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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 EC term (SDEC level: Informative)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
KA1-like	0	DIRECT
L domain-like	0	DIRECT
Concanavalin A-like lectins/glucanases	0	DIRECT
TAF(II)230 TBP-binding fragment	0	DIRECT
FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)	0	DIRECT
DBL homology domain (DH-domain)	0	DIRECT
alpha-D-mannose-specific plant lectins	0	DIRECT
MAST3 pre-PK domain-like	0	DIRECT
Quinoprotein alcohol dehydrogenase-like	0	DIRECT
RNI-like	0	DIRECT
Ankyrin repeat	0	DIRECT
Spectrin repeat	0	DIRECT
DEATH domain	0	DIRECT
Tricorn protease domain 2	0	DIRECT
Penicillin-binding protein 2x (pbp-2x), c-terminal domain	0	DIRECT
G protein-binding domain	0	DIRECT
RCC1/BLIP-II	0	DIRECT
Doublecortin (DC)	0	DIRECT
SMAD/FHA domain	5.111e-16	DIRECT
MIT domain	0.00000000000002415	DIRECT
CRAL/TRIO domain	0.0000000000001107	DIRECT
TPR-like	0.0000000000007194	DIRECT
Myosin rod fragments	0.00000000001292	DIRECT
ARM repeat	0.0000000001055	DIRECT
PX domain	0.000000001944	DIRECT
EF-hand	0.00000007194	DIRECT
GTPase activation domain, GAP	0.0000000996	DIRECT
UBA-like	0.0000001894	DIRECT
PYP-like sensor domain (PAS domain)	0.0000002228	DIRECT
Chaperone J-domain	0.0000008589	DIRECT
Cyclin-like	0.000006743	DIRECT
C-type lectin-like	0.000007587	DIRECT
PDZ domain-like	0.0004172	DIRECT
Bromodomain	0.0004375	DIRECT

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

SCOP term	FDR (all)	Annotation (direct or inherited)
alpha-D-mannose-specific plant lectins	0	DIRECT
Polygalacturonase inhibiting protein PGIP	0	DIRECT
RIO1-like kinases	0	DIRECT
LIM domain	0	DIRECT
Ssp2 C-terminal domain-like	0	DIRECT
Myosin rod fragments	0	DIRECT
MAST3 pre-PK domain-like	0	DIRECT
Legume lectins	0	DIRECT
Doublecortin (DC)	0	DIRECT
beta-lactamase inhibitor protein-II, BLIP-II	0	DIRECT
FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)	0	DIRECT
Ankyrin repeat	0	DIRECT
Phoshoinositide 3-kinase (PI3K), catalytic domain	0	DIRECT
TAF(II)230 TBP-binding fragment	0	DIRECT
Histidine kinase	0	DIRECT
Kinase associated domain 1, KA1	0	DIRECT
RhoA-binding domain	0	DIRECT
DEATH domain, DD	0	DIRECT
Cyclin	0	DIRECT
Spectrin repeat	0	DIRECT
DBL homology domain (DH-domain)	0	DIRECT
FHA domain	3.693e-16	DIRECT
RWD domain	0.000000000000002188	DIRECT
MIT domain	0.000000000000009397	DIRECT
Regulator of chromosome condensation RCC1	0.0000000000004089	DIRECT
Motor proteins	0.00000000001302	DIRECT
Quinoprotein alcohol dehydrogenase-like	0.00000000005121	DIRECT
PX domain	0.000000001029	DIRECT
Flavin-binding PAS domain	0.000000001809	DIRECT
Calmodulin-like	0.00000004874	DIRECT
BCR-homology GTPase activation domain (BH-domain)	0.00000009962	DIRECT
Phoshoinositide 3-kinase (PI3K) helical domain	0.0000001002	DIRECT
Chaperone J-domain	0.0000008289	DIRECT
Tetratricopeptide repeat (TPR)	0.000001892	DIRECT
Sulfatase-modifying factor-like	0.000003044	DIRECT
UBA domain	0.00003211	DIRECT
Bromodomain	0.0004533	DIRECT
Ras-binding domain, RBD	0.0005776	DIRECT
Caspase recruitment domain, CARD	0.0006952	DIRECT

Trees by TreeVector

A presence/absence matrix is generated using protein domain architecture data for all genomes in SUPERFAMILY. The PAUP software is used to produce a single, large tree topology using heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as if individual trees had been produced. However, this data is extracted from the single large tree. This produces a higher quality topology than if the trees had been produced on their own, and allows the trees to be displayed instantly.

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

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Tricorn protease domain 2	0	DIRECT
alpha-D-mannose-specific plant lectins	0	DIRECT
G protein-binding domain	0	DIRECT
Quinoprotein alcohol dehydrogenase-like	0	DIRECT
DEATH domain	0	DIRECT
Doublecortin (DC)	0	DIRECT
RNI-like	0	DIRECT
Concanavalin A-like lectins/glucanases	0	DIRECT
KA1-like	0	DIRECT
MAST3 pre-PK domain-like	0	DIRECT
DBL homology domain (DH-domain)	0	DIRECT
RCC1/BLIP-II	0	DIRECT
TAF(II)230 TBP-binding fragment	0	DIRECT
Ankyrin repeat	0	DIRECT
Penicillin-binding protein 2x (pbp-2x), c-terminal domain	0	DIRECT
L domain-like	0	DIRECT
Spectrin repeat	0	DIRECT
FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)	0	DIRECT
SMAD/FHA domain	3.548e-16	DIRECT
MIT domain	0.00000000000001703	DIRECT
CRAL/TRIO domain	0.00000000000007848	DIRECT
TPR-like	0.000000000000515	DIRECT
Myosin rod fragments	0.00000000000936	DIRECT
ARM repeat	0.00000000007751	DIRECT
PX domain	0.000000001451	DIRECT
EF-hand	0.00000005488	DIRECT
GTPase activation domain, GAP	0.0000000761	DIRECT
UBA-like	0.0000001454	DIRECT
PYP-like sensor domain (PAS domain)	0.0000001713	DIRECT
Chaperone J-domain	0.000000668	DIRECT
Cyclin-like	0.000005309	DIRECT
C-type lectin-like	0.000005981	DIRECT
PDZ domain-like	0.0003403	DIRECT
Bromodomain	0.000357	DIRECT

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

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
53850,56112 53850 - Periplasmic binding protein-like II 56112 - Protein kinase-like (PK-like)	0	DIRECT
55021,56112 55021 - ACT-like 56112 - Protein kinase-like (PK-like)	0	DIRECT
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0	DIRECT
56112,52799 56112 - Protein kinase-like (PK-like) 52799 - (Phosphotyrosine protein) phosphatases II	0	DIRECT
56112,50998 56112 - Protein kinase-like (PK-like) 50998 - Quinoprotein alcohol dehydrogenase-like	0	DIRECT
47212,56112 47212 - FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) 56112 - Protein kinase-like (PK-like)	0	DIRECT
47370,47370 47370 - Bromodomain 47370 - Bromodomain	0	DIRECT
48371,48371 48371 - ARM repeat 48371 - ARM repeat	0	DIRECT
47986,56112 47986 - DEATH domain 56112 - Protein kinase-like (PK-like)	0	DIRECT
56112,48403 56112 - Protein kinase-like (PK-like) 48403 - Ankyrin repeat	0	DIRECT
49879,56112 49879 - SMAD/FHA domain 56112 - Protein kinase-like (PK-like)	0	DIRECT
49265,48726 49265 - Fibronectin type III 48726 - Immunoglobulin	0	DIRECT
52047,56112 52047 - RNI-like 56112 - Protein kinase-like (PK-like)	0	DIRECT
55073,56112 55073 - Nucleotide cyclase 56112 - Protein kinase-like (PK-like)	0	DIRECT
56112,116846 56112 - Protein kinase-like (PK-like) 116846 - MIT domain	0	DIRECT
52047,52047 52047 - RNI-like 52047 - RNI-like	0	DIRECT
56112,48452 56112 - Protein kinase-like (PK-like) 48452 - TPR-like	0	DIRECT
51110,51110 51110 - alpha-D-mannose-specific plant lectins 51110 - alpha-D-mannose-specific plant lectins	0	DIRECT
50729,69322 50729 - PH domain-like 69322 - Tricorn protease domain 2	0	DIRECT
57716,50156 57716 - Glucocorticoid receptor-like (DNA-binding domain) 50156 - PDZ domain-like	0	DIRECT
-9,-7 -9 - PDB -7 - CATH	0	DIRECT
56112,50985 56112 - Protein kinase-like (PK-like) 50985 - RCC1/BLIP-II	0	DIRECT
53067,56112 53067 - Actin-like ATPase domain 56112 - Protein kinase-like (PK-like)	0	DIRECT
56112,48371 56112 - Protein kinase-like (PK-like) 48371 - ARM repeat	0	DIRECT
46785,56112 46785 - "Winged helix" DNA-binding domain 56112 - Protein kinase-like (PK-like)	0	DIRECT
56112,90257 56112 - Protein kinase-like (PK-like) 90257 - Myosin rod fragments	0	DIRECT
50998,56112 50998 - Quinoprotein alcohol dehydrogenase-like 56112 - Protein kinase-like (PK-like)	0	DIRECT
116846,116846 116846 - MIT domain 116846 - MIT domain	0	DIRECT
49899,56112 49899 - Concanavalin A-like lectins/glucanases 56112 - Protein kinase-like (PK-like)	0	DIRECT
52058,52058 52058 - L domain-like 52058 - L domain-like	0	DIRECT
50156,56112 50156 - PDZ domain-like 56112 - Protein kinase-like (PK-like)	0	DIRECT
56112,54928 56112 - Protein kinase-like (PK-like) 54928 - RNA-binding domain, RBD	0	DIRECT
52087,46966 52087 - CRAL/TRIO domain 46966 - Spectrin repeat	0	DIRECT
49562,48350 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48350 - GTPase activation domain, GAP	0	DIRECT
54236,57889 54236 - Ubiquitin-like 57889 - Cysteine-rich domain	0	DIRECT
52058,52047 52058 - L domain-like 52047 - RNI-like	0	DIRECT
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat	0	DIRECT
52058,52540 52058 - L domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
52058,56112 52058 - L domain-like 56112 - Protein kinase-like (PK-like)	0	DIRECT
50729,57889 50729 - PH domain-like 57889 - Cysteine-rich domain	0	DIRECT
56112,103243 56112 - Protein kinase-like (PK-like) 103243 - KA1-like	0	DIRECT
50044,48065 50044 - SH3-domain 48065 - DBL homology domain (DH-domain)	0	DIRECT
89837,89837 89837 - Doublecortin (DC) 89837 - Doublecortin (DC)	0	DIRECT
48726,56112 48726 - Immunoglobulin 56112 - Protein kinase-like (PK-like)	0	DIRECT
64268,56112 64268 - PX domain 56112 - Protein kinase-like (PK-like)	0	DIRECT
48371,56112 48371 - ARM repeat 56112 - Protein kinase-like (PK-like)	0	DIRECT
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0	DIRECT
56112,55681 56112 - Protein kinase-like (PK-like) 55681 - Class II aaRS and biotin synthetases	0	DIRECT
48403,56112 48403 - Ankyrin repeat 56112 - Protein kinase-like (PK-like)	0	DIRECT
52047,52058 52047 - RNI-like 52058 - L domain-like	0	DIRECT
50729,50044 50729 - PH domain-like 50044 - SH3-domain	0.0000000000008289	DIRECT
56112,50044 56112 - Protein kinase-like (PK-like) 50044 - SH3-domain	0.0000000002489	DIRECT
49562,48371 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48371 - ARM repeat	0.00000003441	DIRECT
56112,47473 56112 - Protein kinase-like (PK-like) 47473 - EF-hand	0.00000005488	DIRECT
56112,52540 56112 - Protein kinase-like (PK-like) 52540 - P-loop containing nucleoside triphosphate hydrolases	0.0000002276	DIRECT
48403,47769 48403 - Ankyrin repeat 47769 - SAM/Pointed domain	0.000001529	DIRECT
54768,54768 54768 - dsRNA-binding domain-like 54768 - dsRNA-binding domain-like	0.000002999	DIRECT
53850,53850 53850 - Periplasmic binding protein-like II 53850 - Periplasmic binding protein-like II	0.000008691	DIRECT
48403,52540 48403 - Ankyrin repeat 52540 - P-loop containing nucleoside triphosphate hydrolases	0.00001344	DIRECT
52799,49562 52799 - (Phosphotyrosine protein) phosphatases II 49562 - C2 domain (Calcium/lipid-binding domain, CaLB)	0.00005225	DIRECT
56112,56112 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like)	0.0003403	DIRECT

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

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
52058,52047,52058 52058 - L domain-like 52047 - RNI-like 52058 - L domain-like	0	DIRECT
48065,50729,50044 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like 50044 - SH3-domain	0	DIRECT
50044,48065,50729 50044 - SH3-domain 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0	DIRECT
48726,49265,48726 48726 - Immunoglobulin 49265 - Fibronectin type III 48726 - Immunoglobulin	0	DIRECT
57716,50156,56112 57716 - Glucocorticoid receptor-like (DNA-binding domain) 50156 - PDZ domain-like 56112 - Protein kinase-like (PK-like)	0	DIRECT
57716,57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0	DIRECT
52058,52058,56112 52058 - L domain-like 52058 - L domain-like 56112 - Protein kinase-like (PK-like)	0	DIRECT
53850,53850,56112 53850 - Periplasmic binding protein-like II 53850 - Periplasmic binding protein-like II 56112 - Protein kinase-like (PK-like)	0	DIRECT
-9,-7,56112 -9 - PDB -7 - CATH 56112 - Protein kinase-like (PK-like)	0	DIRECT
49265,48726,49265 49265 - Fibronectin type III 48726 - Immunoglobulin 49265 - Fibronectin type III	0	DIRECT
52087,46966,46966 52087 - CRAL/TRIO domain 46966 - Spectrin repeat 46966 - Spectrin repeat	0	DIRECT
52047,52047,52058 52047 - RNI-like 52047 - RNI-like 52058 - L domain-like	0	DIRECT
57716,57716,50156 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) 50156 - PDZ domain-like	0	DIRECT
56112,52799,49562 56112 - Protein kinase-like (PK-like) 52799 - (Phosphotyrosine protein) phosphatases II 49562 - C2 domain (Calcium/lipid-binding domain, CaLB)	0	DIRECT
56112,116846,116846 56112 - Protein kinase-like (PK-like) 116846 - MIT domain 116846 - MIT domain	0	DIRECT
52058,52047,56112 52058 - L domain-like 52047 - RNI-like 56112 - Protein kinase-like (PK-like)	0	DIRECT
52047,52058,56112 52047 - RNI-like 52058 - L domain-like 56112 - Protein kinase-like (PK-like)	0	DIRECT
48726,48726,56112 48726 - Immunoglobulin 48726 - Immunoglobulin 56112 - Protein kinase-like (PK-like)	0	DIRECT
56112,48726,48726 56112 - Protein kinase-like (PK-like) 48726 - Immunoglobulin 48726 - Immunoglobulin	0	DIRECT
56112,48403,52540 56112 - Protein kinase-like (PK-like) 48403 - Ankyrin repeat 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
52047,52047,56112 52047 - RNI-like 52047 - RNI-like 56112 - Protein kinase-like (PK-like)	0	DIRECT
57889,50729,69322 57889 - Cysteine-rich domain 50729 - PH domain-like 69322 - Tricorn protease domain 2	0	DIRECT
49265,48726,48726 49265 - Fibronectin type III 48726 - Immunoglobulin 48726 - Immunoglobulin	0.0000000000001312	DIRECT
52058,52058,52058 52058 - L domain-like 52058 - L domain-like 52058 - L domain-like	0.000000000001022	DIRECT
49562,48371,56112 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48371 - ARM repeat 56112 - Protein kinase-like (PK-like)	0.00000002715	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.