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

• Disease Ontology (DO) Ontology (DO)
  DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
  
• Human Phenotype (HP) Ontology (HP)
  HP captures phenotypic abnormalities that are described in OMIM, along with the corresponding disease-causing genes. It includes three complementary biological concepts: Mode_of_Inheritance (MI), ONset_and_clinical_course (ON), and Phenotypic_Abnormality (PA).
  
• Mouse Phenotype (MP) Ontology (MP)
  MP describes phenotypes of the mouse after a specific gene is genetically disrupted. Using it, Mouse Genome Informatics (MGI) provides high-coverate gene-level phenotypes for the mouse.
  
• Worm Phenotype (WP) Ontology (WP)
  WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
  
• Yeast Phenotype (YP) Ontology (YP)
  Based on YP which is the major contributor to the Ascomycete phenotype ontology, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
  
• Fly Phenotype (FP) Ontology (FP)
  FP refers to FlyBase controlled vocabulary. Specifically, a structured controlled vocabulary is used for the annotation of alleles (for their mutagen etc) in FlyBase.
  
• Fly Anatomy (FA) Ontology (FA)
  FA is a structured controlled vocabulary of the anatomy of Drosophila melanogaster, used for the description of phenotypes and where a gene is expressed.
  
• Zebrafish Anatomy (ZA) Ontology (ZA)
  ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
  
• Xenopus Anatomy (XA) Ontology (XA)
  XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
  
• Arabidopsis Plant Ontology (AP) Ontology (AP)
  As a major contributor to Plant Ontology which describes plant anatomical and morphological structures (AN) and growth and developmental stages (DE), the Arabidopsis Information Resource (TAIR) provides arabidopsis plant ontology annotations for the model higher plant Arabidopsis thaliana.
  
• Enzyme Commission (EC) Ontology (EC)
  Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed.
  
• DrugBank ATC (DB) Ontology (DB)
  In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
  
• UniProtKB KeyWords (KW) Ontology (KW)
  Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
  
• UniProtKB UniPathway (UP) Ontology (UP)
  UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.
  

Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

• Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).
  

Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

• Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).
  

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

SCOP term	FDR (all)	Annotation (direct or inherited)
PurM C-terminal domain-like	0	DIRECT
Restriction endonuclease-like	0	DIRECT
Blood coagulation inhibitor (disintegrin)	0	DIRECT
PEP carboxykinase-like	0	DIRECT
Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit	0	DIRECT
Ribokinase-like	0	DIRECT
Carbon-nitrogen hydrolase	0	DIRECT
eIF4e-like	0	DIRECT
CO dehydrogenase molybdoprotein N-domain-like	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
ADP-ribosylation	0	DIRECT
Doublecortin (DC)	0	DIRECT
PK beta-barrel domain-like	0	DIRECT
LysM domain	0	DIRECT
3-carboxy-cis,cis-mucoante lactonizing enzyme	0	DIRECT
Pepsin inhibitor-3	0	DIRECT
PurM N-terminal domain-like	0	DIRECT
PHM/PNGase F	0	DIRECT
GYF domain	0	DIRECT
MFPT repeat-like	0	DIRECT
TGS-like	0	DIRECT
Epsilon subunit of mitochondrial F1F0-ATP synthase	0	DIRECT
Outer arm dynein light chain 1	0	DIRECT
FF domain	0	DIRECT
Domain of poly(ADP-ribose) polymerase	0	DIRECT
SAND domain-like	0	DIRECT
L-aspartase-like	0	DIRECT
LEM domain	0	DIRECT
Cystatin/monellin	0	DIRECT
Hormone receptor domain	0	DIRECT
Annexin	0	DIRECT
Phosphoenolpyruvate/pyruvate domain	0	DIRECT
Transducin (heterotrimeric G protein), gamma chain	0	DIRECT
Terpenoid cyclases/Protein prenyltransferases	0	DIRECT
PEP carboxykinase N-terminal domain	0	DIRECT
PP2C-like	0	DIRECT
Fibrinogen C-terminal domain-like	0	DIRECT
Carbohydrate phosphatase	0	DIRECT
Tricorn protease domain 2	0	DIRECT
Ran binding protein zinc finger-like	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
Tubby C-terminal domain-like	0	DIRECT
Oxysterol-binding protein-like	0	DIRECT
Cadherin-like	0	DIRECT
GAS2 domain-like	0	DIRECT
Molybdenum cofactor-binding domain	0	DIRECT
DNA repair protein MutS, domain III	0	DIRECT
Elafin-like	0	DIRECT
MgtE membrane domain-like	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
CBD9-like	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
Proton glutamate symport protein	0	DIRECT
Acid phosphatase/Vanadium-dependent haloperoxidase	0	DIRECT
Rap/Ran-GAP	0	DIRECT
VPS9 domain	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Arginase/deacetylase	0	DIRECT
SPOC domain-like	0	DIRECT
Nop domain	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
Nucleoporin domain	0	DIRECT
WGR domain-like	0	DIRECT
ARID-like	0	DIRECT
AN1-like Zinc finger	0	DIRECT
Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)	0	DIRECT
Complement control module/SCR domain	0	DIRECT
GAT-like domain	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
Hect, E3 ligase catalytic domain	0	DIRECT
R3H domain	0	DIRECT
14-3-3 protein	0	DIRECT
PEBP-like	0	DIRECT
Galactose oxidase, central domain	0	DIRECT
Chitinase insertion domain	0	DIRECT
SWIB/MDM2 domain	0	DIRECT
Small-conductance potassium channel	0	DIRECT
CO dehydrogenase ISP C-domain like	0	DIRECT
Hypothetical protein c14orf129, hspc210	0	DIRECT
PABC (PABP) domain	0	DIRECT
PapD-like	0.000005878	DIRECT
Chromo domain-like	0.01605	INHERITED FROM: maternal effect sterile
SET domain	0.5453	INHERITED FROM: maternal effect sterile
RNA-binding domain, RBD	1	INHERITED FROM: sterile F1

Family domains annotated to this WP term (SDWP level: Least Informative)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
CO dehydrogenase flavoprotein N-terminal domain-like	0	DIRECT
Pancreatic carboxypeptidase, activation domain	0	DIRECT
PhzC/PhzF-like	0	DIRECT
Chitinase insertion domain	0	DIRECT
Hydantoinase (dihydropyrimidinase)	0	DIRECT
MFPT repeat	0	DIRECT
Cadherin	0	DIRECT
Acylamino-acid-releasing enzyme, C-terminal donain	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
PABC (PABP) domain	0	DIRECT
Transducin (heterotrimeric G protein), gamma chain	0	DIRECT
14-3-3 protein	0	DIRECT
GAS2 domain	0	DIRECT
Ran binding protein zinc finger-like	0	DIRECT
First domain of FERM	0	DIRECT
PP2C-like	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
Internalin LRR domain	0	DIRECT
Elafin-like	0	DIRECT
Fibrinogen C-terminal domain-like	0	DIRECT
Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit	0	DIRECT
Nop domain	0	DIRECT
Proton glutamate symport protein	0	DIRECT
Peptidylglycine alpha-hydroxylating monooxygenase, PHM	0	DIRECT
XPF/Rad1/Mus81 nuclease	0	DIRECT
Bactericidal permeability-increasing protein, BPI	0	DIRECT
Oxysterol-binding protein	0	DIRECT
ARID domain	0	DIRECT
Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)	0	DIRECT
Protein prenyltransferases	0	DIRECT
D-aminoacid oxidase-like	0	DIRECT
Phosphatidylethanolamine binding protein	0	DIRECT
Blood coagulation inhibitor (disintegrin)	0	DIRECT
Hormone receptor domain	0	DIRECT
Phoshoinositide 3-kinase (PI3K) helical domain	0	DIRECT
Acyl-CoA thioesterase	0	DIRECT
LEM domain	0	DIRECT
Glycerophosphoryl diester phosphodiesterase	0	DIRECT
Arginine methyltransferase	0	DIRECT
PEP carboxykinase C-terminal domain	0	DIRECT
SAM (sterile alpha motif) domain	0	DIRECT
Inositol monophosphatase/fructose-1,6-bisphosphatase-like	0	DIRECT
FF domain	0	DIRECT
DEATH domain, DD	0	DIRECT
Doublecortin (DC)	0	DIRECT
beta 1,4 galactosyltransferase (b4GalT1)	0	DIRECT
CoA-binding domain	0	DIRECT
Domain of poly(ADP-ribose) polymerase	0	DIRECT
acyl-CoA oxidase C-terminal domains	0	DIRECT
DNA repair protein MutS, domain III	0	DIRECT
Acireductone dioxygenase	0	DIRECT
PUA domain	0	DIRECT
Arfaptin, Rac-binding fragment	0	DIRECT
Glycerol kinase	0	DIRECT
PurM N-terminal domain-like	0	DIRECT
Cell cycle control phosphatase, catalytic domain	0	DIRECT
Glycogenin	0	DIRECT
Ras-binding domain, RBD	0	DIRECT
GYF domain	0	DIRECT
RhoGDI-like	0	DIRECT
Myotubularin-like phosphatases	0	DIRECT
Inositol polyphosphate kinase (IPK)	0	DIRECT
Cytoplasmic domain of inward rectifier potassium channel	0	DIRECT
Type II chitinase	0	DIRECT
CO dehydrogenase ISP C-domain like	0	DIRECT
LysM domain	0	DIRECT
Calpain large subunit, catalytic domain (domain II)	0	DIRECT
AN1-like Zinc finger	0	DIRECT
CO dehydrogenase molybdoprotein N-domain-like	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
SAND domain	0	DIRECT
NOL1/NOP2/sun	0	DIRECT
Histone deacetylase, HDAC	0	DIRECT
Biotin dependent carboxylase carboxyltransferase domain	0	DIRECT
Epsilon subunit of mitochondrial F1F0-ATP synthase	0	DIRECT
DPP6 N-terminal domain-like	0	DIRECT
Annexin	0	DIRECT
PurM C-terminal domain-like	0	DIRECT
Gamma-glutamyltranspeptidase-like	0	DIRECT
Molybdenum cofactor-binding domain	0	DIRECT
SWIB/MDM2 domain	0	DIRECT
GAPDH-like	0	DIRECT
Poly(ADP-ribose) polymerase, C-terminal domain	0	DIRECT
DEP domain	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
Pepsin inhibitor-3	0	DIRECT
U-box	0	DIRECT
Complement control module/SCR domain	0	DIRECT
ATP-dependent protease Lon (La), catalytic domain	0	DIRECT
YihX-like	0	DIRECT
Hect, E3 ligase catalytic domain	0	DIRECT
acyl-CoA oxidase N-terminal domains	0	DIRECT
DPP6 catalytic domain-like	0	DIRECT
Translation initiation factor eIF4e	0	DIRECT
Tetraspanin	0	DIRECT
Hypothetical protein c14orf129, hspc210	0	DIRECT
Ribokinase-like	0	DIRECT
PEP carboxykinase N-terminal domain	0	DIRECT
Double-stranded RNA-binding domain (dsRBD)	0	DIRECT
COMT-like	0	DIRECT
Glutaminase	0	DIRECT
HCDH C-domain-like	0	DIRECT
28-residue LRR	0	DIRECT
Rap/Ran-GAP	0	DIRECT
Arylsulfatase	0	DIRECT
HD domain	0	DIRECT
Paired domain	0	DIRECT
LacY-like proton/sugar symporter	0	DIRECT
Heme-dependent catalases	0	DIRECT
Ubiquitin carboxyl-terminal hydrolase UCH-L	0	DIRECT
RNA editing terminal uridyl transferase 2, RET2, domain 2	0	DIRECT
Inositol polyphosphate 5-phosphatase (IPP5)	0	DIRECT
Epoxide hydrolase	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
Choline kinase	0	DIRECT
Methionine aminopeptidase, insert domain	0	DIRECT
L-aminoacid/polyamine oxidase	0	DIRECT
Serum paraoxonase/arylesterase 1, PON1	0	DIRECT
1,3-glucuronyltransferase	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
D-aminoacid oxidase, N-terminal domain	0	DIRECT
WGR domain	0	DIRECT
AMPK-beta glycogen binding domain-like	0	DIRECT
NHL repeat	0	DIRECT
Small-conductance potassium channel	0	DIRECT
Adenosine/AMP deaminase	0	DIRECT
Hexokinase	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
MSP-like	0.000008913	DIRECT
Protein kinases, catalytic subunit	0.0008439	DIRECT
Mitochondrial carrier	0.0009099	DIRECT
Histone lysine methyltransferases	0.6847	INHERITED FROM: maternal effect sterile
Canonical RBD	0.8877	INHERITED FROM: sterile F1

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 WP term (Not in SPWP)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Elafin-like	0	DIRECT
Carbohydrate phosphatase	0	DIRECT
Nucleoporin domain	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
PP2C-like	0	DIRECT
GAT-like domain	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
3-carboxy-cis,cis-mucoante lactonizing enzyme	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
Hect, E3 ligase catalytic domain	0	DIRECT
TGS-like	0	DIRECT
Tricorn protease domain 2	0	DIRECT
DNA repair protein MutS, domain III	0	DIRECT
CO dehydrogenase ISP C-domain like	0	DIRECT
Ran binding protein zinc finger-like	0	DIRECT
Arginase/deacetylase	0	DIRECT
Molybdenum cofactor-binding domain	0	DIRECT
WGR domain-like	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
ADP-ribosylation	0	DIRECT
Galactose oxidase, central domain	0	DIRECT
Pepsin inhibitor-3	0	DIRECT
Cadherin-like	0	DIRECT
FF domain	0	DIRECT
Proton glutamate symport protein	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
PABC (PABP) domain	0	DIRECT
Fibrinogen C-terminal domain-like	0	DIRECT
Terpenoid cyclases/Protein prenyltransferases	0	DIRECT
Phosphoenolpyruvate/pyruvate domain	0	DIRECT
PK beta-barrel domain-like	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
ARID-like	0	DIRECT
Blood coagulation inhibitor (disintegrin)	0	DIRECT
PEP carboxykinase N-terminal domain	0	DIRECT
L-aspartase-like	0	DIRECT
LysM domain	0	DIRECT
eIF4e-like	0	DIRECT
Rap/Ran-GAP	0	DIRECT
Oxysterol-binding protein-like	0	DIRECT
Nop domain	0	DIRECT
Hormone receptor domain	0	DIRECT
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	0	DIRECT
Restriction endonuclease-like	0	DIRECT
GAS2 domain-like	0	DIRECT
Doublecortin (DC)	0	DIRECT
Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)	0	DIRECT
PEP carboxykinase-like	0	DIRECT
R3H domain	0	DIRECT
Hypothetical protein c14orf129, hspc210	0	DIRECT
GYF domain	0	DIRECT
AN1-like Zinc finger	0	DIRECT
PEBP-like	0	DIRECT
Domain of poly(ADP-ribose) polymerase	0	DIRECT
Chitinase insertion domain	0	DIRECT
Complement control module/SCR domain	0	DIRECT
SAND domain-like	0	DIRECT
CO dehydrogenase molybdoprotein N-domain-like	0	DIRECT
CBD9-like	0	DIRECT
PHM/PNGase F	0	DIRECT
Acid phosphatase/Vanadium-dependent haloperoxidase	0	DIRECT
Annexin	0	DIRECT
SPOC domain-like	0	DIRECT
Carbon-nitrogen hydrolase	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Ribokinase-like	0	DIRECT
SWIB/MDM2 domain	0	DIRECT
14-3-3 protein	0	DIRECT
MgtE membrane domain-like	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
Transducin (heterotrimeric G protein), gamma chain	0	DIRECT
PurM C-terminal domain-like	0	DIRECT
VPS9 domain	0	DIRECT
Epsilon subunit of mitochondrial F1F0-ATP synthase	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
LEM domain	0	DIRECT
Small-conductance potassium channel	0	DIRECT
Outer arm dynein light chain 1	0	DIRECT
Cystatin/monellin	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
PurM N-terminal domain-like	0	DIRECT
Tubby C-terminal domain-like	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit	0	DIRECT
MFPT repeat-like	0	DIRECT
PapD-like	0.000004748	DIRECT
Chromo domain-like	0.01383	INHERITED FROM: maternal effect sterile
SET domain	0.5225	INHERITED FROM: maternal effect sterile
RNA-binding domain, RBD	1	INHERITED FROM: sterile F1

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

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
81324,53850 81324 - Voltage-gated potassium channels 53850 - Periplasmic binding protein-like II	0	DIRECT
53474,53474 53474 - alpha/beta-Hydrolases 53474 - alpha/beta-Hydrolases	0	DIRECT
51338,51556 51338 - Composite domain of metallo-dependent hydrolases 51556 - Metallo-dependent hydrolases	0	DIRECT
47741,56176 47741 - CO dehydrogenase ISP C-domain like 56176 - FAD-binding/transporter-associated domain-like	0	DIRECT
51971,54373 51971 - Nucleotide-binding domain 54373 - FAD-linked reductases, C-terminal domain	0	DIRECT
47473,51695 47473 - EF-hand 51695 - PLC-like phosphodiesterases	0	DIRECT
56601,48403 56601 - beta-lactamase/transpeptidase-like 48403 - Ankyrin repeat	0	DIRECT
54534,54534 54534 - FKBP-like 54534 - FKBP-like	0	DIRECT
57756,50630 57756 - Retrovirus zinc finger-like domains 50630 - Acid proteases	0	DIRECT
141673,50800 141673 - MOSC N-terminal domain-like 50800 - PK beta-barrel domain-like	0	DIRECT
161093,161093 161093 - MgtE membrane domain-like 161093 - MgtE membrane domain-like	0	DIRECT
101690,53098 101690 - PAZ domain 53098 - Ribonuclease H-like	0	DIRECT
47473,103506 47473 - EF-hand 103506 - Mitochondrial carrier	0	DIRECT
54768,54768 54768 - dsRNA-binding domain-like 54768 - dsRNA-binding domain-like	0	DIRECT
50978,50998 50978 - WD40 repeat-like 50998 - Quinoprotein alcohol dehydrogenase-like	0	DIRECT
103473,103473 103473 - MFS general substrate transporter 103473 - MFS general substrate transporter	0	DIRECT
57903,82199 57903 - FYVE/PHD zinc finger 82199 - SET domain	0	DIRECT
46785,46785 46785 - "Winged helix" DNA-binding domain 46785 - "Winged helix" DNA-binding domain	0	DIRECT
55973,55973 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase	0	DIRECT
54495,46934 54495 - UBC-like 46934 - UBA-like	0	DIRECT
48403,52151 48403 - Ankyrin repeat 52151 - FabD/lysophospholipase-like	0	DIRECT
55394,55394 55394 - Bactericidal permeability-increasing protein, BPI 55394 - Bactericidal permeability-increasing protein, BPI	0	DIRECT
81698,81698 81698 - FF domain 81698 - FF domain	0	DIRECT
48425,50729 48425 - Sec7 domain 50729 - PH domain-like	0	DIRECT
54665,56003 54665 - CO dehydrogenase molybdoprotein N-domain-like 56003 - Molybdenum cofactor-binding domain	0	DIRECT
57535,57535 57535 - Complement control module/SCR domain 57535 - Complement control module/SCR domain	0	DIRECT
57850,117839 57850 - RING/U-box 117839 - WWE domain	0	DIRECT
47587,56399 47587 - Domain of poly(ADP-ribose) polymerase 56399 - ADP-ribosylation	0	DIRECT
55326,56042 55326 - PurM N-terminal domain-like 56042 - PurM C-terminal domain-like	0	DIRECT
49742,49742 49742 - PHM/PNGase F 49742 - PHM/PNGase F	0	DIRECT
57903,51197 57903 - FYVE/PHD zinc finger 51197 - Clavaminate synthase-like	0	DIRECT
81383,52047 81383 - F-box domain 52047 - RNI-like	0	DIRECT
48179,48179 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
55486,50923 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0	DIRECT
54292,47741 54292 - 2Fe-2S ferredoxin-like 47741 - CO dehydrogenase ISP C-domain like	0	DIRECT
56112,48371 56112 - Protein kinase-like (PK-like) 48371 - ARM repeat	0	DIRECT
52540,81271 52540 - P-loop containing nucleoside triphosphate hydrolases 81271 - TGS-like	0	DIRECT
47769,47769 47769 - SAM/Pointed domain 47769 - SAM/Pointed domain	0	DIRECT
57196,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
48371,56112 48371 - ARM repeat 56112 - Protein kinase-like (PK-like)	0	DIRECT
81324,81296 81324 - Voltage-gated potassium channels 81296 - E set domains	0	DIRECT
55920,46785 55920 - Creatinase/aminopeptidase 46785 - "Winged helix" DNA-binding domain	0	DIRECT
51045,51045 51045 - WW domain 51045 - WW domain	0	DIRECT
68923,53795 68923 - PEP carboxykinase N-terminal domain 53795 - PEP carboxykinase-like	0	DIRECT
81324,81327 81324 - Voltage-gated potassium channels 81327 - Small-conductance potassium channel	0	DIRECT
49562,48371 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48371 - ARM repeat	0	DIRECT
51735,50129 51735 - NAD(P)-binding Rossmann-fold domains 50129 - GroES-like	0	DIRECT
55486,57552 55486 - Metalloproteases ("zincins"), catalytic domain 57552 - Blood coagulation inhibitor (disintegrin)	0	DIRECT
47203,47203 47203 - Acyl-CoA dehydrogenase C-terminal domain-like 47203 - Acyl-CoA dehydrogenase C-terminal domain-like	0	DIRECT
144232,82199 144232 - HIT/MYND zinc finger-like 82199 - SET domain	0	DIRECT
48334,52540 48334 - DNA repair protein MutS, domain III 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
57863,48403 57863 - ArfGap/RecO-like zinc finger 48403 - Ankyrin repeat	0	DIRECT
54897,53187 54897 - Protease propeptides/inhibitors 53187 - Zn-dependent exopeptidases	0	DIRECT
141739,141739 141739 - MFPT repeat-like 141739 - MFPT repeat-like	0	DIRECT
54001,49758 54001 - Cysteine proteinases 49758 - Calpain large subunit, middle domain (domain III)	0	DIRECT
48464,89009 48464 - ENTH/VHS domain 89009 - GAT-like domain	0	DIRECT
161111,160240 161111 - Cation efflux protein transmembrane domain-like 160240 - Cation efflux protein cytoplasmic domain-like	0	DIRECT
53187,55031 53187 - Zn-dependent exopeptidases 55031 - Bacterial exopeptidase dimerisation domain	0	DIRECT
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like	0	DIRECT
51445,54556 51445 - (Trans)glycosidases 54556 - Chitinase insertion domain	0	DIRECT
51445,51445 51445 - (Trans)glycosidases 51445 - (Trans)glycosidases	0	DIRECT
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.0005333	DIRECT

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

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
47090,55486,50923 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0	DIRECT
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0	DIRECT
48726,49265,48726 48726 - Immunoglobulin 49265 - Fibronectin type III 48726 - Immunoglobulin	0	DIRECT
63411,63411,63411 63411 - LuxS/MPP-like metallohydrolase 63411 - LuxS/MPP-like metallohydrolase 63411 - LuxS/MPP-like metallohydrolase	0	DIRECT
54292,47741,56176 54292 - 2Fe-2S ferredoxin-like 47741 - CO dehydrogenase ISP C-domain like 56176 - FAD-binding/transporter-associated domain-like	0	DIRECT
51735,48179,48179 51735 - NAD(P)-binding Rossmann-fold domains 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
49785,49785,49785 49785 - Galactose-binding domain-like 49785 - Galactose-binding domain-like 49785 - Galactose-binding domain-like	0	DIRECT
56436,49854,49854 56436 - C-type lectin-like 49854 - Spermadhesin, CUB domain 49854 - Spermadhesin, CUB domain	0	DIRECT
55973,55973,55973 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase	0	DIRECT
57535,57535,57535 57535 - Complement control module/SCR domain 57535 - Complement control module/SCR domain 57535 - Complement control module/SCR domain	0	DIRECT
57567,57567,57567 57567 - Serine protease inhibitors 57567 - Serine protease inhibitors 57567 - Serine protease inhibitors	0	DIRECT
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like	0	DIRECT
46938,52087,101576 46938 - CRAL/TRIO N-terminal domain 52087 - CRAL/TRIO domain 101576 - Supernatant protein factor (SPF), C-terminal domain	0	DIRECT
50729,47473,51695 50729 - PH domain-like 47473 - EF-hand 51695 - PLC-like phosphodiesterases	0	DIRECT
50129,51735,50129 50129 - GroES-like 51735 - NAD(P)-binding Rossmann-fold domains 50129 - GroES-like	0	DIRECT
50044,50044,50044 50044 - SH3-domain 50044 - SH3-domain 50044 - SH3-domain	0	DIRECT
49562,48371,56112 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48371 - ARM repeat 56112 - Protein kinase-like (PK-like)	0	DIRECT
56645,47203,47203 56645 - Acyl-CoA dehydrogenase NM domain-like 47203 - Acyl-CoA dehydrogenase C-terminal domain-like 47203 - Acyl-CoA dehydrogenase C-terminal domain-like	0	DIRECT

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.