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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)
Tubby C-terminal domain-like	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
LysM domain	0	DIRECT
Cystatin/monellin	0	DIRECT
CBD9-like	0	DIRECT
AN1-like Zinc finger	0	DIRECT
Carbohydrate phosphatase	0	DIRECT
ADP-ribosylation	0	DIRECT
SAND domain-like	0	DIRECT
R3H domain	0	DIRECT
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
Proton glutamate symport protein	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
3-carboxy-cis,cis-mucoante lactonizing enzyme	0	DIRECT
PurM N-terminal domain-like	0	DIRECT
Galactose oxidase, central domain	0	DIRECT
MgtE membrane domain-like	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
CO dehydrogenase molybdoprotein N-domain-like	0	DIRECT
WGR domain-like	0	DIRECT
Doublecortin (DC)	0	DIRECT
eIF4e-like	0	DIRECT
DNA repair protein MutS, domain III	0	DIRECT
Oxysterol-binding protein-like	0	DIRECT
LEM domain	0	DIRECT
PHM/PNGase F	0	DIRECT
PK beta-barrel domain-like	0	DIRECT
Phoshotransferase/anion transport protein	0	DIRECT
VPS9 domain	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
Arginase/deacetylase	0	DIRECT
Complement control module/SCR domain	0	DIRECT
SWIB/MDM2 domain	0	DIRECT
SPOC domain-like	0	DIRECT
FAD-linked oxidases, C-terminal domain	0	DIRECT
Rap/Ran-GAP	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Nucleoporin domain	0	DIRECT
MFPT repeat-like	0	DIRECT
GAS2 domain-like	0	DIRECT
Terpenoid cyclases/Protein prenyltransferases	0	DIRECT
PEP carboxykinase N-terminal domain	0	DIRECT
Tricorn protease domain 2	0	DIRECT
Hormone receptor domain	0	DIRECT
ARID-like	0	DIRECT
GAT-like domain	0	DIRECT
Transducin (heterotrimeric G protein), gamma chain	0	DIRECT
Phosphoenolpyruvate/pyruvate domain	0	DIRECT
14-3-3 protein	0	DIRECT
Nop domain	0	DIRECT
Blood coagulation inhibitor (disintegrin)	0	DIRECT
Pepsin inhibitor-3	0	DIRECT
Small-conductance potassium channel	0	DIRECT
Hypothetical protein c14orf129, hspc210	0	DIRECT
PABC (PABP) domain	0	DIRECT
Restriction endonuclease-like	0	DIRECT
Chitinase insertion domain	0	DIRECT
Ran binding protein zinc finger-like	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
Annexin	0	DIRECT
PEBP-like	0	DIRECT
FAD-binding/transporter-associated domain-like	0	DIRECT
PurM C-terminal domain-like	0	DIRECT
Molybdenum cofactor-binding domain	0	DIRECT
Domain of poly(ADP-ribose) polymerase	0	DIRECT
Fibrinogen C-terminal domain-like	0	DIRECT
GYF domain	0	DIRECT
Acid phosphatase/Vanadium-dependent haloperoxidase	0	DIRECT
PEP carboxykinase-like	0	DIRECT
TGS-like	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
FF domain	0	DIRECT
Ribokinase-like	0	DIRECT
CO dehydrogenase ISP C-domain like	0	DIRECT
Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)	0	DIRECT
Outer arm dynein light chain 1	0	DIRECT
Elafin-like	0	DIRECT
Cadherin-like	0	DIRECT
Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit	0	DIRECT
Epsilon subunit of mitochondrial F1F0-ATP synthase	0	DIRECT
PapD-like	0.00002149	DIRECT
Chromo domain-like	0.009671	INHERITED FROM: maternal effect sterile
SET domain	0.3456	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)
Transducin (heterotrimeric G protein), gamma chain	0	DIRECT
Ubiquitin carboxyl-terminal hydrolase UCH-L	0	DIRECT
XPF/Rad1/Mus81 nuclease	0	DIRECT
Serum paraoxonase/arylesterase 1, PON1	0	DIRECT
COMT-like	0	DIRECT
Type II chitinase	0	DIRECT
YihX-like	0	DIRECT
Domain of poly(ADP-ribose) polymerase	0	DIRECT
Protein prenyltransferases	0	DIRECT
Paired domain	0	DIRECT
GYF domain	0	DIRECT
AMPK-beta glycogen binding domain-like	0	DIRECT
U-box	0	DIRECT
D-aminoacid oxidase-like	0	DIRECT
Hexokinase	0	DIRECT
Oxysterol-binding protein	0	DIRECT
DPP6 catalytic domain-like	0	DIRECT
Hypothetical protein c14orf129, hspc210	0	DIRECT
CO dehydrogenase flavoprotein N-terminal domain-like	0	DIRECT
Gamma-glutamyltranspeptidase-like	0	DIRECT
LysM domain	0	DIRECT
Chitinase insertion domain	0	DIRECT
Ran binding protein zinc finger-like	0	DIRECT
NHL repeat	0	DIRECT
Inositol monophosphatase/fructose-1,6-bisphosphatase-like	0	DIRECT
SAM (sterile alpha motif) domain	0	DIRECT
Ribokinase-like	0	DIRECT
Poly(ADP-ribose) polymerase, C-terminal domain	0	DIRECT
GAS2 domain	0	DIRECT
Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)	0	DIRECT
PurM C-terminal domain-like	0	DIRECT
CoA-binding domain	0	DIRECT
NOL1/NOP2/sun	0	DIRECT
PEP carboxykinase N-terminal domain	0	DIRECT
Cytoplasmic domain of inward rectifier potassium channel	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
LEM domain	0	DIRECT
Choline kinase	0	DIRECT
DEP domain	0	DIRECT
Phosphatidylethanolamine binding protein	0	DIRECT
Histone deacetylase, HDAC	0	DIRECT
RhoGDI-like	0	DIRECT
Vertebrate phospholipase A2	0	DIRECT
Translation initiation factor eIF4e	0	DIRECT
Tetraspanin	0	DIRECT
Calpain large subunit, catalytic domain (domain II)	0	DIRECT
PUA domain	0	DIRECT
Doublecortin (DC)	0	DIRECT
DNA repair protein MutS, domain III	0	DIRECT
Myotubularin-like phosphatases	0	DIRECT
acyl-CoA oxidase C-terminal domains	0	DIRECT
Rap/Ran-GAP	0	DIRECT
RNA editing terminal uridyl transferase 2, RET2, domain 2	0	DIRECT
PhzC/PhzF-like	0	DIRECT
Fibrinogen C-terminal domain-like	0	DIRECT
Arylsulfatase	0	DIRECT
SAND domain	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
HD domain	0	DIRECT
WGR domain	0	DIRECT
Glycogenin	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
Pepsin inhibitor-3	0	DIRECT
Hydantoinase (dihydropyrimidinase)	0	DIRECT
DEATH domain, DD	0	DIRECT
Annexin	0	DIRECT
Cadherin	0	DIRECT
D-aminoacid oxidase, N-terminal domain	0	DIRECT
Peptidylglycine alpha-hydroxylating monooxygenase, PHM	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
Nop domain	0	DIRECT
PABC (PABP) domain	0	DIRECT
Inositol polyphosphate 5-phosphatase (IPP5)	0	DIRECT
Bactericidal permeability-increasing protein, BPI	0	DIRECT
Elafin-like	0	DIRECT
14-3-3 protein	0	DIRECT
AN1-like Zinc finger	0	DIRECT
Epsilon subunit of mitochondrial F1F0-ATP synthase	0	DIRECT
Internalin LRR domain	0	DIRECT
GAPDH-like	0	DIRECT
1,3-glucuronyltransferase	0	DIRECT
Phoshoinositide 3-kinase (PI3K) helical domain	0	DIRECT
Molybdenum cofactor-binding domain	0	DIRECT
ATP-dependent protease Lon (La), catalytic domain	0	DIRECT
Biotin dependent carboxylase carboxyltransferase domain	0	DIRECT
Ras-binding domain, RBD	0	DIRECT
Acyl-CoA thioesterase	0	DIRECT
CO dehydrogenase ISP C-domain like	0	DIRECT
Acireductone dioxygenase	0	DIRECT
LacY-like proton/sugar symporter	0	DIRECT
Pancreatic carboxypeptidase, activation domain	0	DIRECT
Blood coagulation inhibitor (disintegrin)	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
HCDH C-domain-like	0	DIRECT
28-residue LRR	0	DIRECT
SWIB/MDM2 domain	0	DIRECT
MFPT repeat	0	DIRECT
Small-conductance potassium channel	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
Arfaptin, Rac-binding fragment	0	DIRECT
Glycerol kinase	0	DIRECT
PurM N-terminal domain-like	0	DIRECT
L-aminoacid/polyamine oxidase	0	DIRECT
DPP6 N-terminal domain-like	0	DIRECT
Acylamino-acid-releasing enzyme, C-terminal donain	0	DIRECT
Glycerophosphoryl diester phosphodiesterase	0	DIRECT
Methionine aminopeptidase, insert domain	0	DIRECT
FF domain	0	DIRECT
Arginine methyltransferase	0	DIRECT
PEP carboxykinase C-terminal domain	0	DIRECT
First domain of FERM	0	DIRECT
Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit	0	DIRECT
Hormone receptor domain	0	DIRECT
ARID domain	0	DIRECT
CO dehydrogenase molybdoprotein N-domain-like	0	DIRECT
Heme-dependent catalases	0	DIRECT
Epoxide hydrolase	0	DIRECT
Inositol polyphosphate kinase (IPK)	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Complement control module/SCR domain	0	DIRECT
Cell cycle control phosphatase, catalytic domain	0	DIRECT
Glutaminase	0	DIRECT
Proton glutamate symport protein	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
acyl-CoA oxidase N-terminal domains	0	DIRECT
MSP-like	0.00004243	DIRECT
Mitochondrial carrier	0.0005782	DIRECT
Histone lysine methyltransferases	0.4513	INHERITED FROM: maternal effect sterile
Canonical RBD	0.8636	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 (SPWP level: Least Informative)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Nop domain	0	DIRECT
Cadherin-like	0	DIRECT
AN1-like Zinc finger	0	DIRECT
Hormone receptor domain	0	DIRECT
PEP carboxykinase N-terminal domain	0	DIRECT
FF domain	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
Tricorn protease domain 2	0	DIRECT
Phosphoenolpyruvate/pyruvate domain	0	DIRECT
Ribokinase-like	0	DIRECT
ADP-ribosylation	0	DIRECT
Galactose oxidase, central domain	0	DIRECT
MgtE membrane domain-like	0	DIRECT
Tubby C-terminal domain-like	0	DIRECT
Restriction endonuclease-like	0	DIRECT
SWIB/MDM2 domain	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Chitinase insertion domain	0	DIRECT
Oxysterol-binding protein-like	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
PHM/PNGase F	0	DIRECT
PABC (PABP) domain	0	DIRECT
Phoshotransferase/anion transport protein	0	DIRECT
SAND domain-like	0	DIRECT
Ran binding protein zinc finger-like	0	DIRECT
PurM N-terminal domain-like	0	DIRECT
LysM domain	0	DIRECT
Domain of poly(ADP-ribose) polymerase	0	DIRECT
DNA repair protein MutS, domain III	0	DIRECT
MFPT repeat-like	0	DIRECT
Pepsin inhibitor-3	0	DIRECT
PK beta-barrel domain-like	0	DIRECT
Cystatin/monellin	0	DIRECT
Molybdenum cofactor-binding domain	0	DIRECT
GAT-like domain	0	DIRECT
R3H domain	0	DIRECT
eIF4e-like	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
3-carboxy-cis,cis-mucoante lactonizing enzyme	0	DIRECT
Doublecortin (DC)	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
Rap/Ran-GAP	0	DIRECT
CBD9-like	0	DIRECT
GYF domain	0	DIRECT
Transducin (heterotrimeric G protein), gamma chain	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
Nucleoporin domain	0	DIRECT
Terpenoid cyclases/Protein prenyltransferases	0	DIRECT
PEP carboxykinase-like	0	DIRECT
Hypothetical protein c14orf129, hspc210	0	DIRECT
CO dehydrogenase molybdoprotein N-domain-like	0	DIRECT
PurM C-terminal domain-like	0	DIRECT
SPOC domain-like	0	DIRECT
Blood coagulation inhibitor (disintegrin)	0	DIRECT
ARID-like	0	DIRECT
VPS9 domain	0	DIRECT
LEM domain	0	DIRECT
Proton glutamate symport protein	0	DIRECT
Complement control module/SCR domain	0	DIRECT
Fibrinogen C-terminal domain-like	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
FAD-binding/transporter-associated domain-like	0	DIRECT
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	0	DIRECT
Small-conductance potassium channel	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
Epsilon subunit of mitochondrial F1F0-ATP synthase	0	DIRECT
GAS2 domain-like	0	DIRECT
Acid phosphatase/Vanadium-dependent haloperoxidase	0	DIRECT
Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)	0	DIRECT
PEBP-like	0	DIRECT
Outer arm dynein light chain 1	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
Elafin-like	0	DIRECT
WGR domain-like	0	DIRECT
Arginase/deacetylase	0	DIRECT
CO dehydrogenase ISP C-domain like	0	DIRECT
Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit	0	DIRECT
TGS-like	0	DIRECT
Annexin	0	DIRECT
14-3-3 protein	0	DIRECT
Carbohydrate phosphatase	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
FAD-linked oxidases, C-terminal domain	0	DIRECT
PapD-like	0.00001757	DIRECT
Mitochondrial carrier	0.0008548	DIRECT
Chromo domain-like	0.008322	INHERITED FROM: maternal effect sterile
SET domain	0.3257	INHERITED FROM: maternal effect sterile
RNA-binding domain, RBD	0.9933	INHERITED FROM: sterile F1

Supra-domains annotated to this WP term (SPWP 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)
81324,81296 81324 - Voltage-gated potassium channels 81296 - E set domains	0	DIRECT
48179,48179 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
56176,55103 56176 - FAD-binding/transporter-associated domain-like 55103 - FAD-linked oxidases, C-terminal domain	0	DIRECT
161093,161093 161093 - MgtE membrane domain-like 161093 - MgtE membrane domain-like	0	DIRECT
48334,52540 48334 - DNA repair protein MutS, domain III 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
141739,141739 141739 - MFPT repeat-like 141739 - MFPT repeat-like	0	DIRECT
54495,46934 54495 - UBC-like 46934 - UBA-like	0	DIRECT
48371,56112 48371 - ARM repeat 56112 - Protein kinase-like (PK-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
57903,82199 57903 - FYVE/PHD zinc finger 82199 - SET domain	0	DIRECT
47473,51695 47473 - EF-hand 51695 - PLC-like phosphodiesterases	0	DIRECT
47741,56176 47741 - CO dehydrogenase ISP C-domain like 56176 - FAD-binding/transporter-associated domain-like	0	DIRECT
55486,57552 55486 - Metalloproteases ("zincins"), catalytic domain 57552 - Blood coagulation inhibitor (disintegrin)	0	DIRECT
49742,49742 49742 - PHM/PNGase F 49742 - PHM/PNGase F	0	DIRECT
55973,55973 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase	0	DIRECT
68923,53795 68923 - PEP carboxykinase N-terminal domain 53795 - PEP carboxykinase-like	0	DIRECT
57196,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
54001,49758 54001 - Cysteine proteinases 49758 - Calpain large subunit, middle domain (domain III)	0	DIRECT
57535,57535 57535 - Complement control module/SCR domain 57535 - Complement control module/SCR domain	0	DIRECT
57863,48403 57863 - ArfGap/RecO-like zinc finger 48403 - Ankyrin repeat	0	DIRECT
51971,54373 51971 - Nucleotide-binding domain 54373 - FAD-linked reductases, C-terminal domain	0	DIRECT
47769,47769 47769 - SAM/Pointed domain 47769 - SAM/Pointed domain	0	DIRECT
81383,52047 81383 - F-box domain 52047 - RNI-like	0	DIRECT
81698,81698 81698 - FF domain 81698 - FF domain	0	DIRECT
51338,51556 51338 - Composite domain of metallo-dependent hydrolases 51556 - Metallo-dependent hydrolases	0	DIRECT
55486,50923 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0	DIRECT
51445,54556 51445 - (Trans)glycosidases 54556 - Chitinase insertion domain	0	DIRECT
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
48425,50729 48425 - Sec7 domain 50729 - PH domain-like	0	DIRECT
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like	0	DIRECT
46785,46785 46785 - "Winged helix" DNA-binding domain 46785 - "Winged helix" DNA-binding domain	0	DIRECT
55326,56042 55326 - PurM N-terminal domain-like 56042 - PurM C-terminal domain-like	0	DIRECT
49562,48371 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48371 - ARM repeat	0	DIRECT
47203,47203 47203 - Acyl-CoA dehydrogenase C-terminal domain-like 47203 - Acyl-CoA dehydrogenase C-terminal domain-like	0	DIRECT
54897,53187 54897 - Protease propeptides/inhibitors 53187 - Zn-dependent exopeptidases	0	DIRECT
47587,56399 47587 - Domain of poly(ADP-ribose) polymerase 56399 - ADP-ribosylation	0	DIRECT
54534,54534 54534 - FKBP-like 54534 - FKBP-like	0	DIRECT
144232,82199 144232 - HIT/MYND zinc finger-like 82199 - SET domain	0	DIRECT
48403,52151 48403 - Ankyrin repeat 52151 - FabD/lysophospholipase-like	0	DIRECT
81324,53850 81324 - Voltage-gated potassium channels 53850 - Periplasmic binding protein-like II	0	DIRECT
48464,89009 48464 - ENTH/VHS domain 89009 - GAT-like domain	0	DIRECT
53187,55031 53187 - Zn-dependent exopeptidases 55031 - Bacterial exopeptidase dimerisation domain	0	DIRECT
47473,103506 47473 - EF-hand 103506 - Mitochondrial carrier	0	DIRECT
56601,48403 56601 - beta-lactamase/transpeptidase-like 48403 - Ankyrin repeat	0	DIRECT
54665,56003 54665 - CO dehydrogenase molybdoprotein N-domain-like 56003 - Molybdenum cofactor-binding domain	0	DIRECT
161111,160240 161111 - Cation efflux protein transmembrane domain-like 160240 - Cation efflux protein cytoplasmic domain-like	0	DIRECT
141673,50800 141673 - MOSC N-terminal domain-like 50800 - PK beta-barrel domain-like	0	DIRECT
54292,47741 54292 - 2Fe-2S ferredoxin-like 47741 - CO dehydrogenase ISP C-domain like	0	DIRECT
57903,51197 57903 - FYVE/PHD zinc finger 51197 - Clavaminate synthase-like	0	DIRECT
55920,46785 55920 - Creatinase/aminopeptidase 46785 - "Winged helix" DNA-binding domain	0	DIRECT
81324,81327 81324 - Voltage-gated potassium channels 81327 - Small-conductance potassium channel	0	DIRECT
50978,50998 50978 - WD40 repeat-like 50998 - Quinoprotein alcohol dehydrogenase-like	0	DIRECT
57850,117839 57850 - RING/U-box 117839 - WWE domain	0	DIRECT
55394,55394 55394 - Bactericidal permeability-increasing protein, BPI 55394 - Bactericidal permeability-increasing protein, BPI	0	DIRECT

Supra-domains annotated to this WP term (SPWP 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)
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
46938,52087,101576 46938 - CRAL/TRIO N-terminal domain 52087 - CRAL/TRIO domain 101576 - Supernatant protein factor (SPF), C-terminal domain	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
50729,47473,51695 50729 - PH domain-like 47473 - EF-hand 51695 - PLC-like phosphodiesterases	0	DIRECT
56436,49854,49854 56436 - C-type lectin-like 49854 - Spermadhesin, CUB domain 49854 - Spermadhesin, CUB domain	0	DIRECT
47090,55486,50923 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0	DIRECT
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like	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
50044,50044,50044 50044 - SH3-domain 50044 - SH3-domain 50044 - SH3-domain	0	DIRECT
57567,57567,57567 57567 - Serine protease inhibitors 57567 - Serine protease inhibitors 57567 - Serine protease inhibitors	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
48726,49265,48726 48726 - Immunoglobulin 49265 - Fibronectin type III 48726 - Immunoglobulin	0	DIRECT
49562,48371,56112 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48371 - ARM repeat 56112 - Protein kinase-like (PK-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.