
| Dimethylarginine dimethylaminohydrolase DDAH | 0 | DIRECT |
| Transthyretin (synonym: prealbumin) | 0 | DIRECT |
| LamB/YcsF-like | 0 | DIRECT |
| Z-DNA binding domain | 0 | DIRECT |
| Allantoicase repeat | 0 | DIRECT |
| D-aminoacylase, catalytic domain | 0 | DIRECT |
| Deoxycytidylate deaminase-like | 0 | DIRECT |
| N-acetylglucosamine-6-phosphate deacetylase, NagA | 0 | DIRECT |
| Archaeal IMP cyclohydrolase PurO | 0 | DIRECT |
| Isochorismatase-like hydrolases | 0 | DIRECT |
| Class I glutamine amidotransferases (GAT) | 0 | DIRECT |
| Histone deacetylase, HDAC | 0 | DIRECT |
| GTP cyclohydrolase I | 0 | DIRECT |
| Urease, gamma-subunit | 0 | DIRECT |
| Hydantoinase (dihydropyrimidinase) | 0 | DIRECT |
| D-aminoacylase | 0 | DIRECT |
| Peptidylarginine deiminase Pad4, N-terminal domain | 0 | DIRECT |
| Arginase-like amidino hydrolases | 0 | DIRECT |
| YlbA-like | 0 | DIRECT |
| Cytosine deaminase catalytic domain | 0 | DIRECT |
| Hydantoinase (dihydropyrimidinase), catalytic domain | 0 | DIRECT |
| Aminoacid dehydrogenase-like, C-terminal domain | 0 | DIRECT |
| N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain | 0 | DIRECT |
| SAH/MTA deaminase-like | 0 | DIRECT |
| RibA-like | 0 | DIRECT |
| alpha-subunit of urease, catalytic domain | 0 | DIRECT |
| Bacterial dinuclear zinc exopeptidases | 0 | DIRECT |
| beta-Lactamase/D-ala carboxypeptidase | 0 | DIRECT |
| DJ-1/PfpI | 0 | DIRECT |
| HisI-like | 0 | DIRECT |
| Putative serine hydrolase Ydr428c | 0 | DIRECT |
| NagB-like | 0 | DIRECT |
| Extended PAW domain | 0 | DIRECT |
| AstE/AspA-like | 0 | DIRECT |
| Putative cyclase | 0 | DIRECT |
| Adenosine/AMP deaminase | 0 | DIRECT |
| Peptidylarginine deiminase Pad4, middle domain | 0 | DIRECT |
| Creatininase | 0 | DIRECT |
| GW domain | 0 | DIRECT |
| CheY-related | 0 | DIRECT |
| Imidazolonepropionase-like | 0 | DIRECT |
| Carbamilase | 0 | DIRECT |
| Bacterial exopeptidase dimerisation domain | 0 | DIRECT |
| Succinylarginine dihydrolase-like | 0 | DIRECT |
| Porphyromonas-type peptidylarginine deiminase | 0 | DIRECT |
| AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC | 0 | DIRECT |
| SAH/MTA deaminase-like | 0 | DIRECT |
| Inosicase | 0 | DIRECT |
| Urease, beta-subunit | 0 | DIRECT |
| Acetamidase/Formamidase-like | 0 | DIRECT |
| CheD-like | 0 | DIRECT |
| Imidazolonepropionase-like | 0 | DIRECT |
| Methenyltetrahydromethanopterin cyclohydrolase | 0 | DIRECT |
| dUTPase-like | 0 | DIRECT |
| YdjC-like | 0 | DIRECT |
| N-acetylmuramoyl-L-alanine amidase-like | 0 | DIRECT |
| TENA/THI-4 | 3.693e-16 | DIRECT |
| Transglutaminase core | 0.000000000000001826 | DIRECT |
| HCP-like | 0.00000000000009595 | DIRECT |
| Nitrilase | 0.0000000000001092 | DIRECT |
| RibD C-terminal domain-like | 0.00000000000179 | DIRECT |
| (Glycosyl)asparaginase | 0.00000000001455 | DIRECT |
| PUG domain | 0.00000000001838 | DIRECT |
| YjgF/L-PSP | 0.00000000238 | DIRECT |
| PH0987 C-terminal domain-like | 0.00000001658 | DIRECT |
| PH0987 N-terminal domain-like | 0.0000003362 | DIRECT |
| NodB-like polysaccharide deacetylase | 0.0000006067 | DIRECT |
| Peptidoglycan binding domain, PGBD | 0.00002295 | DIRECT |
| LysM domain | 0.0004719 | DIRECT |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | 0.01144 | INHERITED FROM: 1-aminocyclopropane-1-carboxylate deaminase || In other compounds |
| Amidase signature (AS) enzymes | 0.01865 | INHERITED FROM: In linear amides || Allophanate hydrolase || Amidase || Fatty acid amide hydrolase |
| Ankyrin repeat | 0.02942 | INHERITED FROM: In linear amides || Asparaginase || Glutaminase |
| Cell wall binding repeat | 0.06732 | INHERITED FROM: In linear amides || N-acetylmuramoyl-L-alanine amidase |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | 0.7597 | INHERITED FROM: Dihydroorotase || In cyclic amides |
| Carbamoyl phosphate synthetase, large subunit connection domain | 0.953 | INHERITED FROM: Dihydroorotase || In cyclic amides |
| L-histidinol dehydrogenase HisD | 0.9603 | INHERITED FROM: Phosphoribosyl-AMP cyclohydrolase |
| Zf-UBP | 1 | INHERITED FROM: Histone deacetylase |
| Carboxylesterase | 1 | INHERITED FROM: Arylformamidase |
| Class II glutamine amidotransferases | 1 | INHERITED FROM: Gamma-glutamyl hercynylcysteine S-oxide hydrolase |
| Creatinase/prolidase N-terminal domain | 1 | INHERITED FROM: Creatinase || In linear amidines |
| Formyltransferase | 1 | INHERITED FROM: Formyltetrahydrofolate deformylase |
| Double-stranded RNA-binding domain (dsRBD) | 1 | INHERITED FROM: Double-stranded RNA adenine deaminase |
| BC N-terminal domain-like | 1 | INHERITED FROM: Dihydroorotase |
| Aspartate/ornithine carbamoyltransferase | 1 | INHERITED FROM: Dihydroorotase |
| Creatinase/aminopeptidase | 1 | INHERITED FROM: Creatinase |
| HisE-like (PRA-PH) | 1 | INHERITED FROM: In cyclic amidines || Phosphoribosyl-AMP cyclohydrolase |
| BC ATP-binding domain-like | 1 | INHERITED FROM: Dihydroorotase |
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| Methylesterase CheB, C-terminal domain | 0 | Direct |
| 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB | 0 | Direct |
| Peptidylarginine deiminase Pad4, catalytic C-terminal domain | 0 | Direct |
| alpha-Subunit of urease | 0 | Direct |
| Arginine deiminase | 0 | Direct |
| Dihydroorotase | 0 | Direct |
| LmbE-like | 0 | Direct |
| Zn metallo-beta-lactamase | 0 | Direct |
| CinA-like | 0 | Direct |
| UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC | 0 | Direct |
| Cytidine deaminase | 0 | Direct |
| Glutaminase | 0 | Direct |
| Tetrahydrofolate dehydrogenase/cyclohydrolase | 0 | Direct |
| N-acetylmuramoyl-L-alanine amidase-like | 0 | Direct |
| Peptide deformylase | 0 | Direct |
| Glutaminase/Asparaginase | 0 | Direct |
| Penicillin acylase, catalytic domain | 0 | Direct |
| Dimethylarginine dimethylaminohydrolase DDAH | 0 | Direct |
| Transthyretin (synonym: prealbumin) | 0 | Direct |
| LamB/YcsF-like | 0 | Direct |
| Z-DNA binding domain | 0 | Direct |
| Allantoicase repeat | 0 | Direct |
| D-aminoacylase, catalytic domain | 0 | Direct |
| Deoxycytidylate deaminase-like | 0 | Direct |
| N-acetylglucosamine-6-phosphate deacetylase, NagA | 0 | Direct |
| Archaeal IMP cyclohydrolase PurO | 0 | Direct |
| Isochorismatase-like hydrolases | 0 | Direct |
| Class I glutamine amidotransferases (GAT) | 0 | Direct |
| Histone deacetylase, HDAC | 0 | Direct |
| GTP cyclohydrolase I | 0 | Direct |
| Urease, gamma-subunit | 0 | Direct |
| Hydantoinase (dihydropyrimidinase) | 0 | Direct |
| D-aminoacylase | 0 | Direct |
| Peptidylarginine deiminase Pad4, N-terminal domain | 0 | Direct |
| Arginase-like amidino hydrolases | 0 | Direct |
| YlbA-like | 0 | Direct |
| Cytosine deaminase catalytic domain | 0 | Direct |
| Hydantoinase (dihydropyrimidinase), catalytic domain | 0 | Direct |
| Aminoacid dehydrogenase-like, C-terminal domain | 0 | Direct |
| N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain | 0 | Direct |
| SAH/MTA deaminase-like | 0 | Direct |
| RibA-like | 0 | Direct |
| alpha-subunit of urease, catalytic domain | 0 | Direct |
| Bacterial dinuclear zinc exopeptidases | 0 | Direct |
| beta-Lactamase/D-ala carboxypeptidase | 0 | Direct |
| DJ-1/PfpI | 0 | Direct |
| HisI-like | 0 | Direct |
| Putative serine hydrolase Ydr428c | 0 | Direct |
| NagB-like | 0 | Direct |
| Extended PAW domain | 0 | Direct |
| AstE/AspA-like | 0 | Direct |
| Putative cyclase | 0 | Direct |
| Adenosine/AMP deaminase | 0 | Direct |
| Peptidylarginine deiminase Pad4, middle domain | 0 | Direct |
| Creatininase | 0 | Direct |
| GW domain | 0 | Direct |
| CheY-related | 0 | Direct |
| Imidazolonepropionase-like | 0 | Direct |
| Carbamilase | 0 | Direct |
| Bacterial exopeptidase dimerisation domain | 0 | Direct |
| Succinylarginine dihydrolase-like | 0 | Direct |
| Porphyromonas-type peptidylarginine deiminase | 0 | Direct |
| AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC | 0 | Direct |
| SAH/MTA deaminase-like | 0 | Direct |
| Inosicase | 0 | Direct |
| Urease, beta-subunit | 0 | Direct |
| Acetamidase/Formamidase-like | 0 | Direct |
| CheD-like | 0 | Direct |
| Imidazolonepropionase-like | 0 | Direct |
| Methenyltetrahydromethanopterin cyclohydrolase | 0 | Direct |
| dUTPase-like | 0 | Direct |
| YdjC-like | 0 | Direct |
| N-acetylmuramoyl-L-alanine amidase-like | 0 | Direct |
| TENA/THI-4 | 3.693e-16 | Direct |
| Transglutaminase core | 0.000000000000001826 | Direct |
| HCP-like | 0.00000000000009595 | Direct |
| Nitrilase | 0.0000000000001092 | Direct |
| RibD C-terminal domain-like | 0.00000000000179 | Direct |
| (Glycosyl)asparaginase | 0.00000000001455 | Direct |
| PUG domain | 0.00000000001838 | Direct |
| YjgF/L-PSP | 0.00000000238 | Direct |
| PH0987 C-terminal domain-like | 0.00000001658 | Direct |
| PH0987 N-terminal domain-like | 0.0000003362 | Direct |
| NodB-like polysaccharide deacetylase | 0.0000006067 | Direct |
| Peptidoglycan binding domain, PGBD | 0.00002295 | Direct |
| LysM domain | 0.0004719 | Direct |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | 0.01144 | Inherited |
| Amidase signature (AS) enzymes | 0.01865 | Inherited |
| Ankyrin repeat | 0.02942 | Inherited |
| Cell wall binding repeat | 0.06732 | Inherited |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | 0.7597 | Inherited |
| Carbamoyl phosphate synthetase, large subunit connection domain | 0.953 | Inherited |
| L-histidinol dehydrogenase HisD | 0.9603 | Inherited |
| Zf-UBP | 1 | Inherited |
| Carboxylesterase | 1 | Inherited |
| Class II glutamine amidotransferases | 1 | Inherited |
| Creatinase/prolidase N-terminal domain | 1 | Inherited |
| Formyltransferase | 1 | Inherited |
| Double-stranded RNA-binding domain (dsRBD) | 1 | Inherited |
| BC N-terminal domain-like | 1 | Inherited |
| Aspartate/ornithine carbamoyltransferase | 1 | Inherited |
| Creatinase/aminopeptidase | 1 | Inherited |
| HisE-like (PRA-PH) | 1 | Inherited |
| BC ATP-binding domain-like | 1 | Inherited |
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term
 |
Plot tree as:
| |
Download Newick format tree:
|
(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.
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Supra-domain (including individual superfamily)
(show details)
Supra-domains annotated to this EC term (Not in SPEC)
Highlighted in gray are those with FDR>0.001
(show details)
Supra-domains annotated to this EC term (Not in SPEC)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
51556,51338
51556 - Metallo-dependent hydrolases
51338 - Composite domain of metallo-dependent hydrolases | 0 | DIRECT |
55846,47090
55846 - N-acetylmuramoyl-L-alanine amidase-like
47090 - PGBD-like | 0 | DIRECT |
56601,52091
56601 - beta-lactamase/transpeptidase-like
52091 - SpoIIaa-like | 0 | DIRECT |
54001,49785
54001 - Cysteine proteinases
49785 - Galactose-binding domain-like | 0 | DIRECT |
54111,51278
54111 - Urease, gamma-subunit
51278 - Urease, beta-subunit | 0 | DIRECT |
51338,51556
51338 - Composite domain of metallo-dependent hydrolases
51556 - Metallo-dependent hydrolases | 0 | DIRECT |
53223,51735
53223 - Aminoacid dehydrogenase-like, N-terminal domain
51735 - NAD(P)-binding Rossmann-fold domains | 0 | DIRECT |
101386,53720
101386 - all-alpha NTP pyrophosphatases
53720 - ALDH-like | 0 | DIRECT |
51278,51338
51278 - Urease, beta-subunit
51338 - Composite domain of metallo-dependent hydrolases | 0 | DIRECT |
55021,53328
55021 - ACT-like
53328 - Formyltransferase | 0 | DIRECT |
52335,53927
52335 - Methylglyoxal synthase-like
53927 - Cytidine deaminase-like | 0 | DIRECT |
54211,54637
54211 - Ribosomal protein S5 domain 2-like
54637 - Thioesterase/thiol ester dehydrase-isomerase | 0 | DIRECT |
53927,53927
53927 - Cytidine deaminase-like
53927 - Cytidine deaminase-like | 0 | DIRECT |
49503,110083
49503 - Cupredoxins
110083 - Peptidylarginine deiminase Pad4, middle domain | 0 | DIRECT |
54211,54211
54211 - Ribosomal protein S5 domain 2-like
54211 - Ribosomal protein S5 domain 2-like | 0 | DIRECT |
141734,101386
141734 - HisI-like
101386 - all-alpha NTP pyrophosphatases | 0 | DIRECT |
110083,55909
110083 - Peptidylarginine deiminase Pad4, middle domain
55909 - Pentein | 0 | DIRECT |
52172,52738
52172 - CheY-like
52738 - Methylesterase CheB, C-terminal domain | 0 | DIRECT |
56601,48403
56601 - beta-lactamase/transpeptidase-like
48403 - Ankyrin repeat | 0 | DIRECT |
53927,53597
53927 - Cytidine deaminase-like
53597 - Dihydrofolate reductase-like | 0 | DIRECT |
53774,48403
53774 - Glutaminase/Asparaginase
48403 - Ankyrin repeat | 0 | DIRECT |
143503,54001
143503 - PUG domain-like
54001 - Cysteine proteinases | 0 | DIRECT |
53187,55031
53187 - Zn-dependent exopeptidases
55031 - Bacterial exopeptidase dimerisation domain | 0 | DIRECT |
52768,52768
52768 - Arginase/deacetylase
52768 - Arginase/deacetylase | 0 | DIRECT |
55821,142695
55821 - YrdC/RibB
142695 - RibA-like | 0 | DIRECT |
52335,51556
52335 - Methylglyoxal synthase-like
51556 - Metallo-dependent hydrolases | 0.000000001097 | DIRECT |
160467,50891
160467 - PH0987 N-terminal domain-like
50891 - Cyclophilin-like | 0.00000001247 | DIRECT |
52317,52440
52317 - Class I glutamine amidotransferase-like
52440 - PreATP-grasp domain | 0.0000000596 | DIRECT |
54106,54001
54106 - LysM domain
54001 - Cysteine proteinases | 0.00000225 | DIRECT |
52317,51366
52317 - Class I glutamine amidotransferase-like
51366 - Ribulose-phoshate binding barrel | 0.001239 | INHERITED FROM: Glutaminase || In linear amides |
47090,47090
47090 - PGBD-like
47090 - PGBD-like | 0.003272 | INHERITED FROM: In linear amides || N-acetylmuramoyl-L-alanine amidase |
54768,54768
54768 - dsRNA-binding domain-like
54768 - dsRNA-binding domain-like | 0.01309 | INHERITED FROM: In cyclic amidines || Double-stranded RNA adenine deaminase |
54106,54106
54106 - LysM domain
54106 - LysM domain | 0.01867 | INHERITED FROM: In linear amides || N-acetylmuramoyl-L-alanine amidase |
49785,49785
49785 - Galactose-binding domain-like
49785 - Galactose-binding domain-like | 0.03322 | INHERITED FROM: In linear amidines || Allantoicase |
52021,52317
52021 - Carbamoyl phosphate synthetase, small subunit N-terminal domain
52317 - Class I glutamine amidotransferase-like | 0.6968 | INHERITED FROM: Dihydroorotase || In cyclic amides |
56059,52335
56059 - Glutathione synthetase ATP-binding domain-like
52335 - Methylglyoxal synthase-like | 0.8331 | INHERITED FROM: Dihydroorotase || In cyclic amides |
48108,52440
48108 - Carbamoyl phosphate synthetase, large subunit connection domain
52440 - PreATP-grasp domain | 0.8959 | INHERITED FROM: Dihydroorotase || In cyclic amides |
56059,48108
56059 - Glutathione synthetase ATP-binding domain-like
48108 - Carbamoyl phosphate synthetase, large subunit connection domain | 0.9025 | INHERITED FROM: Dihydroorotase || In cyclic amides |
53092,55920
53092 - Creatinase/prolidase N-terminal domain
55920 - Creatinase/aminopeptidase | 1 | INHERITED FROM: In linear amidines || Creatinase |
52440,56059
52440 - PreATP-grasp domain
56059 - Glutathione synthetase ATP-binding domain-like | 1 | INHERITED FROM: Dihydroorotase |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
51556,51338
51556 - Metallo-dependent hydrolases
51338 - Composite domain of metallo-dependent hydrolases | 0 | Direct |
55846,47090
55846 - N-acetylmuramoyl-L-alanine amidase-like
47090 - PGBD-like | 0 | Direct |
56601,52091
56601 - beta-lactamase/transpeptidase-like
52091 - SpoIIaa-like | 0 | Direct |
54001,49785
54001 - Cysteine proteinases
49785 - Galactose-binding domain-like | 0 | Direct |
54111,51278
54111 - Urease, gamma-subunit
51278 - Urease, beta-subunit | 0 | Direct |
51338,51556
51338 - Composite domain of metallo-dependent hydrolases
51556 - Metallo-dependent hydrolases | 0 | Direct |
53223,51735
53223 - Aminoacid dehydrogenase-like, N-terminal domain
51735 - NAD(P)-binding Rossmann-fold domains | 0 | Direct |
101386,53720
101386 - all-alpha NTP pyrophosphatases
53720 - ALDH-like | 0 | Direct |
51278,51338
51278 - Urease, beta-subunit
51338 - Composite domain of metallo-dependent hydrolases | 0 | Direct |
55021,53328
55021 - ACT-like
53328 - Formyltransferase | 0 | Direct |
52335,53927
52335 - Methylglyoxal synthase-like
53927 - Cytidine deaminase-like | 0 | Direct |
54211,54637
54211 - Ribosomal protein S5 domain 2-like
54637 - Thioesterase/thiol ester dehydrase-isomerase | 0 | Direct |
53927,53927
53927 - Cytidine deaminase-like
53927 - Cytidine deaminase-like | 0 | Direct |
49503,110083
49503 - Cupredoxins
110083 - Peptidylarginine deiminase Pad4, middle domain | 0 | Direct |
54211,54211
54211 - Ribosomal protein S5 domain 2-like
54211 - Ribosomal protein S5 domain 2-like | 0 | Direct |
141734,101386
141734 - HisI-like
101386 - all-alpha NTP pyrophosphatases | 0 | Direct |
110083,55909
110083 - Peptidylarginine deiminase Pad4, middle domain
55909 - Pentein | 0 | Direct |
52172,52738
52172 - CheY-like
52738 - Methylesterase CheB, C-terminal domain | 0 | Direct |
56601,48403
56601 - beta-lactamase/transpeptidase-like
48403 - Ankyrin repeat | 0 | Direct |
53927,53597
53927 - Cytidine deaminase-like
53597 - Dihydrofolate reductase-like | 0 | Direct |
53774,48403
53774 - Glutaminase/Asparaginase
48403 - Ankyrin repeat | 0 | Direct |
143503,54001
143503 - PUG domain-like
54001 - Cysteine proteinases | 0 | Direct |
53187,55031
53187 - Zn-dependent exopeptidases
55031 - Bacterial exopeptidase dimerisation domain | 0 | Direct |
52768,52768
52768 - Arginase/deacetylase
52768 - Arginase/deacetylase | 0 | Direct |
55821,142695
55821 - YrdC/RibB
142695 - RibA-like | 0 | Direct |
52335,51556
52335 - Methylglyoxal synthase-like
51556 - Metallo-dependent hydrolases | 0.000000001097 | Direct |
160467,50891
160467 - PH0987 N-terminal domain-like
50891 - Cyclophilin-like | 0.00000001247 | Direct |
52317,52440
52317 - Class I glutamine amidotransferase-like
52440 - PreATP-grasp domain | 0.0000000596 | Direct |
54106,54001
54106 - LysM domain
54001 - Cysteine proteinases | 0.00000225 | Direct |
52317,51366
52317 - Class I glutamine amidotransferase-like
51366 - Ribulose-phoshate binding barrel | 0.001239 | Inherited |
47090,47090
47090 - PGBD-like
47090 - PGBD-like | 0.003272 | Inherited |
54768,54768
54768 - dsRNA-binding domain-like
54768 - dsRNA-binding domain-like | 0.01309 | Inherited |
54106,54106
54106 - LysM domain
54106 - LysM domain | 0.01867 | Inherited |
49785,49785
49785 - Galactose-binding domain-like
49785 - Galactose-binding domain-like | 0.03322 | Inherited |
52021,52317
52021 - Carbamoyl phosphate synthetase, small subunit N-terminal domain
52317 - Class I glutamine amidotransferase-like | 0.6968 | Inherited |
56059,52335
56059 - Glutathione synthetase ATP-binding domain-like
52335 - Methylglyoxal synthase-like | 0.8331 | Inherited |
48108,52440
48108 - Carbamoyl phosphate synthetase, large subunit connection domain
52440 - PreATP-grasp domain | 0.8959 | Inherited |
56059,48108
56059 - Glutathione synthetase ATP-binding domain-like
48108 - Carbamoyl phosphate synthetase, large subunit connection domain | 0.9025 | Inherited |
53092,55920
53092 - Creatinase/prolidase N-terminal domain
55920 - Creatinase/aminopeptidase | 1 | Inherited |
52440,56059
52440 - PreATP-grasp domain
56059 - Glutathione synthetase ATP-binding domain-like | 1 | Inherited |
(show details)
Supra-domains annotated to this EC term (Not in SPEC)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
51338,51556,51338
51338 - Composite domain of metallo-dependent hydrolases
51556 - Metallo-dependent hydrolases
51338 - Composite domain of metallo-dependent hydrolases | 0 | DIRECT |
51278,51338,51556
51278 - Urease, beta-subunit
51338 - Composite domain of metallo-dependent hydrolases
51556 - Metallo-dependent hydrolases | 0 | DIRECT |
49503,110083,55909
49503 - Cupredoxins
110083 - Peptidylarginine deiminase Pad4, middle domain
55909 - Pentein | 0 | DIRECT |
54768,54768,54768
54768 - dsRNA-binding domain-like
54768 - dsRNA-binding domain-like
54768 - dsRNA-binding domain-like | 0 | DIRECT |
54111,51278,51338
54111 - Urease, gamma-subunit
51278 - Urease, beta-subunit
51338 - Composite domain of metallo-dependent hydrolases | 0 | DIRECT |
143503,54001,49785
143503 - PUG domain-like
54001 - Cysteine proteinases
49785 - Galactose-binding domain-like | 0 | DIRECT |
54211,54211,54637
54211 - Ribosomal protein S5 domain 2-like
54211 - Ribosomal protein S5 domain 2-like
54637 - Thioesterase/thiol ester dehydrase-isomerase | 0 | DIRECT |
141734,101386,53720
141734 - HisI-like
101386 - all-alpha NTP pyrophosphatases
53720 - ALDH-like | 0 | DIRECT |
52335,51556,51338
52335 - Methylglyoxal synthase-like
51556 - Metallo-dependent hydrolases
51338 - Composite domain of metallo-dependent hydrolases | 0.00000000002742 | DIRECT |
56059,52335,51556
56059 - Glutathione synthetase ATP-binding domain-like
52335 - Methylglyoxal synthase-like
51556 - Metallo-dependent hydrolases | 0.000000001097 | DIRECT |
52317,52440,56059
52317 - Class I glutamine amidotransferase-like
52440 - PreATP-grasp domain
56059 - Glutathione synthetase ATP-binding domain-like | 0.0000000596 | DIRECT |
52021,52317,52440
52021 - Carbamoyl phosphate synthetase, small subunit N-terminal domain
52317 - Class I glutamine amidotransferase-like
52440 - PreATP-grasp domain | 0.0000000596 | DIRECT |
54106,54106,54001
54106 - LysM domain
54106 - LysM domain
54001 - Cysteine proteinases | 0.000009675 | DIRECT |
54106,54106,54106
54106 - LysM domain
54106 - LysM domain
54106 - LysM domain | 0.005279 | INHERITED FROM: In linear amides || N-acetylmuramoyl-L-alanine amidase |
52440,56059,52335
52440 - PreATP-grasp domain
56059 - Glutathione synthetase ATP-binding domain-like
52335 - Methylglyoxal synthase-like | 0.8287 | INHERITED FROM: Dihydroorotase || In cyclic amides |
56059,48108,52440
56059 - Glutathione synthetase ATP-binding domain-like
48108 - Carbamoyl phosphate synthetase, large subunit connection domain
52440 - PreATP-grasp domain | 0.8924 | INHERITED FROM: Dihydroorotase || In cyclic amides |
48108,52440,56059
48108 - Carbamoyl phosphate synthetase, large subunit connection domain
52440 - PreATP-grasp domain
56059 - Glutathione synthetase ATP-binding domain-like | 0.8959 | INHERITED FROM: Dihydroorotase || In cyclic amides |
52440,56059,48108
52440 - PreATP-grasp domain
56059 - Glutathione synthetase ATP-binding domain-like
48108 - Carbamoyl phosphate synthetase, large subunit connection domain | 0.9025 | INHERITED FROM: Dihydroorotase || In cyclic amides |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
51338,51556,51338
51338 - Composite domain of metallo-dependent hydrolases
51556 - Metallo-dependent hydrolases
51338 - Composite domain of metallo-dependent hydrolases | 0 | Direct |
51278,51338,51556
51278 - Urease, beta-subunit
51338 - Composite domain of metallo-dependent hydrolases
51556 - Metallo-dependent hydrolases | 0 | Direct |
49503,110083,55909
49503 - Cupredoxins
110083 - Peptidylarginine deiminase Pad4, middle domain
55909 - Pentein | 0 | Direct |
54768,54768,54768
54768 - dsRNA-binding domain-like
54768 - dsRNA-binding domain-like
54768 - dsRNA-binding domain-like | 0 | Direct |
54111,51278,51338
54111 - Urease, gamma-subunit
51278 - Urease, beta-subunit
51338 - Composite domain of metallo-dependent hydrolases | 0 | Direct |
143503,54001,49785
143503 - PUG domain-like
54001 - Cysteine proteinases
49785 - Galactose-binding domain-like | 0 | Direct |
54211,54211,54637
54211 - Ribosomal protein S5 domain 2-like
54211 - Ribosomal protein S5 domain 2-like
54637 - Thioesterase/thiol ester dehydrase-isomerase | 0 | Direct |
141734,101386,53720
141734 - HisI-like
101386 - all-alpha NTP pyrophosphatases
53720 - ALDH-like | 0 | Direct |
52335,51556,51338
52335 - Methylglyoxal synthase-like
51556 - Metallo-dependent hydrolases
51338 - Composite domain of metallo-dependent hydrolases | 0.00000000002742 | Direct |
56059,52335,51556
56059 - Glutathione synthetase ATP-binding domain-like
52335 - Methylglyoxal synthase-like
51556 - Metallo-dependent hydrolases | 0.000000001097 | Direct |
52317,52440,56059
52317 - Class I glutamine amidotransferase-like
52440 - PreATP-grasp domain
56059 - Glutathione synthetase ATP-binding domain-like | 0.0000000596 | Direct |
52021,52317,52440
52021 - Carbamoyl phosphate synthetase, small subunit N-terminal domain
52317 - Class I glutamine amidotransferase-like
52440 - PreATP-grasp domain | 0.0000000596 | Direct |
54106,54106,54001
54106 - LysM domain
54106 - LysM domain
54001 - Cysteine proteinases | 0.000009675 | Direct |
54106,54106,54106
54106 - LysM domain
54106 - LysM domain
54106 - LysM domain | 0.005279 | Inherited |
52440,56059,52335
52440 - PreATP-grasp domain
56059 - Glutathione synthetase ATP-binding domain-like
52335 - Methylglyoxal synthase-like | 0.8287 | Inherited |
56059,48108,52440
56059 - Glutathione synthetase ATP-binding domain-like
48108 - Carbamoyl phosphate synthetase, large subunit connection domain
52440 - PreATP-grasp domain | 0.8924 | Inherited |
48108,52440,56059
48108 - Carbamoyl phosphate synthetase, large subunit connection domain
52440 - PreATP-grasp domain
56059 - Glutathione synthetase ATP-binding domain-like | 0.8959 | Inherited |
52440,56059,48108
52440 - PreATP-grasp domain
56059 - Glutathione synthetase ATP-binding domain-like
48108 - Carbamoyl phosphate synthetase, large subunit connection domain | 0.9025 | Inherited |
Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term
|
Plot tree as:
| |
Download Newick format tree:
|
(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.
|
