•  SEARCH

  • Keyword search
  • Sequence search
• 
  

•  BROWSE

  •   Organisms
  • Taxonomy
  • Statistics
  •   SCOP
  • Hierarchy
  •   Ontologies
  • GO
  • EC
  • Phenotype
• 
  

•  TOOLS

  • Compare genomes
  • Phylogenetic trees
  • Web services
  • Downloads
• 
  

•  ABOUT

  • Description
  • Publications
  • Documentation
• 
  

•  HELP

  • User support
  • Contact us
  • Email list
  • Sitemap

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

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

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

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

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

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

Superfamily domains annotated to this KW term (SDKW level: Informative)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
RCC1/BLIP-II	0	DIRECT
USP8 N-terminal domain-like	0	DIRECT
SAP domain	0	DIRECT
TRAF domain-like	0	DIRECT
UBC-like	0	DIRECT
PA domain	0	DIRECT
TPR-like	0	DIRECT
RNI-like	0	DIRECT
Macro domain-like	0	DIRECT
Skp1 dimerisation domain-like	0	DIRECT
MoaD/ThiS	0	DIRECT
Galactose oxidase, central domain	0	DIRECT
Galactose-binding domain-like	0	DIRECT
WW domain	0	DIRECT
SOCS box-like	0	DIRECT
RING/U-box	0	DIRECT
Activating enzymes of the ubiquitin-like proteins	0	DIRECT
Coronavirus NSP7-like	0	DIRECT
Mib/herc2 domain-like	0	DIRECT
SH2 domain	0	DIRECT
F-box domain	0	DIRECT
EndoU-like	0	DIRECT
Calcyclin-binding protein-like	0	DIRECT
Ankyrin repeat	0	DIRECT
Cysteine proteinases	0	DIRECT
WWE domain	0	DIRECT
CCCH zinc finger	0	DIRECT
NHL repeat	0	DIRECT
Hect, E3 ligase catalytic domain	0	DIRECT
UBA-like	0	DIRECT
ARM repeat	0	DIRECT
DUSP-like	0	DIRECT
SARS Nsp1-like	0	DIRECT
Ubiquitin-like	0	DIRECT
NSP3A-like	0	DIRECT
POZ domain	0	DIRECT
N-terminal domain of cbl (N-cbl)	0	DIRECT
JAB1/MPN domain	0	DIRECT
Inhibitor of apoptosis (IAP) repeat	0	DIRECT
Cullin homology domain	0	DIRECT
Kelch motif	0	DIRECT
Coronavirus NSP8-like	0	DIRECT
FYVE/PHD zinc finger	0	DIRECT
WD40 repeat-like	0	DIRECT
VHL	0	DIRECT
B-box zinc-binding domain	0	DIRECT
C2 domain (Calcium/lipid-binding domain, CaLB)	0	DIRECT
Ran binding protein zinc finger-like	0	DIRECT
Replicase NSP9	0	DIRECT
Concanavalin A-like lectins/glucanases	0	DIRECT
Coronavirus NSP10-like	0	DIRECT
Cullin repeat-like	0	DIRECT
Trypsin-like serine proteases	1.514e-14	DIRECT
Pentapeptide repeat-like	1.353e-13	DIRECT
ApaG-like	1.503e-11	DIRECT
XPC-binding domain	4.513e-11	DIRECT
SMAD/FHA domain	1.698e-10	DIRECT
Quinoprotein alcohol dehydrogenase-like	3.852e-10	DIRECT
SMI1/KNR4-like	1.766e-09	DIRECT
SWIB/MDM2 domain	3.171e-09	DIRECT
PUG domain-like	5.54e-09	DIRECT
HIT/MYND zinc finger-like	6.39e-09	DIRECT
HSP20-like chaperones	1.423e-07	DIRECT
TAZ domain	4.15e-07	DIRECT
MIT domain	1.228e-06	DIRECT
VPS9 domain	4.361e-06	DIRECT
Cap-Gly domain	1.675e-05	DIRECT
Formin homology 2 domain (FH2 domain)	0.0007081	DIRECT
E set domains	0.000807	DIRECT

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

SCOP term	FDR (all)	Annotation (direct or inherited)
Coronavirus NSP8-like	0	DIRECT
Nsp15 C-terminal domain-like	0	DIRECT
SOCS box-like	0	DIRECT
Cyclin A/CDK2-associated p19, Skp2	0	DIRECT
Molybdenum cofactor biosynthesis protein MoeB	0	DIRECT
Ubiquitin thiolesterase protein OTUB2 (Otubain-2)	0	DIRECT
Ran binding protein zinc finger-like	0	DIRECT
Replicase NSP9	0	DIRECT
C9orf74 homolog	0	DIRECT
Mib/herc2 domain	0	DIRECT
Siah interacting protein N terminal domain-like	0	DIRECT
HEAT repeat	0	DIRECT
M48USP-like	0	DIRECT
B-box zinc-binding domain	0	DIRECT
SAP domain	0	DIRECT
WW domain	0	DIRECT
CPH domain	0	DIRECT
Regulator of chromosome condensation RCC1	0	DIRECT
UBC-related	0	DIRECT
Adenain-like	0	DIRECT
Filamin repeat (rod domain)	0	DIRECT
WD40-repeat	0	DIRECT
SH2 domain	0	DIRECT
RING finger domain, C3HC4	0	DIRECT
Cullin homology domain	0	DIRECT
NHL repeat	0	DIRECT
NSP3A-like	0	DIRECT
Macro domain	0	DIRECT
Skp1 dimerisation domain-like	0	DIRECT
Kelch motif	0	DIRECT
CCCH zinc finger	0	DIRECT
ZZ domain	0	DIRECT
Ubiquitin-related	0	DIRECT
Coronavirus NSP10-like	0	DIRECT
JAB1/MPN domain	0	DIRECT
Zf-UBP	0	DIRECT
N-terminal domain of cbl (N-cbl)	0	DIRECT
WWE domain	0	DIRECT
BM-002-like	0	DIRECT
F-box domain	0	DIRECT
MATH domain	0	DIRECT
GS domain	0	DIRECT
APG12-like	0	DIRECT
Ubiquitin carboxyl-terminal hydrolase UCH-L	0	DIRECT
UBA domain	0	DIRECT
Ubiquitin carboxyl-terminal hydrolase, UCH	0	DIRECT
PHD domain	0	DIRECT
BTB/POZ domain	0	DIRECT
VHL	0	DIRECT
Cullin repeat	0	DIRECT
Autophagin-like	0	DIRECT
U-box	0	DIRECT
Nsp15 N-terminal domain-like	0	DIRECT
SARS Nsp1-like	0	DIRECT
Hect, E3 ligase catalytic domain	0	DIRECT
SRA domain-like	0	DIRECT
SCF ubiquitin ligase complex WHB domain	0	DIRECT
GABARAP-like	0	DIRECT
Variant RING domain	0	DIRECT
SPRY domain	0	DIRECT
UFC1-like	0	DIRECT
Coronavirus NSP7-like	0	DIRECT
F-box associated region, FBA	0	DIRECT
DUSP, domain in ubiquitin-specific proteases	0	DIRECT
USP8 N-terminal domain-like	0	DIRECT
Inhibitor of apoptosis (IAP) repeat	0	DIRECT
Ubiquitin activating enzymes (UBA)	0	DIRECT
Ankyrin repeat	0	DIRECT
APC10-like	0	DIRECT
Viral cysteine protease of trypsin fold	0	DIRECT
SIAH, seven in absentia homolog	0	DIRECT
Tetratricopeptide repeat (TPR)	1.843e-16	DIRECT
BRCT domain	5.48e-16	DIRECT
Pentapeptide repeats	3.586e-15	DIRECT
FHA domain	4.827e-15	DIRECT
Leucine rich effector protein YopM	3.548e-13	DIRECT
Armadillo repeat	1.024e-12	DIRECT
ApaG-like	8.763e-12	DIRECT
XPC-binding domain	2.3e-11	DIRECT
A20-like zinc finger	8.02e-11	DIRECT
SWIB/MDM2 domain	2.113e-10	DIRECT
Galactose oxidase, central domain	2.461e-10	DIRECT
PUG domain	3.295e-09	DIRECT
MYND zinc finger	3.79e-08	DIRECT
PA domain	6.517e-08	DIRECT
TAZ domain	2.438e-07	DIRECT
MIT domain	4.795e-07	DIRECT
EF-hand modules in multidomain proteins	6.13e-07	DIRECT
FYVE, a phosphatidylinositol-3-phosphate binding domain	8.877e-07	DIRECT
VPS9 domain	2.665e-06	DIRECT
SWIRM domain	3.207e-06	DIRECT
Cap-Gly domain	1.034e-05	DIRECT
Flavin-binding PAS domain	2.079e-05	DIRECT
First domain of FERM	0.0003148	DIRECT
PLC-like (P variant)	0.0008222	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 KW term (SPKW level: Informative)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
WD40 repeat-like	0	DIRECT
RING/U-box	0	DIRECT
Ubiquitin-like	0	DIRECT
Inhibitor of apoptosis (IAP) repeat	0	DIRECT
Skp1 dimerisation domain-like	0	DIRECT
ApaG-like	0	DIRECT
MoaD/ThiS	0	DIRECT
POZ domain	0	DIRECT
Ran binding protein zinc finger-like	0	DIRECT
Trypsin-like serine proteases	0	DIRECT
C2 domain (Calcium/lipid-binding domain, CaLB)	0	DIRECT
RCC1/BLIP-II	0	DIRECT
Concanavalin A-like lectins/glucanases	0	DIRECT
PA domain	0	DIRECT
ClpS-like	0	DIRECT
WW domain	0	DIRECT
NHL repeat	0	DIRECT
EndoU-like	0	DIRECT
F-box domain	0	DIRECT
Galactose-binding domain-like	0	DIRECT
WWE domain	0	DIRECT
Activating enzymes of the ubiquitin-like proteins	0	DIRECT
Coronavirus NSP10-like	0	DIRECT
Coronavirus NSP7-like	0	DIRECT
Kelch motif	0	DIRECT
Ankyrin repeat	0	DIRECT
SAP domain	0	DIRECT
ARM repeat	0	DIRECT
UBA-like	0	DIRECT
TPR-like	0	DIRECT
SOCS box-like	0	DIRECT
USP8 N-terminal domain-like	0	DIRECT
VHL	0	DIRECT
Coronavirus NSP8-like	0	DIRECT
N-terminal domain of cbl (N-cbl)	0	DIRECT
Galactose oxidase, central domain	0	DIRECT
JAB1/MPN domain	0	DIRECT
Calcyclin-binding protein-like	0	DIRECT
TRAF domain-like	0	DIRECT
RNI-like	0	DIRECT
Replicase NSP9	0	DIRECT
FYVE/PHD zinc finger	0	DIRECT
B-box zinc-binding domain	0	DIRECT
NSP3A-like	0	DIRECT
Mib/herc2 domain-like	0	DIRECT
DUSP-like	0	DIRECT
UBC-like	0	DIRECT
Hect, E3 ligase catalytic domain	0	DIRECT
CCCH zinc finger	0	DIRECT
Macro domain-like	0	DIRECT
Cullin homology domain	0	DIRECT
SARS Nsp1-like	0	DIRECT
Cullin repeat-like	0	DIRECT
Cysteine proteinases	0	DIRECT
SH2 domain	0	DIRECT
Quinoprotein alcohol dehydrogenase-like	5.696e-15	DIRECT
Pentapeptide repeat-like	4.588e-14	DIRECT
PUG domain-like	2.405e-11	DIRECT
XPC-binding domain	3.573e-11	DIRECT
HIT/MYND zinc finger-like	1.171e-10	DIRECT
SMAD/FHA domain	1.35e-10	DIRECT
SMI1/KNR4-like	6.318e-10	DIRECT
SWIB/MDM2 domain	2.558e-09	DIRECT
HSP20-like chaperones	1.166e-07	DIRECT
Cap-Gly domain	1.534e-07	DIRECT
TAZ domain	3.432e-07	DIRECT
VPS9 domain	6.915e-07	DIRECT
MIT domain	1.023e-06	DIRECT
Formin homology 2 domain (FH2 domain)	5.576e-06	DIRECT
Rhodanese/Cell cycle control phosphatase	9.686e-06	DIRECT
L domain-like	9.54e-05	DIRECT
Second domain of FERM	0.0001759	DIRECT
E set domains	0.000694	DIRECT

Supra-domains annotated to this KW term (SPKW level: 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)
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0	DIRECT
69572,69572 69572 - Activating enzymes of the ubiquitin-like proteins 69572 - Activating enzymes of the ubiquitin-like proteins	0	DIRECT
81383,117281 81383 - F-box domain 117281 - Kelch motif	0	DIRECT
143791,54236 143791 - DUSP-like 54236 - Ubiquitin-like	0	DIRECT
116846,81383 116846 - MIT domain 81383 - F-box domain	0	DIRECT
47668,47473 47668 - N-terminal domain of cbl (N-cbl) 47473 - EF-hand	0	DIRECT
159936,52949 159936 - NSP3A-like 52949 - Macro domain-like	0	DIRECT
52047,48371 52047 - RNI-like 48371 - ARM repeat	0	DIRECT
54695,50965 54695 - POZ domain 50965 - Galactose oxidase, central domain	0	DIRECT
49599,49599 49599 - TRAF domain-like 49599 - TRAF domain-like	0	DIRECT
81383,50998 81383 - F-box domain 50998 - Quinoprotein alcohol dehydrogenase-like	0	DIRECT
52025,57850 52025 - PA domain 57850 - RING/U-box	0	DIRECT
49599,54695 49599 - TRAF domain-like 54695 - POZ domain	0	DIRECT
57850,117839 57850 - RING/U-box 117839 - WWE domain	0	DIRECT
48371,49785 48371 - ARM repeat 49785 - Galactose-binding domain-like	0	DIRECT
54236,54236 54236 - Ubiquitin-like 54236 - Ubiquitin-like	0	DIRECT
74788,75632 74788 - Cullin repeat-like 75632 - Cullin homology domain	0	DIRECT
57850,49599 57850 - RING/U-box 49599 - TRAF domain-like	0	DIRECT
90229,90229 90229 - CCCH zinc finger 90229 - CCCH zinc finger	0	DIRECT
57850,159034 57850 - RING/U-box 159034 - Mib/herc2 domain-like	0	DIRECT
54695,48403 54695 - POZ domain 48403 - Ankyrin repeat	0	DIRECT
57850,57667 57850 - RING/U-box 57667 - beta-beta-alpha zinc fingers	0	DIRECT
48371,117839 48371 - ARM repeat 117839 - WWE domain	0	DIRECT
54001,46934 54001 - Cysteine proteinases 46934 - UBA-like	0	DIRECT
140367,143076 140367 - Coronavirus NSP7-like 143076 - Coronavirus NSP8-like	0	DIRECT
51045,56204 51045 - WW domain 56204 - Hect, E3 ligase catalytic domain	0	DIRECT
57850,57850 57850 - RING/U-box 57850 - RING/U-box	0	DIRECT
56112,57850 56112 - Protein kinase-like (PK-like) 57850 - RING/U-box	0	DIRECT
48403,158235 48403 - Ankyrin repeat 158235 - SOCS box-like	0	DIRECT
53335,142877 53335 - S-adenosyl-L-methionine-dependent methyltransferases 142877 - EndoU-like	0	DIRECT
54695,81382 54695 - POZ domain 81382 - Skp1 dimerisation domain-like	0	DIRECT
48403,48403 48403 - Ankyrin repeat 48403 - Ankyrin repeat	0	DIRECT
49879,57850 49879 - SMAD/FHA domain 57850 - RING/U-box	0	DIRECT
140106,49764 140106 - Calcyclin-binding protein-like 49764 - HSP20-like chaperones	0	DIRECT
159936,53335 159936 - NSP3A-like 53335 - S-adenosyl-L-methionine-dependent methyltransferases	0	DIRECT
101816,144246 101816 - Replicase NSP9 144246 - Coronavirus NSP10-like	0	DIRECT
48403,57850 48403 - Ankyrin repeat 57850 - RING/U-box	0	DIRECT
143076,101816 143076 - Coronavirus NSP8-like 101816 - Replicase NSP9	0	DIRECT
54236,54001 54236 - Ubiquitin-like 54001 - Cysteine proteinases	0	DIRECT
143791,143791 143791 - DUSP-like 143791 - DUSP-like	0	DIRECT
49265,49899 49265 - Fibronectin type III 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
52540,158235 52540 - P-loop containing nucleoside triphosphate hydrolases 158235 - SOCS box-like	0	DIRECT
47592,90209 47592 - SWIB/MDM2 domain 90209 - Ran binding protein zinc finger-like	0	DIRECT
55550,57850 55550 - SH2 domain 57850 - RING/U-box	0	DIRECT
75632,46785 75632 - Cullin homology domain 46785 - "Winged helix" DNA-binding domain	0	DIRECT
50978,158235 50978 - WD40 repeat-like 158235 - SOCS box-like	0	DIRECT
48403,48452 48403 - Ankyrin repeat 48452 - TPR-like	0	DIRECT
54001,143791 54001 - Cysteine proteinases 143791 - DUSP-like	0	DIRECT
159034,57850 159034 - Mib/herc2 domain-like 57850 - RING/U-box	0	DIRECT
90209,57850 90209 - Ran binding protein zinc finger-like 57850 - RING/U-box	0	DIRECT
54495,46934 54495 - UBC-like 46934 - UBA-like	0	DIRECT
74924,54001 74924 - Cap-Gly domain 54001 - Cysteine proteinases	0	DIRECT
55550,158235 55550 - SH2 domain 158235 - SOCS box-like	0	DIRECT
57850,48371 57850 - RING/U-box 48371 - ARM repeat	0	DIRECT
51045,51045 51045 - WW domain 51045 - WW domain	0	DIRECT
63748,48371 63748 - Tudor/PWWP/MBT 48371 - ARM repeat	0	DIRECT
57850,57845 57850 - RING/U-box 57845 - B-box zinc-binding domain	0	DIRECT
81383,49785 81383 - F-box domain 49785 - Galactose-binding domain-like	0	DIRECT
50965,117281 50965 - Galactose oxidase, central domain 117281 - Kelch motif	0	DIRECT
68906,57850 68906 - SAP domain 57850 - RING/U-box	0	DIRECT
81383,49899 81383 - F-box domain 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
48452,49764 48452 - TPR-like 49764 - HSP20-like chaperones	0	DIRECT
49562,51045 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 51045 - WW domain	0	DIRECT
81296,101898 81296 - E set domains 101898 - NHL repeat	0	DIRECT
81383,50978 81383 - F-box domain 50978 - WD40 repeat-like	0	DIRECT
81383,51126 81383 - F-box domain 51126 - Pectin lyase-like	0	DIRECT
47473,55550 47473 - EF-hand 55550 - SH2 domain	0	DIRECT
54236,90209 54236 - Ubiquitin-like 90209 - Ran binding protein zinc finger-like	0	DIRECT
81383,160631 81383 - F-box domain 160631 - SMI1/KNR4-like	0	DIRECT
49899,158235 49899 - Concanavalin A-like lectins/glucanases 158235 - SOCS box-like	0	DIRECT
81383,52047 81383 - F-box domain 52047 - RNI-like	0	DIRECT
49599,54001 49599 - TRAF domain-like 54001 - Cysteine proteinases	0	DIRECT
55785,81383 55785 - PYP-like sensor domain (PAS domain) 81383 - F-box domain	0	DIRECT
48452,48452 48452 - TPR-like 48452 - TPR-like	1.768e-16	DIRECT
52113,52113 52113 - BRCT domain 52113 - BRCT domain	5.546e-14	DIRECT
117839,117839 117839 - WWE domain 117839 - WWE domain	3.103e-12	DIRECT
50044,50044 50044 - SH3-domain 50044 - SH3-domain	3.989e-12	DIRECT
101238,46934 101238 - XPC-binding domain 46934 - UBA-like	3.573e-11	DIRECT
52047,52047 52047 - RNI-like 52047 - RNI-like	4.041e-11	DIRECT
74924,74924 74924 - Cap-Gly domain 74924 - Cap-Gly domain	6.318e-10	DIRECT
90209,90209 90209 - Ran binding protein zinc finger-like 90209 - Ran binding protein zinc finger-like	1.147e-09	DIRECT
48452,48403 48452 - TPR-like 48403 - Ankyrin repeat	4.523e-09	DIRECT
57903,47370 57903 - FYVE/PHD zinc finger 47370 - Bromodomain	9.847e-09	DIRECT
90229,57850 90229 - CCCH zinc finger 57850 - RING/U-box	1.53e-08	DIRECT
117281,117281 117281 - Kelch motif 117281 - Kelch motif	1.905e-08	DIRECT
51126,51126 51126 - Pectin lyase-like 51126 - Pectin lyase-like	5.967e-08	DIRECT
57850,52540 57850 - RING/U-box 52540 - P-loop containing nucleoside triphosphate hydrolases	2.349e-07	DIRECT
54236,47031 54236 - Ubiquitin-like 47031 - Second domain of FERM	2.9e-06	DIRECT
47031,50729 47031 - Second domain of FERM 50729 - PH domain-like	4.267e-05	DIRECT
48371,48371 48371 - ARM repeat 48371 - ARM repeat	0.0009824	DIRECT

Supra-domains annotated to this KW term (SPKW level: 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)
49599,49599,49599 49599 - TRAF domain-like 49599 - TRAF domain-like 49599 - TRAF domain-like	0	DIRECT
81383,51126,51126 81383 - F-box domain 51126 - Pectin lyase-like 51126 - Pectin lyase-like	0	DIRECT
81383,52047,52047 81383 - F-box domain 52047 - RNI-like 52047 - RNI-like	0	DIRECT
54695,50965,117281 54695 - POZ domain 50965 - Galactose oxidase, central domain 117281 - Kelch motif	0	DIRECT
140367,143076,101816 140367 - Coronavirus NSP7-like 143076 - Coronavirus NSP8-like 101816 - Replicase NSP9	0	DIRECT
57850,57850,57850 57850 - RING/U-box 57850 - RING/U-box 57850 - RING/U-box	0	DIRECT
48403,48403,158235 48403 - Ankyrin repeat 48403 - Ankyrin repeat 158235 - SOCS box-like	0	DIRECT
48403,48452,48403 48403 - Ankyrin repeat 48452 - TPR-like 48403 - Ankyrin repeat	0	DIRECT
47668,47473,55550 47668 - N-terminal domain of cbl (N-cbl) 47473 - EF-hand 55550 - SH2 domain	0	DIRECT
54001,143791,143791 54001 - Cysteine proteinases 143791 - DUSP-like 143791 - DUSP-like	0	DIRECT
51126,51126,51126 51126 - Pectin lyase-like 51126 - Pectin lyase-like 51126 - Pectin lyase-like	0	DIRECT
51045,51045,56204 51045 - WW domain 51045 - WW domain 56204 - Hect, E3 ligase catalytic domain	0	DIRECT
74788,75632,46785 74788 - Cullin repeat-like 75632 - Cullin homology domain 46785 - "Winged helix" DNA-binding domain	0	DIRECT
47473,55550,57850 47473 - EF-hand 55550 - SH2 domain 57850 - RING/U-box	0	DIRECT
90209,57850,57850 90209 - Ran binding protein zinc finger-like 57850 - RING/U-box 57850 - RING/U-box	0	DIRECT
159034,57850,159034 159034 - Mib/herc2 domain-like 57850 - RING/U-box 159034 - Mib/herc2 domain-like	0	DIRECT
143076,101816,144246 143076 - Coronavirus NSP8-like 101816 - Replicase NSP9 144246 - Coronavirus NSP10-like	0	DIRECT
51045,51045,51045 51045 - WW domain 51045 - WW domain 51045 - WW domain	0	DIRECT
57850,49599,49599 57850 - RING/U-box 49599 - TRAF domain-like 49599 - TRAF domain-like	0	DIRECT
57924,57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	3.516e-16	DIRECT
54236,54236,54236 54236 - Ubiquitin-like 54236 - Ubiquitin-like 54236 - Ubiquitin-like	3.516e-16	DIRECT
54236,47031,50729 54236 - Ubiquitin-like 47031 - Second domain of FERM 50729 - PH domain-like	2.244e-06	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.