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

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

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

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

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

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

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

SCOP term	FDR (all)	Annotation (direct or inherited)
alpha/beta-Hydrolases	0	DIRECT
NHL repeat	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Transglutaminase, two C-terminal domains	0	DIRECT
Kix domain of CBP (creb binding protein)	0	DIRECT
Docking domain B of the erythromycin polyketide synthase (DEBS)	0	DIRECT
Mib/herc2 domain-like	0	DIRECT
FabD/lysophospholipase-like	0	DIRECT
TRAF domain-like	0	DIRECT
Nucleotide-diphospho-sugar transferases	0	DIRECT
UBC-like	0	DIRECT
PABC (PABP) domain	0	DIRECT
RING/U-box	0	DIRECT
Hect, E3 ligase catalytic domain	0	DIRECT
TAZ domain	0	DIRECT
HLH, helix-loop-helix DNA-binding domain	0	DIRECT
Probable ACP-binding domain of malonyl-CoA ACP transacylase	0	DIRECT
Single hybrid motif	0	DIRECT
CCHHC domain	0	DIRECT
CHY zinc finger-like	0	DIRECT
HprK N-terminal domain-like	0	DIRECT
TTHA0583/YokD-like	0	DIRECT
WWE domain	0	DIRECT
CoA-dependent acyltransferases	0	DIRECT
ARM repeat	0	DIRECT
Isocitrate/Isopropylmalate dehydrogenase-like	0	DIRECT
DmpA/ArgJ-like	0	DIRECT
PA domain	0	DIRECT
Malate synthase G	0	DIRECT
Citrate synthase	0	DIRECT
Actin-like ATPase domain	0	DIRECT
Leucine zipper domain	0	DIRECT
Inhibitor of apoptosis (IAP) repeat	0	DIRECT
Zinc hairpin stack	0	DIRECT
CCCH zinc finger	0	DIRECT
Formylmethanofuran:tetrahydromethanopterin formyltransferase	0	DIRECT
WW domain	0	DIRECT
Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
Thiolase-like	0	DIRECT
NRDP1 C-terminal domain-like	0	DIRECT
SWIB/MDM2 domain	0	DIRECT
B-box zinc-binding domain	0	DIRECT
Nuclear receptor coactivator interlocking domain	0	DIRECT
Ankyrin repeat	0	DIRECT
Trimerization domain of TRAF	0	DIRECT
FYVE/PHD zinc finger	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
Concanavalin A-like lectins/glucanases	0	DIRECT
Trimeric LpxA-like enzymes	0	DIRECT
post-HMGL domain-like	0	DIRECT
2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain	0	DIRECT
ACP-like	0	DIRECT
OMPA-like	0	DIRECT
N-terminal domain of cbl (N-cbl)	0	DIRECT
ClpS-like	0	DIRECT
Aldolase	0	DIRECT
Bromodomain	0	DIRECT
Ran binding protein zinc finger-like	5.003e-16	DIRECT
Chromo domain-like	0.000000000000006368	DIRECT
WD40 repeat-like	0.0000000000000268	DIRECT
Class II aaRS and biotin synthetases	0.00000000000009501	DIRECT
SAP domain	0.0000000003001	DIRECT
Class I glutamine amidotransferase-like	0.000000000583	DIRECT
Pentapeptide repeat-like	0.00000000239	DIRECT
SMAD/FHA domain	0.00000001341	DIRECT
UBA-like	0.00000009417	DIRECT
SCP-like	0.00000009603	DIRECT
RCC1/BLIP-II	0.0000003805	DIRECT
beta-beta-alpha zinc fingers	0.0000005195	DIRECT
Galactose oxidase, central domain	0.0000005682	DIRECT
C2 domain (Calcium/lipid-binding domain, CaLB)	0.00000499	DIRECT
Cyclin-like	0.00002218	DIRECT
Cysteine proteinases	0.00002572	DIRECT
Ubiquitin-like	0.00008703	DIRECT
Tropomyosin	0.0001053	DIRECT
TAF(II)230 TBP-binding fragment	0.0003717	DIRECT
vWA-like	0.0004191	DIRECT
CBS-domain pair	0.0006691	DIRECT
Formin homology 2 domain (FH2 domain)	0.0009572	DIRECT
Kelch motif	0.001577	INHERITED FROM: Transferring groups other than amino-acyl groups || methoxycarbonyltransferase
Acetyl-CoA synthetase-like	0.002511	INHERITED FROM: Transferring groups other than amino-acyl groups || Acyl-[acyl-carrier-protein]--phospholipid O-acyltransferase
PFL-like glycyl radical enzymes	0.002676	INHERITED FROM: Formate C-acetyltransferase || Transferring groups other than amino-acyl groups
Homeodomain-like	0.0139	INHERITED FROM: Sphingosine N-acyltransferase
EF-hand	0.05284	INHERITED FROM: 1-acylglycerol-3-phosphate O-acyltransferase || 1-alkylglycerophosphocholine O-acetyltransferase || 1-acylglycerophosphocholine O-acyltransferase || RING-type E3 ubiquitin transferase
Prismane protein-like	0.07225	INHERITED FROM: CO-methylating acetyl-CoA synthase
Zinc beta-ribbon	0.07787	INHERITED FROM: Histone acetyltransferase
DEATH domain	0.07789	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Second domain of FERM	0.1089	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
PDZ domain-like	0.3022	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Cyclophilin-like	0.5079	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Tudor/PWWP/MBT	0.5283	INHERITED FROM: HECT-type E3 ubiquitin transferase
Dimeric alpha+beta barrel	0.7626	INHERITED FROM: Homocitrate synthase || Acyl groups converted into alkyl groups on transfer
RNA-binding domain, RBD	0.7757	INHERITED FROM: RING-type E3 ubiquitin transferase
PYP-like sensor domain (PAS domain)	0.8398	INHERITED FROM: Histone acetyltransferase || Transferring groups other than amino-acyl groups
TPR-like	0.9176	INHERITED FROM: RING-type E3 ubiquitin transferase
PLP-dependent transferases	0.9846	INHERITED FROM: 5-aminolevulinate synthase || Transferring groups other than amino-acyl groups || Serine C-palmitoyltransferase || Glycine C-acetyltransferase || 8-amino-7-oxononanoate synthase
E set domains	0.985	INHERITED FROM: Protein-glutamine gamma-glutamyltransferase || Aminoacyltransferases
Thioesterase/thiol ester dehydrase-isomerase	1	INHERITED FROM: Fatty-acyl-CoA synthase || [Acyl-carrier-protein] S-malonyltransferase || [Acyl-carrier-protein] S-acetyltransferase
Clavaminate synthase-like	1	INHERITED FROM: methoxycarbonyltransferase
BRCT domain	1	INHERITED FROM: RING-type E3 ubiquitin transferase
tRNA-binding arm	1	INHERITED FROM: glycyltransferase
Nucleic acid-binding proteins	1	INHERITED FROM: Lysyltransferase
P-loop containing nucleoside triphosphate hydrolases	1	INHERITED FROM: tRNA(Met) cytidine acetyltransferase || Phosphate acetyltransferase
FMN-linked oxidoreductases	1	INHERITED FROM: [Acyl-carrier-protein] S-malonyltransferase
Carbamate kinase-like	1	INHERITED FROM: Amino-acid N-acetyltransferase
Zn-dependent exopeptidases	1	INHERITED FROM: Glutaminyl-peptide cyclotransferase
4'-phosphopantetheinyl transferase	1	INHERITED FROM: Fatty-acyl-CoA synthase || Beta-ketoacyl-[acyl-carrier-protein] synthase I
NAD(P)-binding Rossmann-fold domains	1	INHERITED FROM: 6-deoxyerythronolide-B synthase || Fatty-acyl-CoA synthase || Beta-ketoacyl-[acyl-carrier-protein] synthase I || Fatty-acid synthase || Lovastatin nonaketide synthase || [Acyl-carrier-protein] S-acetyltransferase || Narbonolide synthase || 10-deoxymethynolide syntase || ATP citrate synthase || 6-methylsalicylic acid synthase
Succinyl-CoA synthetase domains	1	INHERITED FROM: Acyl groups converted into alkyl groups on transfer || ATP citrate synthase
GroES-like	1	INHERITED FROM: [Acyl-carrier-protein] S-malonyltransferase || Beta-ketoacyl-[acyl-carrier-protein] synthase I || Fatty-acid synthase || [Acyl-carrier-protein] S-acetyltransferase
Inosine monophosphate dehydrogenase (IMPDH)	1	INHERITED FROM: Fatty-acyl-CoA synthase || [Acyl-carrier-protein] S-malonyltransferase || [Acyl-carrier-protein] S-acetyltransferase
Thiamin diphosphate-binding fold (THDP-binding)	1	INHERITED FROM: Sulfoacetaldehyde acetyltransferase || Dihydrolipoyllysine-residue succinyltransferase
PUA domain-like	1	INHERITED FROM: RING-type E3 ubiquitin transferase
Fibronectin type III	1	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
S-adenosyl-L-methionine-dependent methyltransferases	1	INHERITED FROM: Fatty-acid synthase || Lovastatin nonaketide synthase || [Acyl-carrier-protein] S-acetyltransferase || methoxycarbonyltransferase
Radical SAM enzymes	1	INHERITED FROM: Histone acetyltransferase
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	1	INHERITED FROM: Gamma-glutamyltransferase || Aminoacyltransferases
"Winged helix" DNA-binding domain	1	INHERITED FROM: Histone acetyltransferase
Glutathione synthetase ATP-binding domain-like	1	INHERITED FROM: ATP citrate synthase
Phosphoenolpyruvate/pyruvate domain	1	INHERITED FROM: Malate synthase
DHS-like NAD/FAD-binding domain	1	INHERITED FROM: Sulfoacetaldehyde acetyltransferase || Acyl groups converted into alkyl groups on transfer
L domain-like	1	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Galactose-binding domain-like	1	INHERITED FROM: HECT-type E3 ubiquitin transferase
SH2 domain	1	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
SH3-domain	1	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase

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

SCOP term	FDR (all)	Annotation (direct or inherited)
RING finger domain, C3HC4	0	DIRECT
YeaZ-like	0	DIRECT
Malate synthase G	0	DIRECT
Outer membrane enzyme PagP	0	DIRECT
U-box	0	DIRECT
FabD-like	0	DIRECT
SWIB/MDM2 domain	0	DIRECT
Zinc hairpin stack	0	DIRECT
Serine acetyltransferase	0	DIRECT
Hypoxia-inducible factor Hif2a, C-terminal domain	0	DIRECT
Homeodomain	0	DIRECT
Armadillo repeat	0	DIRECT
FemXAB nonribosomal peptidyltransferases	0	DIRECT
Autoinducer synthetase	0	DIRECT
Probable ACP-binding domain of malonyl-CoA ACP transacylase	0	DIRECT
Transglutaminase, two C-terminal domains	0	DIRECT
UDP N-acetylglucosamine acyltransferase	0	DIRECT
Docking domain B of the erythromycin polyketide synthase (DEBS)	0	DIRECT
Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD	0	DIRECT
2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain	0	DIRECT
HTS-like	0	DIRECT
B-box zinc-binding domain	0	DIRECT
Transglutaminase core	0	DIRECT
ZZ domain	0	DIRECT
Thiolase-related	0	DIRECT
Nuclear receptor coactivator interlocking domain	0	DIRECT
Transcriptional factor domain	0	DIRECT
Phytochelatin synthase	0	DIRECT
SPRY domain	0	DIRECT
CHY zinc finger	0	DIRECT
Choline/Carnitine O-acyltransferase	0	DIRECT
USP8 interacting domain	0	DIRECT
APC10-like	0	DIRECT
Trimerization domain of TRAF	0	DIRECT
HMGL-like	0	DIRECT
BRCT domain	0	DIRECT
Methicillin resistance protein FemA probable tRNA-binding arm	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Transcription factor IIB (TFIIB), core domain	0	DIRECT
Biotinyl/lipoyl-carrier proteins and domains	0	DIRECT
Variant RING domain	0	DIRECT
Mycobacterial antigens	0	DIRECT
Acyl-carrier protein (ACP)	0	DIRECT
GABA-aminotransferase-like	0	DIRECT
CAT-like	0	DIRECT
HLH, helix-loop-helix DNA-binding domain	0	DIRECT
Transglutaminase N-terminal domain	0	DIRECT
Ankyrin repeat	0	DIRECT
Citrate synthase	0	DIRECT
PHD domain	0	DIRECT
Kix domain of CBP (creb binding protein)	0	DIRECT
Acetyl-CoA synthase	0	DIRECT
Ran binding protein zinc finger-like	0	DIRECT
LFTR-like	0	DIRECT
Aminoglycoside 3-N-acetyltransferase-like	0	DIRECT
WWE domain	0	DIRECT
UBC-related	0	DIRECT
N-terminal domain of cbl (N-cbl)	0	DIRECT
PABC (PABP) domain	0	DIRECT
N-acetyl transferase, NAT	0	DIRECT
UDP-glucose pyrophosphorylase	0	DIRECT
TAZ domain	0	DIRECT
Bromodomain	0	DIRECT
CCHHC domain	0	DIRECT
Glutaminyl-peptide cyclotransferase-like	0	DIRECT
Gamma-glutamyltranspeptidase-like	0	DIRECT
LplA-like	0	DIRECT
CPH domain	0	DIRECT
NHL repeat	0	DIRECT
DmpG/LeuA communication domain-like	0	DIRECT
Mib/herc2 domain	0	DIRECT
CCCH zinc finger	0	DIRECT
N-myristoyl transferase, NMT	0	DIRECT
Filamin repeat (rod domain)	0	DIRECT
Chalcone synthase-like	0	DIRECT
Leucine zipper domain	0	DIRECT
SIAH, seven in absentia homolog	0	DIRECT
AstA-like	0	DIRECT
Arylamine N-acetyltransferase	0	DIRECT
Hect, E3 ligase catalytic domain	0	DIRECT
PlsX-like	0	DIRECT
WW domain	0	DIRECT
Galactoside acetyltransferase-like	0	DIRECT
Lrp/AsnC-like transcriptional regulator C-terminal domain	0	DIRECT
Inhibitor of apoptosis (IAP) repeat	0	DIRECT
Formylmethanofuran:tetrahydromethanopterin formyltransferase	0	DIRECT
PAS domain of steroid receptor coactivator 1A, NCo-A1	0	DIRECT
ArgJ-like	0	DIRECT
Phosphotransacetylase	0	DIRECT
Chromo barrel domain	0	DIRECT
O-acetyltransferase	0	DIRECT
GlmU C-terminal domain-like	0	DIRECT
MATH domain	7.291e-16	DIRECT
PFL-like	0.000000000000004316	DIRECT
WD40-repeat	0.0000000000001098	DIRECT
DRTGG domain	0.0000000000008827	DIRECT
Classic zinc finger, C2H2	0.00000000002062	DIRECT
Pentapeptide repeats	0.0000000001533	DIRECT
SAP domain	0.0000000001923	DIRECT
SRA domain-like	0.000000001189	DIRECT
Ubiquitin-related	0.000000002514	DIRECT
Thioesterase domain of polypeptide, polyketide and fatty acid synthases	0.000000003215	DIRECT
Leucine rich effector protein YopM	0.000000007837	DIRECT
FHA domain	0.000000008316	DIRECT
Sterol carrier protein, SCP	0.00000004471	DIRECT
CoA-binding domain	0.000003021	DIRECT
FYVE, a phosphatidylinositol-3-phosphate binding domain	0.000003963	DIRECT
Regulator of chromosome condensation RCC1	0.000004337	DIRECT
MaoC-like	0.000004673	DIRECT
Tropomyosin	0.000004765	DIRECT
Leucine carboxy methyltransferase Ppm1	0.000008857	DIRECT
EF-hand modules in multidomain proteins	0.00001208	DIRECT
Hypoxia-inducible factor HIF ihhibitor (FIH1)	0.00001809	DIRECT
PA domain	0.00005767	DIRECT
PDZ domain	0.0001166	DIRECT
UBA domain	0.0001166	DIRECT
CBS-domain pair	0.0002508	DIRECT
TAF(II)230 TBP-binding fragment	0.0002911	DIRECT
Acetyl-CoA synthetase-like	0.0004863	DIRECT
Third domain of FERM	0.003385	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
First domain of FERM	0.003385	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Caspase recruitment domain, CARD	0.03314	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
RWD domain	0.04368	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Branched-chain alpha-keto acid dehydrogenase Pyr module	0.04663	INHERITED FROM: Dihydrolipoyllysine-residue succinyltransferase
Branched-chain alpha-keto acid dehydrogenase PP module	0.04992	INHERITED FROM: Dihydrolipoyllysine-residue succinyltransferase
Second domain of FERM	0.07745	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Tetratricopeptide repeat (TPR)	0.1011	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
PLC-like (P variant)	0.2598	INHERITED FROM: HECT-type E3 ubiquitin transferase || Aminoacyltransferases
Cyclophilin (peptidylprolyl isomerase)	0.3066	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
HpcH/HpaI aldolase	0.4385	INHERITED FROM: Malate synthase || Acyl groups converted into alkyl groups on transfer
Chromo domain	0.4487	INHERITED FROM: Histone acetyltransferase
Pyruvate oxidase and decarboxylase, middle domain	0.6336	INHERITED FROM: Sulfoacetaldehyde acetyltransferase || Acyl groups converted into alkyl groups on transfer
Serine carboxypeptidase-like	0.8215	INHERITED FROM: Sinapoylglucose--sinapoylglucose O-sinapoyltransferase
Alcohol dehydrogenase-like, C-terminal domain	0.9234	INHERITED FROM: [Acyl-carrier-protein] S-malonyltransferase || Beta-ketoacyl-[acyl-carrier-protein] synthase I || Fatty-acid synthase || [Acyl-carrier-protein] S-acetyltransferase
Fibronectin type III	0.9334	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
SH3-domain	0.9629	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Succinyl-CoA synthetase domains	1	INHERITED FROM: Acyl groups converted into alkyl groups on transfer || ATP citrate synthase
Anticodon-binding domain	1	INHERITED FROM: Lysyltransferase
Pyruvate oxidase and decarboxylase Pyr module	1	INHERITED FROM: Sulfoacetaldehyde acetyltransferase
Calmodulin-like	1	INHERITED FROM: 1-acylglycerol-3-phosphate O-acyltransferase || 1-alkylglycerophosphocholine O-acetyltransferase || 1-acylglycerophosphocholine O-acyltransferase
Alcohol dehydrogenase-like, N-terminal domain	1	INHERITED FROM: [Acyl-carrier-protein] S-malonyltransferase || Beta-ketoacyl-[acyl-carrier-protein] synthase I || Fatty-acid synthase || [Acyl-carrier-protein] S-acetyltransferase
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	1	INHERITED FROM: Lysyltransferase
Class I aldolase	1	INHERITED FROM: 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase
Pyruvate oxidase and decarboxylase PP module	1	INHERITED FROM: Sulfoacetaldehyde acetyltransferase || Acyl groups converted into alkyl groups on transfer
Tyrosine-dependent oxidoreductases	1	INHERITED FROM: 6-deoxyerythronolide-B synthase || [Acyl-carrier-protein] S-malonyltransferase || Beta-ketoacyl-[acyl-carrier-protein] synthase I || Fatty-acid synthase || Lovastatin nonaketide synthase || [Acyl-carrier-protein] S-acetyltransferase || Narbonolide synthase || 10-deoxymethynolide syntase || 6-methylsalicylic acid synthase
SH2 domain	1	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Succinyl-CoA synthetase, beta-chain, N-terminal domain	1	INHERITED FROM: ATP citrate synthase
Holo-(acyl carrier protein) synthase ACPS	1	INHERITED FROM: Fatty-acyl-CoA synthase || Beta-ketoacyl-[acyl-carrier-protein] synthase I
N-acetyl-l-glutamate kinase	1	INHERITED FROM: Amino-acid N-acetyltransferase || Transferring groups other than amino-acyl groups
Crotonase-like	1	INHERITED FROM: Histone acetyltransferase

Trees by TreeVector

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

Supra-domains annotated to this EC term (SPEC level: Moderately Informative)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
NHL repeat	0	DIRECT
CCCH zinc finger	0	DIRECT
FabD/lysophospholipase-like	0	DIRECT
NRDP1 C-terminal domain-like	0	DIRECT
alpha/beta-Hydrolases	0	DIRECT
TAZ domain	0	DIRECT
Isocitrate/Isopropylmalate dehydrogenase-like	0	DIRECT
Concanavalin A-like lectins/glucanases	0	DIRECT
Malate synthase G	0	DIRECT
B-box zinc-binding domain	0	DIRECT
ARM repeat	0	DIRECT
Probable ACP-binding domain of malonyl-CoA ACP transacylase	0	DIRECT
UBC-like	0	DIRECT
Ankyrin repeat	0	DIRECT
CCHHC domain	0	DIRECT
ClpS-like	0	DIRECT
TRAF domain-like	0	DIRECT
DmpA/ArgJ-like	0	DIRECT
SWIB/MDM2 domain	0	DIRECT
RING/U-box	0	DIRECT
Aldolase	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Kix domain of CBP (creb binding protein)	0	DIRECT
N-terminal domain of cbl (N-cbl)	0	DIRECT
FYVE/PHD zinc finger	0	DIRECT
HprK N-terminal domain-like	0	DIRECT
CoA-dependent acyltransferases	0	DIRECT
OMPA-like	0	DIRECT
Single hybrid motif	0	DIRECT
post-HMGL domain-like	0	DIRECT
Transglutaminase, two C-terminal domains	0	DIRECT
HLH, helix-loop-helix DNA-binding domain	0	DIRECT
Docking domain B of the erythromycin polyketide synthase (DEBS)	0	DIRECT
2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
PA domain	0	DIRECT
Leucine zipper domain	0	DIRECT
Actin-like ATPase domain	0	DIRECT
Formylmethanofuran:tetrahydromethanopterin formyltransferase	0	DIRECT
CHY zinc finger-like	0	DIRECT
Citrate synthase	0	DIRECT
Hect, E3 ligase catalytic domain	0	DIRECT
Nuclear receptor coactivator interlocking domain	0	DIRECT
TTHA0583/YokD-like	0	DIRECT
Bromodomain	0	DIRECT
WW domain	0	DIRECT
Zinc hairpin stack	0	DIRECT
Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
Trimeric LpxA-like enzymes	0	DIRECT
Nucleotide-diphospho-sugar transferases	0	DIRECT
Trimerization domain of TRAF	0	DIRECT
WWE domain	0	DIRECT
Inhibitor of apoptosis (IAP) repeat	0	DIRECT
ACP-like	0	DIRECT
PABC (PABP) domain	0	DIRECT
Mib/herc2 domain-like	0	DIRECT
Thiolase-like	0	DIRECT
Ran binding protein zinc finger-like	3.506e-16	DIRECT
Chromo domain-like	0.0000000000000045	DIRECT
WD40 repeat-like	0.00000000000001906	DIRECT
Class II aaRS and biotin synthetases	0.00000000000006779	DIRECT
SAP domain	0.0000000002229	DIRECT
Class I glutamine amidotransferase-like	0.0000000004349	DIRECT
Pentapeptide repeat-like	0.000000001798	DIRECT
SMAD/FHA domain	0.00000001019	DIRECT
UBA-like	0.00000007221	DIRECT
SCP-like	0.00000007364	DIRECT
RCC1/BLIP-II	0.0000002949	DIRECT
beta-beta-alpha zinc fingers	0.0000004039	DIRECT
Galactose oxidase, central domain	0.0000004423	DIRECT
C2 domain (Calcium/lipid-binding domain, CaLB)	0.00000394	DIRECT
Cyclin-like	0.00001774	DIRECT
Cysteine proteinases	0.0000206	DIRECT
Ubiquitin-like	0.00007043	DIRECT
Tropomyosin	0.0000855	DIRECT
TAF(II)230 TBP-binding fragment	0.0003042	DIRECT
vWA-like	0.000344	DIRECT
CBS-domain pair	0.0005526	DIRECT
Formin homology 2 domain (FH2 domain)	0.0007922	DIRECT
Kelch motif	0.001313	INHERITED FROM: methoxycarbonyltransferase || Transferring groups other than amino-acyl groups
Acetyl-CoA synthetase-like	0.002102	INHERITED FROM: Transferring groups other than amino-acyl groups || Acyl-[acyl-carrier-protein]--phospholipid O-acyltransferase
PFL-like glycyl radical enzymes	0.002242	INHERITED FROM: Formate C-acetyltransferase || Transferring groups other than amino-acyl groups
Homeodomain-like	0.01185	INHERITED FROM: Sphingosine N-acyltransferase
EF-hand	0.04577	INHERITED FROM: 1-acylglycerol-3-phosphate O-acyltransferase || RING-type E3 ubiquitin transferase || 1-alkylglycerophosphocholine O-acetyltransferase || 1-acylglycerophosphocholine O-acyltransferase
Prismane protein-like	0.06287	INHERITED FROM: CO-methylating acetyl-CoA synthase
Zinc beta-ribbon	0.06785	INHERITED FROM: Histone acetyltransferase
DEATH domain	0.06786	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
Second domain of FERM	0.09543	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
PDZ domain-like	0.2727	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
Cyclophilin-like	0.4642	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
Tudor/PWWP/MBT	0.4833	INHERITED FROM: HECT-type E3 ubiquitin transferase
Dimeric alpha+beta barrel	0.7016	INHERITED FROM: Acyl groups converted into alkyl groups on transfer || Homocitrate synthase
RNA-binding domain, RBD	0.7138	INHERITED FROM: RING-type E3 ubiquitin transferase
PYP-like sensor domain (PAS domain)	0.774	INHERITED FROM: Transferring groups other than amino-acyl groups || Histone acetyltransferase
TPR-like	0.847	INHERITED FROM: RING-type E3 ubiquitin transferase
PLP-dependent transferases	0.9107	INHERITED FROM: Transferring groups other than amino-acyl groups || 8-amino-7-oxononanoate synthase || 5-aminolevulinate synthase || Serine C-palmitoyltransferase || Glycine C-acetyltransferase
E set domains	0.9111	INHERITED FROM: Protein-glutamine gamma-glutamyltransferase || Aminoacyltransferases
Fibronectin type III	0.9311	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
SH3-domain	0.9591	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
tRNA-binding arm	1	INHERITED FROM: glycyltransferase
Inosine monophosphate dehydrogenase (IMPDH)	1	INHERITED FROM: [Acyl-carrier-protein] S-malonyltransferase || Fatty-acyl-CoA synthase || [Acyl-carrier-protein] S-acetyltransferase
PUA domain-like	1	INHERITED FROM: RING-type E3 ubiquitin transferase
Nucleic acid-binding proteins	1	INHERITED FROM: Lysyltransferase
NAD(P)-binding Rossmann-fold domains	1	INHERITED FROM: 6-methylsalicylic acid synthase || Lovastatin nonaketide synthase || Fatty-acid synthase || ATP citrate synthase || Fatty-acyl-CoA synthase || Narbonolide synthase || [Acyl-carrier-protein] S-acetyltransferase || 10-deoxymethynolide syntase || 6-deoxyerythronolide-B synthase || Beta-ketoacyl-[acyl-carrier-protein] synthase I
GroES-like	1	INHERITED FROM: [Acyl-carrier-protein] S-malonyltransferase || Fatty-acid synthase || [Acyl-carrier-protein] S-acetyltransferase || Beta-ketoacyl-[acyl-carrier-protein] synthase I
Succinyl-CoA synthetase domains	1	INHERITED FROM: ATP citrate synthase || Acyl groups converted into alkyl groups on transfer
Carbamate kinase-like	1	INHERITED FROM: Amino-acid N-acetyltransferase
BRCT domain	1	INHERITED FROM: RING-type E3 ubiquitin transferase
L domain-like	1	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
Glutathione synthetase ATP-binding domain-like	1	INHERITED FROM: ATP citrate synthase
Phosphoenolpyruvate/pyruvate domain	1	INHERITED FROM: Malate synthase
Galactose-binding domain-like	1	INHERITED FROM: HECT-type E3 ubiquitin transferase
Zn-dependent exopeptidases	1	INHERITED FROM: Glutaminyl-peptide cyclotransferase
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	1	INHERITED FROM: Gamma-glutamyltransferase || Aminoacyltransferases
Clavaminate synthase-like	1	INHERITED FROM: methoxycarbonyltransferase
FMN-linked oxidoreductases	1	INHERITED FROM: [Acyl-carrier-protein] S-malonyltransferase
Thioesterase/thiol ester dehydrase-isomerase	1	INHERITED FROM: [Acyl-carrier-protein] S-malonyltransferase || Fatty-acyl-CoA synthase || [Acyl-carrier-protein] S-acetyltransferase
P-loop containing nucleoside triphosphate hydrolases	1	INHERITED FROM: tRNA(Met) cytidine acetyltransferase || Phosphate acetyltransferase
S-adenosyl-L-methionine-dependent methyltransferases	1	INHERITED FROM: Lovastatin nonaketide synthase || Fatty-acid synthase || methoxycarbonyltransferase || [Acyl-carrier-protein] S-acetyltransferase
DHS-like NAD/FAD-binding domain	1	INHERITED FROM: Sulfoacetaldehyde acetyltransferase || Acyl groups converted into alkyl groups on transfer
4'-phosphopantetheinyl transferase	1	INHERITED FROM: Fatty-acyl-CoA synthase || Beta-ketoacyl-[acyl-carrier-protein] synthase I
Thiamin diphosphate-binding fold (THDP-binding)	1	INHERITED FROM: Dihydrolipoyllysine-residue succinyltransferase || Sulfoacetaldehyde acetyltransferase
SH2 domain	1	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
Radical SAM enzymes	1	INHERITED FROM: Histone acetyltransferase
"Winged helix" DNA-binding domain	1	INHERITED FROM: Histone acetyltransferase

Supra-domains annotated to this EC term (SPEC level: Moderately Informative)
Highlighted in gray are those with FDR>0.001

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
49785,159034 49785 - Galactose-binding domain-like 159034 - Mib/herc2 domain-like	0	DIRECT
54495,46934 54495 - UBC-like 46934 - UBA-like	0	DIRECT
51569,54909 51569 - Aldolase 54909 - Dimeric alpha+beta barrel	0	DIRECT
56112,57850 56112 - Protein kinase-like (PK-like) 57850 - RING/U-box	0	DIRECT
47668,47473 47668 - N-terminal domain of cbl (N-cbl) 47473 - EF-hand	0	DIRECT
57850,117839 57850 - RING/U-box 117839 - WWE domain	0	DIRECT
55550,57850 55550 - SH2 domain 57850 - RING/U-box	0	DIRECT
51230,52777 51230 - Single hybrid motif 52777 - CoA-dependent acyltransferases	0	DIRECT
51045,51045 51045 - WW domain 51045 - WW domain	0	DIRECT
57850,57850 57850 - RING/U-box 57850 - RING/U-box	0	DIRECT
75138,53659 75138 - HprK N-terminal domain-like 53659 - Isocitrate/Isopropylmalate dehydrogenase-like	0	DIRECT
81296,54001 81296 - E set domains 54001 - Cysteine proteinases	0	DIRECT
51569,89000 51569 - Aldolase 89000 - post-HMGL domain-like	0	DIRECT
57850,57845 57850 - RING/U-box 57845 - B-box zinc-binding domain	0	DIRECT
48403,57850 48403 - Ankyrin repeat 57850 - RING/U-box	0	DIRECT
51735,51735 51735 - NAD(P)-binding Rossmann-fold domains 51735 - NAD(P)-binding Rossmann-fold domains	0	DIRECT
49785,50985 49785 - Galactose-binding domain-like 50985 - RCC1/BLIP-II	0	DIRECT
161245,57850 161245 - Zinc hairpin stack 57850 - RING/U-box	0	DIRECT
49599,49599 49599 - TRAF domain-like 49599 - TRAF domain-like	0	DIRECT
53633,55729 53633 - Carbamate kinase-like 55729 - Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
90209,57850 90209 - Ran binding protein zinc finger-like 57850 - RING/U-box	0	DIRECT
55729,55729 55729 - Acyl-CoA N-acyltransferases (Nat) 55729 - Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
51230,51230 51230 - Single hybrid motif 51230 - Single hybrid motif	0	DIRECT
47592,90209 47592 - SWIB/MDM2 domain 90209 - Ran binding protein zinc finger-like	0	DIRECT
54495,57850 54495 - UBC-like 57850 - RING/U-box	0	DIRECT
57850,101898 57850 - RING/U-box 101898 - NHL repeat	0	DIRECT
117281,51197 117281 - Kelch motif 51197 - Clavaminate synthase-like	0	DIRECT
48403,52113 48403 - Ankyrin repeat 52113 - BRCT domain	0	DIRECT
90229,57850 90229 - CCCH zinc finger 57850 - RING/U-box	0	DIRECT
53300,57850 53300 - vWA-like 57850 - RING/U-box	0	DIRECT
49265,49899 49265 - Fibronectin type III 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
81296,101898 81296 - E set domains 101898 - NHL repeat	0	DIRECT
57850,57933 57850 - RING/U-box 57933 - TAZ domain	0	DIRECT
54160,55729 54160 - Chromo domain-like 55729 - Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
54236,90209 54236 - Ubiquitin-like 90209 - Ran binding protein zinc finger-like	0	DIRECT
55729,46589 55729 - Acyl-CoA N-acyltransferases (Nat) 46589 - tRNA-binding arm	0	DIRECT
54637,52151 54637 - Thioesterase/thiol ester dehydrase-isomerase 52151 - FabD/lysophospholipase-like	0	DIRECT
54001,49309 54001 - Cysteine proteinases 49309 - Transglutaminase, two C-terminal domains	0	DIRECT
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0	DIRECT
161219,161245 161219 - CHY zinc finger-like 161245 - Zinc hairpin stack	0	DIRECT
57783,47954 57783 - Zinc beta-ribbon 47954 - Cyclin-like	0	DIRECT
49879,57850 49879 - SMAD/FHA domain 57850 - RING/U-box	0	DIRECT
69593,56801 69593 - Glycerol-3-phosphate (1)-acyltransferase 56801 - Acetyl-CoA synthetase-like	0	DIRECT
53901,55718 53901 - Thiolase-like 55718 - SCP-like	0	DIRECT
57903,57850 57903 - FYVE/PHD zinc finger 57850 - RING/U-box	0	DIRECT
57850,48371 57850 - RING/U-box 48371 - ARM repeat	0	DIRECT
55112,55112 55112 - Formylmethanofuran:tetrahydromethanopterin formyltransferase 55112 - Formylmethanofuran:tetrahydromethanopterin formyltransferase	0	DIRECT
63570,56204 63570 - PABC (PABP) domain 56204 - Hect, E3 ligase catalytic domain	0	DIRECT
90229,90229 90229 - CCCH zinc finger 90229 - CCCH zinc finger	0	DIRECT
55729,47370 55729 - Acyl-CoA N-acyltransferases (Nat) 47370 - Bromodomain	0	DIRECT
57850,159034 57850 - RING/U-box 159034 - Mib/herc2 domain-like	0	DIRECT
53335,50965 53335 - S-adenosyl-L-methionine-dependent methyltransferases 50965 - Galactose oxidase, central domain	0	DIRECT
51735,48256 51735 - NAD(P)-binding Rossmann-fold domains 48256 - Citrate synthase	0	DIRECT
46589,55729 46589 - tRNA-binding arm 55729 - Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
52540,55729 52540 - P-loop containing nucleoside triphosphate hydrolases 55729 - Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
50044,50044 50044 - SH3-domain 50044 - SH3-domain	0	DIRECT
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain)	0	DIRECT
69593,47473 69593 - Glycerol-3-phosphate (1)-acyltransferase 47473 - EF-hand	0	DIRECT
53474,54631 53474 - alpha/beta-Hydrolases 54631 - CBS-domain pair	0	DIRECT
53067,56112 53067 - Actin-like ATPase domain 56112 - Protein kinase-like (PK-like)	0	DIRECT
49599,50156 49599 - TRAF domain-like 50156 - PDZ domain-like	0	DIRECT
51735,47336 51735 - NAD(P)-binding Rossmann-fold domains 47336 - ACP-like	0	DIRECT
49599,160088 49599 - TRAF domain-like 160088 - NRDP1 C-terminal domain-like	0	DIRECT
50965,51197 50965 - Galactose oxidase, central domain 51197 - Clavaminate synthase-like	0	DIRECT
68906,57850 68906 - SAP domain 57850 - RING/U-box	0	DIRECT
57850,57667 57850 - RING/U-box 57667 - beta-beta-alpha zinc fingers	0	DIRECT
46785,57903 46785 - "Winged helix" DNA-binding domain 57903 - FYVE/PHD zinc finger	0	DIRECT
52540,75138 52540 - P-loop containing nucleoside triphosphate hydrolases 75138 - HprK N-terminal domain-like	0	DIRECT
117839,117839 117839 - WWE domain 117839 - WWE domain	0	DIRECT
57953,49599 57953 - Trimerization domain of TRAF 49599 - TRAF domain-like	0	DIRECT
52777,52777 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases	0	DIRECT
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0	DIRECT
47005,52777 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases	0	DIRECT
48452,57850 48452 - TPR-like 57850 - RING/U-box	0	DIRECT
47473,55550 47473 - EF-hand 55550 - SH2 domain	0	DIRECT
49562,51045 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 51045 - WW domain	0	DIRECT
49309,49309 49309 - Transglutaminase, two C-terminal domains 49309 - Transglutaminase, two C-terminal domains	0	DIRECT
52210,51735 52210 - Succinyl-CoA synthetase domains 51735 - NAD(P)-binding Rossmann-fold domains	0	DIRECT
57850,50978 57850 - RING/U-box 50978 - WD40 repeat-like	0	DIRECT
48371,117839 48371 - ARM repeat 117839 - WWE domain	0	DIRECT
52025,57850 52025 - PA domain 57850 - RING/U-box	0	DIRECT
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain	0	DIRECT
102114,55729 102114 - Radical SAM enzymes 55729 - Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
51230,47005 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
57850,49599 57850 - RING/U-box 49599 - TRAF domain-like	0	DIRECT
49599,57953 49599 - TRAF domain-like 57953 - Trimerization domain of TRAF	0	DIRECT
53901,53901 53901 - Thiolase-like 53901 - Thiolase-like	0	DIRECT
57850,52540 57850 - RING/U-box 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
89000,110921 89000 - post-HMGL domain-like 110921 - 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain	0	DIRECT
53448,51161 53448 - Nucleotide-diphospho-sugar transferases 51161 - Trimeric LpxA-like enzymes	0	DIRECT
159034,57850 159034 - Mib/herc2 domain-like 57850 - RING/U-box	0	DIRECT
52151,51412 52151 - FabD/lysophospholipase-like 51412 - Inosine monophosphate dehydrogenase (IMPDH)	0	DIRECT
51045,56204 51045 - WW domain 56204 - Hect, E3 ligase catalytic domain	0	DIRECT
52151,55048 52151 - FabD/lysophospholipase-like 55048 - Probable ACP-binding domain of malonyl-CoA ACP transacylase	0	DIRECT
47336,53474 47336 - ACP-like 53474 - alpha/beta-Hydrolases	0.00000000000008169	DIRECT
52113,52113 52113 - BRCT domain 52113 - BRCT domain	0.00000000000008947	DIRECT
49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0.000000001355	DIRECT
53335,51735 53335 - S-adenosyl-L-methionine-dependent methyltransferases 51735 - NAD(P)-binding Rossmann-fold domains	0.0000003101	DIRECT
57903,47370 57903 - FYVE/PHD zinc finger 47370 - Bromodomain	0.00001774	DIRECT
48371,48403 48371 - ARM repeat 48403 - Ankyrin repeat	0.00003919	DIRECT
47336,52777 47336 - ACP-like 52777 - CoA-dependent acyltransferases	0.0001072	DIRECT
47370,47370 47370 - Bromodomain 47370 - Bromodomain	0.0003042	DIRECT
54236,47031 54236 - Ubiquitin-like 47031 - Second domain of FERM	0.003601	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.003601	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
47031,50729 47031 - Second domain of FERM 50729 - PH domain-like	0.0285	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
55785,55785 55785 - PYP-like sensor domain (PAS domain) 55785 - PYP-like sensor domain (PAS domain)	0.05108	INHERITED FROM: Transferring groups other than amino-acyl groups || Histone acetyltransferase
57903,57903 57903 - FYVE/PHD zinc finger 57903 - FYVE/PHD zinc finger	0.07933	INHERITED FROM: Transferring groups other than amino-acyl groups || Histone acetyltransferase
48371,48371 48371 - ARM repeat 48371 - ARM repeat	0.09543	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
48452,48452 48452 - TPR-like 48452 - TPR-like	0.1742	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
51735,50129 51735 - NAD(P)-binding Rossmann-fold domains 50129 - GroES-like	0.1796	INHERITED FROM: Beta-ketoacyl-[acyl-carrier-protein] synthase I
52518,52518 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52518 - Thiamin diphosphate-binding fold (THDP-binding)	1	INHERITED FROM: Dihydrolipoyllysine-residue succinyltransferase
52518,52467 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52467 - DHS-like NAD/FAD-binding domain	1	INHERITED FROM: Sulfoacetaldehyde acetyltransferase || Acyl groups converted into alkyl groups on transfer
52467,52518 52467 - DHS-like NAD/FAD-binding domain 52518 - Thiamin diphosphate-binding fold (THDP-binding)	1	INHERITED FROM: Sulfoacetaldehyde acetyltransferase || Acyl groups converted into alkyl groups on transfer
50249,55681 50249 - Nucleic acid-binding proteins 55681 - Class II aaRS and biotin synthetases	1	INHERITED FROM: Lysyltransferase
56059,52210 56059 - Glutathione synthetase ATP-binding domain-like 52210 - Succinyl-CoA synthetase domains	1	INHERITED FROM: ATP citrate synthase || Acyl groups converted into alkyl groups on transfer
50129,51735 50129 - GroES-like 51735 - NAD(P)-binding Rossmann-fold domains	1	INHERITED FROM: [Acyl-carrier-protein] S-malonyltransferase || Fatty-acid synthase || [Acyl-carrier-protein] S-acetyltransferase || Beta-ketoacyl-[acyl-carrier-protein] synthase I