•  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 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 FA term (Not in SDFA)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	DIRECT
RCC1/BLIP-II	0	DIRECT
NAD kinase/diacylglycerol kinase-like	0	DIRECT
SAP domain	0	DIRECT
PurM N-terminal domain-like	0	DIRECT
Cullin repeat-like	0	DIRECT
PriA/YqbF domain	0	DIRECT
Rhodanese/Cell cycle control phosphatase	0	DIRECT
Integrin domains	0	DIRECT
Arginase/deacetylase	0	DIRECT
Cytokine	0	DIRECT
PapD-like	0	DIRECT
Prefoldin	0	DIRECT
PurM C-terminal domain-like	0	DIRECT
RNase III domain-like	0	DIRECT
Plexin repeat	0	DIRECT
Tropomyosin	0	DIRECT
Tubulin C-terminal domain-like	0	DIRECT
Translation proteins	0	DIRECT
MIR domain	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Snake toxin-like	0	DIRECT
Metal cation-transporting ATPase, ATP-binding domain N	0	DIRECT
NHL repeat	0	DIRECT
TIMP-like	0	DIRECT
Terpenoid synthases	0	DIRECT
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	0	DIRECT
Tubulin nucleotide-binding domain-like	0	DIRECT
t-snare proteins	0	DIRECT
CAD & PB1 domains	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
Metallo-hydrolase/oxidoreductase	0	DIRECT
Smc hinge domain	0	DIRECT
Ferritin-like	0	DIRECT
Frizzled cysteine-rich domain	0	DIRECT
GINS helical bundle-like	0	DIRECT
alpha-catenin/vinculin-like	0	DIRECT
YVTN repeat-like/Quinoprotein amine dehydrogenase	0	DIRECT
Ribosomal protein S5 domain 2-like	0	DIRECT
post-AAA+ oligomerization domain-like	0	DIRECT
Mob1/phocein	0	DIRECT
YWTD domain	0	DIRECT
Aminoacid dehydrogenase-like, N-terminal domain	0	DIRECT
SMAD MH1 domain	0	DIRECT
B-box zinc-binding domain	0	DIRECT
Class II aaRS ABD-related	0	DIRECT
Cullin homology domain	0	DIRECT
Sema domain	0	DIRECT
Ankyrin repeat	0.01972	INHERITED FROM: Johnston organ neuron
dsRNA-binding domain-like	0.04385	INHERITED FROM: mushroom body intrinsic neuron || projection neuron || germline cell || Kenyon cell || uniglomerular antennal lobe projection neuron || mushroom body extrinsic neuron || female germline stem cell || adult antennal lobe projection neuron || persistent antennal lobe projection neuron || BAmv3 lineage neuron || antennal lobe projection neuron adPN || adult MBp lineage neuron || cholinergic neuron || unilateral ACT relay interneuron || alpha/beta Kenyon cell || antennal lobe projection neuron iPN
RING/U-box	0.05657	INHERITED FROM: garland cell || embryonic/larval garland cell
p53-like transcription factors	0.08745	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte
EGF/Laminin	0.1036	INHERITED FROM: nephrocyte || syncytium || sensory neuron || abdominal 3 acute muscle || sensory organ cell || abdominal 5 acute muscle || abdominal 2 acute muscle || muscle cell || pericardial cell || abdominal 6 acute muscle || hub cell || ventral longitudinal muscle || adult midgut progenitor cell || embryonic/larval midgut cell || abdominal 4 acute muscle || abdominal 7 acute muscle || embryonic/larval somatic muscle || tendon cell || eye photoreceptor cell stalk
Spectrin repeat	0.1178	INHERITED FROM: copper cell || midgut enterocyte || enterocyte
Calponin-homology domain, CH-domain	0.1315	INHERITED FROM: skeletal muscle of mesothorax || indirect flight muscle || flight muscle || skeletal muscle of thorax
BAR/IMD domain-like	0.1603	INHERITED FROM: NMJ bouton || bouton || synapse
Protein kinase-like (PK-like)	0.1741	INHERITED FROM: epithelial cell || intestinal stem cell
E set domains	0.2035	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte
Homeodomain-like	0.2331	INHERITED FROM: thoracic neuroblast || syncytium || uniglomerular antennal lobe projection neuron || prothoracic ventral intersegmental muscle || embryonic neuroblast || dorsal margin photoreceptor || muscle cell || adult antennal lobe projection neuron VM2 adPN || adult antennal lobe projection neuron VA1v adPN || interneuron || U neuron || embryonic/larval neuron
Transducin (alpha subunit), insertion domain	0.2433	INHERITED FROM: eo neuron
CoA-dependent acyltransferases	0.3085	INHERITED FROM: skeletal muscle of mesothorax || flight muscle || adult somatic muscle || skeletal muscle of thorax
PAZ domain	0.3085	INHERITED FROM: pole cell
Cadherin-like	0.3418	INHERITED FROM: photoreceptor cell R4
Immunoglobulin	0.3443	INHERITED FROM: cardioblast || embryonic heart cardioblast || adult pacemaker neuron || longitudinal muscle || LN period neuron || glial cell || embryonic cardioblast || leg taste bristle chemosensory neuron || interface glial cell || pacemaker neuron || LNv neuron
L domain-like	0.385	INHERITED FROM: BAlc1 lineage neuron
Cap-Gly domain	0.3911	INHERITED FROM: interneuron
Fibronectin type III	0.4445	INHERITED FROM: embryonic heart cardioblast || adult pacemaker neuron || LN period neuron || leg taste bristle chemosensory neuron || s-LNv neuron || pacemaker neuron || LNv neuron || dendritic arborizing neuron
ENTH/VHS domain	0.4869	INHERITED FROM: imaginal disc epithelial cell
Caspase-like	0.4869	INHERITED FROM: interommatidial precursor cell || male germline cell || peptidergic neuron
HAD-like	0.5134	INHERITED FROM: rhabdomere of eye photoreceptor cell
Metalloproteases ("zincins"), catalytic domain	0.5208	INHERITED FROM: embryonic heart cardioblast || embryonic cardioblast
SMAD/FHA domain	0.5404	INHERITED FROM: female germline stem cell
FYVE/PHD zinc finger	0.5627	INHERITED FROM: embryonic/larval garland cell
HLH, helix-loop-helix DNA-binding domain	0.5735	INHERITED FROM: 5-6I of thorax || sensory mother cell
Nuclear receptor ligand-binding domain	0.604	INHERITED FROM: mushroom body intrinsic neuron || supraesophageal ganglion neuron || interneuron
Cytochrome P450	0.7108	INHERITED FROM: embryonic/larval glial cell || neuropil associated CNS glial cell || larval neuropil glial cell || larval VNC neuropil glial cell || CNS glial cell || midline glial cell
Cyclin-like	0.7238	INHERITED FROM: female germline cell
Growth factor receptor domain	0.7349	INHERITED FROM: somatic cell of testis || neuroblast NB5-2 || dorsal acute muscle || hub cell || vMP2 neuron || head mesoderm derived embryonic hemocyte || GABAergic neuron || RP2sib neuron || embryonic hemocyte || stage 1 neuroblast || dMP2 neuron || photoreceptor cell R7
Orange domain-like	0.7792	INHERITED FROM: 5-6I of thorax || EL neuron || EG neuron
SH2 domain	0.7969	INHERITED FROM: histaminergic neuron || sensory organ cell || photoreceptor cell || optic lobe neuron || rhabdomeric photoreceptor cell || cyst progenitor cell || photoreceptor cell R7
Tetraspanin	0.844	INHERITED FROM: sensory mother cell
beta-beta-alpha zinc fingers	1	INHERITED FROM: serotonergic neuron || subesophageal ganglion neuron

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

SCOP term	FDR (all)	Annotation (direct or inherited)
SAP domain	0	DIRECT
Cullin repeat	0	DIRECT
Cell cycle control phosphatase, catalytic domain	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
SMAD MH1 domain	0	DIRECT
Fibroblast growth factors (FGF)	0	DIRECT
Group II chaperonin (CCT, TRIC), intermediate domain	0	DIRECT
PurM N-terminal domain-like	0	DIRECT
Tropomyosin	0	DIRECT
Integrin domains	0	DIRECT
POU-specific domain	0	DIRECT
MSP-like	0	DIRECT
Choline/Carnitine O-acyltransferase	0	DIRECT
BAR domain	0	DIRECT
Pointed domain	0	DIRECT
Tubulin, GTPase domain	0	DIRECT
2Fe-2S ferredoxin domains from multidomain proteins	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Sema domain	0	DIRECT
beta-CASP RNA-metabolising hydrolases	0	DIRECT
NHL repeat	0	DIRECT
PurM C-terminal domain-like	0	DIRECT
Histone deacetylase, HDAC	0	DIRECT
Proteasome subunits	0	DIRECT
Laminin-type module	0	DIRECT
Smc hinge domain	0	DIRECT
Extracellular domain of cell surface receptors	0	DIRECT
Isoprenyl diphosphate synthases	0	DIRECT
Laminin G-like module	0	DIRECT
YWTD domain	0	DIRECT
SPRY domain	0	DIRECT
MIR domain	0	DIRECT
RNase III catalytic domain-like	0	DIRECT
CAD domain	0	DIRECT
t-snare proteins	0	DIRECT
Eps15 homology domain (EH domain)	0	DIRECT
Anticodon-binding domain of Class II aaRS	0	DIRECT
MBT repeat	0	DIRECT
Prefoldin	0	DIRECT
B-box zinc-binding domain	0	DIRECT
Plexin repeat	0	DIRECT
Zf-UBP	0	DIRECT
Nitrogenase iron protein-like	0	DIRECT
Aminoacid dehydrogenase-like, C-terminal domain	0	DIRECT
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	DIRECT
Elongation factors	0	DIRECT
Tubulin, C-terminal domain	0	DIRECT
DNA polymerase III clamp loader subunits, C-terminal domain	0	DIRECT
Armadillo repeat	0	DIRECT
Tetramerization domain of potassium channels	0	DIRECT
SCF ubiquitin ligase complex WHB domain	0	DIRECT
CoA-binding domain	0	DIRECT
Inositol polyphosphate 5-phosphatase (IPP5)	0	DIRECT
Glutathione S-transferase (GST), N-terminal domain	0	DIRECT
Diacylglycerol kinase-like	0	DIRECT
Cullin homology domain	0	DIRECT
Transforming growth factor (TGF)-beta	0	DIRECT
Mob1/phocein	0	DIRECT
Arrestin/Vps26-like	0	DIRECT
Metal cation-transporting ATPase, ATP-binding domain N	0	DIRECT
Myb/SANT domain	0	DIRECT
Kelch motif	0	DIRECT
Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta	0	DIRECT
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	0	DIRECT
Frizzled cysteine-rich domain	0	DIRECT
Extended AAA-ATPase domain	0	DIRECT
Ankyrin repeat	0.02	INHERITED FROM: Johnston organ neuron || ventral multidendritic neuron
Double-stranded RNA-binding domain (dsRBD)	0.08231	INHERITED FROM: germline cell
Spectrin repeat	0.1058	INHERITED FROM: copper cell || oocyte || midgut enterocyte || enterocyte
Calponin-homology domain, CH-domain	0.1218	INHERITED FROM: skeletal muscle of mesothorax || indirect flight muscle || flight muscle || skeletal muscle of thorax
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.1742	INHERITED FROM: intestinal stem cell
Ubiquitin-related	0.2219	INHERITED FROM: mushroom body extrinsic neuron
Transducin (alpha subunit), insertion domain	0.2226	INHERITED FROM: eo neuron
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.2226	INHERITED FROM: head mesoderm derived embryonic hemocyte || lamellocyte || embryonic hemocyte
Protein kinases, catalytic subunit	0.2554	INHERITED FROM: somatic cell of ovary || intestinal stem cell || photoreceptor cell R8 of pale ommatidium
I set domains	0.2563	INHERITED FROM: cardioblast || adult descending neuron || embryonic heart cardioblast || abdominal neuron || adult pacemaker neuron || LN period neuron || embryonic cardioblast || embryonic/larval lateral glial cell || visceral muscle fiber || leg taste bristle chemosensory neuron || abdominal sensory neuron || mechanosensory system neuron || interface glial cell || s-LNv neuron || embryonic somatic muscle || gustatory system neuron || pacemaker neuron || LNv neuron || gustatory receptor neuron || dendritic arborizing neuron
RecA protein-like (ATPase-domain)	0.2864	INHERITED FROM: oocyte || presumptive oocyte || nurse cell || female germline cell
Pancreatic lipase, N-terminal domain	0.2864	INHERITED FROM: ganglion mother cell
SMAD domain	0.2864	INHERITED FROM: female germline stem cell || germline stem cell
ZZ domain	0.2864	INHERITED FROM: skeletal muscle of mesothorax || indirect flight muscle || flight muscle || adult somatic muscle || skeletal muscle of thorax
G proteins	0.3527	INHERITED FROM: hemocyte
Cap-Gly domain	0.3672	INHERITED FROM: interneuron
PDZ domain	0.3782	INHERITED FROM: somatic cell of ovary || epithelial cell
Motor proteins	0.3842	INHERITED FROM: germline cell
PLC-like (P variant)	0.3909	INHERITED FROM: dorsal multidendritic neuron || dorsal multidendritic neuron ddaC
Cadherin	0.3909	INHERITED FROM: photoreceptor cell R4 || outer photoreceptor cell
Fibronectin type III	0.4559	INHERITED FROM: embryonic heart cardioblast || abdominal neuron || adult pacemaker neuron || LN period neuron || leg taste bristle chemosensory neuron || s-LNv neuron || pacemaker neuron || LNv neuron || gustatory receptor neuron || dendritic arborizing neuron
EGF-type module	0.486	INHERITED FROM: embryonic pericardial cell || somatic cell of testis || dorsal acute muscle || hub cell || adult midgut progenitor cell || embryonic/larval midgut cell || head mesoderm derived embryonic hemocyte || pigment cell
Paired domain	0.5264	INHERITED FROM: RP2 motor neuron || EL neuron || EG neuron || U neuron
Cyclin	0.5264	INHERITED FROM: female germline cell
Homeodomain	0.5463	INHERITED FROM: adult antennal lobe projection neuron VA3 adPN || thoracic neuroblast || syncytium || uniglomerular antennal lobe projection neuron || prothoracic ventral intersegmental muscle || embryonic neuroblast || ventral intersegmental muscle || dorsal margin photoreceptor || muscle cell || glial cell || maxillary palp olfactory receptor neuron || adult antennal lobe projection neuron VM2 adPN || hypodermal muscle of prothorax || adult antennal lobe projection neuron VA1v adPN || interneuron || U neuron || embryonic/larval neuron
Caspase catalytic domain	0.557	INHERITED FROM: peptidergic neuron
HLH, helix-loop-helix DNA-binding domain	0.5922	INHERITED FROM: 5-6I of thorax || sensory mother cell || EL neuron
Nuclear receptor ligand-binding domain	0.6007	INHERITED FROM: mushroom body intrinsic neuron || supraesophageal ganglion neuron || interneuron
Nuclear receptor	0.6256	INHERITED FROM: mushroom body intrinsic neuron || supraesophageal ganglion neuron || interneuron
Cytochrome P450	0.705	INHERITED FROM: embryonic/larval glial cell || neuropil associated CNS glial cell || larval neuropil glial cell || larval VNC neuropil glial cell || CNS glial cell || midline glial cell
Growth factor receptor domain	0.774	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte
SH2 domain	0.8037	INHERITED FROM: histaminergic neuron || sensory organ cell || photoreceptor cell || optic lobe neuron || rhabdomeric photoreceptor cell || cyst progenitor cell || photoreceptor cell R7
Forkhead DNA-binding domain	0.8389	INHERITED FROM: RP2sib neuron
FYVE, a phosphatidylinositol-3-phosphate binding domain	0.8408	INHERITED FROM: nephrocyte || garland cell || embryonic/larval garland cell
Hairy Orange domain	0.8408	INHERITED FROM: EL neuron || EG neuron
Classic zinc finger, C2H2	1	INHERITED FROM: embryonic ganglion mother cell

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 FA term (Not in SPFA)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
TIMP-like	0	DIRECT
t-snare proteins	0	DIRECT
alpha-catenin/vinculin-like	0	DIRECT
YVTN repeat-like/Quinoprotein amine dehydrogenase	0	DIRECT
PurM C-terminal domain-like	0	DIRECT
Smc hinge domain	0	DIRECT
MIR domain	0	DIRECT
Metallo-hydrolase/oxidoreductase	0	DIRECT
GINS helical bundle-like	0	DIRECT
RCC1/BLIP-II	0	DIRECT
Tubulin nucleotide-binding domain-like	0	DIRECT
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	0	DIRECT
post-AAA+ oligomerization domain-like	0	DIRECT
Cullin repeat-like	0	DIRECT
PriA/YqbF domain	0	DIRECT
Frizzled cysteine-rich domain	0	DIRECT
Translation proteins	0	DIRECT
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	DIRECT
Tropomyosin	0	DIRECT
Prefoldin	0	DIRECT
RNase III domain-like	0	DIRECT
Cullin homology domain	0	DIRECT
Ferritin-like	0	DIRECT
Plexin repeat	0	DIRECT
Arginase/deacetylase	0	DIRECT
SMAD MH1 domain	0	DIRECT
Rhodanese/Cell cycle control phosphatase	0	DIRECT
Sema domain	0	DIRECT
Cytokine	0	DIRECT
Integrin domains	0	DIRECT
Metal cation-transporting ATPase, ATP-binding domain N	0	DIRECT
Class II aaRS ABD-related	0	DIRECT
NHL repeat	0	DIRECT
B-box zinc-binding domain	0	DIRECT
Snake toxin-like	0	DIRECT
Aminoacid dehydrogenase-like, N-terminal domain	0	DIRECT
SAP domain	0	DIRECT
NAD kinase/diacylglycerol kinase-like	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
PurM N-terminal domain-like	0	DIRECT
Terpenoid synthases	0	DIRECT
Mob1/phocein	0	DIRECT
Ribosomal protein S5 domain 2-like	0	DIRECT
YWTD domain	0	DIRECT
Tubulin C-terminal domain-like	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
PapD-like	0	DIRECT
CAD & PB1 domains	0	DIRECT
Ankyrin repeat	0.01517	INHERITED FROM: Johnston organ neuron
dsRNA-binding domain-like	0.03455	INHERITED FROM: adult MBp lineage neuron || antennal lobe projection neuron adPN || antennal lobe projection neuron iPN || alpha/beta Kenyon cell || uniglomerular antennal lobe projection neuron || mushroom body extrinsic neuron || Kenyon cell || BAmv3 lineage neuron || female germline stem cell || germline cell || mushroom body intrinsic neuron || projection neuron || cholinergic neuron || adult antennal lobe projection neuron || unilateral ACT relay interneuron || persistent antennal lobe projection neuron
RING/U-box	0.04525	INHERITED FROM: garland cell || embryonic/larval garland cell
p53-like transcription factors	0.0722	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte
EGF/Laminin	0.08642	INHERITED FROM: abdominal 4 acute muscle || abdominal 7 acute muscle || abdominal 2 acute muscle || pericardial cell || pigment cell || somatic cell of testis || embryonic/larval midgut cell || adult midgut progenitor cell || muscle cell || sensory organ cell || eye photoreceptor cell stalk || sensory neuron || syncytium || abdominal 6 acute muscle || ventral longitudinal muscle || nephrocyte || abdominal 5 acute muscle || hub cell || abdominal 3 acute muscle || embryonic/larval somatic muscle || tendon cell
Spectrin repeat	0.09912	INHERITED FROM: enterocyte || oocyte || midgut enterocyte || copper cell
Calponin-homology domain, CH-domain	0.1113	INHERITED FROM: flight muscle || somatic muscle || skeletal muscle of mesothorax || skeletal muscle of thorax || indirect flight muscle
BAR/IMD domain-like	0.1373	INHERITED FROM: NMJ bouton || synapse || bouton
Protein kinase-like (PK-like)	0.1503	INHERITED FROM: intestinal stem cell || somatic cell of ovary || epithelial cell || photoreceptor cell R8 of pale ommatidium
Actin depolymerizing proteins	0.1657	INHERITED FROM: follicle cell
E set domains	0.1772	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte
Homeodomain-like	0.2045	INHERITED FROM: adult antennal lobe projection neuron VA3 adPN || embryonic neuroblast || uniglomerular antennal lobe projection neuron || adult antennal lobe projection neuron VA1v adPN || interneuron || thoracic neuroblast || muscle cell || prothoracic ventral intersegmental muscle || syncytium || embryonic/larval neuron || adult antennal lobe projection neuron VM2 adPN || dorsal margin photoreceptor || U neuron
Transducin (alpha subunit), insertion domain	0.2146	INHERITED FROM: eo neuron
CoA-dependent acyltransferases	0.277	INHERITED FROM: flight muscle || adult somatic muscle || skeletal muscle of mesothorax || skeletal muscle of thorax
PAZ domain	0.277	INHERITED FROM: pole cell
Cadherin-like	0.3098	INHERITED FROM: photoreceptor cell R4
Immunoglobulin	0.3124	INHERITED FROM: embryonic cardioblast || 3-1M || embryonic heart cardioblast || pacemaker neuron || glial cell || LNv neuron || longitudinal muscle || adult pacemaker neuron || leg taste bristle chemosensory neuron || LN period neuron || cardioblast || interface glial cell
L domain-like	0.3531	INHERITED FROM: BAlc1 lineage neuron
Cap-Gly domain	0.3591	INHERITED FROM: interneuron
POZ domain	0.4051	INHERITED FROM: adult descending neuron
Fibronectin type III	0.4133	INHERITED FROM: embryonic heart cardioblast || pacemaker neuron || abdominal neuron || dendritic arborizing neuron || LNv neuron || adult pacemaker neuron || s-LNv neuron || leg taste bristle chemosensory neuron || LN period neuron
Caspase-like	0.4557	INHERITED FROM: male germline cell || peptidergic neuron || interommatidial precursor cell
ENTH/VHS domain	0.4557	INHERITED FROM: imaginal disc epithelial cell
PDZ domain-like	0.4713	INHERITED FROM: epithelial cell
HAD-like	0.4827	INHERITED FROM: rhabdomere of eye photoreceptor cell
Metalloproteases ("zincins"), catalytic domain	0.4901	INHERITED FROM: embryonic cardioblast || embryonic heart cardioblast
SMAD/FHA domain	0.5103	INHERITED FROM: female germline stem cell
FYVE/PHD zinc finger	0.533	INHERITED FROM: embryonic/larval garland cell
HLH, helix-loop-helix DNA-binding domain	0.5443	INHERITED FROM: EL neuron || sensory mother cell || 5-6I of thorax
Nuclear receptor ligand-binding domain	0.5758	INHERITED FROM: interneuron || supraesophageal ganglion neuron || mushroom body intrinsic neuron
Cytochrome P450	0.6869	INHERITED FROM: larval neuropil glial cell || embryonic/larval glial cell || midline glial cell || neuropil associated CNS glial cell || larval VNC neuropil glial cell || CNS glial cell
Cyclin-like	0.7004	INHERITED FROM: female germline cell
Growth factor receptor domain	0.7121	INHERITED FROM: head mesoderm derived embryonic hemocyte || stage 1 neuroblast || dMP2 neuron || GABAergic neuron || surface associated glial cell || pigment cell || vMP2 neuron || somatic cell of testis || dorsal acute muscle || retinal pigment cell || neuroblast of ventral nerve cord primordium || embryonic hemocyte || photoreceptor cell R7 || neuroblast NB5-2 || hub cell || RP2sib neuron
Orange domain-like	0.7584	INHERITED FROM: EL neuron || thoracic neuron || 5-6I of thorax || EG neuron
SH2 domain	0.7776	INHERITED FROM: rhabdomeric photoreceptor cell || sensory organ cell || optic lobe neuron || photoreceptor cell R7 || photoreceptor cell || cyst progenitor cell || histaminergic neuron
Tetraspanin	0.8278	INHERITED FROM: sensory mother cell
beta-beta-alpha zinc fingers	1	INHERITED FROM: serotonergic neuron || subesophageal ganglion neuron || embryonic ganglion mother cell

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

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
101912,103575 101912 - Sema domain 103575 - Plexin repeat	0	DIRECT
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat	0	DIRECT
47220,47220 47220 - alpha-catenin/vinculin-like 47220 - alpha-catenin/vinculin-like	0	DIRECT
49899,57196 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin	0	DIRECT
63748,63748 63748 - Tudor/PWWP/MBT 63748 - Tudor/PWWP/MBT	0	DIRECT
52777,52777 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases	0	DIRECT
55753,55753 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins	0	DIRECT
81660,56784 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like	0	DIRECT
51206,51206 51206 - cAMP-binding domain-like 51206 - cAMP-binding domain-like	0	DIRECT
52540,48019 52540 - P-loop containing nucleoside triphosphate hydrolases 48019 - post-AAA+ oligomerization domain-like	0	DIRECT
48403,48403 48403 - Ankyrin repeat 48403 - Ankyrin repeat	0	DIRECT
52540,50447 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins	0	DIRECT
54768,54768 54768 - dsRNA-binding domain-like 54768 - dsRNA-binding domain-like	0	DIRECT
52490,55307 52490 - Tubulin nucleotide-binding domain-like 55307 - Tubulin C-terminal domain-like	0	DIRECT
57196,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
57850,57850 57850 - RING/U-box 57850 - RING/U-box	0	DIRECT
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like	0	DIRECT
53223,51735 53223 - Aminoacid dehydrogenase-like, N-terminal domain 51735 - NAD(P)-binding Rossmann-fold domains	0	DIRECT
81296,81296 81296 - E set domains 81296 - E set domains	0	DIRECT
50447,50465 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	DIRECT
49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain)	0	DIRECT
54534,48452 54534 - FKBP-like 48452 - TPR-like	0	DIRECT
75632,46785 75632 - Cullin homology domain 46785 - "Winged helix" DNA-binding domain	0	DIRECT
57903,47370 57903 - FYVE/PHD zinc finger 47370 - Bromodomain	0	DIRECT
55326,56042 55326 - PurM N-terminal domain-like 56042 - PurM C-terminal domain-like	0	DIRECT
74788,75632 74788 - Cullin repeat-like 75632 - Cullin homology domain	0	DIRECT
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.1319	INHERITED FROM: embryonic/larval pericardial cell || secondary pigment cell || pericardial cell || somatic cell of testis || rhabdomeric photoreceptor cell || sensory organ cell || eye photoreceptor cell stalk || nephrocyte || hub cell || somatic muscle || tertiary pigment cell || embryonic/larval somatic muscle
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin	0.2056	INHERITED FROM: embryonic cardioblast || embryonic heart cardioblast || pacemaker neuron || interommatidial precursor cell || LNv neuron || longitudinal muscle || adult pacemaker neuron || s-LNv neuron || leg taste bristle chemosensory neuron || cardioblast
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.2146	INHERITED FROM: eo neuron
55550,50044 55550 - SH2 domain 50044 - SH3-domain	0.3591	INHERITED FROM: photoreceptor cell R7 || inner photoreceptor cell
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like	0.3758	INHERITED FROM: photoreceptor cell R4 || outer photoreceptor cell
50978,50978 50978 - WD40 repeat-like 50978 - WD40 repeat-like	0.3758	INHERITED FROM: mechanosensory system neuron || mechanosensory neuron
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.4557	INHERITED FROM: multidendritic neuron || abdominal neuron || dendritic arborizing neuron || abdominal sensory neuron
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III	0.5981	INHERITED FROM: giant fiber neuron || embryonic heart cardioblast || pacemaker neuron || chemosensory system neuron || LNv neuron || adult pacemaker neuron || neuropil associated CNS glial cell || adult descending neuron || mechanosensory system neuron || gustatory receptor neuron || s-LNv neuron || leg taste bristle chemosensory neuron || chemosensory neuron || mechanosensory neuron
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.6869	INHERITED FROM: female germline cell
47473,47473 47473 - EF-hand 47473 - EF-hand	0.7563	INHERITED FROM: synapse || bouton
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like	0.7584	INHERITED FROM: EL neuron || thoracic neuron || 5-6I of thorax || EG neuron
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.8408	INHERITED FROM: head mesoderm derived embryonic hemocyte || pigment cell || somatic cell of testis || embryonic hemocyte || photoreceptor cell R7 || hub cell || crystal cell || inner photoreceptor cell
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	1	INHERITED FROM: embryonic ganglion mother cell

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

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat	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
49899,49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
57850,57850,57850 57850 - RING/U-box 57850 - RING/U-box 57850 - RING/U-box	0	DIRECT
81660,56784,81665 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like 81665 - Calcium ATPase, transmembrane domain M	0	DIRECT
48452,48452,48452 48452 - TPR-like 48452 - TPR-like 48452 - TPR-like	0	DIRECT
52540,50447,50465 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	DIRECT
74788,75632,46785 74788 - Cullin repeat-like 75632 - Cullin homology domain 46785 - "Winged helix" DNA-binding domain	0	DIRECT
57196,49899,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains	0	DIRECT
52540,52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin	0.04521	INHERITED FROM: embryonic/larval pericardial cell || head mesoderm derived embryonic hemocyte || secondary pigment cell || photoreceptor cell R1 || glial cell || pericardial cell || somatic cell of testis || rhabdomeric photoreceptor cell || embryonic hemocyte || sensory organ cell || eye photoreceptor cell stalk || optic lobe neuron || sensory neuron || nephrocyte || hub cell || tertiary pigment cell || embryonic/larval somatic muscle || photoreceptor cell R6 || histaminergic neuron || embryonic/larval hypodermal muscle
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III	0.3659	INHERITED FROM: giant fiber neuron || embryonic heart cardioblast || pacemaker neuron || chemosensory system neuron || LNv neuron || adult pacemaker neuron || neuropil associated CNS glial cell || adult descending neuron || mechanosensory system neuron || gustatory receptor neuron || s-LNv neuron || leg taste bristle chemosensory neuron || chemosensory neuron || mechanosensory neuron
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like	0.3758	INHERITED FROM: photoreceptor cell R4 || outer photoreceptor cell
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.4713	INHERITED FROM: embryonic cardioblast || embryonic heart cardioblast || pacemaker neuron || interommatidial precursor cell || LNv neuron || adult pacemaker neuron || adult descending neuron || mechanosensory system neuron || embryonic/larval garland cell || gustatory receptor neuron || s-LNv neuron || leg taste bristle chemosensory neuron
57667,57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	1	INHERITED FROM: embryonic ganglion mother cell

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.