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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 AP term (Not in SDAP)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
FAH	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
Alpha-L RNA-binding motif	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
AlbA-like	0	DIRECT
Enolase C-terminal domain-like	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
Granulin repeat	0	DIRECT
Ribosomal protein L31e	0	DIRECT
Clc chloride channel	0	DIRECT
Tim10-like	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
Cytochrome c	0	DIRECT
AMPKBI-like	0	DIRECT
Nicotinate/Quinolinate PRTase C-terminal domain-like	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
SIS domain	0	DIRECT
GroEL-intermediate domain like	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
V-type ATPase subunit E-like	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
LanC-like	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
FF domain	0	DIRECT
L9 N-domain-like	0	DIRECT
LuxS/MPP-like metallohydrolase	0	DIRECT
Globin-like	0	DIRECT
Folate-binding domain	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Peptidase/esterase 'gauge' domain	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
MurD-like peptide ligases, catalytic domain	0	DIRECT
beta-N-acetylhexosaminidase-like domain	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
Smc hinge domain	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
Ribosomal protein L39e	0	DIRECT
MurD-like peptide ligases, peptide-binding domain	0	DIRECT
GroEL apical domain-like	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
DLC	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
Preprotein translocase SecY subunit	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
SH3-domain	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
Glutamine synthetase/guanido kinase	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
Enolase N-terminal domain-like	0	DIRECT
Tautomerase/MIF	0	DIRECT
Ribosomal protein L13	0	DIRECT
Inosine monophosphate dehydrogenase (IMPDH)	0	DIRECT
Electron transport accessory proteins	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
RNA polymerase subunits	0	DIRECT
TATA-box binding protein-like	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
NHL repeat	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
Ribosomal protein S2	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
RraA-like	0	DIRECT
Ribosomal protein L14	0	DIRECT
DNA repair protein MutS, domain II	0	DIRECT
VHP, Villin headpiece domain	0	DIRECT
ADC-like	0	DIRECT
R3H domain	0	DIRECT
PABC (PABP) domain	0	DIRECT
Families 57/38 glycoside transferase middle domain	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
Flavoproteins	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
FKBP-like	0	DIRECT
eIF1-like	0	DIRECT
Expressed protein At2g23090/F21P24.15	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
alpha-helical ferredoxin	0	DIRECT
Protease propeptides/inhibitors	0	DIRECT
Inorganic pyrophosphatase	0	DIRECT
N-terminal domain of the delta subunit of the F1F0-ATP synthase	0	DIRECT
Ribosomal protein S8	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
Ribosomal protein L4	0	DIRECT
Nicotinate/Quinolinate PRTase N-terminal domain-like	0	DIRECT
BolA-like	0	DIRECT
Pentein	0	DIRECT
Mitochondrial glycoprotein MAM33-like	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
Composite domain of metallo-dependent hydrolases	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
S13-like H2TH domain	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
FAD-dependent thiol oxidase	0	DIRECT
GlnB-like	0	DIRECT
HesB-like domain	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
Saposin	0	DIRECT
Putative isomerase YbhE	0	DIRECT
Serine metabolism enzymes domain	0	DIRECT
YrdC/RibB	0	DIRECT
tRNA-binding arm	0	DIRECT
Chelatase	0	DIRECT
CYTH-like phosphatases	0	DIRECT
Metallo-dependent hydrolases	0	DIRECT
Single hybrid motif	0	DIRECT
Tetrapyrrole methylase	0	DIRECT
SufE/NifU	0	DIRECT
XPC-binding domain	0	DIRECT
E2F-DP heterodimerization region	0	DIRECT
Tetrahydrobiopterin biosynthesis enzymes-like	0	DIRECT
Cation efflux protein transmembrane domain-like	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
Sec7 domain	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
RibA-like	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
Ricin B-like lectins	0	DIRECT
Ribosomal proteins S24e, L23 and L15e	0	DIRECT
Signal peptide-binding domain	0	DIRECT
ssDNA-binding transcriptional regulator domain	0	DIRECT
Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0	DIRECT
Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
Chorismate mutase II	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
LeuD/IlvD-like	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
Lipoxigenase	0	DIRECT
SMR domain-like	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
Phosphofructokinase	0	DIRECT
GroEL equatorial domain-like	0	DIRECT
Pentapeptide repeat-like	0	DIRECT
LysM domain	0	DIRECT
Lipocalins	0	DIRECT
Glutamine synthetase, N-terminal domain	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
Ribosomal protein S6	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Glycoside hydrolase/deacetylase	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
Lesion bypass DNA polymerase (Y-family), little finger domain	0	DIRECT
DNA clamp	0	DIRECT
Ribosomal protein L16p/L10e	0	DIRECT

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

SCOP term	FDR (all)	Annotation (direct or inherited)
Ribosomal protein L31e	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
HEAT repeat	0	DIRECT
Choline kinase	0	DIRECT
Ferritin	0	DIRECT
LEA14-like	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
alpha-mannosidase, domain 2	0	DIRECT
E2F dimerization segment	0	DIRECT
PCI domain (PINT motif)	0	DIRECT
Ribosomal protein S13	0	DIRECT
Enolase N-terminal domain-like	0	DIRECT
Allosteric chorismate mutase	0	DIRECT
Ribosomal protein S8	0	DIRECT
GroEL-like chaperone, apical domain	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Spermidine synthase	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Protein prenyltransferases	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
MIF-related	0	DIRECT
Aminoacid dehydrogenases	0	DIRECT
Prolyl oligopeptidase, N-terminal domain	0	DIRECT
Cystatins	0	DIRECT
beta-sandwich domain of Sec23/24	0	DIRECT
Glycerophosphoryl diester phosphodiesterase	0	DIRECT
La domain	0	DIRECT
PaaI/YdiI-like	0	DIRECT
RNB domain-like	0	DIRECT
RhoGDI-like	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Phosphofructokinase	0	DIRECT
SerA intervening domain-like	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
Methionine aminopeptidase, insert domain	0	DIRECT
V-type ATPase subunit E	0	DIRECT
LON domain-like	0	DIRECT
GDI-like N domain	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
Gelsolin-like	0	DIRECT
gamma-carbonic anhydrase-like	0	DIRECT
Lipoxigenase N-terminal domain	0	DIRECT
Clc chloride channel	0	DIRECT
Ran-binding domain	0	DIRECT
Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
RWD domain	0	DIRECT
DNA repair glycosylase, 2 C-terminal domains	0	DIRECT
ATP sulfurylase catalytic domain	0	DIRECT
Starch-binding domain	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
Succinyl-CoA synthetase, beta-chain, N-terminal domain	0	DIRECT
Tetramerization domain of potassium channels	0	DIRECT
Receiver domain of the ethylene receptor	0	DIRECT
Ubiquitin carboxyl-terminal hydrolase UCH-L	0	DIRECT
Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain	0	DIRECT
Glucose 6-phosphate dehydrogenase-like	0	DIRECT
L23p	0	DIRECT
Glyoxalase II (hydroxyacylglutathione hydrolase)	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Transcriptional coactivator PC4 C-terminal domain	0	DIRECT
Aminomethyltransferase folate-binding domain	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
RNase Z-like	0	DIRECT
Signal peptide-binding domain	0	DIRECT
IPP isomerase-like	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
MYND zinc finger	0	DIRECT
2Fe-2S ferredoxin-related	0	DIRECT
GAF domain	0	DIRECT
rRNA adenine dimethylase-like	0	DIRECT
Phosphoenolpyruvate carboxylase	0	DIRECT
PAPS reductase-like	0	DIRECT
STAR domain	0	DIRECT
Ribosomal protein L3	0	DIRECT
BolA-like	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
Tetrapyrrole methylase	0	DIRECT
NifU/IscU domain	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
FKBP immunophilin/proline isomerase	0	DIRECT
WrbA-like	0	DIRECT
Ribosomal protein L39e	0	DIRECT
BphP N-terminal domain-like	0	DIRECT
Myf domain	0	DIRECT
Cytochrome p450 reductase N-terminal domain-like	0	DIRECT
eIF1-like	0	DIRECT
Ribosomal protein S27e	0	DIRECT
Granulin repeat	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
Hypothetical protein HI1317	0	DIRECT
GABARAP-like	0	DIRECT
Ribosomal protein L10e	0	DIRECT
Folylpolyglutamate synthetase	0	DIRECT
D-ribulose-5-phosphate 3-epimerase	0	DIRECT
3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
Acyl-ACP thioesterase-like	0	DIRECT
Molybdenum-containing oxidoreductases-like dimerisation domain	0	DIRECT
GroES	0	DIRECT
Cytidylyltransferase	0	DIRECT
Amylase, catalytic domain	0	DIRECT
PABC (PABP) domain	0	DIRECT
NHL repeat	0	DIRECT
Inorganic pyrophosphatase	0	DIRECT
Thiolase-related	0	DIRECT
AlkB-like	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
LysM domain	0	DIRECT
Group II chaperonin (CCT, TRIC), ATPase domain	0	DIRECT
PUA domain	0	DIRECT
Group II chaperonin (CCT, TRIC), intermediate domain	0	DIRECT
alpha-mannosidase, C-terminal domain	0	DIRECT
HAT/Suf repeat	0	DIRECT
Pentapeptide repeats	0	DIRECT
HAL/PAL-like	0	DIRECT
Cell cycle arrest protein BUB3	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
Ribosomal protein L37e	0	DIRECT
Sec7 domain	0	DIRECT
Gastric lipase	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
MPP-like	0	DIRECT
Pseudouridine synthase II TruB	0	DIRECT
CoA-binding domain	0	DIRECT
Rubredoxin	0	DIRECT
Ring hydroxylating alpha subunit ISP domain	0	DIRECT
DNase I-like	0	DIRECT
NADPH-cytochrome p450 reductase FAD-binding domain-like	0	DIRECT
Sedlin (SEDL)	0	DIRECT
Biotinyl/lipoyl-carrier proteins and domains	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
ZZ domain	0	DIRECT
Class I aldolase	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
Subtilase propeptides/inhibitors	0	DIRECT
Chromo barrel domain	0	DIRECT
Ribosomal protein L14	0	DIRECT
Branched-chain alpha-keto acid dehydrogenase Pyr module	0	DIRECT
5' nucleotidase-like	0	DIRECT
Gtf glycosyltransferase	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase dimerisation domain	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
Poly(ADP-ribose) polymerase, C-terminal domain	0	DIRECT
Prolyl oligopeptidase, C-terminal domain	0	DIRECT
R3H domain	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
Class-II DAHP synthetase	0	DIRECT
NOL1/NOP2/sun	0	DIRECT
Inosine monophosphate dehydrogenase (IMPDH)	0	DIRECT
Glutamine synthetase, N-terminal domain	0	DIRECT
Calnexin/calreticulin	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
RelA/SpoT domain	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
Cdc48 N-terminal domain-like	0	DIRECT
Ribosomal protein S6	0	DIRECT
Plant lipoxigenases	0	DIRECT
Preprotein translocase SecY subunit	0	DIRECT
Ribosomal protein S15	0	DIRECT
Dihydrodipicolinate reductase-like	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
GroEL chaperone, ATPase domain	0	DIRECT
Biotin dependent carboxylase carboxyltransferase domain	0	DIRECT
Adenosine-5'phosphosulfate kinase (APS kinase)	0	DIRECT
N-type ATP pyrophosphatases	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
Exostosin	0	DIRECT
FAH	0	DIRECT
Trunk domain of Sec23/24	0	DIRECT
Sec63 N-terminal domain	0	DIRECT
Plant stress-induced protein	0	DIRECT
Cation efflux protein transmembrane domain-like	0	DIRECT
alpha-mannosidase	0	DIRECT
AMPK-beta glycogen binding domain-like	0	DIRECT
Ribosomal protein L4	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
N-acetyl-l-glutamate kinase	0	DIRECT
(Glycosyl)asparaginase	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
Plant transcriptional regulator PBF-2	0	DIRECT
Glycerol-3-phosphate dehydrogenase	0	DIRECT
HesB-like domain	0	DIRECT
Glyoxalase I (lactoylglutathione lyase)	0	DIRECT
LIM domain	0	DIRECT
Tim10/DDP	0	DIRECT
1,3-glucuronyltransferase	0	DIRECT
Clp protease, ClpP subunit	0	DIRECT
VHP, Villin headpiece domain	0	DIRECT
Cyclin A/CDK2-associated p19, Skp2	0	DIRECT
Galactosyltransferase LgtC	0	DIRECT
eIF5a N-terminal domain-like	0	DIRECT
YicI N-terminal domain-like	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
ATP sulfurylase N-terminal domain	0	DIRECT
Macro domain	0	DIRECT
TRM1-like	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), catalytic domain	0	DIRECT
LeuD-like	0	DIRECT
Smr domain	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
SufE-like	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
CAT-like	0	DIRECT
Ribosomal protein S2	0	DIRECT
Smc hinge domain	0	DIRECT
Glutamine synthetase catalytic domain	0	DIRECT
NADPH-cytochrome p450 reductase-like	0	DIRECT
EDF1-like	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
Mitochondrial glycoprotein MAM33-like	0	DIRECT
Ribosomal protein L13	0	DIRECT
Homoserine dehydrogenase-like	0	DIRECT
HMGL-like	0	DIRECT
Phytochrome-specific domain	0	DIRECT
beta-Phosphoglucomutase-like	0	DIRECT
RNA-polymerase beta-prime	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
Enolase	0	DIRECT
Rps19E-like	0	DIRECT
Heme-dependent catalases	0	DIRECT
Thioesterases	0	DIRECT
6-phosphogluconate dehydrogenase-like, N-terminal domain	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
beta-N-acetylhexosaminidase catalytic domain	0	DIRECT
UDP-glucose pyrophosphorylase	0	DIRECT
Lesion bypass DNA polymerase (Y-family), catalytic domain	0	DIRECT
XPC-binding domain	0	DIRECT
Shikimate kinase (AroK)	0	DIRECT
FucT-like	0	DIRECT
monodomain cytochrome c	0	DIRECT
Class I alpha-1;2-mannosidase, catalytic domain	0	DIRECT
FF domain	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
DLC	0	DIRECT
alpha-Amylases, C-terminal beta-sheet domain	0	DIRECT
Anti-sigma factor antagonist SpoIIaa	0	DIRECT
RibA-like	0	DIRECT
Hypothetical protein At2g34160	0	DIRECT
PDI-like	0	DIRECT
SWIRM domain	0	DIRECT
SH3-domain	0	DIRECT
RraA-like	0	DIRECT
G domain-linked domain	0	DIRECT
Sec63 C-terminal domain-like	0	DIRECT
Leukotriene A4 hydrolase catalytic domain	0	DIRECT
DNA polymerase processivity factor	0	DIRECT
Eps15 homology domain (EH domain)	0	DIRECT
Molybdenum cofactor biosynthesis protein MoeB	0	DIRECT
B56-like	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
BAR domain	0	DIRECT
Swaposin	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
Tail specific protease, catalytic domain	0	DIRECT
Reductases	0	DIRECT
FAD-dependent thiol oxidase	0	DIRECT
AMPKBI-like	0	DIRECT
GroEL-like chaperone, intermediate domain	0	DIRECT
Group II chaperonin (CCT, TRIC), apical domain	0	DIRECT
PhzC/PhzF-like	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
NadC C-terminal domain-like	0	DIRECT
Sigma4 domain	0	DIRECT
NadC N-terminal domain-like	0	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 AP term (SPAP level: Least Informative)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Tim10-like	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Single hybrid motif	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
Glutamine synthetase/guanido kinase	0	DIRECT
Cytochrome c	0	DIRECT
Sec7 domain	0	DIRECT
Clc chloride channel	0	DIRECT
Inosine monophosphate dehydrogenase (IMPDH)	0	DIRECT
Saposin	0	DIRECT
Glutamine synthetase, N-terminal domain	0	DIRECT
Enolase C-terminal domain-like	0	DIRECT
TATA-box binding protein-like	0	DIRECT
Lipocalins	0	DIRECT
Nicotinate/Quinolinate PRTase N-terminal domain-like	0	DIRECT
SufE/NifU	0	DIRECT
Cation efflux protein transmembrane domain-like	0	DIRECT
Preprotein translocase SecY subunit	0	DIRECT
Signal peptide-binding domain	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
SH3-domain	0	DIRECT
FKBP-like	0	DIRECT
FF domain	0	DIRECT
PABC (PABP) domain	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
Ribosomal protein S6	0	DIRECT
Electron transport accessory proteins	0	DIRECT
Tetrahydrobiopterin biosynthesis enzymes-like	0	DIRECT
Glycoside hydrolase/deacetylase	0	DIRECT
Globin-like	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
Metallo-dependent hydrolases	0	DIRECT
Enolase N-terminal domain-like	0	DIRECT
Composite domain of metallo-dependent hydrolases	0	DIRECT
Ribosomal protein L4	0	DIRECT
Ribosomal protein S8	0	DIRECT
Protease propeptides/inhibitors	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
NHL repeat	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
Inorganic pyrophosphatase	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
GroEL apical domain-like	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
eIF1-like	0	DIRECT
Ribosomal protein L31e	0	DIRECT
RibA-like	0	DIRECT
FAD-dependent thiol oxidase	0	DIRECT
DNA repair protein MutS, domain II	0	DIRECT
Pentapeptide repeat-like	0	DIRECT
alpha-helical ferredoxin	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
Chelatase	0	DIRECT
R3H domain	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
Ricin B-like lectins	0	DIRECT
Putative isomerase YbhE	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
MurD-like peptide ligases, catalytic domain	0	DIRECT
Phosphofructokinase	0	DIRECT
VHP, Villin headpiece domain	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
Tautomerase/MIF	0	DIRECT
GroEL-intermediate domain like	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
Folate-binding domain	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
ssDNA-binding transcriptional regulator domain	0	DIRECT
FAH	0	DIRECT
L9 N-domain-like	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0	DIRECT
Families 57/38 glycoside transferase middle domain	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
AMPKBI-like	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
ADC-like	0	DIRECT
XPC-binding domain	0	DIRECT
YrdC/RibB	0	DIRECT
LeuD/IlvD-like	0	DIRECT
S13-like H2TH domain	0	DIRECT
Ribosomal protein L16p/L10e	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
Ribosomal protein L39e	0	DIRECT
Mitochondrial glycoprotein MAM33-like	0	DIRECT
RraA-like	0	DIRECT
N-terminal domain of the delta subunit of the F1F0-ATP synthase	0	DIRECT
RNA polymerase subunits	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
E2F-DP heterodimerization region	0	DIRECT
Chorismate mutase II	0	DIRECT
DNA clamp	0	DIRECT
beta-N-acetylhexosaminidase-like domain	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
Expressed protein At2g23090/F21P24.15	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
Serine metabolism enzymes domain	0	DIRECT
Tetrapyrrole methylase	0	DIRECT
BolA-like	0	DIRECT
HesB-like domain	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
V-type ATPase subunit E-like	0	DIRECT
Alpha-L RNA-binding motif	0	DIRECT
6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
MurD-like peptide ligases, peptide-binding domain	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
Smc hinge domain	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
tRNA-binding arm	0	DIRECT
Pentein	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
Ribosomal protein L14	0	DIRECT
Granulin repeat	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
SMR domain-like	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
GroEL equatorial domain-like	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
Lesion bypass DNA polymerase (Y-family), little finger domain	0	DIRECT
GlnB-like	0	DIRECT
LuxS/MPP-like metallohydrolase	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
LanC-like	0	DIRECT
AlbA-like	0	DIRECT
DLC	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
LysM domain	0	DIRECT
CYTH-like phosphatases	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
Flavoproteins	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
Ribosomal protein L13	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
Lipoxigenase	0	DIRECT
Nicotinate/Quinolinate PRTase C-terminal domain-like	0	DIRECT
Ribosomal protein S2	0	DIRECT
SIS domain	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
Ribosomal proteins S24e, L23 and L15e	0	DIRECT
Peptidase/esterase 'gauge' domain	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
Aldolase	0.0007976	DIRECT