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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)
Doublecortin (DC)	0	DIRECT
GAT-like domain	0	DIRECT
FF domain	0	DIRECT
ARID-like	0	DIRECT
Transducin (heterotrimeric G protein), gamma chain	0	DIRECT
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	0	DIRECT
Arginase/deacetylase	0	DIRECT
Tubby C-terminal domain-like	0	DIRECT
Annexin	0	DIRECT
Phosphoenolpyruvate/pyruvate domain	0	DIRECT
FAD-linked oxidases, C-terminal domain	0	DIRECT
SWIB/MDM2 domain	0	DIRECT
PK beta-barrel domain-like	0	DIRECT
eIF4e-like	0	DIRECT
Acid phosphatase/Vanadium-dependent haloperoxidase	0	DIRECT
Pepsin inhibitor-3	0	DIRECT
Elafin-like	0	DIRECT
Outer arm dynein light chain 1	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)	0	DIRECT
Proton glutamate symport protein	0	DIRECT
CO dehydrogenase molybdoprotein N-domain-like	0	DIRECT
Fibrinogen C-terminal domain-like	0	DIRECT
WGR domain-like	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
FAD-binding/transporter-associated domain-like	0	DIRECT
CO dehydrogenase ISP C-domain like	0	DIRECT
Rap/Ran-GAP	0	DIRECT
Carbohydrate phosphatase	0	DIRECT
Blood coagulation inhibitor (disintegrin)	0	DIRECT
LEM domain	0	DIRECT
MgtE membrane domain-like	0	DIRECT
ADP-ribosylation	0	DIRECT
Terpenoid cyclases/Protein prenyltransferases	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit	0	DIRECT
Ran binding protein zinc finger-like	0	DIRECT
CBD9-like	0	DIRECT
Hormone receptor domain	0	DIRECT
DNA repair protein MutS, domain III	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
Phoshotransferase/anion transport protein	0	DIRECT
14-3-3 protein	0	DIRECT
Complement control module/SCR domain	0	DIRECT
VPS9 domain	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Oxysterol-binding protein-like	0	DIRECT
Cystatin/monellin	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
Small-conductance potassium channel	0	DIRECT
GYF domain	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
LysM domain	0	DIRECT
Cadherin-like	0	DIRECT
PEBP-like	0	DIRECT
Molybdenum cofactor-binding domain	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Nop domain	0	DIRECT
MFPT repeat-like	0	DIRECT
3-carboxy-cis,cis-mucoante lactonizing enzyme	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
Ribokinase-like	0	DIRECT
PurM C-terminal domain-like	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
AN1-like Zinc finger	0	DIRECT
SPOC domain-like	0	DIRECT
Chitinase insertion domain	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
Galactose oxidase, central domain	0	DIRECT
SAND domain-like	0	DIRECT
Epsilon subunit of mitochondrial F1F0-ATP synthase	0	DIRECT
PEP carboxykinase N-terminal domain	0	DIRECT
Nucleoporin domain	0	DIRECT
PurM N-terminal domain-like	0	DIRECT
PABC (PABP) domain	0	DIRECT
Restriction endonuclease-like	0	DIRECT
Domain of poly(ADP-ribose) polymerase	0	DIRECT
TGS-like	0	DIRECT
Hypothetical protein c14orf129, hspc210	0	DIRECT
GAS2 domain-like	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
PEP carboxykinase-like	0	DIRECT
PHM/PNGase F	0	DIRECT
Tricorn protease domain 2	0	DIRECT
R3H domain	0	DIRECT
PapD-like	0.00002136	DIRECT
Chromo domain-like	0.009667	INHERITED FROM: maternal effect sterile
SET domain	0.3453	INHERITED FROM: maternal effect sterile
RNA-binding domain, RBD	0.9914	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)
Chitinase insertion domain	0	DIRECT
GAPDH-like	0	DIRECT
Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit	0	DIRECT
Ras-binding domain, RBD	0	DIRECT
D-aminoacid oxidase-like	0	DIRECT
Ran binding protein zinc finger-like	0	DIRECT
PABC (PABP) domain	0	DIRECT
RNA editing terminal uridyl transferase 2, RET2, domain 2	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
DPP6 catalytic domain-like	0	DIRECT
Cell cycle control phosphatase, catalytic domain	0	DIRECT
Nop domain	0	DIRECT
Internalin LRR domain	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
PEP carboxykinase C-terminal domain	0	DIRECT
Pancreatic carboxypeptidase, activation domain	0	DIRECT
Inositol polyphosphate 5-phosphatase (IPP5)	0	DIRECT
Type II chitinase	0	DIRECT
Annexin	0	DIRECT
DNA repair protein MutS, domain III	0	DIRECT
Cytoplasmic domain of inward rectifier potassium channel	0	DIRECT
Heme-dependent catalases	0	DIRECT
Hydantoinase (dihydropyrimidinase)	0	DIRECT
RhoGDI-like	0	DIRECT
Epsilon subunit of mitochondrial F1F0-ATP synthase	0	DIRECT
WGR domain	0	DIRECT
Domain of poly(ADP-ribose) polymerase	0	DIRECT
First domain of FERM	0	DIRECT
FF domain	0	DIRECT
Ribokinase-like	0	DIRECT
Blood coagulation inhibitor (disintegrin)	0	DIRECT
DPP6 N-terminal domain-like	0	DIRECT
ATP-dependent protease Lon (La), catalytic domain	0	DIRECT
Acylamino-acid-releasing enzyme, C-terminal donain	0	DIRECT
Proton glutamate symport protein	0	DIRECT
ARID domain	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Inositol monophosphatase/fructose-1,6-bisphosphatase-like	0	DIRECT
Small-conductance potassium channel	0	DIRECT
28-residue LRR	0	DIRECT
XPF/Rad1/Mus81 nuclease	0	DIRECT
PurM N-terminal domain-like	0	DIRECT
Fibrinogen C-terminal domain-like	0	DIRECT
Translation initiation factor eIF4e	0	DIRECT
Myotubularin-like phosphatases	0	DIRECT
COMT-like	0	DIRECT
Hexokinase	0	DIRECT
PUA domain	0	DIRECT
U-box	0	DIRECT
Tetraspanin	0	DIRECT
Doublecortin (DC)	0	DIRECT
Adenosine/AMP deaminase	0	DIRECT
Ubiquitin carboxyl-terminal hydrolase UCH-L	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
Methionine aminopeptidase, insert domain	0	DIRECT
Vertebrate phospholipase A2	0	DIRECT
acyl-CoA oxidase C-terminal domains	0	DIRECT
Rap/Ran-GAP	0	DIRECT
GAS2 domain	0	DIRECT
Glycogenin	0	DIRECT
D-aminoacid oxidase, N-terminal domain	0	DIRECT
NOL1/NOP2/sun	0	DIRECT
Protein prenyltransferases	0	DIRECT
14-3-3 protein	0	DIRECT
Biotin dependent carboxylase carboxyltransferase domain	0	DIRECT
Calpain large subunit, catalytic domain (domain II)	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
GYF domain	0	DIRECT
Epoxide hydrolase	0	DIRECT
Acireductone dioxygenase	0	DIRECT
PhzC/PhzF-like	0	DIRECT
LysM domain	0	DIRECT
Cadherin	0	DIRECT
MFPT repeat	0	DIRECT
Acyl-CoA thioesterase	0	DIRECT
Phoshoinositide 3-kinase (PI3K) helical domain	0	DIRECT
Histone deacetylase, HDAC	0	DIRECT
Pepsin inhibitor-3	0	DIRECT
Paired domain	0	DIRECT
Poly(ADP-ribose) polymerase, C-terminal domain	0	DIRECT
LEM domain	0	DIRECT
DEP domain	0	DIRECT
acyl-CoA oxidase N-terminal domains	0	DIRECT
L-aminoacid/polyamine oxidase	0	DIRECT
PEP carboxykinase N-terminal domain	0	DIRECT
CO dehydrogenase molybdoprotein N-domain-like	0	DIRECT
1,3-glucuronyltransferase	0	DIRECT
LacY-like proton/sugar symporter	0	DIRECT
DEATH domain, DD	0	DIRECT
Transducin (heterotrimeric G protein), gamma chain	0	DIRECT
Inositol polyphosphate kinase (IPK)	0	DIRECT
Phosphatidylethanolamine binding protein	0	DIRECT
CO dehydrogenase flavoprotein N-terminal domain-like	0	DIRECT
Serum paraoxonase/arylesterase 1, PON1	0	DIRECT
AMPK-beta glycogen binding domain-like	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
Molybdenum cofactor-binding domain	0	DIRECT
HCDH C-domain-like	0	DIRECT
SWIB/MDM2 domain	0	DIRECT
Peptidylglycine alpha-hydroxylating monooxygenase, PHM	0	DIRECT
Choline kinase	0	DIRECT
Elafin-like	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
Glycerol kinase	0	DIRECT
Glutaminase	0	DIRECT
Bactericidal permeability-increasing protein, BPI	0	DIRECT
Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Complement control module/SCR domain	0	DIRECT
Oxysterol-binding protein	0	DIRECT
Arylsulfatase	0	DIRECT
YihX-like	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
CO dehydrogenase ISP C-domain like	0	DIRECT
Hypothetical protein c14orf129, hspc210	0	DIRECT
Glycerophosphoryl diester phosphodiesterase	0	DIRECT
SAM (sterile alpha motif) domain	0	DIRECT
AN1-like Zinc finger	0	DIRECT
Gamma-glutamyltranspeptidase-like	0	DIRECT
CoA-binding domain	0	DIRECT
HD domain	0	DIRECT
SAND domain	0	DIRECT
Hormone receptor domain	0	DIRECT
NHL repeat	0	DIRECT
PurM C-terminal domain-like	0	DIRECT
Arfaptin, Rac-binding fragment	0	DIRECT
Arginine methyltransferase	0	DIRECT
MSP-like	0.00004127	DIRECT
Mitochondrial carrier	0.00057	DIRECT
Histone lysine methyltransferases	0.4498	INHERITED FROM: maternal effect sterile
Canonical RBD	0.8303	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)
PEP carboxykinase-like	0	DIRECT
Epsilon subunit of mitochondrial F1F0-ATP synthase	0	DIRECT
Hypothetical protein c14orf129, hspc210	0	DIRECT
Elafin-like	0	DIRECT
Outer arm dynein light chain 1	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
Oxysterol-binding protein-like	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
Tubby C-terminal domain-like	0	DIRECT
Cystatin/monellin	0	DIRECT
CO dehydrogenase molybdoprotein N-domain-like	0	DIRECT
14-3-3 protein	0	DIRECT
ADP-ribosylation	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Proton glutamate symport protein	0	DIRECT
ARID-like	0	DIRECT
GAT-like domain	0	DIRECT
Hormone receptor domain	0	DIRECT
Annexin	0	DIRECT
Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)	0	DIRECT
LEM domain	0	DIRECT
Acid phosphatase/Vanadium-dependent haloperoxidase	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
PEP carboxykinase N-terminal domain	0	DIRECT
R3H domain	0	DIRECT
LysM domain	0	DIRECT
CBD9-like	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
Nucleoporin domain	0	DIRECT
DNA repair protein MutS, domain III	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
SWIB/MDM2 domain	0	DIRECT
Fibrinogen C-terminal domain-like	0	DIRECT
Tricorn protease domain 2	0	DIRECT
Pepsin inhibitor-3	0	DIRECT
Cadherin-like	0	DIRECT
PurM N-terminal domain-like	0	DIRECT
VPS9 domain	0	DIRECT
Complement control module/SCR domain	0	DIRECT
MFPT repeat-like	0	DIRECT
Galactose oxidase, central domain	0	DIRECT
Carbohydrate phosphatase	0	DIRECT
PHM/PNGase F	0	DIRECT
FF domain	0	DIRECT
Blood coagulation inhibitor (disintegrin)	0	DIRECT
3-carboxy-cis,cis-mucoante lactonizing enzyme	0	DIRECT
PK beta-barrel domain-like	0	DIRECT
Ran binding protein zinc finger-like	0	DIRECT
GAS2 domain-like	0	DIRECT
AN1-like Zinc finger	0	DIRECT
Nop domain	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
PurM C-terminal domain-like	0	DIRECT
PABC (PABP) domain	0	DIRECT
Transducin (heterotrimeric G protein), gamma chain	0	DIRECT
Restriction endonuclease-like	0	DIRECT
eIF4e-like	0	DIRECT
Rap/Ran-GAP	0	DIRECT
Molybdenum cofactor-binding domain	0	DIRECT
SAND domain-like	0	DIRECT
MgtE membrane domain-like	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
TGS-like	0	DIRECT
Small-conductance potassium channel	0	DIRECT
Chitinase insertion domain	0	DIRECT
Doublecortin (DC)	0	DIRECT
CO dehydrogenase ISP C-domain like	0	DIRECT
GYF domain	0	DIRECT
Phosphoenolpyruvate/pyruvate domain	0	DIRECT
SPOC domain-like	0	DIRECT
Ribokinase-like	0	DIRECT
Arginase/deacetylase	0	DIRECT
WGR domain-like	0	DIRECT
FAD-linked oxidases, C-terminal domain	0	DIRECT
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	0	DIRECT
Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit	0	DIRECT
Phoshotransferase/anion transport protein	0	DIRECT
Domain of poly(ADP-ribose) polymerase	0	DIRECT
FAD-binding/transporter-associated domain-like	0	DIRECT
Terpenoid cyclases/Protein prenyltransferases	0	DIRECT
PEBP-like	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
PapD-like	0.00001741	DIRECT
Mitochondrial carrier	0.0008515	DIRECT
Chromo domain-like	0.008306	INHERITED FROM: maternal effect sterile
SET domain	0.3253	INHERITED FROM: maternal effect sterile
RNA-binding domain, RBD	0.9807	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)
56176,55103 56176 - FAD-binding/transporter-associated domain-like 55103 - FAD-linked oxidases, C-terminal domain	0	DIRECT
47473,51695 47473 - EF-hand 51695 - PLC-like phosphodiesterases	0	DIRECT
48425,50729 48425 - Sec7 domain 50729 - PH domain-like	0	DIRECT
51971,54373 51971 - Nucleotide-binding domain 54373 - FAD-linked reductases, C-terminal domain	0	DIRECT
48464,89009 48464 - ENTH/VHS domain 89009 - GAT-like domain	0	DIRECT
81324,53850 81324 - Voltage-gated potassium channels 53850 - Periplasmic binding protein-like II	0	DIRECT
47741,56176 47741 - CO dehydrogenase ISP C-domain like 56176 - FAD-binding/transporter-associated domain-like	0	DIRECT
54897,53187 54897 - Protease propeptides/inhibitors 53187 - Zn-dependent exopeptidases	0	DIRECT
81383,52047 81383 - F-box domain 52047 - RNI-like	0	DIRECT
54495,46934 54495 - UBC-like 46934 - UBA-like	0	DIRECT
54665,56003 54665 - CO dehydrogenase molybdoprotein N-domain-like 56003 - Molybdenum cofactor-binding domain	0	DIRECT
55486,50923 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0	DIRECT
49742,49742 49742 - PHM/PNGase F 49742 - PHM/PNGase F	0	DIRECT
51338,51556 51338 - Composite domain of metallo-dependent hydrolases 51556 - Metallo-dependent hydrolases	0	DIRECT
50978,50998 50978 - WD40 repeat-like 50998 - Quinoprotein alcohol dehydrogenase-like	0	DIRECT
56601,48403 56601 - beta-lactamase/transpeptidase-like 48403 - Ankyrin repeat	0	DIRECT
81324,81296 81324 - Voltage-gated potassium channels 81296 - E set domains	0	DIRECT
144232,82199 144232 - HIT/MYND zinc finger-like 82199 - SET 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
47587,56399 47587 - Domain of poly(ADP-ribose) polymerase 56399 - ADP-ribosylation	0	DIRECT
47203,47203 47203 - Acyl-CoA dehydrogenase C-terminal domain-like 47203 - Acyl-CoA dehydrogenase C-terminal domain-like	0	DIRECT
49562,48371 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48371 - ARM repeat	0	DIRECT
53187,55031 53187 - Zn-dependent exopeptidases 55031 - Bacterial exopeptidase dimerisation domain	0	DIRECT
55920,46785 55920 - Creatinase/aminopeptidase 46785 - "Winged helix" DNA-binding domain	0	DIRECT
55326,56042 55326 - PurM N-terminal domain-like 56042 - PurM C-terminal domain-like	0	DIRECT
48334,52540 48334 - DNA repair protein MutS, domain III 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
54534,54534 54534 - FKBP-like 54534 - FKBP-like	0	DIRECT
141739,141739 141739 - MFPT repeat-like 141739 - MFPT repeat-like	0	DIRECT
47473,103506 47473 - EF-hand 103506 - Mitochondrial carrier	0	DIRECT
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like	0	DIRECT
57196,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
81698,81698 81698 - FF domain 81698 - FF domain	0	DIRECT
51445,54556 51445 - (Trans)glycosidases 54556 - Chitinase insertion domain	0	DIRECT
54001,49758 54001 - Cysteine proteinases 49758 - Calpain large subunit, middle domain (domain III)	0	DIRECT
161093,161093 161093 - MgtE membrane domain-like 161093 - MgtE membrane domain-like	0	DIRECT
55973,55973 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase	0	DIRECT
55394,55394 55394 - Bactericidal permeability-increasing protein, BPI 55394 - Bactericidal permeability-increasing protein, BPI	0	DIRECT
57903,51197 57903 - FYVE/PHD zinc finger 51197 - Clavaminate synthase-like	0	DIRECT
56112,48371 56112 - Protein kinase-like (PK-like) 48371 - ARM repeat	0	DIRECT
47769,47769 47769 - SAM/Pointed domain 47769 - SAM/Pointed domain	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
48371,56112 48371 - ARM repeat 56112 - Protein kinase-like (PK-like)	0	DIRECT
57850,117839 57850 - RING/U-box 117839 - WWE domain	0	DIRECT
48403,52151 48403 - Ankyrin repeat 52151 - FabD/lysophospholipase-like	0	DIRECT
48179,48179 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
141673,50800 141673 - MOSC N-terminal domain-like 50800 - PK beta-barrel domain-like	0	DIRECT
161111,160240 161111 - Cation efflux protein transmembrane domain-like 160240 - Cation efflux protein cytoplasmic domain-like	0	DIRECT
52540,81271 52540 - P-loop containing nucleoside triphosphate hydrolases 81271 - TGS-like	0	DIRECT
57863,48403 57863 - ArfGap/RecO-like zinc finger 48403 - Ankyrin repeat	0	DIRECT
55486,57552 55486 - Metalloproteases ("zincins"), catalytic domain 57552 - Blood coagulation inhibitor (disintegrin)	0	DIRECT
57535,57535 57535 - Complement control module/SCR domain 57535 - Complement control module/SCR domain	0	DIRECT
54292,47741 54292 - 2Fe-2S ferredoxin-like 47741 - CO dehydrogenase ISP C-domain like	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)
56436,49854,49854 56436 - C-type lectin-like 49854 - Spermadhesin, CUB domain 49854 - Spermadhesin, CUB domain	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
57535,57535,57535 57535 - Complement control module/SCR domain 57535 - Complement control module/SCR domain 57535 - Complement control module/SCR domain	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
49562,48371,56112 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48371 - ARM repeat 56112 - Protein kinase-like (PK-like)	0	DIRECT
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like	0	DIRECT
47090,55486,50923 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0	DIRECT
50729,47473,51695 50729 - PH domain-like 47473 - EF-hand 51695 - PLC-like phosphodiesterases	0	DIRECT
55973,55973,55973 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase	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
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
48726,49265,48726 48726 - Immunoglobulin 49265 - Fibronectin type III 48726 - Immunoglobulin	0	DIRECT
57567,57567,57567 57567 - Serine protease inhibitors 57567 - Serine protease inhibitors 57567 - Serine protease inhibitors	0	DIRECT
50044,50044,50044 50044 - SH3-domain 50044 - SH3-domain 50044 - SH3-domain	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.