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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)
RibA-like	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
YrdC/RibB	0	DIRECT
Ribosomal protein S2	0	DIRECT
SMR domain-like	0	DIRECT
FF domain	0	DIRECT
Expressed protein At2g23090/F21P24.15	0	DIRECT
L9 N-domain-like	0	DIRECT
Alpha-L RNA-binding motif	0	DIRECT
Signal peptide-binding domain	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
PABC (PABP) domain	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
beta-N-acetylhexosaminidase-like domain	0	DIRECT
Electron transport accessory proteins	0	DIRECT
Phosphofructokinase	0	DIRECT
DNA repair protein MutS, domain II	0	DIRECT
Sec7 domain	0	DIRECT
RraA-like	0	DIRECT
CYTH-like phosphatases	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Serine metabolism enzymes domain	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
LuxS/MPP-like metallohydrolase	0	DIRECT
SIS domain	0	DIRECT
Inosine monophosphate dehydrogenase (IMPDH)	0	DIRECT
Folate-binding domain	0	DIRECT
Chelatase	0	DIRECT
Tetrahydrobiopterin biosynthesis enzymes-like	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
Ribosomal protein L4	0	DIRECT
Tetrapyrrole methylase	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
Lipoxigenase	0	DIRECT
GroEL-intermediate domain like	0	DIRECT
Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
Peptidase/esterase 'gauge' domain	0	DIRECT
Single hybrid motif	0	DIRECT
Protease propeptides/inhibitors	0	DIRECT
Mitochondrial glycoprotein MAM33-like	0	DIRECT
Enolase N-terminal domain-like	0	DIRECT
GroEL equatorial domain-like	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
N-terminal domain of the delta subunit of the F1F0-ATP synthase	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Composite domain of metallo-dependent hydrolases	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
Ribosomal protein L14	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
Smc hinge domain	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
Preprotein translocase SecY subunit	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
DLC	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
Tautomerase/MIF	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
Tim10-like	0	DIRECT
MurD-like peptide ligases, catalytic domain	0	DIRECT
Ribosomal proteins S24e, L23 and L15e	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
MurD-like peptide ligases, peptide-binding domain	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
BolA-like	0	DIRECT
Lesion bypass DNA polymerase (Y-family), little finger domain	0	DIRECT
LeuD/IlvD-like	0	DIRECT
LysM domain	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
LanC-like	0	DIRECT
Enolase C-terminal domain-like	0	DIRECT
AMPKBI-like	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Nicotinate/Quinolinate PRTase N-terminal domain-like	0	DIRECT
ssDNA-binding transcriptional regulator domain	0	DIRECT
Nicotinate/Quinolinate PRTase C-terminal domain-like	0	DIRECT
Ribosomal protein S6	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
TATA-box binding protein-like	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
Ribosomal protein L39e	0	DIRECT
Cation efflux protein transmembrane domain-like	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
XPC-binding domain	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
tRNA-binding arm	0	DIRECT
FKBP-like	0	DIRECT
Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0	DIRECT
Pentapeptide repeat-like	0	DIRECT
GroEL apical domain-like	0	DIRECT
Pentein	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
Inorganic pyrophosphatase	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
Cytochrome c	0	DIRECT
Flavoproteins	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
Glycoside hydrolase/deacetylase	0	DIRECT
Ribosomal protein S8	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
eIF1-like	0	DIRECT
V-type ATPase subunit E-like	0	DIRECT
Ribosomal protein L31e	0	DIRECT
R3H domain	0	DIRECT
FAD-dependent thiol oxidase	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
Granulin repeat	0	DIRECT
alpha-helical ferredoxin	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
SH3-domain	0	DIRECT
NHL repeat	0	DIRECT
Ribosomal protein L13	0	DIRECT
Metallo-dependent hydrolases	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
Globin-like	0	DIRECT
RNA polymerase subunits	0	DIRECT
Glutamine synthetase/guanido kinase	0	DIRECT
Lipocalins	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
Putative isomerase YbhE	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Saposin	0	DIRECT
FAH	0	DIRECT
Ricin B-like lectins	0	DIRECT
ADC-like	0	DIRECT
E2F-DP heterodimerization region	0	DIRECT
VHP, Villin headpiece domain	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
GlnB-like	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
SufE/NifU	0	DIRECT
Families 57/38 glycoside transferase middle domain	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
AlbA-like	0	DIRECT
Glutamine synthetase, N-terminal domain	0	DIRECT
HesB-like domain	0	DIRECT
S13-like H2TH domain	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
DNA clamp	0	DIRECT
Chorismate mutase II	0	DIRECT
Clc chloride channel	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
Glycolipid transfer protein, GLTP	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)
SH3-domain	0	DIRECT
Lesion bypass DNA polymerase (Y-family), catalytic domain	0	DIRECT
RelA/SpoT domain	0	DIRECT
Tail specific protease, catalytic domain	0	DIRECT
Smr domain	0	DIRECT
PAPS reductase-like	0	DIRECT
Glucose 6-phosphate dehydrogenase-like	0	DIRECT
Phytochrome-specific domain	0	DIRECT
Ran-binding domain	0	DIRECT
ZZ domain	0	DIRECT
Cytidylyltransferase	0	DIRECT
Branched-chain alpha-keto acid dehydrogenase Pyr module	0	DIRECT
Subtilase propeptides/inhibitors	0	DIRECT
DNA repair glycosylase, 2 C-terminal domains	0	DIRECT
AMPKBI-like	0	DIRECT
NADPH-cytochrome p450 reductase-like	0	DIRECT
GAF domain	0	DIRECT
Acyl-ACP thioesterase-like	0	DIRECT
RNA-polymerase beta-prime	0	DIRECT
Homoserine dehydrogenase-like	0	DIRECT
HAT/Suf repeat	0	DIRECT
La domain	0	DIRECT
Glycerophosphoryl diester phosphodiesterase	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
Tim10/DDP	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
Cytochrome p450 reductase N-terminal domain-like	0	DIRECT
RhoGDI-like	0	DIRECT
ATP sulfurylase catalytic domain	0	DIRECT
Gelsolin-like	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Ribosomal protein L39e	0	DIRECT
TRM1-like	0	DIRECT
Ribosomal protein L4	0	DIRECT
beta-N-acetylhexosaminidase catalytic domain	0	DIRECT
Protein prenyltransferases	0	DIRECT
Trunk domain of Sec23/24	0	DIRECT
(Glycosyl)asparaginase	0	DIRECT
Ribosomal protein S2	0	DIRECT
Lipoxigenase N-terminal domain	0	DIRECT
GroES	0	DIRECT
VHP, Villin headpiece domain	0	DIRECT
eIF5a N-terminal domain-like	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
NADPH-cytochrome p450 reductase FAD-binding domain-like	0	DIRECT
Pentapeptide repeats	0	DIRECT
RWD domain	0	DIRECT
Tetrapyrrole methylase	0	DIRECT
D-ribulose-5-phosphate 3-epimerase	0	DIRECT
LEA14-like	0	DIRECT
Ribosomal protein S8	0	DIRECT
Clp protease, ClpP subunit	0	DIRECT
Enolase	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
PDI-like	0	DIRECT
Glutamine synthetase catalytic domain	0	DIRECT
BolA-like	0	DIRECT
Glyoxalase II (hydroxyacylglutathione hydrolase)	0	DIRECT
Cell cycle arrest protein BUB3	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
GroEL chaperone, ATPase domain	0	DIRECT
Transcriptional coactivator PC4 C-terminal domain	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Heme-dependent catalases	0	DIRECT
Reductases	0	DIRECT
GroEL-like chaperone, intermediate domain	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
ATP sulfurylase N-terminal domain	0	DIRECT
Sec63 N-terminal domain	0	DIRECT
Dihydrodipicolinate reductase-like	0	DIRECT
Swaposin	0	DIRECT
Thiolase-related	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Ribosomal protein L14	0	DIRECT
Cdc48 N-terminal domain-like	0	DIRECT
Preprotein translocase SecY subunit	0	DIRECT
Leukotriene A4 hydrolase catalytic domain	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
FF domain	0	DIRECT
Ring hydroxylating alpha subunit ISP domain	0	DIRECT
HAL/PAL-like	0	DIRECT
5' nucleotidase-like	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
Methionine aminopeptidase, insert domain	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
PCI domain (PINT motif)	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
Plant transcriptional regulator PBF-2	0	DIRECT
Group II chaperonin (CCT, TRIC), intermediate domain	0	DIRECT
Glycerol-3-phosphate dehydrogenase	0	DIRECT
DLC	0	DIRECT
Cyclin A/CDK2-associated p19, Skp2	0	DIRECT
Plant stress-induced protein	0	DIRECT
Mitochondrial glycoprotein MAM33-like	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Class I alpha-1;2-mannosidase, catalytic domain	0	DIRECT
GABARAP-like	0	DIRECT
Eps15 homology domain (EH domain)	0	DIRECT
Gtf glycosyltransferase	0	DIRECT
SWIRM domain	0	DIRECT
G domain-linked domain	0	DIRECT
GroEL-like chaperone, apical domain	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
1,3-glucuronyltransferase	0	DIRECT
Chromo barrel domain	0	DIRECT
Ribosomal protein L3	0	DIRECT
AlkB-like	0	DIRECT
Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0	DIRECT
RNB domain-like	0	DIRECT
Ribosomal protein L10e	0	DIRECT
alpha-mannosidase, C-terminal domain	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
PUA domain	0	DIRECT
FucT-like	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
Signal peptide-binding domain	0	DIRECT
PaaI/YdiI-like	0	DIRECT
DNase I-like	0	DIRECT
NadC N-terminal domain-like	0	DIRECT
Pseudouridine synthase II TruB	0	DIRECT
Choline kinase	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), catalytic domain	0	DIRECT
Ribosomal protein S6	0	DIRECT
Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain	0	DIRECT
alpha-mannosidase	0	DIRECT
Molybdenum cofactor biosynthesis protein MoeB	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
HesB-like domain	0	DIRECT
Gastric lipase	0	DIRECT
LON domain-like	0	DIRECT
Aminoacid dehydrogenases	0	DIRECT
STAR domain	0	DIRECT
Poly(ADP-ribose) polymerase, C-terminal domain	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
beta-sandwich domain of Sec23/24	0	DIRECT
YicI N-terminal domain-like	0	DIRECT
Ribosomal protein L31e	0	DIRECT
MYND zinc finger	0	DIRECT
Adenosine-5'phosphosulfate kinase (APS kinase)	0	DIRECT
NadC C-terminal domain-like	0	DIRECT
2Fe-2S ferredoxin-related	0	DIRECT
Ribosomal protein L13	0	DIRECT
Amylase, catalytic domain	0	DIRECT
Glyoxalase I (lactoylglutathione lyase)	0	DIRECT
LIM domain	0	DIRECT
Group II chaperonin (CCT, TRIC), ATPase domain	0	DIRECT
CAT-like	0	DIRECT
Plant lipoxigenases	0	DIRECT
B56-like	0	DIRECT
alpha-Amylases, C-terminal beta-sheet domain	0	DIRECT
FAD-dependent thiol oxidase	0	DIRECT
Calnexin/calreticulin	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
HEAT repeat	0	DIRECT
Inosine monophosphate dehydrogenase (IMPDH)	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
Biotinyl/lipoyl-carrier proteins and domains	0	DIRECT
Group II chaperonin (CCT, TRIC), apical domain	0	DIRECT
Ubiquitin carboxyl-terminal hydrolase UCH-L	0	DIRECT
SerA intervening domain-like	0	DIRECT
Rps19E-like	0	DIRECT
Prolyl oligopeptidase, N-terminal domain	0	DIRECT
UDP-glucose pyrophosphorylase	0	DIRECT
Glutamine synthetase, N-terminal domain	0	DIRECT
LeuD-like	0	DIRECT
Shikimate kinase (AroK)	0	DIRECT
PhzC/PhzF-like	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
Thioesterases	0	DIRECT
Ribosomal protein S27e	0	DIRECT
Sec63 C-terminal domain-like	0	DIRECT
Molybdenum-containing oxidoreductases-like dimerisation domain	0	DIRECT
Aminomethyltransferase folate-binding domain	0	DIRECT
FKBP immunophilin/proline isomerase	0	DIRECT
Class I aldolase	0	DIRECT
Phosphofructokinase	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
Spermidine synthase	0	DIRECT
RNase Z-like	0	DIRECT
Rubredoxin	0	DIRECT
alpha-mannosidase, domain 2	0	DIRECT
GDI-like N domain	0	DIRECT
rRNA adenine dimethylase-like	0	DIRECT
Receiver domain of the ethylene receptor	0	DIRECT
IPP isomerase-like	0	DIRECT
6-phosphogluconate dehydrogenase-like, N-terminal domain	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
Smc hinge domain	0	DIRECT
Hypothetical protein At2g34160	0	DIRECT
Prolyl oligopeptidase, C-terminal domain	0	DIRECT
Starch-binding domain	0	DIRECT
Cation efflux protein transmembrane domain-like	0	DIRECT
Folylpolyglutamate synthetase	0	DIRECT
Ribosomal protein S13	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
EDF1-like	0	DIRECT
Cystatins	0	DIRECT
Tetramerization domain of potassium channels	0	DIRECT
Macro domain	0	DIRECT
AMPK-beta glycogen binding domain-like	0	DIRECT
BAR domain	0	DIRECT
NOL1/NOP2/sun	0	DIRECT
L23p	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
MPP-like	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
RraA-like	0	DIRECT
Clc chloride channel	0	DIRECT
LysM domain	0	DIRECT
V-type ATPase subunit E	0	DIRECT
Galactosyltransferase LgtC	0	DIRECT
Enolase N-terminal domain-like	0	DIRECT
Sigma4 domain	0	DIRECT
N-acetyl-l-glutamate kinase	0	DIRECT
HMGL-like	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
NifU/IscU domain	0	DIRECT
gamma-carbonic anhydrase-like	0	DIRECT
Hypothetical protein HI1317	0	DIRECT
R3H domain	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
Succinyl-CoA synthetase, beta-chain, N-terminal domain	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
Allosteric chorismate mutase	0	DIRECT
Sedlin (SEDL)	0	DIRECT
MIF-related	0	DIRECT
BphP N-terminal domain-like	0	DIRECT
CoA-binding domain	0	DIRECT
Anti-sigma factor antagonist SpoIIaa	0	DIRECT
eIF1-like	0	DIRECT
DNA polymerase processivity factor	0	DIRECT
FAH	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
E2F dimerization segment	0	DIRECT
Biotin dependent carboxylase carboxyltransferase domain	0	DIRECT
WrbA-like	0	DIRECT
N-type ATP pyrophosphatases	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase dimerisation domain	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
PABC (PABP) domain	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
Ferritin	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
Class-II DAHP synthetase	0	DIRECT
monodomain cytochrome c	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
Inorganic pyrophosphatase	0	DIRECT
Ribosomal protein L37e	0	DIRECT
Granulin repeat	0	DIRECT
Exostosin	0	DIRECT
beta-Phosphoglucomutase-like	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
XPC-binding domain	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
Phosphoenolpyruvate carboxylase	0	DIRECT
NHL repeat	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
SufE-like	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
RibA-like	0	DIRECT
Sec7 domain	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
Ribosomal protein S15	0	DIRECT
Myf domain	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)
Homocysteine S-methyltransferase	0	DIRECT
Ribosomal protein L31e	0	DIRECT
Ribosomal protein L13	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
Inosine monophosphate dehydrogenase (IMPDH)	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
FKBP-like	0	DIRECT
LanC-like	0	DIRECT
Ribosomal protein L14	0	DIRECT
GroEL apical domain-like	0	DIRECT
Enolase N-terminal domain-like	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
Ribosomal protein L39e	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
MurD-like peptide ligases, peptide-binding domain	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Ribosomal proteins S24e, L23 and L15e	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
AMPKBI-like	0	DIRECT
FF domain	0	DIRECT
FAH	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
L9 N-domain-like	0	DIRECT
Smc hinge domain	0	DIRECT
Signal peptide-binding domain	0	DIRECT
LuxS/MPP-like metallohydrolase	0	DIRECT
eIF1-like	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
Tetrahydrobiopterin biosynthesis enzymes-like	0	DIRECT
Serine metabolism enzymes domain	0	DIRECT
Pentein	0	DIRECT
S13-like H2TH domain	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
Inorganic pyrophosphatase	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
Ribosomal protein S8	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
Electron transport accessory proteins	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
Peptidase/esterase 'gauge' domain	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
FAD-dependent thiol oxidase	0	DIRECT
Metallo-dependent hydrolases	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
Glycoside hydrolase/deacetylase	0	DIRECT
Nicotinate/Quinolinate PRTase C-terminal domain-like	0	DIRECT
V-type ATPase subunit E-like	0	DIRECT
NHL repeat	0	DIRECT
ssDNA-binding transcriptional regulator domain	0	DIRECT
E2F-DP heterodimerization region	0	DIRECT
N-terminal domain of the delta subunit of the F1F0-ATP synthase	0	DIRECT
Lipocalins	0	DIRECT
Ribosomal protein S6	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
Enolase C-terminal domain-like	0	DIRECT
Phosphofructokinase	0	DIRECT
DNA clamp	0	DIRECT
Preprotein translocase SecY subunit	0	DIRECT
Folate-binding domain	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
Chorismate mutase II	0	DIRECT
BolA-like	0	DIRECT
Protease propeptides/inhibitors	0	DIRECT
Cation efflux protein transmembrane domain-like	0	DIRECT
CYTH-like phosphatases	0	DIRECT
Families 57/38 glycoside transferase middle domain	0	DIRECT
AlbA-like	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
Ribosomal protein L16p/L10e	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
LysM domain	0	DIRECT
LeuD/IlvD-like	0	DIRECT
tRNA-binding arm	0	DIRECT
Cytochrome c	0	DIRECT
Glutamine synthetase/guanido kinase	0	DIRECT
Putative isomerase YbhE	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
Globin-like	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
Flavoproteins	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
Tim10-like	0	DIRECT
SIS domain	0	DIRECT
GroEL equatorial domain-like	0	DIRECT
Ricin B-like lectins	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
DLC	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0	DIRECT
Tetrapyrrole methylase	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
Mitochondrial glycoprotein MAM33-like	0	DIRECT
SH3-domain	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
Saposin	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
Tautomerase/MIF	0	DIRECT
RNA polymerase subunits	0	DIRECT
Pentapeptide repeat-like	0	DIRECT
Ribosomal protein L4	0	DIRECT
YrdC/RibB	0	DIRECT
GlnB-like	0	DIRECT
MurD-like peptide ligases, catalytic domain	0	DIRECT
R3H domain	0	DIRECT
Glutamine synthetase, N-terminal domain	0	DIRECT
alpha-helical ferredoxin	0	DIRECT
VHP, Villin headpiece domain	0	DIRECT
SMR domain-like	0	DIRECT
XPC-binding domain	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
TATA-box binding protein-like	0	DIRECT
Ribosomal protein S2	0	DIRECT
Alpha-L RNA-binding motif	0	DIRECT
GroEL-intermediate domain like	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Lipoxigenase	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
beta-N-acetylhexosaminidase-like domain	0	DIRECT
SufE/NifU	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
Clc chloride channel	0	DIRECT
6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
Nicotinate/Quinolinate PRTase N-terminal domain-like	0	DIRECT
DNA repair protein MutS, domain II	0	DIRECT
Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
Single hybrid motif	0	DIRECT
RraA-like	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
Sec7 domain	0	DIRECT
PABC (PABP) domain	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
RibA-like	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
Chelatase	0	DIRECT
Granulin repeat	0	DIRECT
HesB-like domain	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
Expressed protein At2g23090/F21P24.15	0	DIRECT
Composite domain of metallo-dependent hydrolases	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
Lesion bypass DNA polymerase (Y-family), little finger domain	0	DIRECT
ADC-like	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
Aldolase	0.0007976	DIRECT