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Phenotype Ontology
Like Gene Ontology (GO), phenotypy ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Phenotype ontologies we have incorporated are as follows:

• Disease Ontology (DO) Ontology (DO)
  DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI’s 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 (SPHP) 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:SPHP.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).
  

Superfamily domains annotated to this YP term (Not in SDYP)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
Tim10-like	0	DIRECT
Cytidine deaminase-like	0	DIRECT
ArfGap/RecO-like zinc finger	0	DIRECT
FMN-binding split barrel	0	DIRECT
Rudiment single hybrid motif	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
Cation efflux protein transmembrane domain-like	0	DIRECT
Ribosomal protein S8	0	DIRECT
EPT/RTPC-like	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
PR-1-like	0	DIRECT
Subtilisin-like	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
YAP1 redox domain	0	DIRECT
Rhodanese/Cell cycle control phosphatase	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Galactose-binding domain-like	0	DIRECT
Tropomyosin	0	DIRECT
The spindle assembly checkpoint protein mad2	0	DIRECT
LeuD/IlvD-like	0	DIRECT
WW domain	0	DIRECT
Galactose mutarotase-like	0	DIRECT
Ribosomal protein L14	0	DIRECT
EF-G C-terminal domain-like	0	DIRECT
Clathrin adaptor appendage domain	0	DIRECT
LDH C-terminal domain-like	0	DIRECT
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	0	DIRECT
L-aspartase-like	0	DIRECT
PH domain-like	0	DIRECT
Oxysterol-binding protein-like	0	DIRECT
GroEL-intermediate domain like	0	DIRECT
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	DIRECT
RCC1/BLIP-II	0	DIRECT
Ammonium transporter	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
Formate/glycerate dehydrogenase catalytic domain-like	0	DIRECT
Cupredoxins	0	DIRECT
Carbohydrate phosphatase	0	DIRECT
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	0	DIRECT
Activating enzymes of the ubiquitin-like proteins	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
SAP domain	0	DIRECT
Prefoldin	0	DIRECT
Nudix	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
Glutathione synthetase ATP-binding domain-like	0	DIRECT
FabD/lysophospholipase-like	0	DIRECT
Pseudouridine synthase	0	DIRECT
PP2C-like	0	DIRECT
Cytochrome P450	0	DIRECT
Oligoxyloglucan reducing end-specific cellobiohydrolase	0	DIRECT
4'-phosphopantetheinyl transferase	0	DIRECT
NAD kinase/diacylglycerol kinase-like	0	DIRECT
PLP-binding barrel	0	DIRECT
ClpP/crotonase	0	DIRECT
DPP6 N-terminal domain-like	0	DIRECT
DNA ligase/mRNA capping enzyme, catalytic domain	0	DIRECT
Trimeric LpxA-like enzymes	0	DIRECT
Mitochondrial cytochrome c oxidase subunit IV	0	DIRECT
Protease propeptides/inhibitors	0	DIRECT
HLH, helix-loop-helix DNA-binding domain	0	DIRECT
Ferritin-like	0	DIRECT
PriA/YqbF domain	0	DIRECT
Endosomal sorting complex assembly domain	0	DIRECT
Glucocorticoid receptor-like (DNA-binding domain)	0	DIRECT
Ribokinase-like	0	DIRECT
HD-domain/PDEase-like	0	DIRECT
HMG-box	0	DIRECT
ValRS/IleRS/LeuRS editing domain	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
HSP20-like chaperones	0	DIRECT
HRDC-like	0	DIRECT
Ribosomal protein L22	0	DIRECT
FKBP-like	0	DIRECT
DNA repair protein MutS, domain II	0	DIRECT
GYF domain	0	DIRECT
Methylglyoxal synthase-like	0	DIRECT
VPS9 domain	0	DIRECT
KA1-like	0	DIRECT
Alpha-L RNA-binding motif	0	DIRECT
Hect, E3 ligase catalytic domain	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
Multidrug resistance efflux transporter EmrE	0	DIRECT
PLC-like phosphodiesterases	0	DIRECT
Tubulin nucleotide-binding domain-like	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
GroEL apical domain-like	0	DIRECT
Fumarate reductase respiratory complex transmembrane subunits	0	DIRECT
Protein prenylyltransferase	0	DIRECT
Glutamine synthetase/guanido kinase	0	DIRECT
PEBP-like	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
Clavaminate synthase-like	0	DIRECT
DNA-glycosylase	0	DIRECT
HIT/MYND zinc finger-like	0	DIRECT
Smc hinge domain	0	DIRECT
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	0	DIRECT
Quinoprotein alcohol dehydrogenase-like	0	DIRECT
DNase I-like	0	DIRECT
Tricorn protease domain 2	0	DIRECT
GHMP Kinase, C-terminal domain	0	DIRECT
Ras GEF	0	DIRECT
Zinc domain conserved in yeast copper-regulated transcription factors	0	DIRECT
Heme oxygenase-like	0	DIRECT
Chromo domain-like	0	DIRECT
post-AAA+ oligomerization domain-like	0	DIRECT
Family A G protein-coupled receptor-like	0	DIRECT
Nucleoporin domain	0	DIRECT
Rhomboid-like	0	DIRECT
HMA, heavy metal-associated domain	0	DIRECT
Radical SAM enzymes	0	DIRECT
Calponin-homology domain, CH-domain	0	DIRECT
YjgF-like	0	DIRECT
Thioesterase/thiol ester dehydrase-isomerase	0	DIRECT
FAD-linked oxidases, C-terminal domain	0	DIRECT
Nucleotide-binding domain	0	DIRECT
PA domain	0	DIRECT
CorA soluble domain-like	0	DIRECT
L domain-like	0	DIRECT
t-snare proteins	0	DIRECT
GST C-terminal domain-like	0	DIRECT
PYP-like sensor domain (PAS domain)	0	DIRECT
Restriction endonuclease-like	0	DIRECT
FAD-linked reductases, C-terminal domain	0	DIRECT
Tubulin C-terminal domain-like	0	DIRECT
Ribosomal protein L13	0	DIRECT
Carbamate kinase-like	0	DIRECT
RNI-like	0	DIRECT
DNA repair protein MutS, domain III	0	DIRECT
AMPKBI-like	0	DIRECT
Transferrin receptor-like dimerisation domain	0	DIRECT
GAT-like domain	0	DIRECT
MurD-like peptide ligases, peptide-binding domain	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Ribosomal protein L6	0	DIRECT
Cullin homology domain	0	DIRECT
ThrRS/AlaRS common domain	0	DIRECT
eIF1-like	0	DIRECT
RBP11-like subunits of RNA polymerase	0	DIRECT
Alkaline phosphatase-like	0	DIRECT
Cytochrome b5-like heme/steroid binding domain	0	DIRECT
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
Homo-oligomeric flavin-containing Cys decarboxylases, HFCD	0	DIRECT
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	DIRECT
Zinc beta-ribbon	0	DIRECT
ACT-like	0	DIRECT
Isocitrate/Isopropylmalate dehydrogenase-like	0	DIRECT
Nop domain	0	DIRECT
NagB/RpiA/CoA transferase-like	0	DIRECT
PAP/OAS1 substrate-binding domain	0	DIRECT
HSP40/DnaJ peptide-binding domain	0	DIRECT
S13-like H2TH domain	0	DIRECT
Ankyrin repeat	0	DIRECT
Concanavalin A-like lectins/glucanases	0	DIRECT
Phospholipase D/nuclease	0	DIRECT
Tryptophan synthase beta subunit-like PLP-dependent enzymes	0	DIRECT
post-HMGL domain-like	0	DIRECT
ABC transporter transmembrane region	0	DIRECT
beta-beta-alpha zinc fingers	0	DIRECT
GINS helical bundle-like	0	DIRECT
Amidase signature (AS) enzymes	0	DIRECT
SRF-like	0	DIRECT
GroEL equatorial domain-like	0	DIRECT
Sialidases	0	DIRECT
Acid proteases	0	DIRECT
CheY-like	0	DIRECT
FtsH protease domain-like	0	DIRECT
Translational machinery components	0	DIRECT
F1F0 ATP synthase subunit C	0	DIRECT
MurD-like peptide ligases, catalytic domain	0	DIRECT
Six-hairpin glycosidases	0	DIRECT
PreATP-grasp domain	0	DIRECT
GTPase activation domain, GAP	0	DIRECT
Ubiquitin-like	0	DIRECT
Aldolase	0	DIRECT
DnaJ/Hsp40 cysteine-rich domain	0	DIRECT
UBA-like	0	DIRECT
Ypt/Rab-GAP domain of gyp1p	0	DIRECT
FAD-linked oxidoreductase	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Thiolase-like	0	DIRECT
Cap-Gly domain	0	DIRECT
Kelch motif	0	DIRECT
R3H domain	0	DIRECT
TGS-like	0	DIRECT
Aquaporin-like	0	DIRECT
Cytochrome c	0	DIRECT
Sec63 N-terminal domain-like	0	DIRECT
(Phosphotyrosine protein) phosphatases II	0	DIRECT
tRNA-intron endonuclease catalytic domain-like	0	DIRECT
Regulator of G-protein signaling, RGS	0	DIRECT
Phosphoenolpyruvate/pyruvate domain	0	DIRECT
Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
Citrate synthase	0	DIRECT
CCCH zinc finger	0	DIRECT
SpoIIaa-like	0	DIRECT
DNA-binding domain of Mlu1-box binding protein MBP1	0	DIRECT
Actin depolymerizing proteins	0	DIRECT
Nucleotidyltransferase	0	DIRECT
Metallo-dependent hydrolases	0	DIRECT
Cullin repeat-like	0	DIRECT
Mss4-like	0	DIRECT
Metallo-dependent phosphatases	0.2916	INHERITED FROM: viability

Family domains annotated to this YP term (Not in SDYP)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
Ribosomal protein L13	0	DIRECT
Oxysterol-binding protein	0	DIRECT
DnaQ-like 3'-5' exonuclease	0	DIRECT
Ribokinase-like	0	DIRECT
SAP domain	0	DIRECT
Cyclin	0	DIRECT
WW domain	0	DIRECT
TENA/THI-4	0	DIRECT
Glutathione S-transferase (GST), N-terminal domain	0	DIRECT
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain	0	DIRECT
FabD-like	0	DIRECT
GAPDH-like	0	DIRECT
Dual specificity phosphatase-like	0	DIRECT
VPS9 domain	0	DIRECT
Inositol monophosphatase/fructose-1,6-bisphosphatase-like	0	DIRECT
ABC transporter transmembrane region	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Ras GEF	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
Forkhead DNA-binding domain	0	DIRECT
HLH, helix-loop-helix DNA-binding domain	0	DIRECT
HSP40/DnaJ peptide-binding domain	0	DIRECT
HMGL-like	0	DIRECT
Glycolipid 2-alpha-mannosyltransferase	0	DIRECT
Vacuolar sorting protein domain	0	DIRECT
C-terminal domain of ribosomal protein L2	0	DIRECT
Motor proteins	0	DIRECT
Hect, E3 ligase catalytic domain	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
VHS domain	0	DIRECT
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	DIRECT
Histidine acid phosphatase	0	DIRECT
RuBisCo LSMT catalytic domain	0	DIRECT
Ribosomal protein S8	0	DIRECT
PR-1-like	0	DIRECT
Ribosomal protein L14	0	DIRECT
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	0	DIRECT
YAP1 redox domain	0	DIRECT
Ubiquitin-related	0	DIRECT
Ribosomal protein S13	0	DIRECT
Erythroid transcription factor GATA-1	0	DIRECT
Lysophospholipase	0	DIRECT
Choline/Carnitine O-acyltransferase	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
Group II chaperonin (CCT, TRIC), ATPase domain	0	DIRECT
RecA protein-like (ATPase-domain)	0	DIRECT
AMPK-beta glycogen binding domain-like	0	DIRECT
TBP-associated factors, TAFs	0	DIRECT
DNA gyrase/MutL, N-terminal domain	0	DIRECT
Subtilase propeptides/inhibitors	0	DIRECT
Pyruvate oxidase and decarboxylase PP module	0	DIRECT
Hexokinase	0	DIRECT
UBA domain	0	DIRECT
Phosphatidylethanolamine binding protein	0	DIRECT
Thiamin biosynthesis kinases	0	DIRECT
Single strand DNA-binding domain, SSB	0	DIRECT
GYF domain	0	DIRECT
RING finger domain, C3HC4	0	DIRECT
NADPH-cytochrome p450 reductase FAD-binding domain-like	0	DIRECT
DNA ligase/mRNA capping enzyme postcatalytic domain	0	DIRECT
Lactate & malate dehydrogenases, C-terminal domain	0	DIRECT
Transcriptional factor domain	0	DIRECT
FCH domain	0	DIRECT
Cullin homology domain	0	DIRECT
ALDH-like	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	0	DIRECT
Pseudouridine synthase RsuA/RluD	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
Class I alpha-1;2-mannosidase, catalytic domain	0	DIRECT
Pyk2-associated protein beta ARF-GAP domain	0	DIRECT
Group II chaperonin (CCT, TRIC), intermediate domain	0	DIRECT
Homo-oligomeric flavin-containing Cys decarboxylases, HFCD	0	DIRECT
Heat-shock transcription factor	0	DIRECT
Zinc domain conserved in yeast copper-regulated transcription factors	0	DIRECT
LeuD-like	0	DIRECT
Bacteriorhodopsin-like	0	DIRECT
FYVE, a phosphatidylinositol-3-phosphate binding domain	0	DIRECT
Crotonase-like	0	DIRECT
Trehalose-6-phosphate synthase, OtsA	0	DIRECT
Ubiquitin activating enzymes (UBA)	0	DIRECT
NADPH-cytochrome p450 reductase-like	0	DIRECT
Cofilin-like	0	DIRECT
AMPKBI-like	0	DIRECT
Cytochrome b5	0	DIRECT
NAD kinase-like	0	DIRECT
PP2C-like	0	DIRECT
Pyruvate oxidase and decarboxylase Pyr module	0	DIRECT
PyrH-like	0	DIRECT
SWIRM domain	0	DIRECT
Glutathione S-transferase (GST), C-terminal domain	0	DIRECT
Ribosomal protein L18 and S11	0	DIRECT
NLI interacting factor-like phosphatase	0	DIRECT
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain	0	DIRECT
Translational machinery components	0	DIRECT
Ankyrin repeat	0	DIRECT
N-acetyl transferase, NAT	0	DIRECT
DNA-binding domain of Mlu1-box binding protein MBP1	0	DIRECT
tRNA-intron endonuclease catalytic domain-like	0	DIRECT
Tubulin, C-terminal domain	0	DIRECT
Formate/glycerate dehydrogenases, substrate-binding domain	0	DIRECT
Clathrin coat assembly domain	0	DIRECT
Prefoldin	0	DIRECT
Calponin-homology domain, CH-domain	0	DIRECT
Amidase signature (AS) enzymes	0	DIRECT
Leukotriene A4 hydrolase catalytic domain	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
TRAPP components	0	DIRECT
Class I aldolase	0	DIRECT
Tetratricopeptide repeat (TPR)	0	DIRECT
Thiolase-related	0	DIRECT
Serine carboxypeptidase-like	0	DIRECT
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	DIRECT
Citrate synthase	0	DIRECT
L-aspartase/fumarase	0	DIRECT
Multidomain cupredoxins	0	DIRECT
Smc hinge domain	0	DIRECT
PDI-like	0	DIRECT
Transferrin receptor-like dimerisation domain	0	DIRECT
Tryptophan synthase beta subunit-like PLP-dependent enzymes	0	DIRECT
Ribosomal protein S4	0	DIRECT
DNA polymerase III clamp loader subunits, C-terminal domain	0	DIRECT
Formate/glycerate dehydrogenases, NAD-domain	0	DIRECT
SCF ubiquitin ligase complex WHB domain	0	DIRECT
HMG-box	0	DIRECT
Pleckstrin-homology domain (PH domain)	0	DIRECT
Aldose 1-epimerase (mutarotase)	0	DIRECT
Glycosyl hydrolases family 16	0	DIRECT
Myb/SANT domain	0	DIRECT
RNA-polymerase beta-prime	0	DIRECT
Cytochrome P450	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
t-snare proteins	0	DIRECT
BC C-terminal domain-like	0	DIRECT
Pseudouridine synthase I TruA	0	DIRECT
IF2B-like	0	DIRECT
Subtilases	0	DIRECT
Eps15 homology domain (EH domain)	0	DIRECT
La domain	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
Ran-binding domain	0	DIRECT
Phosphoribulokinase/pantothenate kinase	0	DIRECT
BC N-terminal domain-like	0	DIRECT
Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain	0	DIRECT
DnaJ/Hsp40 cysteine-rich domain	0	DIRECT
Cation efflux protein transmembrane domain-like	0	DIRECT
RNB domain-like	0	DIRECT
PA domain	0	DIRECT
ValRS/IleRS/LeuRS editing domain	0	DIRECT
FKBP immunophilin/proline isomerase	0	DIRECT
Regulator of G-protein signaling, RGS	0	DIRECT
Aquaporin-like	0	DIRECT
Tropomyosin	0	DIRECT
DNA gyrase/MutL, second domain	0	DIRECT
Dimeric isocitrate & isopropylmalate dehydrogenases	0	DIRECT
EF-G/eEF-2 domains III and V	0	DIRECT
Glutathione peroxidase-like	0	DIRECT
GHMP Kinase, N-terminal domain	0	DIRECT
Pepsin-like	0	DIRECT
Cap-Gly domain	0	DIRECT
YjgF/L-PSP	0	DIRECT
eIF1-like	0	DIRECT
DNA repair protein MutS, domain III	0	DIRECT
Higher-molecular-weight phosphotyrosine protein phosphatases	0	DIRECT
Inositol polyphosphate 5-phosphatase (IPP5)	0	DIRECT
Gastric lipase	0	DIRECT
Deoxycytidylate deaminase-like	0	DIRECT
Tryptophan biosynthesis enzymes	0	DIRECT
Ribosomal protein L22	0	DIRECT
Adenosine/AMP deaminase	0	DIRECT
FtsH protease domain-like	0	DIRECT
Ammonium transporter	0	DIRECT
BCR-homology GTPase activation domain (BH-domain)	0	DIRECT
Tubulin, GTPase domain	0	DIRECT
LDH N-terminal domain-like	0	DIRECT
Nop domain	0	DIRECT
ENTH domain	0	DIRECT
Tim10/DDP	0	DIRECT
Protein serine/threonine phosphatase	0	DIRECT
NagB-like	0	DIRECT
Pyruvate oxidase and decarboxylase, middle domain	0	DIRECT
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	DIRECT
PX domain	0	DIRECT
NOL1/NOP2/sun	0	DIRECT
beta-glycanases	0	DIRECT
Pumilio repeat	0	DIRECT
HMA, heavy metal-associated domain	0	DIRECT
Cytochrome p450 reductase N-terminal domain-like	0	DIRECT
FAD-linked reductases, N-terminal domain	0	DIRECT
Glycosyl transferases group 1	0	DIRECT
p120GAP domain-like	0	DIRECT
SRF-like	0	DIRECT
RNA methyltransferase FtsJ	0	DIRECT
Folylpolyglutamate synthetase	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Group II chaperonin (CCT, TRIC), apical domain	0	DIRECT
Ribosomal protein L6	0	DIRECT
Classic zinc finger, C2H2	0	DIRECT
CheY-related	0	DIRECT
CorA soluble domain-like	0	DIRECT
CCCH zinc finger	0	DIRECT
XPF/Rad1/Mus81 nuclease	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Ypt/Rab-GAP domain of gyp1p	0	DIRECT
Aminoacid dehydrogenases	0	DIRECT
Glucose 6-phosphate dehydrogenase-like	0	DIRECT
BC ATP-binding domain-like	0	DIRECT
HCP-like	0	DIRECT

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.

Supra-domains annotated to this YP term (Not in SPYP)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
SAP domain	0	DIRECT
Ribosomal protein L22	0	DIRECT
L domain-like	0	DIRECT
GroEL equatorial domain-like	0	DIRECT
R3H domain	0	DIRECT
HIT/MYND zinc finger-like	0	DIRECT
F1F0 ATP synthase subunit C	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
HRDC-like	0	DIRECT
Nucleotidyltransferase	0	DIRECT
TGS-like	0	DIRECT
Glutathione synthetase ATP-binding domain-like	0	DIRECT
HMA, heavy metal-associated domain	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Heme oxygenase-like	0	DIRECT
YjgF-like	0	DIRECT
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	DIRECT
GYF domain	0	DIRECT
LeuD/IlvD-like	0	DIRECT
Sialidases	0	DIRECT
RBP11-like subunits of RNA polymerase	0	DIRECT
Zinc domain conserved in yeast copper-regulated transcription factors	0	DIRECT
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	0	DIRECT
Actin depolymerizing proteins	0	DIRECT
GroEL apical domain-like	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
PLP-binding barrel	0	DIRECT
Radical SAM enzymes	0	DIRECT
UBA-like	0	DIRECT
GAT-like domain	0	DIRECT
Zinc beta-ribbon	0	DIRECT
FKBP-like	0	DIRECT
Regulator of G-protein signaling, RGS	0	DIRECT
S13-like H2TH domain	0	DIRECT
DNase I-like	0	DIRECT
NagB/RpiA/CoA transferase-like	0	DIRECT
Rhomboid-like	0	DIRECT
GST C-terminal domain-like	0	DIRECT
Hect, E3 ligase catalytic domain	0	DIRECT
Rudiment single hybrid motif	0	DIRECT
PA domain	0	DIRECT
MurD-like peptide ligases, peptide-binding domain	0	DIRECT
Cullin repeat-like	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
Cupredoxins	0	DIRECT
Thiolase-like	0	DIRECT
Tubulin nucleotide-binding domain-like	0	DIRECT
Nop domain	0	DIRECT
ThrRS/AlaRS common domain	0	DIRECT
Cytidine deaminase-like	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
HD-domain/PDEase-like	0	DIRECT
beta-beta-alpha zinc fingers	0	DIRECT
PR-1-like	0	DIRECT
DPP6 N-terminal domain-like	0	DIRECT
DNA repair protein MutS, domain II	0	DIRECT
EPT/RTPC-like	0	DIRECT
Ammonium transporter	0	DIRECT
KA1-like	0	DIRECT
Oligoxyloglucan reducing end-specific cellobiohydrolase	0	DIRECT
FAD-linked oxidoreductase	0	DIRECT
Tropomyosin	0	DIRECT
Tubulin C-terminal domain-like	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
Six-hairpin glycosidases	0	DIRECT
Cytochrome b5-like heme/steroid binding domain	0	DIRECT
CCCH zinc finger	0	DIRECT
CorA soluble domain-like	0	DIRECT
Clavaminate synthase-like	0	DIRECT
Ribosomal protein L6	0	DIRECT
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Amidase signature (AS) enzymes	0	DIRECT
Subtilisin-like	0	DIRECT
VPS9 domain	0	DIRECT
NAD kinase/diacylglycerol kinase-like	0	DIRECT
PriA/YqbF domain	0	DIRECT
L-aspartase-like	0	DIRECT
FabD/lysophospholipase-like	0	DIRECT
HSP20-like chaperones	0	DIRECT
ArfGap/RecO-like zinc finger	0	DIRECT
Kelch motif	0	DIRECT
Trimeric LpxA-like enzymes	0	DIRECT
Nucleoporin domain	0	DIRECT
LDH C-terminal domain-like	0	DIRECT
Ribosomal protein L14	0	DIRECT
Calponin-homology domain, CH-domain	0	DIRECT
PAP/OAS1 substrate-binding domain	0	DIRECT
Mss4-like	0	DIRECT
WW domain	0	DIRECT
Protein prenylyltransferase	0	DIRECT
Carbohydrate phosphatase	0	DIRECT
Ypt/Rab-GAP domain of gyp1p	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
HMG-box	0	DIRECT
Alpha-L RNA-binding motif	0	DIRECT
Nucleotide-binding domain	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Quinoprotein alcohol dehydrogenase-like	0	DIRECT
SpoIIaa-like	0	DIRECT
Galactose mutarotase-like	0	DIRECT
Glucocorticoid receptor-like (DNA-binding domain)	0	DIRECT
AMPKBI-like	0	DIRECT
DNA-glycosylase	0	DIRECT
GHMP Kinase, C-terminal domain	0	DIRECT
Acid proteases	0	DIRECT
Aquaporin-like	0	DIRECT
PEBP-like	0	DIRECT
DNA repair protein MutS, domain III	0	DIRECT
Cap-Gly domain	0	DIRECT
Cytochrome P450	0	DIRECT
Clathrin adaptor appendage domain	0	DIRECT
Protease propeptides/inhibitors	0	DIRECT
t-snare proteins	0	DIRECT
ClpP/crotonase	0	DIRECT
DNA ligase/mRNA capping enzyme, catalytic domain	0	DIRECT
Pseudouridine synthase	0	DIRECT
Tricorn protease domain 2	0	DIRECT
Endosomal sorting complex assembly domain	0	DIRECT
Citrate synthase	0	DIRECT
Oxysterol-binding protein-like	0	DIRECT
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	0	DIRECT
GTPase activation domain, GAP	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
RCC1/BLIP-II	0	DIRECT
PLC-like phosphodiesterases	0	DIRECT
Ferritin-like	0	DIRECT
PYP-like sensor domain (PAS domain)	0	DIRECT
PH domain-like	0	DIRECT
Multidrug resistance efflux transporter EmrE	0	DIRECT
Family A G protein-coupled receptor-like	0	DIRECT
Galactose-binding domain-like	0	DIRECT
Restriction endonuclease-like	0	DIRECT
Cullin homology domain	0	DIRECT
SRF-like	0	DIRECT
Formate/glycerate dehydrogenase catalytic domain-like	0	DIRECT
Ubiquitin-like	0	DIRECT
Smc hinge domain	0	DIRECT
Phospholipase D/nuclease	0	DIRECT
Transferrin receptor-like dimerisation domain	0	DIRECT
Ribosomal protein S8	0	DIRECT
Ras GEF	0	DIRECT
Sec63 N-terminal domain-like	0	DIRECT
Isocitrate/Isopropylmalate dehydrogenase-like	0	DIRECT
Phosphoenolpyruvate/pyruvate domain	0	DIRECT
FAD-linked oxidases, C-terminal domain	0	DIRECT
(Phosphotyrosine protein) phosphatases II	0	DIRECT
DNA-binding domain of Mlu1-box binding protein MBP1	0	DIRECT
EF-G C-terminal domain-like	0	DIRECT
Ankyrin repeat	0	DIRECT
Fumarate reductase respiratory complex transmembrane subunits	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
Prefoldin	0	DIRECT
Activating enzymes of the ubiquitin-like proteins	0	DIRECT
GroEL-intermediate domain like	0	DIRECT
eIF1-like	0	DIRECT
HLH, helix-loop-helix DNA-binding domain	0	DIRECT
Carbamate kinase-like	0	DIRECT
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	0	DIRECT
DnaJ/Hsp40 cysteine-rich domain	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
The spindle assembly checkpoint protein mad2	0	DIRECT
ACT-like	0	DIRECT
FAD-linked reductases, C-terminal domain	0	DIRECT
Nudix	0	DIRECT
FMN-binding split barrel	0	DIRECT
Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
MurD-like peptide ligases, catalytic domain	0	DIRECT
Glutamine synthetase/guanido kinase	0	DIRECT
post-AAA+ oligomerization domain-like	0	DIRECT
FtsH protease domain-like	0	DIRECT
Tim10-like	0	DIRECT
RNI-like	0	DIRECT
PreATP-grasp domain	0	DIRECT
post-HMGL domain-like	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
Thioesterase/thiol ester dehydrase-isomerase	0	DIRECT
Cation efflux protein transmembrane domain-like	0	DIRECT
ABC transporter transmembrane region	0	DIRECT
Aldolase	0	DIRECT
Alkaline phosphatase-like	0	DIRECT
Chromo domain-like	0	DIRECT
Homo-oligomeric flavin-containing Cys decarboxylases, HFCD	0	DIRECT
tRNA-intron endonuclease catalytic domain-like	0	DIRECT
Translational machinery components	0	DIRECT
Tryptophan synthase beta subunit-like PLP-dependent enzymes	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
Methylglyoxal synthase-like	0	DIRECT
Rhodanese/Cell cycle control phosphatase	0	DIRECT
Concanavalin A-like lectins/glucanases	0	DIRECT
Mitochondrial cytochrome c oxidase subunit IV	0	DIRECT
GINS helical bundle-like	0	DIRECT
4'-phosphopantetheinyl transferase	0	DIRECT
Ribokinase-like	0	DIRECT
Ribosomal protein L13	0	DIRECT
Cytochrome c	0	DIRECT
PP2C-like	0	DIRECT
Metallo-dependent hydrolases	0	DIRECT
ValRS/IleRS/LeuRS editing domain	0	DIRECT
YAP1 redox domain	0	DIRECT
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	DIRECT
HSP40/DnaJ peptide-binding domain	0	DIRECT
CheY-like	0	DIRECT
Metallo-dependent phosphatases	0.2803	INHERITED FROM: viability