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Enzyme Commission (EC): Carboxy-lyases
(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)
Superfamily domains annotated to this EC term (SDEC level: Informative)
Highlighted in gray are those with FDR_all>0.001
SCOP term | FDR (all) | Annotation (direct or inherited) |
Ornithine decarboxylase C-terminal domain | 0 | DIRECT |
CoaB-like | 0 | DIRECT |
PEP carboxykinase N-terminal domain | 0 | DIRECT |
Homo-oligomeric flavin-containing Cys decarboxylases, HFCD | 0 | DIRECT |
PLP-binding barrel | 0 | DIRECT |
Acetoacetate decarboxylase-like | 0 | DIRECT |
UbiD C-terminal domain-like | 0 | DIRECT |
RuBisCo, C-terminal domain | 0 | DIRECT |
PEP carboxykinase-like | 0 | DIRECT |
N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | 0 | DIRECT |
Pyruvoyl-dependent histidine and arginine decarboxylases | 0 | DIRECT |
RuBisCO, large subunit, small (N-terminal) domain | 0 | DIRECT |
Ribulose-phoshate binding barrel | 0 | DIRECT |
Alanine racemase C-terminal domain-like | 0 | DIRECT |
S-adenosylmethionine decarboxylase | 0 | DIRECT |
RuBisCO, small subunit | 0 | DIRECT |
AF0104/ALDC/Ptd012-like | 0 | DIRECT |
ADC-like | 0 | DIRECT |
UROD/MetE-like | 0 | DIRECT |
FMN-binding split barrel | 0 | DIRECT |
UraD-Like | 0 | DIRECT |
RraA-like | 0.000000000006246 | DIRECT |
FAH | 0.000000005395 | DIRECT |
Thiamin diphosphate-binding fold (THDP-binding) | 0.00000001308 | DIRECT |
Tautomerase/MIF | 0.00000002838 | DIRECT |
DHS-like NAD/FAD-binding domain | 0.00000009504 | DIRECT |
2-methylcitrate dehydratase PrpD | 0.00002931 | DIRECT |
Rudiment single hybrid motif | 0.004635 | INHERITED FROM: Phosphoribosylaminoimidazole carboxylase |
CoA-dependent acyltransferases | 0.02916 | INHERITED FROM: 2-oxoglutarate decarboxylase |
PFL-like glycyl radical enzymes | 0.1971 | INHERITED FROM: 4-hydroxyphenylacetate decarboxylase |
C2 domain (Calcium/lipid-binding domain, CaLB) | 0.4997 | INHERITED FROM: Phosphatidylserine decarboxylase |
GHMP Kinase, C-terminal domain | 0.6993 | INHERITED FROM: Diphosphomevalonate decarboxylase |
PLP-dependent transferases | 0.7009 | INHERITED FROM: Aspartate 1-decarboxylase || Aromatic-L-amino-acid decarboxylase || Histidine decarboxylase || Glutamate decarboxylase || Threonine-phosphate decarboxylase || 3,4-dihydroxyphenylacetaldehyde synthase || Sulfinoalanine decarboxylase || Diaminobutyrate decarboxylase || L-tryptophan decarboxylase || Tyrosine decarboxylase || Lysine decarboxylase |
SAICAR synthase-like | 0.9006 | INHERITED FROM: Phosphoribosylaminoimidazole carboxylase |
CheY-like | 0.9668 | INHERITED FROM: Ornithine decarboxylase |
RmlC-like cupins | 0.9703 | INHERITED FROM: Oxalate decarboxylase || Peptidyl-glutamate 4-carboxylase |
EF-hand | 1 | INHERITED FROM: Phosphatidylserine decarboxylase |
Metallo-dependent hydrolases | 1 | INHERITED FROM: Aminocarboxymuconate-semialdehyde decarboxylase |
ClpP/crotonase | 1 | INHERITED FROM: Ethylmalonyl-CoA decarboxylase |
Phosphoenolpyruvate/pyruvate domain | 1 | INHERITED FROM: Oxaloacetate decarboxylase || Phosphoenolpyruvate carboxylase |
AraD/HMP-PK domain-like | 1 | INHERITED FROM: 3-dehydro-4-phosphotetronate decarboxylase |
PRTase-like | 1 | INHERITED FROM: Orotidine-5'-phosphate decarboxylase |
Aminoacid dehydrogenase-like, N-terminal domain | 1 | INHERITED FROM: Malolactic enzyme |
PreATP-grasp domain | 1 | INHERITED FROM: Phosphoribosylaminoimidazole carboxylase |
Class I glutamine amidotransferase-like | 1 | INHERITED FROM: Indole-3-glycerol-phosphate synthase |
Ribosomal protein S5 domain 2-like | 1 | INHERITED FROM: Bisphosphomevalonate decarboxylase || Diphosphomevalonate decarboxylase |
Glutathione synthetase ATP-binding domain-like | 1 | INHERITED FROM: Phosphoribosylaminoimidazole carboxylase |
NAD(P)-binding Rossmann-fold domains | 1 | INHERITED FROM: UDP-glucuronate decarboxylase || Malolactic enzyme |
Periplasmic binding protein-like II | 1 | INHERITED FROM: Prephenate decarboxylase |
Isocitrate/Isopropylmalate dehydrogenase-like | 1 | INHERITED FROM: Tartrate decarboxylase |
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Family(show details)
Family domains annotated to this EC term (SDEC level: Informative)
Highlighted in gray are those with FDR_all>0.001
SCOP term | FDR (all) | Annotation (direct or inherited) |
Ornithine decarboxylase C-terminal domain | 0 | DIRECT |
Eukaryotic ODC-like | 0 | DIRECT |
Mevalonate 5-diphosphate decarboxylase | 0 | DIRECT |
Pyruvoyl dependent aspartate decarboxylase, ADC | 0 | DIRECT |
Homo-oligomeric flavin-containing Cys decarboxylases, HFCD | 0 | DIRECT |
S-adenosylmethionine decarboxylase | 0 | DIRECT |
RuBisCO, small subunit | 0 | DIRECT |
Alanine racemase-like, N-terminal domain | 0 | DIRECT |
Ornithine decarboxylase N-terminal "wing" domain | 0 | DIRECT |
CoaB-like | 0 | DIRECT |
Ornithine decarboxylase major domain | 0 | DIRECT |
Tryptophan biosynthesis enzymes | 0 | DIRECT |
UraD-like | 0 | DIRECT |
PEP carboxykinase N-terminal domain | 0 | DIRECT |
Ribulose 1,5-bisphosphate carboxylase-oxygenase | 0 | DIRECT |
Arginine decarboxylase | 0 | DIRECT |
PEP carboxykinase C-terminal domain | 0 | DIRECT |
N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | 0 | DIRECT |
Uroporphyrinogen decarboxylase, UROD | 0 | DIRECT |
Alpha-acetolactate decarboxylase-like | 0 | DIRECT |
UbiD middle domain-like | 0 | DIRECT |
UbiD C-terminal domain-like | 0 | DIRECT |
Decarboxylase | 0 | DIRECT |
Histidine decarboxylase | 0 | DIRECT |
Acetoacetate decarboxylase-like | 0 | DIRECT |
Bacterial S-adenosylmethionine decarboxylase | 0 | DIRECT |
RuBisCo, large subunit, C-terminal domain | 0 | DIRECT |
Phosphoenolpyruvate carboxylase | 0 | DIRECT |
PP1699/LP2961-like | 0.00000000000000237 | DIRECT |
RraA-like | 0.000000000009917 | DIRECT |
MIF-related | 0.0000000006959 | DIRECT |
Pyridoxal-dependent decarboxylase | 0.00000000502 | DIRECT |
FAH | 0.000000006542 | DIRECT |
Pyruvate oxidase and decarboxylase PP module | 0.00000001749 | DIRECT |
Pyruvate oxidase and decarboxylase, middle domain | 0.0000001099 | DIRECT |
Pyruvate oxidase and decarboxylase Pyr module | 0.0000001587 | DIRECT |
Germin/Seed storage 7S protein | 0.000002137 | DIRECT |
2-methylcitrate dehydratase PrpD | 0.00003163 | DIRECT |
CAT-like | 0.0007191 | DIRECT |
Branched-chain alpha-keto acid dehydrogenase Pyr module | 0.00102 | INHERITED FROM: 2-oxoglutarate decarboxylase |
Branched-chain alpha-keto acid dehydrogenase PP module | 0.003035 | INHERITED FROM: 2-oxoglutarate decarboxylase |
BC C-terminal domain-like | 0.005459 | INHERITED FROM: Phosphoribosylaminoimidazole carboxylase |
Malic enzyme N-domain | 0.1883 | INHERITED FROM: Malolactic enzyme |
PFL-like | 0.2548 | INHERITED FROM: 4-hydroxyphenylacetate decarboxylase |
BC ATP-binding domain-like | 0.4159 | INHERITED FROM: Phosphoribosylaminoimidazole carboxylase |
BC N-terminal domain-like | 0.5133 | INHERITED FROM: Phosphoribosylaminoimidazole carboxylase |
Dimeric isocitrate & isopropylmalate dehydrogenases | 0.7136 | INHERITED FROM: Tartrate decarboxylase |
SAICAR synthase | 0.8438 | INHERITED FROM: Phosphoribosylaminoimidazole carboxylase |
GHMP Kinase, N-terminal domain | 0.8656 | INHERITED FROM: Bisphosphomevalonate decarboxylase || Diphosphomevalonate decarboxylase |
Phosphoenolpyruvate mutase/Isocitrate lyase-like | 1 | INHERITED FROM: Oxaloacetate decarboxylase |
AraD-like aldolase/epimerase | 1 | INHERITED FROM: 3-dehydro-4-phosphotetronate decarboxylase |
AAT-like | 1 | INHERITED FROM: Threonine-phosphate decarboxylase |
Class I glutamine amidotransferases (GAT) | 1 | INHERITED FROM: Indole-3-glycerol-phosphate synthase |
Tyrosine-dependent oxidoreductases | 1 | INHERITED FROM: UDP-glucuronate decarboxylase |
Aminoacid dehydrogenase-like, C-terminal domain | 1 | INHERITED FROM: Malolactic enzyme |
Phosphoribosyltransferases (PRTases) | 1 | INHERITED FROM: Orotidine-5'-phosphate decarboxylase |
Crotonase-like | 1 | INHERITED FROM: Ethylmalonyl-CoA decarboxylase |
SCOP term | FDR (all) | Annotation (direct or inherited) |
Ornithine decarboxylase C-terminal domain | 0 | Direct |
Eukaryotic ODC-like | 0 | Direct |
Mevalonate 5-diphosphate decarboxylase | 0 | Direct |
Pyruvoyl dependent aspartate decarboxylase, ADC | 0 | Direct |
Homo-oligomeric flavin-containing Cys decarboxylases, HFCD | 0 | Direct |
S-adenosylmethionine decarboxylase | 0 | Direct |
RuBisCO, small subunit | 0 | Direct |
Alanine racemase-like, N-terminal domain | 0 | Direct |
Ornithine decarboxylase N-terminal "wing" domain | 0 | Direct |
CoaB-like | 0 | Direct |
Ornithine decarboxylase major domain | 0 | Direct |
Tryptophan biosynthesis enzymes | 0 | Direct |
UraD-like | 0 | Direct |
PEP carboxykinase N-terminal domain | 0 | Direct |
Ribulose 1,5-bisphosphate carboxylase-oxygenase | 0 | Direct |
Arginine decarboxylase | 0 | Direct |
PEP carboxykinase C-terminal domain | 0 | Direct |
N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | 0 | Direct |
Uroporphyrinogen decarboxylase, UROD | 0 | Direct |
Alpha-acetolactate decarboxylase-like | 0 | Direct |
UbiD middle domain-like | 0 | Direct |
UbiD C-terminal domain-like | 0 | Direct |
Decarboxylase | 0 | Direct |
Histidine decarboxylase | 0 | Direct |
Acetoacetate decarboxylase-like | 0 | Direct |
Bacterial S-adenosylmethionine decarboxylase | 0 | Direct |
RuBisCo, large subunit, C-terminal domain | 0 | Direct |
Phosphoenolpyruvate carboxylase | 0 | Direct |
PP1699/LP2961-like | 0.00000000000000237 | Direct |
RraA-like | 0.000000000009917 | Direct |
MIF-related | 0.0000000006959 | Direct |
Pyridoxal-dependent decarboxylase | 0.00000000502 | Direct |
FAH | 0.000000006542 | Direct |
Pyruvate oxidase and decarboxylase PP module | 0.00000001749 | Direct |
Pyruvate oxidase and decarboxylase, middle domain | 0.0000001099 | Direct |
Pyruvate oxidase and decarboxylase Pyr module | 0.0000001587 | Direct |
Germin/Seed storage 7S protein | 0.000002137 | Direct |
2-methylcitrate dehydratase PrpD | 0.00003163 | Direct |
CAT-like | 0.0007191 | Direct |
Branched-chain alpha-keto acid dehydrogenase Pyr module | 0.00102 | Inherited |
Branched-chain alpha-keto acid dehydrogenase PP module | 0.003035 | Inherited |
BC C-terminal domain-like | 0.005459 | Inherited |
Malic enzyme N-domain | 0.1883 | Inherited |
PFL-like | 0.2548 | Inherited |
BC ATP-binding domain-like | 0.4159 | Inherited |
BC N-terminal domain-like | 0.5133 | Inherited |
Dimeric isocitrate & isopropylmalate dehydrogenases | 0.7136 | Inherited |
SAICAR synthase | 0.8438 | Inherited |
GHMP Kinase, N-terminal domain | 0.8656 | Inherited |
Phosphoenolpyruvate mutase/Isocitrate lyase-like | 1 | Inherited |
AraD-like aldolase/epimerase | 1 | Inherited |
AAT-like | 1 | Inherited |
Class I glutamine amidotransferases (GAT) | 1 | Inherited |
Tyrosine-dependent oxidoreductases | 1 | Inherited |
Aminoacid dehydrogenase-like, C-terminal domain | 1 | Inherited |
Phosphoribosyltransferases (PRTases) | 1 | Inherited |
Crotonase-like | 1 | Inherited |
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term
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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
Supra-domain (Single) |
FDR (all) |
Annotation (direct or inherited) |
AF0104/ALDC/Ptd012-like | 0 | DIRECT |
Acetoacetate decarboxylase-like | 0 | DIRECT |
UraD-Like | 0 | DIRECT |
PEP carboxykinase-like | 0 | DIRECT |
FMN-binding split barrel | 0 | DIRECT |
RuBisCO, large subunit, small (N-terminal) domain | 0 | DIRECT |
UbiD C-terminal domain-like | 0 | DIRECT |
Ornithine decarboxylase C-terminal domain | 0 | DIRECT |
PLP-binding barrel | 0 | DIRECT |
ADC-like | 0 | DIRECT |
UROD/MetE-like | 0 | DIRECT |
S-adenosylmethionine decarboxylase | 0 | DIRECT |
PEP carboxykinase N-terminal domain | 0 | DIRECT |
Homo-oligomeric flavin-containing Cys decarboxylases, HFCD | 0 | DIRECT |
RuBisCO, small subunit | 0 | DIRECT |
RuBisCo, C-terminal domain | 0 | DIRECT |
N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | 0 | DIRECT |
Pyruvoyl-dependent histidine and arginine decarboxylases | 0 | DIRECT |
CoaB-like | 0 | DIRECT |
Alanine racemase C-terminal domain-like | 0 | DIRECT |
Ribulose-phoshate binding barrel | 0 | DIRECT |
RraA-like | 0.000000000004508 | DIRECT |
FAH | 0.000000004055 | DIRECT |
Thiamin diphosphate-binding fold (THDP-binding) | 0.000000009887 | DIRECT |
Tautomerase/MIF | 0.00000002155 | DIRECT |
DHS-like NAD/FAD-binding domain | 0.00000007255 | DIRECT |
2-methylcitrate dehydratase PrpD | 0.00002337 | DIRECT |
Rudiment single hybrid motif | 0.003885 | INHERITED FROM: Phosphoribosylaminoimidazole carboxylase |
CoA-dependent acyltransferases | 0.02502 | INHERITED FROM: 2-oxoglutarate decarboxylase |
PFL-like glycyl radical enzymes | 0.1746 | INHERITED FROM: 4-hydroxyphenylacetate decarboxylase |
C2 domain (Calcium/lipid-binding domain, CaLB) | 0.4564 | INHERITED FROM: Phosphatidylserine decarboxylase |
GHMP Kinase, C-terminal domain | 0.6428 | INHERITED FROM: Diphosphomevalonate decarboxylase |
PLP-dependent transferases | 0.6443 | INHERITED FROM: Sulfinoalanine decarboxylase || Aspartate 1-decarboxylase || Threonine-phosphate decarboxylase || L-tryptophan decarboxylase || Histidine decarboxylase || Diaminobutyrate decarboxylase || 3,4-dihydroxyphenylacetaldehyde synthase || Glutamate decarboxylase || Aromatic-L-amino-acid decarboxylase || Tyrosine decarboxylase || Lysine decarboxylase |
SAICAR synthase-like | 0.8312 | INHERITED FROM: Phosphoribosylaminoimidazole carboxylase |
CheY-like | 0.8945 | INHERITED FROM: Ornithine decarboxylase |
RmlC-like cupins | 0.8978 | INHERITED FROM: Oxalate decarboxylase || Peptidyl-glutamate 4-carboxylase |
EF-hand | 0.9528 | INHERITED FROM: Phosphatidylserine decarboxylase |
Phosphoenolpyruvate/pyruvate domain | 0.9995 | INHERITED FROM: Oxaloacetate decarboxylase || Phosphoenolpyruvate carboxylase |
PreATP-grasp domain | 1 | INHERITED FROM: Phosphoribosylaminoimidazole carboxylase |
ClpP/crotonase | 1 | INHERITED FROM: Ethylmalonyl-CoA decarboxylase |
Glutathione synthetase ATP-binding domain-like | 1 | INHERITED FROM: Phosphoribosylaminoimidazole carboxylase |
Periplasmic binding protein-like II | 1 | INHERITED FROM: Prephenate decarboxylase |
Metallo-dependent hydrolases | 1 | INHERITED FROM: Aminocarboxymuconate-semialdehyde decarboxylase |
AraD/HMP-PK domain-like | 1 | INHERITED FROM: 3-dehydro-4-phosphotetronate decarboxylase |
NAD(P)-binding Rossmann-fold domains | 1 | INHERITED FROM: Malolactic enzyme || UDP-glucuronate decarboxylase |
PRTase-like | 1 | INHERITED FROM: Orotidine-5'-phosphate decarboxylase |
Ribosomal protein S5 domain 2-like | 1 | INHERITED FROM: Bisphosphomevalonate decarboxylase || Diphosphomevalonate decarboxylase |
Isocitrate/Isopropylmalate dehydrogenase-like | 1 | INHERITED FROM: Tartrate decarboxylase |
Class I glutamine amidotransferase-like | 1 | INHERITED FROM: Indole-3-glycerol-phosphate synthase |
Aminoacid dehydrogenase-like, N-terminal domain | 1 | INHERITED FROM: Malolactic enzyme |
(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) |
52172,53383 52172 - CheY-like 53383 - PLP-dependent transferases | 0 | DIRECT |
68923,53795 68923 - PEP carboxykinase N-terminal domain 53795 - PEP carboxykinase-like | 0 | DIRECT |
50475,143968 50475 - FMN-binding split barrel 143968 - UbiD C-terminal domain-like | 0 | DIRECT |
56104,52255 56104 - SAICAR synthase-like 52255 - N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | 0 | DIRECT |
51246,52255 51246 - Rudiment single hybrid motif 52255 - N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | 0 | DIRECT |
51366,51366 51366 - Ribulose-phoshate binding barrel 51366 - Ribulose-phoshate binding barrel | 0 | DIRECT |
51419,50621 51419 - PLP-binding barrel 50621 - Alanine racemase C-terminal domain-like | 0 | DIRECT |
53383,55904 53383 - PLP-dependent transferases 55904 - Ornithine decarboxylase C-terminal domain | 0 | DIRECT |
56529,56529 56529 - FAH 56529 - FAH | 0 | DIRECT |
54966,51649 54966 - RuBisCO, large subunit, small (N-terminal) domain 51649 - RuBisCo, C-terminal domain | 0 | DIRECT |
52317,51366 52317 - Class I glutamine amidotransferase-like 51366 - Ribulose-phoshate binding barrel | 0 | DIRECT |
52507,102645 52507 - Homo-oligomeric flavin-containing Cys decarboxylases, HFCD 102645 - CoaB-like | 0 | DIRECT |
53271,51366 53271 - PRTase-like 51366 - Ribulose-phoshate binding barrel | 0 | DIRECT |
52467,52518 52467 - DHS-like NAD/FAD-binding domain 52518 - Thiamin diphosphate-binding fold (THDP-binding) | 0.00000007255 | DIRECT |
52518,52467 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52467 - DHS-like NAD/FAD-binding domain | 0.0000001048 | DIRECT |
56059,51246 56059 - Glutathione synthetase ATP-binding domain-like 51246 - Rudiment single hybrid motif | 0.003885 | INHERITED FROM: Phosphoribosylaminoimidazole carboxylase |
54211,55060 54211 - Ribosomal protein S5 domain 2-like 55060 - GHMP Kinase, C-terminal domain | 0.6185 | INHERITED FROM: Diphosphomevalonate decarboxylase |
52518,52518 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52518 - Thiamin diphosphate-binding fold (THDP-binding) | 0.6718 | INHERITED FROM: 2-oxoglutarate decarboxylase |
52440,56059 52440 - PreATP-grasp domain 56059 - Glutathione synthetase ATP-binding domain-like | 1 | INHERITED FROM: Phosphoribosylaminoimidazole carboxylase |
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
52172,53383 52172 - CheY-like 53383 - PLP-dependent transferases | 0 | Direct |
68923,53795 68923 - PEP carboxykinase N-terminal domain 53795 - PEP carboxykinase-like | 0 | Direct |
50475,143968 50475 - FMN-binding split barrel 143968 - UbiD C-terminal domain-like | 0 | Direct |
56104,52255 56104 - SAICAR synthase-like 52255 - N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | 0 | Direct |
51246,52255 51246 - Rudiment single hybrid motif 52255 - N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | 0 | Direct |
51366,51366 51366 - Ribulose-phoshate binding barrel 51366 - Ribulose-phoshate binding barrel | 0 | Direct |
51419,50621 51419 - PLP-binding barrel 50621 - Alanine racemase C-terminal domain-like | 0 | Direct |
53383,55904 53383 - PLP-dependent transferases 55904 - Ornithine decarboxylase C-terminal domain | 0 | Direct |
56529,56529 56529 - FAH 56529 - FAH | 0 | Direct |
54966,51649 54966 - RuBisCO, large subunit, small (N-terminal) domain 51649 - RuBisCo, C-terminal domain | 0 | Direct |
52317,51366 52317 - Class I glutamine amidotransferase-like 51366 - Ribulose-phoshate binding barrel | 0 | Direct |
52507,102645 52507 - Homo-oligomeric flavin-containing Cys decarboxylases, HFCD 102645 - CoaB-like | 0 | Direct |
53271,51366 53271 - PRTase-like 51366 - Ribulose-phoshate binding barrel | 0 | Direct |
52467,52518 52467 - DHS-like NAD/FAD-binding domain 52518 - Thiamin diphosphate-binding fold (THDP-binding) | 0.00000007255 | Direct |
52518,52467 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52467 - DHS-like NAD/FAD-binding domain | 0.0000001048 | Direct |
56059,51246 56059 - Glutathione synthetase ATP-binding domain-like 51246 - Rudiment single hybrid motif | 0.003885 | Inherited |
54211,55060 54211 - Ribosomal protein S5 domain 2-like 55060 - GHMP Kinase, C-terminal domain | 0.6185 | Inherited |
52518,52518 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52518 - Thiamin diphosphate-binding fold (THDP-binding) | 0.6718 | 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) |
56059,51246,52255 56059 - Glutathione synthetase ATP-binding domain-like 51246 - Rudiment single hybrid motif 52255 - N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | 0 | DIRECT |
52317,51366,51366 52317 - Class I glutamine amidotransferase-like 51366 - Ribulose-phoshate binding barrel 51366 - Ribulose-phoshate binding barrel | 0 | DIRECT |
52172,53383,55904 52172 - CheY-like 53383 - PLP-dependent transferases 55904 - Ornithine decarboxylase C-terminal domain | 0 | DIRECT |
52518,52467,52518 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52467 - DHS-like NAD/FAD-binding domain 52518 - Thiamin diphosphate-binding fold (THDP-binding) | 0.0000001048 | DIRECT |
52440,56059,51246 52440 - PreATP-grasp domain 56059 - Glutathione synthetase ATP-binding domain-like 51246 - Rudiment single hybrid motif | 0.003744 | INHERITED FROM: Phosphoribosylaminoimidazole carboxylase |
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
56059,51246,52255 56059 - Glutathione synthetase ATP-binding domain-like 51246 - Rudiment single hybrid motif 52255 - N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | 0 | Direct |
52317,51366,51366 52317 - Class I glutamine amidotransferase-like 51366 - Ribulose-phoshate binding barrel 51366 - Ribulose-phoshate binding barrel | 0 | Direct |
52172,53383,55904 52172 - CheY-like 53383 - PLP-dependent transferases 55904 - Ornithine decarboxylase C-terminal domain | 0 | Direct |
52518,52467,52518 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52467 - DHS-like NAD/FAD-binding domain 52518 - Thiamin diphosphate-binding fold (THDP-binding) | 0.0000001048 | Direct |
52440,56059,51246 52440 - PreATP-grasp domain 56059 - Glutathione synthetase ATP-binding domain-like 51246 - Rudiment single hybrid motif | 0.003744 | Inherited |
Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term
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A presence/absence matrix is generated using protein domains and supradomains
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