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Yeast Phenotype (YP): metabolism and growth
(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: YP Hierarchy (yeast phenotype from Ascomycete phenotype ontology)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Superfamily(show details)
Superfamily domains annotated to this YP term (SDYP level: Least Informative)
Highlighted in gray are those with FDR_all>0.001
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| FAD-linked oxidoreductase | 0 | DIRECT |
| F1F0 ATP synthase subunit C | 0 | DIRECT |
| Formate/glycerate dehydrogenase catalytic domain-like | 0 | DIRECT |
| The spindle assembly checkpoint protein mad2 | 0 | DIRECT |
| S13-like H2TH domain | 0 | DIRECT |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 0 | DIRECT |
| YAP1 redox domain | 0 | DIRECT |
| Periplasmic binding protein-like II | 0 | DIRECT |
| HRDC-like | 0 | DIRECT |
| Seven-hairpin glycosidases | 0 | DIRECT |
| Chromo domain-like | 0 | DIRECT |
| Fe,Mn superoxide dismutase (SOD), C-terminal domain | 0 | DIRECT |
| FAD-linked oxidases, C-terminal domain | 0 | DIRECT |
| SAP domain | 0 | DIRECT |
| PLP-binding barrel | 0 | DIRECT |
| Tubulin C-terminal domain-like | 0 | DIRECT |
| Nucleotide-binding domain | 0 | DIRECT |
| DNA-glycosylase | 0 | DIRECT |
| Cupredoxins | 0 | DIRECT |
| HLH, helix-loop-helix DNA-binding domain | 0 | DIRECT |
| Endosomal sorting complex assembly domain | 0 | DIRECT |
| HMA, heavy metal-associated domain | 0 | DIRECT |
| Ribosomal protein S2 | 0 | DIRECT |
| SAM/Pointed domain | 0 | DIRECT |
| Ribosomal protein L14 | 0 | DIRECT |
| GYF domain | 0 | DIRECT |
| SAICAR synthase-like | 0 | DIRECT |
| DNA repair protein MutS, domain II | 0 | DIRECT |
| YVTN repeat-like/Quinoprotein amine dehydrogenase | 0 | DIRECT |
| Ras GEF | 0 | DIRECT |
| tRNA-binding arm | 0 | DIRECT |
| Ribosomal protein S8 | 0 | DIRECT |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
| Prefoldin | 0 | DIRECT |
| Actin depolymerizing proteins | 0 | DIRECT |
| FAD-binding/transporter-associated domain-like | 0 | DIRECT |
| Subtilisin-like | 0 | DIRECT |
| Pseudouridine synthase | 0 | DIRECT |
| Helical domain of Sec23/24 | 0 | DIRECT |
| FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0 | DIRECT |
| Ammonium transporter | 0 | DIRECT |
| Ribosomal L11/L12e N-terminal domain | 0 | DIRECT |
| C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
| Methylglyoxal synthase-like | 0 | DIRECT |
| Tubulin nucleotide-binding domain-like | 0 | DIRECT |
| CheY-like | 0 | DIRECT |
| PAP/OAS1 substrate-binding domain | 0 | DIRECT |
| Phospholipase D/nuclease | 0 | DIRECT |
| FtsH protease domain-like | 0 | DIRECT |
| HSP40/DnaJ peptide-binding domain | 0 | DIRECT |
| 4'-phosphopantetheinyl transferase | 0 | DIRECT |
| AMPKBI-like | 0 | DIRECT |
| Ribosomal protein L11, C-terminal domain | 0 | DIRECT |
| DnaJ/Hsp40 cysteine-rich domain | 0 | DIRECT |
| Ribosomal protein L13 | 0 | DIRECT |
| Cytochrome c | 0 | DIRECT |
| beta-sandwich domain of Sec23/24 | 0 | DIRECT |
| Ribosomal protein L6 | 0 | DIRECT |
| PLC-like phosphodiesterases | 0 | DIRECT |
| RNase III domain-like | 0 | DIRECT |
| Mitochondrial carrier | 0.00005139 | DIRECT |
| Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 0.03513 | INHERITED FROM: utilization of nitrogen source |
| EF-G C-terminal domain-like | 0.1352 | INHERITED FROM: mitochondrial genome maintenance |
| Protein kinase-like (PK-like) | 0.1826 | INHERITED FROM: protein/peptide modification |
| Ubiquitin-like | 0.1854 | INHERITED FROM: protein/peptide accumulation |
| S-adenosyl-L-methionine-dependent methyltransferases | 0.2032 | INHERITED FROM: RNA modification |
| PreATP-grasp domain | 0.2097 | INHERITED FROM: utilization of nitrogen source |
| TK C-terminal domain-like | 0.252 | INHERITED FROM: utilization of nitrogen source |
| Glutathione synthetase ATP-binding domain-like | 0.3189 | INHERITED FROM: utilization of nitrogen source |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | 0.4224 | INHERITED FROM: utilization of nitrogen source |
| ARM repeat | 0.4541 | INHERITED FROM: protein/peptide distribution |
| Nucleotidyltransferase | 0.5144 | INHERITED FROM: RNA accumulation |
| Class II aaRS and biotin synthetases | 0.5217 | INHERITED FROM: respiratory growth || mitochondrial genome maintenance || respiratory metabolism |
| NAD(P)-binding Rossmann-fold domains | 0.7306 | INHERITED FROM: utilization of nitrogen source |
| MFS general substrate transporter | 0.7796 | INHERITED FROM: nutrient uptake |
| Nucleotidylyl transferase | 0.9548 | INHERITED FROM: mitochondrial genome maintenance |
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| FAD-linked oxidoreductase | 0 | Direct |
| F1F0 ATP synthase subunit C | 0 | Direct |
| Formate/glycerate dehydrogenase catalytic domain-like | 0 | Direct |
| The spindle assembly checkpoint protein mad2 | 0 | Direct |
| S13-like H2TH domain | 0 | Direct |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 0 | Direct |
| YAP1 redox domain | 0 | Direct |
| Periplasmic binding protein-like II | 0 | Direct |
| HRDC-like | 0 | Direct |
| Seven-hairpin glycosidases | 0 | Direct |
| Chromo domain-like | 0 | Direct |
| Fe,Mn superoxide dismutase (SOD), C-terminal domain | 0 | Direct |
| FAD-linked oxidases, C-terminal domain | 0 | Direct |
| SAP domain | 0 | Direct |
| PLP-binding barrel | 0 | Direct |
| Tubulin C-terminal domain-like | 0 | Direct |
| Nucleotide-binding domain | 0 | Direct |
| DNA-glycosylase | 0 | Direct |
| Cupredoxins | 0 | Direct |
| HLH, helix-loop-helix DNA-binding domain | 0 | Direct |
| Endosomal sorting complex assembly domain | 0 | Direct |
| HMA, heavy metal-associated domain | 0 | Direct |
| Ribosomal protein S2 | 0 | Direct |
| SAM/Pointed domain | 0 | Direct |
| Ribosomal protein L14 | 0 | Direct |
| GYF domain | 0 | Direct |
| SAICAR synthase-like | 0 | Direct |
| DNA repair protein MutS, domain II | 0 | Direct |
| YVTN repeat-like/Quinoprotein amine dehydrogenase | 0 | Direct |
| Ras GEF | 0 | Direct |
| tRNA-binding arm | 0 | Direct |
| Ribosomal protein S8 | 0 | Direct |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
| Prefoldin | 0 | Direct |
| Actin depolymerizing proteins | 0 | Direct |
| FAD-binding/transporter-associated domain-like | 0 | Direct |
| Subtilisin-like | 0 | Direct |
| Pseudouridine synthase | 0 | Direct |
| Helical domain of Sec23/24 | 0 | Direct |
| FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0 | Direct |
| Ammonium transporter | 0 | Direct |
| Ribosomal L11/L12e N-terminal domain | 0 | Direct |
| C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
| Methylglyoxal synthase-like | 0 | Direct |
| Tubulin nucleotide-binding domain-like | 0 | Direct |
| CheY-like | 0 | Direct |
| PAP/OAS1 substrate-binding domain | 0 | Direct |
| Phospholipase D/nuclease | 0 | Direct |
| FtsH protease domain-like | 0 | Direct |
| HSP40/DnaJ peptide-binding domain | 0 | Direct |
| 4'-phosphopantetheinyl transferase | 0 | Direct |
| AMPKBI-like | 0 | Direct |
| Ribosomal protein L11, C-terminal domain | 0 | Direct |
| DnaJ/Hsp40 cysteine-rich domain | 0 | Direct |
| Ribosomal protein L13 | 0 | Direct |
| Cytochrome c | 0 | Direct |
| beta-sandwich domain of Sec23/24 | 0 | Direct |
| Ribosomal protein L6 | 0 | Direct |
| PLC-like phosphodiesterases | 0 | Direct |
| RNase III domain-like | 0 | Direct |
| Mitochondrial carrier | 0.00005139 | Direct |
| Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 0.03513 | Inherited |
| EF-G C-terminal domain-like | 0.1352 | Inherited |
| Protein kinase-like (PK-like) | 0.1826 | Inherited |
| Ubiquitin-like | 0.1854 | Inherited |
| S-adenosyl-L-methionine-dependent methyltransferases | 0.2032 | Inherited |
| PreATP-grasp domain | 0.2097 | Inherited |
| TK C-terminal domain-like | 0.252 | Inherited |
| Glutathione synthetase ATP-binding domain-like | 0.3189 | Inherited |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | 0.4224 | Inherited |
| ARM repeat | 0.4541 | Inherited |
| Nucleotidyltransferase | 0.5144 | Inherited |
| Class II aaRS and biotin synthetases | 0.5217 | Inherited |
| NAD(P)-binding Rossmann-fold domains | 0.7306 | Inherited |
| MFS general substrate transporter | 0.7796 | Inherited |
| Nucleotidylyl transferase | 0.9548 | Inherited |
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Family(show details)
Family domains annotated to this YP term (SDYP level: Least Informative)
Highlighted in gray are those with FDR_all>0.001
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| beta-sandwich domain of Sec23/24 | 0 | DIRECT |
| RecA protein-like (ATPase-domain) | 0 | DIRECT |
| Glucose 6-phosphate dehydrogenase-like | 0 | DIRECT |
| AMPKBI-like | 0 | DIRECT |
| FAD-linked oxidases, N-terminal domain | 0 | DIRECT |
| Serine carboxypeptidase-like | 0 | DIRECT |
| Phoshoinositide 3-kinase (PI3K), catalytic domain | 0 | DIRECT |
| FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0 | DIRECT |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 0 | DIRECT |
| Cofilin-like | 0 | DIRECT |
| RNB domain-like | 0 | DIRECT |
| CheY-related | 0 | DIRECT |
| Adenosine/AMP deaminase | 0 | DIRECT |
| C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
| Pseudouridine synthase I TruA | 0 | DIRECT |
| Formate/glycerate dehydrogenases, NAD-domain | 0 | DIRECT |
| Ribosomal protein S8 | 0 | DIRECT |
| HLH, helix-loop-helix DNA-binding domain | 0 | DIRECT |
| Multidomain cupredoxins | 0 | DIRECT |
| Ribosomal protein L14e | 0 | DIRECT |
| FabD-like | 0 | DIRECT |
| Ribosomal protein L14 | 0 | DIRECT |
| C-terminal domain of ribosomal protein L2 | 0 | DIRECT |
| Helical domain of Sec23/24 | 0 | DIRECT |
| SAP domain | 0 | DIRECT |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
| 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain | 0 | DIRECT |
| Ribosomal protein L6 | 0 | DIRECT |
| HSP40/DnaJ peptide-binding domain | 0 | DIRECT |
| Subtilases | 0 | DIRECT |
| FtsH protease domain-like | 0 | DIRECT |
| Prefoldin | 0 | DIRECT |
| Ribosomal protein L13 | 0 | DIRECT |
| Ribosomal protein S13 | 0 | DIRECT |
| Ammonium transporter | 0 | DIRECT |
| F1F0 ATP synthase subunit C | 0 | DIRECT |
| Formate/glycerate dehydrogenases, substrate-binding domain | 0 | DIRECT |
| HMA, heavy metal-associated domain | 0 | DIRECT |
| Ribosomal protein S2 | 0 | DIRECT |
| La domain | 0 | DIRECT |
| Myb/SANT domain | 0 | DIRECT |
| DnaJ/Hsp40 cysteine-rich domain | 0 | DIRECT |
| Ribosomal protein L11, C-terminal domain | 0 | DIRECT |
| NAD kinase-like | 0 | DIRECT |
| Class I alpha-1;2-mannosidase, catalytic domain | 0 | DIRECT |
| Tetrahydrofolate dehydrogenase/cyclohydrolase | 0 | DIRECT |
| Pseudouridine synthase RsuA/RluD | 0 | DIRECT |
| Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain | 0 | DIRECT |
| GYF domain | 0 | DIRECT |
| Vacuolar sorting protein domain | 0 | DIRECT |
| SAM (sterile alpha motif) domain | 0 | DIRECT |
| Ras GEF | 0 | DIRECT |
| Tryptophan biosynthesis enzymes | 0 | DIRECT |
| YAP1 redox domain | 0 | DIRECT |
| Ribosomal L11/L12e N-terminal domain | 0 | DIRECT |
| DJ-1/PfpI | 0 | DIRECT |
| Ran-binding domain | 0 | DIRECT |
| Phosphate binding protein-like | 0 | DIRECT |
| Mitochondrial carrier | 0.0001964 | DIRECT |
| Elongation factors | 0.02229 | INHERITED FROM: vegetative growth |
| Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain | 0.03159 | INHERITED FROM: utilization of nitrogen source |
| EF-G/eEF-2 domains III and V | 0.1222 | INHERITED FROM: mitochondrial genome maintenance |
| DNA polymerase I | 0.2278 | INHERITED FROM: protein/peptide accumulation |
| FYVE, a phosphatidylinositol-3-phosphate binding domain | 0.2278 | INHERITED FROM: protein/peptide modification || chemical compound excretion || protein/peptide distribution |
| BC ATP-binding domain-like | 0.2501 | INHERITED FROM: utilization of nitrogen source |
| BC N-terminal domain-like | 0.2501 | INHERITED FROM: utilization of nitrogen source |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | 0.3971 | INHERITED FROM: utilization of nitrogen source |
| Protein kinases, catalytic subunit | 0.4557 | INHERITED FROM: protein/peptide modification |
| Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | 0.5193 | INHERITED FROM: mitochondrial genome maintenance |
| Ubiquitin-related | 0.5552 | INHERITED FROM: protein/peptide accumulation |
| Class I glutamine amidotransferases (GAT) | 0.6317 | INHERITED FROM: utilization of nitrogen source |
| Class I aminoacyl-tRNA synthetases (RS), catalytic domain | 0.9321 | INHERITED FROM: mitochondrial genome maintenance |
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| beta-sandwich domain of Sec23/24 | 0 | Direct |
| RecA protein-like (ATPase-domain) | 0 | Direct |
| Glucose 6-phosphate dehydrogenase-like | 0 | Direct |
| AMPKBI-like | 0 | Direct |
| FAD-linked oxidases, N-terminal domain | 0 | Direct |
| Serine carboxypeptidase-like | 0 | Direct |
| Phoshoinositide 3-kinase (PI3K), catalytic domain | 0 | Direct |
| FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0 | Direct |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 0 | Direct |
| Cofilin-like | 0 | Direct |
| RNB domain-like | 0 | Direct |
| CheY-related | 0 | Direct |
| Adenosine/AMP deaminase | 0 | Direct |
| C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
| Pseudouridine synthase I TruA | 0 | Direct |
| Formate/glycerate dehydrogenases, NAD-domain | 0 | Direct |
| Ribosomal protein S8 | 0 | Direct |
| HLH, helix-loop-helix DNA-binding domain | 0 | Direct |
| Multidomain cupredoxins | 0 | Direct |
| Ribosomal protein L14e | 0 | Direct |
| FabD-like | 0 | Direct |
| Ribosomal protein L14 | 0 | Direct |
| C-terminal domain of ribosomal protein L2 | 0 | Direct |
| Helical domain of Sec23/24 | 0 | Direct |
| SAP domain | 0 | Direct |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
| 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain | 0 | Direct |
| Ribosomal protein L6 | 0 | Direct |
| HSP40/DnaJ peptide-binding domain | 0 | Direct |
| Subtilases | 0 | Direct |
| FtsH protease domain-like | 0 | Direct |
| Prefoldin | 0 | Direct |
| Ribosomal protein L13 | 0 | Direct |
| Ribosomal protein S13 | 0 | Direct |
| Ammonium transporter | 0 | Direct |
| F1F0 ATP synthase subunit C | 0 | Direct |
| Formate/glycerate dehydrogenases, substrate-binding domain | 0 | Direct |
| HMA, heavy metal-associated domain | 0 | Direct |
| Ribosomal protein S2 | 0 | Direct |
| La domain | 0 | Direct |
| Myb/SANT domain | 0 | Direct |
| DnaJ/Hsp40 cysteine-rich domain | 0 | Direct |
| Ribosomal protein L11, C-terminal domain | 0 | Direct |
| NAD kinase-like | 0 | Direct |
| Class I alpha-1;2-mannosidase, catalytic domain | 0 | Direct |
| Tetrahydrofolate dehydrogenase/cyclohydrolase | 0 | Direct |
| Pseudouridine synthase RsuA/RluD | 0 | Direct |
| Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain | 0 | Direct |
| GYF domain | 0 | Direct |
| Vacuolar sorting protein domain | 0 | Direct |
| SAM (sterile alpha motif) domain | 0 | Direct |
| Ras GEF | 0 | Direct |
| Tryptophan biosynthesis enzymes | 0 | Direct |
| YAP1 redox domain | 0 | Direct |
| Ribosomal L11/L12e N-terminal domain | 0 | Direct |
| DJ-1/PfpI | 0 | Direct |
| Ran-binding domain | 0 | Direct |
| Phosphate binding protein-like | 0 | Direct |
| Mitochondrial carrier | 0.0001964 | Direct |
| Elongation factors | 0.02229 | Inherited |
| Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain | 0.03159 | Inherited |
| EF-G/eEF-2 domains III and V | 0.1222 | Inherited |
| DNA polymerase I | 0.2278 | Inherited |
| FYVE, a phosphatidylinositol-3-phosphate binding domain | 0.2278 | Inherited |
| BC ATP-binding domain-like | 0.2501 | Inherited |
| BC N-terminal domain-like | 0.2501 | Inherited |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | 0.3971 | Inherited |
| Protein kinases, catalytic subunit | 0.4557 | Inherited |
| Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | 0.5193 | Inherited |
| Ubiquitin-related | 0.5552 | Inherited |
| Class I glutamine amidotransferases (GAT) | 0.6317 | Inherited |
| Class I aminoacyl-tRNA synthetases (RS), catalytic domain | 0.9321 | Inherited |
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term
 |
Plot tree as:
| |
Download Newick format tree:
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(show help)
Trees by TreeVector
A presence/absence matrix is generated using protein domain
architecture data for all genomes in SUPERFAMILY. The PAUP
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Supra-domain (including individual superfamily)
(show details)
Supra-domains annotated to this YP term (SPYP level: Least Informative)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Single) |
FDR (all) |
Annotation (direct or inherited) |
| RNase III domain-like | 0 | DIRECT |
| tRNA-binding arm | 0 | DIRECT |
| Pseudouridine synthase | 0 | DIRECT |
| SAICAR synthase-like | 0 | DIRECT |
| Formate/glycerate dehydrogenase catalytic domain-like | 0 | DIRECT |
| S13-like H2TH domain | 0 | DIRECT |
| Tubulin C-terminal domain-like | 0 | DIRECT |
| Fe,Mn superoxide dismutase (SOD), C-terminal domain | 0 | DIRECT |
| beta-sandwich domain of Sec23/24 | 0 | DIRECT |
| SAM/Pointed domain | 0 | DIRECT |
| The spindle assembly checkpoint protein mad2 | 0 | DIRECT |
| FtsH protease domain-like | 0 | DIRECT |
| FAD-binding/transporter-associated domain-like | 0 | DIRECT |
| Cupredoxins | 0 | DIRECT |
| Cytochrome c | 0 | DIRECT |
| HRDC-like | 0 | DIRECT |
| Phospholipase D/nuclease | 0 | DIRECT |
| DnaJ/Hsp40 cysteine-rich domain | 0 | DIRECT |
| Helical domain of Sec23/24 | 0 | DIRECT |
| CheY-like | 0 | DIRECT |
| Ribosomal L11/L12e N-terminal domain | 0 | DIRECT |
| DNA repair protein MutS, domain II | 0 | DIRECT |
| Nucleotide-binding domain | 0 | DIRECT |
| YAP1 redox domain | 0 | DIRECT |
| C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
| Seven-hairpin glycosidases | 0 | DIRECT |
| HMA, heavy metal-associated domain | 0 | DIRECT |
| Ribosomal protein S2 | 0 | DIRECT |
| SAP domain | 0 | DIRECT |
| Tubulin nucleotide-binding domain-like | 0 | DIRECT |
| YVTN repeat-like/Quinoprotein amine dehydrogenase | 0 | DIRECT |
| 4'-phosphopantetheinyl transferase | 0 | DIRECT |
| Chromo domain-like | 0 | DIRECT |
| Endosomal sorting complex assembly domain | 0 | DIRECT |
| Periplasmic binding protein-like II | 0 | DIRECT |
| PLC-like phosphodiesterases | 0 | DIRECT |
| FAD-linked oxidases, C-terminal domain | 0 | DIRECT |
| Ribosomal protein L6 | 0 | DIRECT |
| DNA-glycosylase | 0 | DIRECT |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
| Ras GEF | 0 | DIRECT |
| FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0 | DIRECT |
| AMPKBI-like | 0 | DIRECT |
| GYF domain | 0 | DIRECT |
| Ribosomal protein L13 | 0 | DIRECT |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 0 | DIRECT |
| Ribosomal protein L14 | 0 | DIRECT |
| HLH, helix-loop-helix DNA-binding domain | 0 | DIRECT |
| Subtilisin-like | 0 | DIRECT |
| Prefoldin | 0 | DIRECT |
| PLP-binding barrel | 0 | DIRECT |
| Ammonium transporter | 0 | DIRECT |
| Ribosomal protein L11, C-terminal domain | 0 | DIRECT |
| Ribosomal protein S8 | 0 | DIRECT |
| Actin depolymerizing proteins | 0 | DIRECT |
| FAD-linked oxidoreductase | 0 | DIRECT |
| HSP40/DnaJ peptide-binding domain | 0 | DIRECT |
| Methylglyoxal synthase-like | 0 | DIRECT |
| F1F0 ATP synthase subunit C | 0 | DIRECT |
| PAP/OAS1 substrate-binding domain | 0 | DIRECT |
| Mitochondrial carrier | 0.0000421 | DIRECT |
| Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 0.03076 | INHERITED FROM: utilization of nitrogen source |
| EF-G C-terminal domain-like | 0.1234 | INHERITED FROM: mitochondrial genome maintenance |
| Protein kinase-like (PK-like) | 0.169 | INHERITED FROM: protein/peptide modification |
| Ubiquitin-like | 0.1719 | INHERITED FROM: protein/peptide accumulation |
| S-adenosyl-L-methionine-dependent methyltransferases | 0.1894 | INHERITED FROM: RNA modification |
| PreATP-grasp domain | 0.1956 | INHERITED FROM: utilization of nitrogen source |
| TK C-terminal domain-like | 0.237 | INHERITED FROM: utilization of nitrogen source |
| Glutathione synthetase ATP-binding domain-like | 0.3031 | INHERITED FROM: utilization of nitrogen source |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | 0.4041 | INHERITED FROM: utilization of nitrogen source |
| ARM repeat | 0.4368 | INHERITED FROM: protein/peptide distribution |
| Nucleotidyltransferase | 0.4985 | INHERITED FROM: RNA accumulation |
| Class II aaRS and biotin synthetases | 0.5058 | INHERITED FROM: mitochondrial genome maintenance || respiratory metabolism || respiratory growth |
| Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor | 0.6046 | INHERITED FROM: protein/peptide distribution |
| NAD(P)-binding Rossmann-fold domains | 0.7193 | INHERITED FROM: utilization of nitrogen source |
| MFS general substrate transporter | 0.7696 | INHERITED FROM: nutrient uptake |
| Nucleotidylyl transferase | 0.9496 | INHERITED FROM: mitochondrial genome maintenance |
| Supra-domain (Single) |
FDR (all) |
Annotation (direct or inherited) |
| RNase III domain-like | 0 | Direct |
| tRNA-binding arm | 0 | Direct |
| Pseudouridine synthase | 0 | Direct |
| SAICAR synthase-like | 0 | Direct |
| Formate/glycerate dehydrogenase catalytic domain-like | 0 | Direct |
| S13-like H2TH domain | 0 | Direct |
| Tubulin C-terminal domain-like | 0 | Direct |
| Fe,Mn superoxide dismutase (SOD), C-terminal domain | 0 | Direct |
| beta-sandwich domain of Sec23/24 | 0 | Direct |
| SAM/Pointed domain | 0 | Direct |
| The spindle assembly checkpoint protein mad2 | 0 | Direct |
| FtsH protease domain-like | 0 | Direct |
| FAD-binding/transporter-associated domain-like | 0 | Direct |
| Cupredoxins | 0 | Direct |
| Cytochrome c | 0 | Direct |
| HRDC-like | 0 | Direct |
| Phospholipase D/nuclease | 0 | Direct |
| DnaJ/Hsp40 cysteine-rich domain | 0 | Direct |
| Helical domain of Sec23/24 | 0 | Direct |
| CheY-like | 0 | Direct |
| Ribosomal L11/L12e N-terminal domain | 0 | Direct |
| DNA repair protein MutS, domain II | 0 | Direct |
| Nucleotide-binding domain | 0 | Direct |
| YAP1 redox domain | 0 | Direct |
| C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
| Seven-hairpin glycosidases | 0 | Direct |
| HMA, heavy metal-associated domain | 0 | Direct |
| Ribosomal protein S2 | 0 | Direct |
| SAP domain | 0 | Direct |
| Tubulin nucleotide-binding domain-like | 0 | Direct |
| YVTN repeat-like/Quinoprotein amine dehydrogenase | 0 | Direct |
| 4'-phosphopantetheinyl transferase | 0 | Direct |
| Chromo domain-like | 0 | Direct |
| Endosomal sorting complex assembly domain | 0 | Direct |
| Periplasmic binding protein-like II | 0 | Direct |
| PLC-like phosphodiesterases | 0 | Direct |
| FAD-linked oxidases, C-terminal domain | 0 | Direct |
| Ribosomal protein L6 | 0 | Direct |
| DNA-glycosylase | 0 | Direct |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
| Ras GEF | 0 | Direct |
| FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0 | Direct |
| AMPKBI-like | 0 | Direct |
| GYF domain | 0 | Direct |
| Ribosomal protein L13 | 0 | Direct |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 0 | Direct |
| Ribosomal protein L14 | 0 | Direct |
| HLH, helix-loop-helix DNA-binding domain | 0 | Direct |
| Subtilisin-like | 0 | Direct |
| Prefoldin | 0 | Direct |
| PLP-binding barrel | 0 | Direct |
| Ammonium transporter | 0 | Direct |
| Ribosomal protein L11, C-terminal domain | 0 | Direct |
| Ribosomal protein S8 | 0 | Direct |
| Actin depolymerizing proteins | 0 | Direct |
| FAD-linked oxidoreductase | 0 | Direct |
| HSP40/DnaJ peptide-binding domain | 0 | Direct |
| Methylglyoxal synthase-like | 0 | Direct |
| F1F0 ATP synthase subunit C | 0 | Direct |
| PAP/OAS1 substrate-binding domain | 0 | Direct |
| Mitochondrial carrier | 0.0000421 | Direct |
| Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 0.03076 | Inherited |
| EF-G C-terminal domain-like | 0.1234 | Inherited |
| Protein kinase-like (PK-like) | 0.169 | Inherited |
| Ubiquitin-like | 0.1719 | Inherited |
| S-adenosyl-L-methionine-dependent methyltransferases | 0.1894 | Inherited |
| PreATP-grasp domain | 0.1956 | Inherited |
| TK C-terminal domain-like | 0.237 | Inherited |
| Glutathione synthetase ATP-binding domain-like | 0.3031 | Inherited |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | 0.4041 | Inherited |
| ARM repeat | 0.4368 | Inherited |
| Nucleotidyltransferase | 0.4985 | Inherited |
| Class II aaRS and biotin synthetases | 0.5058 | Inherited |
| Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor | 0.6046 | Inherited |
| NAD(P)-binding Rossmann-fold domains | 0.7193 | Inherited |
| MFS general substrate transporter | 0.7696 | Inherited |
| Nucleotidylyl transferase | 0.9496 | Inherited |
(show details)
Supra-domains annotated to this YP term (SPYP level: Least Informative)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
52540,140990
52540 - P-loop containing nucleoside triphosphate hydrolases
140990 - FtsH protease domain-like | 0 | DIRECT |
56024,56024
56024 - Phospholipase D/nuclease
56024 - Phospholipase D/nuclease | 0 | DIRECT |
52490,55307
52490 - Tubulin nucleotide-binding domain-like
55307 - Tubulin C-terminal domain-like | 0 | DIRECT |
46689,46689
46689 - Homeodomain-like
46689 - Homeodomain-like | 0 | DIRECT |
56235,52402
56235 - N-terminal nucleophile aminohydrolases (Ntn hydrolases)
52402 - Adenine nucleotide alpha hydrolases-like | 0 | DIRECT |
56053,56053
56053 - Ribosomal protein L6
56053 - Ribosomal protein L6 | 0 | DIRECT |
49493,49493
49493 - HSP40/DnaJ peptide-binding domain
49493 - HSP40/DnaJ peptide-binding domain | 0 | DIRECT |
81301,81631
81301 - Nucleotidyltransferase
81631 - PAP/OAS1 substrate-binding domain | 0 | DIRECT |
81811,82754
81811 - Helical domain of Sec23/24
82754 - C-terminal, gelsolin-like domain of Sec23/24 | 0 | DIRECT |
50615,52540
50615 - N-terminal domain of alpha and beta subunits of F1 ATP synthase
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
50249,50104
50249 - Nucleic acid-binding proteins
50104 - Translation proteins SH3-like domain | 0 | DIRECT |
46565,57938
46565 - Chaperone J-domain
57938 - DnaJ/Hsp40 cysteine-rich domain | 0 | DIRECT |
81995,82919
81995 - beta-sandwich domain of Sec23/24
82919 - Zn-finger domain of Sec23/24 | 0 | DIRECT |
49879,56112
49879 - SMAD/FHA domain
56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
88723,47807
88723 - PIN domain-like
47807 - 5' to 3' exonuclease, C-terminal subdomain | 0 | DIRECT |
52283,51735
52283 - Formate/glycerate dehydrogenase catalytic domain-like
51735 - NAD(P)-binding Rossmann-fold domains | 0 | DIRECT |
57701,57959
57701 - Zn2/Cys6 DNA-binding domain
57959 - Leucine zipper domain | 0 | DIRECT |
51905,56425
51905 - FAD/NAD(P)-binding domain
56425 - Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 0 | DIRECT |
56176,55103
56176 - FAD-binding/transporter-associated domain-like
55103 - FAD-linked oxidases, C-terminal domain | 0 | DIRECT |
57938,49493
57938 - DnaJ/Hsp40 cysteine-rich domain
49493 - HSP40/DnaJ peptide-binding domain | 0 | DIRECT |
54791,54791
54791 - Eukaryotic type KH-domain (KH-domain type I)
54791 - Eukaryotic type KH-domain (KH-domain type I) | 0 | DIRECT |
52540,47917
52540 - P-loop containing nucleoside triphosphate hydrolases
47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
54747,46906
54747 - Ribosomal L11/L12e N-terminal domain
46906 - Ribosomal protein L11, C-terminal domain | 0 | DIRECT |
51905,55424
51905 - FAD/NAD(P)-binding domain
55424 - FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0 | DIRECT |
49503,49503
49503 - Cupredoxins
49503 - Cupredoxins | 0 | DIRECT |
81333,81333
81333 - F1F0 ATP synthase subunit C
81333 - F1F0 ATP synthase subunit C | 0 | DIRECT |
103657,50729
103657 - BAR/IMD domain-like
50729 - PH domain-like | 0 | DIRECT |
53150,48334
53150 - DNA repair protein MutS, domain II
48334 - DNA repair protein MutS, domain III | 0 | DIRECT |
54897,52743
54897 - Protease propeptides/inhibitors
52743 - Subtilisin-like | 0 | DIRECT |
52540,53254
52540 - P-loop containing nucleoside triphosphate hydrolases
53254 - Phosphoglycerate mutase-like | 0 | DIRECT |
51735,55347
51735 - NAD(P)-binding Rossmann-fold domains
55347 - Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 0.03076 | INHERITED FROM: utilization of nitrogen source |
53067,53067
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain | 0.1911 | INHERITED FROM: growth in exponential phase |
52440,56059
52440 - PreATP-grasp domain
56059 - Glutathione synthetase ATP-binding domain-like | 0.2515 | INHERITED FROM: utilization of nitrogen source |
50249,55681
50249 - Nucleic acid-binding proteins
55681 - Class II aaRS and biotin synthetases | 0.4985 | INHERITED FROM: respiratory growth |
52540,-9
52540 - P-loop containing nucleoside triphosphate hydrolases
-9 - PDB | 0.7486 | INHERITED FROM: protein/peptide accumulation |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
52540,140990
52540 - P-loop containing nucleoside triphosphate hydrolases
140990 - FtsH protease domain-like | 0 | Direct |
56024,56024
56024 - Phospholipase D/nuclease
56024 - Phospholipase D/nuclease | 0 | Direct |
52490,55307
52490 - Tubulin nucleotide-binding domain-like
55307 - Tubulin C-terminal domain-like | 0 | Direct |
46689,46689
46689 - Homeodomain-like
46689 - Homeodomain-like | 0 | Direct |
56235,52402
56235 - N-terminal nucleophile aminohydrolases (Ntn hydrolases)
52402 - Adenine nucleotide alpha hydrolases-like | 0 | Direct |
56053,56053
56053 - Ribosomal protein L6
56053 - Ribosomal protein L6 | 0 | Direct |
49493,49493
49493 - HSP40/DnaJ peptide-binding domain
49493 - HSP40/DnaJ peptide-binding domain | 0 | Direct |
81301,81631
81301 - Nucleotidyltransferase
81631 - PAP/OAS1 substrate-binding domain | 0 | Direct |
81811,82754
81811 - Helical domain of Sec23/24
82754 - C-terminal, gelsolin-like domain of Sec23/24 | 0 | Direct |
50615,52540
50615 - N-terminal domain of alpha and beta subunits of F1 ATP synthase
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
50249,50104
50249 - Nucleic acid-binding proteins
50104 - Translation proteins SH3-like domain | 0 | Direct |
46565,57938
46565 - Chaperone J-domain
57938 - DnaJ/Hsp40 cysteine-rich domain | 0 | Direct |
81995,82919
81995 - beta-sandwich domain of Sec23/24
82919 - Zn-finger domain of Sec23/24 | 0 | Direct |
49879,56112
49879 - SMAD/FHA domain
56112 - Protein kinase-like (PK-like) | 0 | Direct |
88723,47807
88723 - PIN domain-like
47807 - 5' to 3' exonuclease, C-terminal subdomain | 0 | Direct |
52283,51735
52283 - Formate/glycerate dehydrogenase catalytic domain-like
51735 - NAD(P)-binding Rossmann-fold domains | 0 | Direct |
57701,57959
57701 - Zn2/Cys6 DNA-binding domain
57959 - Leucine zipper domain | 0 | Direct |
51905,56425
51905 - FAD/NAD(P)-binding domain
56425 - Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 0 | Direct |
56176,55103
56176 - FAD-binding/transporter-associated domain-like
55103 - FAD-linked oxidases, C-terminal domain | 0 | Direct |
57938,49493
57938 - DnaJ/Hsp40 cysteine-rich domain
49493 - HSP40/DnaJ peptide-binding domain | 0 | Direct |
54791,54791
54791 - Eukaryotic type KH-domain (KH-domain type I)
54791 - Eukaryotic type KH-domain (KH-domain type I) | 0 | Direct |
52540,47917
52540 - P-loop containing nucleoside triphosphate hydrolases
47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
54747,46906
54747 - Ribosomal L11/L12e N-terminal domain
46906 - Ribosomal protein L11, C-terminal domain | 0 | Direct |
51905,55424
51905 - FAD/NAD(P)-binding domain
55424 - FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0 | Direct |
49503,49503
49503 - Cupredoxins
49503 - Cupredoxins | 0 | Direct |
81333,81333
81333 - F1F0 ATP synthase subunit C
81333 - F1F0 ATP synthase subunit C | 0 | Direct |
103657,50729
103657 - BAR/IMD domain-like
50729 - PH domain-like | 0 | Direct |
53150,48334
53150 - DNA repair protein MutS, domain II
48334 - DNA repair protein MutS, domain III | 0 | Direct |
54897,52743
54897 - Protease propeptides/inhibitors
52743 - Subtilisin-like | 0 | Direct |
52540,53254
52540 - P-loop containing nucleoside triphosphate hydrolases
53254 - Phosphoglycerate mutase-like | 0 | Direct |
51735,55347
51735 - NAD(P)-binding Rossmann-fold domains
55347 - Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 0.03076 | Inherited |
53067,53067
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain | 0.1911 | Inherited |
52440,56059
52440 - PreATP-grasp domain
56059 - Glutathione synthetase ATP-binding domain-like | 0.2515 | Inherited |
50249,55681
50249 - Nucleic acid-binding proteins
55681 - Class II aaRS and biotin synthetases | 0.4985 | Inherited |
52540,-9
52540 - P-loop containing nucleoside triphosphate hydrolases
-9 - PDB | 0.7486 | Inherited |
(show details)
Supra-domains annotated to this YP term (SPYP level: Least Informative)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
46565,57938,49493
46565 - Chaperone J-domain
57938 - DnaJ/Hsp40 cysteine-rich domain
49493 - HSP40/DnaJ peptide-binding domain | 0 | DIRECT |
57938,49493,49493
57938 - DnaJ/Hsp40 cysteine-rich domain
49493 - HSP40/DnaJ peptide-binding domain
49493 - HSP40/DnaJ peptide-binding domain | 0 | DIRECT |
53150,48334,52540
53150 - DNA repair protein MutS, domain II
48334 - DNA repair protein MutS, domain III
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
48371,48371,48371
48371 - ARM repeat
48371 - ARM repeat
48371 - ARM repeat | 0 | DIRECT |
81995,82919,53300
81995 - beta-sandwich domain of Sec23/24
82919 - Zn-finger domain of Sec23/24
53300 - vWA-like | 0 | DIRECT |
49503,49503,49503
49503 - Cupredoxins
49503 - Cupredoxins
49503 - Cupredoxins | 0 | DIRECT |
50615,52540,47917
50615 - N-terminal domain of alpha and beta subunits of F1 ATP synthase
52540 - P-loop containing nucleoside triphosphate hydrolases
47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
46565,57938,49493
46565 - Chaperone J-domain
57938 - DnaJ/Hsp40 cysteine-rich domain
49493 - HSP40/DnaJ peptide-binding domain | 0 | Direct |
57938,49493,49493
57938 - DnaJ/Hsp40 cysteine-rich domain
49493 - HSP40/DnaJ peptide-binding domain
49493 - HSP40/DnaJ peptide-binding domain | 0 | Direct |
53150,48334,52540
53150 - DNA repair protein MutS, domain II
48334 - DNA repair protein MutS, domain III
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
48371,48371,48371
48371 - ARM repeat
48371 - ARM repeat
48371 - ARM repeat | 0 | Direct |
81995,82919,53300
81995 - beta-sandwich domain of Sec23/24
82919 - Zn-finger domain of Sec23/24
53300 - vWA-like | 0 | Direct |
49503,49503,49503
49503 - Cupredoxins
49503 - Cupredoxins
49503 - Cupredoxins | 0 | Direct |
50615,52540,47917
50615 - N-terminal domain of alpha and beta subunits of F1 ATP synthase
52540 - P-loop containing nucleoside triphosphate hydrolases
47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
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.
|
