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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 (Not in SDEC)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain	0	DIRECT
Thiolase-like	0	DIRECT
NRDP1 C-terminal domain-like	0	DIRECT
Actin-like ATPase domain	0	DIRECT
DmpA/ArgJ-like	0	DIRECT
HLH, helix-loop-helix DNA-binding domain	0	DIRECT
Trimerization domain of TRAF	0	DIRECT
Transglutaminase, two C-terminal domains	0	DIRECT
Formylmethanofuran:tetrahydromethanopterin formyltransferase	0	DIRECT
HprK N-terminal domain-like	0	DIRECT
Docking domain B of the erythromycin polyketide synthase (DEBS)	0	DIRECT
Mib/herc2 domain-like	0	DIRECT
Malate synthase G	0	DIRECT
CCCH zinc finger	0	DIRECT
DHS-like NAD/FAD-binding domain	0	DIRECT
FabD/lysophospholipase-like	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
ClpS-like	0	DIRECT
FYVE/PHD zinc finger	0	DIRECT
N-terminal domain of cbl (N-cbl)	0	DIRECT
ACP-like	0	DIRECT
Nucleotide-diphospho-sugar transferases	0	DIRECT
TRAF domain-like	0	DIRECT
Aldolase	0	DIRECT
PABC (PABP) domain	0	DIRECT
Carbon-nitrogen hydrolase	0	DIRECT
Nuclear receptor coactivator interlocking domain	0	DIRECT
Leucine zipper domain	0	DIRECT
PA domain	0	DIRECT
TTHA0583/YokD-like	0	DIRECT
Bromodomain	0	DIRECT
Ankyrin repeat	0	DIRECT
TAZ domain	0	DIRECT
Concanavalin A-like lectins/glucanases	0	DIRECT
CoA-dependent acyltransferases	0	DIRECT
Single hybrid motif	0	DIRECT
UBC-like	0	DIRECT
Probable ACP-binding domain of malonyl-CoA ACP transacylase	0	DIRECT
Kix domain of CBP (creb binding protein)	0	DIRECT
CCHHC domain	0	DIRECT
Inhibitor of apoptosis (IAP) repeat	0	DIRECT
Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
Isocitrate/Isopropylmalate dehydrogenase-like	0	DIRECT
OMPA-like	0	DIRECT
RING/U-box	0	DIRECT
B-box zinc-binding domain	0	DIRECT
CHY zinc finger-like	0	DIRECT
Hect, E3 ligase catalytic domain	0	DIRECT
SWIB/MDM2 domain	0	DIRECT
WW domain	0	DIRECT
Trimeric LpxA-like enzymes	0	DIRECT
Zinc hairpin stack	0	DIRECT
Citrate synthase	0	DIRECT
NHL repeat	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
WWE domain	0	DIRECT
post-HMGL domain-like	0	DIRECT
ARM repeat	0	DIRECT
alpha/beta-Hydrolases	0	DIRECT
Ran binding protein zinc finger-like	5.103e-16	DIRECT
Chromo domain-like	0.00000000000001579	DIRECT
WD40 repeat-like	0.00000000000006414	DIRECT
Class II aaRS and biotin synthetases	0.000000000005738	DIRECT
SAP domain	0.00000000006859	DIRECT
Pentapeptide repeat-like	0.000000003393	DIRECT
SMAD/FHA domain	0.00000004071	DIRECT
SCP-like	0.0000001195	DIRECT
UBA-like	0.00000018	DIRECT
RCC1/BLIP-II	0.0000005772	DIRECT
Galactose oxidase, central domain	0.00000075	DIRECT
Class I glutamine amidotransferase-like	0.000003775	DIRECT
beta-beta-alpha zinc fingers	0.000005653	DIRECT
Homeodomain-like	0.00001206	DIRECT
C2 domain (Calcium/lipid-binding domain, CaLB)	0.00001254	DIRECT
Cyclin-like	0.00002757	DIRECT
Cysteine proteinases	0.0001079	DIRECT
Tropomyosin	0.0001196	DIRECT
Ubiquitin-like	0.0001454	DIRECT
TAF(II)230 TBP-binding fragment	0.0004238	DIRECT
vWA-like	0.0004794	DIRECT
CBS-domain pair	0.001096	INHERITED FROM: Transferring groups other than amino-acyl groups || Homoserine O-acetyltransferase
Formin homology 2 domain (FH2 domain)	0.001108	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Kelch motif	0.001927	INHERITED FROM: Transferring groups other than amino-acyl groups || methoxycarbonyltransferase
PFL-like glycyl radical enzymes	0.003055	INHERITED FROM: Transferring groups other than amino-acyl groups || Formate C-acetyltransferase
Acetyl-CoA synthetase-like	0.02404	INHERITED FROM: Transferring groups other than amino-acyl groups || Acyl-[acyl-carrier-protein]--phospholipid O-acyltransferase
EF-hand	0.07187	INHERITED FROM: 1-acylglycerophosphocholine O-acyltransferase || RING-type E3 ubiquitin transferase || 1-alkylglycerophosphocholine O-acetyltransferase || 1-acylglycerol-3-phosphate O-acyltransferase
Zinc beta-ribbon	0.0803	INHERITED FROM: Histone acetyltransferase
Prismane protein-like	0.08754	INHERITED FROM: CO-methylating acetyl-CoA synthase
DEATH domain	0.08843	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Second domain of FERM	0.1229	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Glutamine synthetase, N-terminal domain	0.2744	INHERITED FROM: Protein S-acyltransferase
PDZ domain-like	0.3312	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
SGNH hydrolase	0.3923	INHERITED FROM: Diglucosylglycerate octanoyltransferase
RNA-binding domain, RBD	0.4621	INHERITED FROM: RING-type E3 ubiquitin transferase
Tudor/PWWP/MBT	0.5567	INHERITED FROM: HECT-type E3 ubiquitin transferase
Cyclophilin-like	0.5657	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Dimeric alpha+beta barrel	0.6161	INHERITED FROM: Acyl groups converted into alkyl groups on transfer || Homocitrate synthase
PYP-like sensor domain (PAS domain)	0.9096	INHERITED FROM: Transferring groups other than amino-acyl groups || Histone acetyltransferase
SH2 domain	1	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
PUA domain-like	1	INHERITED FROM: RING-type E3 ubiquitin transferase
Zn-dependent exopeptidases	1	INHERITED FROM: Glutaminyl-peptide cyclotransferase
Galactose-binding domain-like	1	INHERITED FROM: HECT-type E3 ubiquitin transferase
Glutamine synthetase/guanido kinase	1	INHERITED FROM: Protein S-acyltransferase
Thiamin diphosphate-binding fold (THDP-binding)	1	INHERITED FROM: Sulfoacetaldehyde acetyltransferase || Dihydrolipoyllysine-residue succinyltransferase
4'-phosphopantetheinyl transferase	1	INHERITED FROM: Beta-ketoacyl-[acyl-carrier-protein] synthase I || Fatty-acyl-CoA synthase system
PLP-dependent transferases	1	INHERITED FROM: 5-aminolevulinate synthase || Serine C-palmitoyltransferase || Transferring groups other than amino-acyl groups || 8-amino-7-oxononanoate synthase || Glycine C-acetyltransferase
Fibronectin type III	1	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
P-loop containing nucleoside triphosphate hydrolases	1	INHERITED FROM: Phosphate acetyltransferase || tRNA(Met) cytidine acetyltransferase
Phosphoenolpyruvate/pyruvate domain	1	INHERITED FROM: Malate synthase
Nucleic acid-binding proteins	1	INHERITED FROM: Lysyltransferase
BRCT domain	1	INHERITED FROM: RING-type E3 ubiquitin transferase
GroES-like	1	INHERITED FROM: Beta-ketoacyl-[acyl-carrier-protein] synthase I || 2-methylbutanoate polyketide synthase || [Acyl-carrier-protein] S-acetyltransferase || [Acyl-carrier-protein] S-malonyltransferase || Fatty-acid synthase system
Carbamate kinase-like	1	INHERITED FROM: Amino-acid N-acetyltransferase
S-adenosyl-L-methionine-dependent methyltransferases	1	INHERITED FROM: Lovastatin nonaketide synthase || 2-methylbutanoate polyketide synthase || [Acyl-carrier-protein] S-acetyltransferase || methoxycarbonyltransferase || Fatty-acid synthase system
SH3-domain	1	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
tRNA-binding arm	1	INHERITED FROM: glycyltransferase
Inosine monophosphate dehydrogenase (IMPDH)	1	INHERITED FROM: Fatty-acyl-CoA synthase system || [Acyl-carrier-protein] S-acetyltransferase || [Acyl-carrier-protein] S-malonyltransferase
FMN-linked oxidoreductases	1	INHERITED FROM: [Acyl-carrier-protein] S-malonyltransferase
NAD(P)-binding Rossmann-fold domains	1	INHERITED FROM: Beta-ketoacyl-[acyl-carrier-protein] synthase I || Lovastatin nonaketide synthase || 6-deoxyerythronolide-B synthase || Narbonolide synthase || 2-methylbutanoate polyketide synthase || Fatty-acyl-CoA synthase system || ATP citrate synthase || [Acyl-carrier-protein] S-acetyltransferase || 10-deoxymethynolide syntase || 6-methylsalicylic acid synthase || Fatty-acid synthase system
L domain-like	1	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
"Winged helix" DNA-binding domain	1	INHERITED FROM: Histone acetyltransferase
TPR-like	1	INHERITED FROM: RING-type E3 ubiquitin transferase
E set domains	1	INHERITED FROM: Aminoacyltransferases || Protein-glutamine gamma-glutamyltransferase
Clavaminate synthase-like	1	INHERITED FROM: methoxycarbonyltransferase
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	1	INHERITED FROM: Aminoacyltransferases || Gamma-glutamyltransferase
Succinyl-CoA synthetase domains	1	INHERITED FROM: Acyl groups converted into alkyl groups on transfer || ATP citrate synthase
Glutathione synthetase ATP-binding domain-like	1	INHERITED FROM: ATP citrate synthase
Thioesterase/thiol ester dehydrase-isomerase	1	INHERITED FROM: Fatty-acyl-CoA synthase system || [Acyl-carrier-protein] S-acetyltransferase || [Acyl-carrier-protein] S-malonyltransferase

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)
SWIB/MDM2 domain	0	DIRECT
GABA-aminotransferase-like	0	DIRECT
TAZ domain	0	DIRECT
Inhibitor of apoptosis (IAP) repeat	0	DIRECT
CCCH zinc finger	0	DIRECT
U-box	0	DIRECT
BRCT domain	0	DIRECT
LFTR-like	0	DIRECT
Thiolase-related	0	DIRECT
Lrp/AsnC-like transcriptional regulator C-terminal domain	0	DIRECT
B-box zinc-binding domain	0	DIRECT
GlmU C-terminal domain-like	0	DIRECT
Phosphotransacetylase	0	DIRECT
Autoinducer synthetase	0	DIRECT
Leucine zipper domain	0	DIRECT
HTS-like	0	DIRECT
Biotinyl/lipoyl-carrier proteins and domains	0	DIRECT
NHL repeat	0	DIRECT
Hypoxia-inducible factor Hif2a, C-terminal domain	0	DIRECT
Zinc hairpin stack	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
CPH domain	0	DIRECT
Outer membrane enzyme PagP	0	DIRECT
PABC (PABP) domain	0	DIRECT
Glutaminyl-peptide cyclotransferase-like	0	DIRECT
UBC-related	0	DIRECT
PlsX-like	0	DIRECT
Arylamine N-acetyltransferase	0	DIRECT
Armadillo repeat	0	DIRECT
CHY zinc finger	0	DIRECT
APC10-like	0	DIRECT
YeaZ-like	0	DIRECT
Chromo barrel domain	0	DIRECT
HLH, helix-loop-helix DNA-binding domain	0	DIRECT
Mib/herc2 domain	0	DIRECT
N-acetyl transferase, NAT	0	DIRECT
UDP-glucose pyrophosphorylase	0	DIRECT
Choline/Carnitine O-acyltransferase	0	DIRECT
RING finger domain, C3HC4	0	DIRECT
Trimerization domain of TRAF	0	DIRECT
AstA-like	0	DIRECT
Acyl-carrier protein (ACP)	0	DIRECT
USP8 interacting domain	0	DIRECT
Phytochelatin synthase	0	DIRECT
PHD domain	0	DIRECT
CAT-like	0	DIRECT
Ran binding protein zinc finger-like	0	DIRECT
ZZ domain	0	DIRECT
Aminoglycoside 3-N-acetyltransferase-like	0	DIRECT
FemXAB nonribosomal peptidyltransferases	0	DIRECT
Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD	0	DIRECT
Malate synthase G	0	DIRECT
Hect, E3 ligase catalytic domain	0	DIRECT
Homeodomain	0	DIRECT
Transcriptional factor domain	0	DIRECT
PAS domain of steroid receptor coactivator 1A, NCo-A1	0	DIRECT
HMGL-like	0	DIRECT
Docking domain B of the erythromycin polyketide synthase (DEBS)	0	DIRECT
FabD-like	0	DIRECT
Transglutaminase core	0	DIRECT
Methicillin resistance protein FemA probable tRNA-binding arm	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
Gamma-glutamyltranspeptidase-like	0	DIRECT
Galactoside acetyltransferase-like	0	DIRECT
WWE domain	0	DIRECT
Ankyrin repeat	0	DIRECT
Mycobacterial antigens	0	DIRECT
DmpG/LeuA communication domain-like	0	DIRECT
Sir2 family of transcriptional regulators	0	DIRECT
Formylmethanofuran:tetrahydromethanopterin formyltransferase	0	DIRECT
Probable ACP-binding domain of malonyl-CoA ACP transacylase	0	DIRECT
Transglutaminase, two C-terminal domains	0	DIRECT
Chalcone synthase-like	0	DIRECT
Nuclear receptor coactivator interlocking domain	0	DIRECT
UDP N-acetylglucosamine acyltransferase	0	DIRECT
Transglutaminase N-terminal domain	0	DIRECT
Transcription factor IIB (TFIIB), core domain	0	DIRECT
ArgJ-like	0	DIRECT
N-terminal domain of cbl (N-cbl)	0	DIRECT
LplA-like	0	DIRECT
Serine acetyltransferase	0	DIRECT
Citrate synthase	0	DIRECT
Acetyl-CoA synthase	0	DIRECT
SPRY domain	0	DIRECT
2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain	0	DIRECT
SIAH, seven in absentia homolog	0	DIRECT
O-acetyltransferase	0	DIRECT
Bromodomain	0	DIRECT
Variant RING domain	0	DIRECT
CCHHC domain	0	DIRECT
N-myristoyl transferase, NMT	0	DIRECT
Kix domain of CBP (creb binding protein)	0	DIRECT
WW domain	0	DIRECT
MATH domain	9.193e-16	DIRECT
PFL-like	0.000000000000001826	DIRECT
WD40-repeat	0.0000000000009973	DIRECT
DRTGG domain	0.000000000001088	DIRECT
Classic zinc finger, C2H2	0.00000000002921	DIRECT
SAP domain	0.0000000000384	DIRECT
Pentapeptide repeats	0.0000000001995	DIRECT
SRA domain-like	0.000000001697	DIRECT
Filamin repeat (rod domain)	0.00000000245	DIRECT
Ubiquitin-related	0.000000003511	DIRECT
Thioesterase domain of polypeptide, polyketide and fatty acid synthases	0.000000003933	DIRECT
Leucine rich effector protein YopM	0.000000009387	DIRECT
FHA domain	0.00000001234	DIRECT
Sterol carrier protein, SCP	0.00000005232	DIRECT
NRPS condensation domain (amide synthase)	0.0000007976	DIRECT
CoA-binding domain	0.00000387	DIRECT
FYVE, a phosphatidylinositol-3-phosphate binding domain	0.000005022	DIRECT
Tropomyosin	0.000005235	DIRECT
Regulator of chromosome condensation RCC1	0.000005402	DIRECT
Hypoxia-inducible factor HIF ihhibitor (FIH1)	0.000009442	DIRECT
EF-hand modules in multidomain proteins	0.00001514	DIRECT
PA domain	0.00003564	DIRECT
Leucine carboxy methyltransferase Ppm1	0.00003999	DIRECT
MaoC-like	0.00004232	DIRECT
PDZ domain	0.0001364	DIRECT
UBA domain	0.0001364	DIRECT
CBS-domain pair	0.0003088	DIRECT
TAF(II)230 TBP-binding fragment	0.0003212	DIRECT
Third domain of FERM	0.003843	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
First domain of FERM	0.003843	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Acetyl-CoA synthetase-like	0.005042	INHERITED FROM: Transferring groups other than amino-acyl groups || Acyl-[acyl-carrier-protein]--phospholipid O-acyltransferase
Caspase recruitment domain, CARD	0.03572	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
RWD domain	0.0473	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Branched-chain alpha-keto acid dehydrogenase Pyr module	0.05258	INHERITED FROM: Dihydrolipoyllysine-residue succinyltransferase
Branched-chain alpha-keto acid dehydrogenase PP module	0.05669	INHERITED FROM: Dihydrolipoyllysine-residue succinyltransferase
Second domain of FERM	0.08523	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Glutamine synthetase, N-terminal domain	0.1674	INHERITED FROM: Protein S-acyltransferase
Glutamine synthetase catalytic domain	0.2026	INHERITED FROM: Protein S-acyltransferase
PLC-like (P variant)	0.2802	INHERITED FROM: Aminoacyltransferases || HECT-type E3 ubiquitin transferase
Tetratricopeptide repeat (TPR)	0.2895	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Cyclophilin (peptidylprolyl isomerase)	0.337	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
HpcH/HpaI aldolase	0.4341	INHERITED FROM: Acyl groups converted into alkyl groups on transfer || Malate synthase
Chromo domain	0.4679	INHERITED FROM: Histone acetyltransferase
Pyruvate oxidase and decarboxylase, middle domain	0.4981	INHERITED FROM: Sulfoacetaldehyde acetyltransferase || Acyl groups converted into alkyl groups on transfer
Serine carboxypeptidase-like	0.8396	INHERITED FROM: Sinapoylglucose--sinapoylglucose O-sinapoyltransferase
Alcohol dehydrogenase-like, C-terminal domain	0.895	INHERITED FROM: Beta-ketoacyl-[acyl-carrier-protein] synthase I || 2-methylbutanoate polyketide synthase || [Acyl-carrier-protein] S-acetyltransferase || [Acyl-carrier-protein] S-malonyltransferase || Fatty-acid synthase system
Alcohol dehydrogenase-like, N-terminal domain	0.9506	INHERITED FROM: Beta-ketoacyl-[acyl-carrier-protein] synthase I || 2-methylbutanoate polyketide synthase || [Acyl-carrier-protein] S-acetyltransferase || [Acyl-carrier-protein] S-malonyltransferase || Fatty-acid synthase system
Fibronectin type III	0.9665	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
SH3-domain	0.9814	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
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: Beta-ketoacyl-[acyl-carrier-protein] synthase I || Lovastatin nonaketide synthase || 6-deoxyerythronolide-B synthase || Narbonolide synthase || 2-methylbutanoate polyketide synthase || [Acyl-carrier-protein] S-acetyltransferase || [Acyl-carrier-protein] S-malonyltransferase || 10-deoxymethynolide syntase || 6-methylsalicylic acid synthase || Fatty-acid synthase system
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
N-acetyl-l-glutamate kinase	1	INHERITED FROM: Amino-acid N-acetyltransferase || Transferring groups other than amino-acyl groups
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	1	INHERITED FROM: Lysyltransferase
Succinyl-CoA synthetase, beta-chain, N-terminal domain	1	INHERITED FROM: ATP citrate synthase
Holo-(acyl carrier protein) synthase ACPS	1	INHERITED FROM: Beta-ketoacyl-[acyl-carrier-protein] synthase I || Fatty-acyl-CoA synthase system
Class I aldolase	1	INHERITED FROM: 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase
Crotonase-like	1	INHERITED FROM: Histone acetyltransferase
Calmodulin-like	1	INHERITED FROM: 1-acylglycerophosphocholine O-acyltransferase || 1-alkylglycerophosphocholine O-acetyltransferase || 1-acylglycerol-3-phosphate O-acyltransferase
SH2 domain	1	INHERITED FROM: Aminoacyltransferases || RING-type E3 ubiquitin transferase
Pyruvate oxidase and decarboxylase Pyr module	1	INHERITED FROM: Sulfoacetaldehyde acetyltransferase || Acyl groups converted into alkyl groups on transfer

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)
NRDP1 C-terminal domain-like	0	DIRECT
Actin-like ATPase domain	0	DIRECT
TAZ domain	0	DIRECT
WWE domain	0	DIRECT
Aldolase	0	DIRECT
post-HMGL domain-like	0	DIRECT
ACP-like	0	DIRECT
B-box zinc-binding domain	0	DIRECT
CHY zinc finger-like	0	DIRECT
Mib/herc2 domain-like	0	DIRECT
HprK N-terminal domain-like	0	DIRECT
Malate synthase G	0	DIRECT
Kix domain of CBP (creb binding protein)	0	DIRECT
Carbon-nitrogen hydrolase	0	DIRECT
ClpS-like	0	DIRECT
Docking domain B of the erythromycin polyketide synthase (DEBS)	0	DIRECT
WW domain	0	DIRECT
2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain	0	DIRECT
TRAF domain-like	0	DIRECT
alpha/beta-Hydrolases	0	DIRECT
Trimeric LpxA-like enzymes	0	DIRECT
SWIB/MDM2 domain	0	DIRECT
Zinc hairpin stack	0	DIRECT
Nuclear receptor coactivator interlocking domain	0	DIRECT
RING/U-box	0	DIRECT
HLH, helix-loop-helix DNA-binding domain	0	DIRECT
UBC-like	0	DIRECT
N-terminal domain of cbl (N-cbl)	0	DIRECT
FYVE/PHD zinc finger	0	DIRECT
FabD/lysophospholipase-like	0	DIRECT
PA domain	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
Ankyrin repeat	0	DIRECT
CoA-dependent acyltransferases	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Thiolase-like	0	DIRECT
Trimerization domain of TRAF	0	DIRECT
DHS-like NAD/FAD-binding domain	0	DIRECT
OMPA-like	0	DIRECT
Hect, E3 ligase catalytic domain	0	DIRECT
CCHHC domain	0	DIRECT
Bromodomain	0	DIRECT
Leucine zipper domain	0	DIRECT
Probable ACP-binding domain of malonyl-CoA ACP transacylase	0	DIRECT
TTHA0583/YokD-like	0	DIRECT
CCCH zinc finger	0	DIRECT
Inhibitor of apoptosis (IAP) repeat	0	DIRECT
DmpA/ArgJ-like	0	DIRECT
Isocitrate/Isopropylmalate dehydrogenase-like	0	DIRECT
Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
NHL repeat	0	DIRECT
Concanavalin A-like lectins/glucanases	0	DIRECT
Formylmethanofuran:tetrahydromethanopterin formyltransferase	0	DIRECT
PABC (PABP) domain	0	DIRECT
ARM repeat	0	DIRECT
Single hybrid motif	0	DIRECT
Transglutaminase, two C-terminal domains	0	DIRECT
Citrate synthase	0	DIRECT
Nucleotide-diphospho-sugar transferases	0	DIRECT
Ran binding protein zinc finger-like	3.545e-16	DIRECT
Chromo domain-like	0.00000000000001114	DIRECT
WD40 repeat-like	0.00000000000004548	DIRECT
Class II aaRS and biotin synthetases	0.000000000004146	DIRECT
SAP domain	0.00000000005024	DIRECT
Pentapeptide repeat-like	0.000000002545	DIRECT
SMAD/FHA domain	0.00000003095	DIRECT
SCP-like	0.00000009149	DIRECT
UBA-like	0.0000001383	DIRECT
RCC1/BLIP-II	0.000000448	DIRECT
Galactose oxidase, central domain	0.0000005839	DIRECT
Class I glutamine amidotransferase-like	0.00000297	DIRECT
beta-beta-alpha zinc fingers	0.00000445	DIRECT
Homeodomain-like	0.00000957	DIRECT
C2 domain (Calcium/lipid-binding domain, CaLB)	0.000009951	DIRECT
Cyclin-like	0.000022	DIRECT
Cysteine proteinases	0.00008718	DIRECT
Tropomyosin	0.00009673	DIRECT
Ubiquitin-like	0.0001177	DIRECT
TAF(II)230 TBP-binding fragment	0.0003459	DIRECT
vWA-like	0.000392	DIRECT
CBS-domain pair	0.000904	DIRECT
Formin homology 2 domain (FH2 domain)	0.0009144	DIRECT
Kelch motif	0.001603	INHERITED FROM: Transferring groups other than amino-acyl groups || methoxycarbonyltransferase
PFL-like glycyl radical enzymes	0.002553	INHERITED FROM: Transferring groups other than amino-acyl groups || Formate C-acetyltransferase
Acetyl-CoA synthetase-like	0.02059	INHERITED FROM: Transferring groups other than amino-acyl groups || Acyl-[acyl-carrier-protein]--phospholipid O-acyltransferase
EF-hand	0.06242	INHERITED FROM: 1-acylglycerol-3-phosphate O-acyltransferase || RING-type E3 ubiquitin transferase || 1-acylglycerophosphocholine O-acyltransferase || 1-alkylglycerophosphocholine O-acetyltransferase
Zinc beta-ribbon	0.06986	INHERITED FROM: Histone acetyltransferase
Prismane protein-like	0.07622	INHERITED FROM: CO-methylating acetyl-CoA synthase
DEATH domain	0.07704	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
Second domain of FERM	0.1076	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
Glutamine synthetase, N-terminal domain	0.2466	INHERITED FROM: Protein S-acyltransferase
PDZ domain-like	0.2993	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
SGNH hydrolase	0.3555	INHERITED FROM: Diglucosylglycerate octanoyltransferase
RNA-binding domain, RBD	0.4212	INHERITED FROM: RING-type E3 ubiquitin transferase
Tudor/PWWP/MBT	0.5102	INHERITED FROM: HECT-type E3 ubiquitin transferase
Cyclophilin-like	0.5188	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
Dimeric alpha+beta barrel	0.5654	INHERITED FROM: Acyl groups converted into alkyl groups on transfer || Homocitrate synthase
PYP-like sensor domain (PAS domain)	0.8397	INHERITED FROM: Transferring groups other than amino-acyl groups || Histone acetyltransferase
Fibronectin type III	0.9683	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
GroES-like	0.9725	INHERITED FROM: [Acyl-carrier-protein] S-acetyltransferase || Fatty-acid synthase system || [Acyl-carrier-protein] S-malonyltransferase || 2-methylbutanoate polyketide synthase || Beta-ketoacyl-[acyl-carrier-protein] synthase I
SH3-domain	0.9817	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
E set domains	0.983	INHERITED FROM: Aminoacyltransferases || Protein-glutamine gamma-glutamyltransferase
TPR-like	0.9865	INHERITED FROM: RING-type E3 ubiquitin transferase
SH2 domain	1	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
4'-phosphopantetheinyl transferase	1	INHERITED FROM: Beta-ketoacyl-[acyl-carrier-protein] synthase I || Fatty-acyl-CoA synthase system
Zn-dependent exopeptidases	1	INHERITED FROM: Glutaminyl-peptide cyclotransferase
Thioesterase/thiol ester dehydrase-isomerase	1	INHERITED FROM: [Acyl-carrier-protein] S-acetyltransferase || [Acyl-carrier-protein] S-malonyltransferase || Fatty-acyl-CoA synthase system
PLP-dependent transferases	1	INHERITED FROM: 8-amino-7-oxononanoate synthase || Transferring groups other than amino-acyl groups || 5-aminolevulinate synthase || Serine C-palmitoyltransferase || Glycine C-acetyltransferase
NAD(P)-binding Rossmann-fold domains	1	INHERITED FROM: [Acyl-carrier-protein] S-acetyltransferase || Fatty-acid synthase system || Lovastatin nonaketide synthase || 6-methylsalicylic acid synthase || Narbonolide synthase || 2-methylbutanoate polyketide synthase || Beta-ketoacyl-[acyl-carrier-protein] synthase I || 10-deoxymethynolide syntase || 6-deoxyerythronolide-B synthase || Fatty-acyl-CoA synthase system || ATP citrate synthase
Carbamate kinase-like	1	INHERITED FROM: Amino-acid N-acetyltransferase
Nucleic acid-binding proteins	1	INHERITED FROM: Lysyltransferase
Inosine monophosphate dehydrogenase (IMPDH)	1	INHERITED FROM: [Acyl-carrier-protein] S-acetyltransferase || [Acyl-carrier-protein] S-malonyltransferase || Fatty-acyl-CoA synthase system
Phosphoenolpyruvate/pyruvate domain	1	INHERITED FROM: Malate synthase
Galactose-binding domain-like	1	INHERITED FROM: HECT-type E3 ubiquitin transferase
Thiamin diphosphate-binding fold (THDP-binding)	1	INHERITED FROM: Sulfoacetaldehyde acetyltransferase || Dihydrolipoyllysine-residue succinyltransferase
FMN-linked oxidoreductases	1	INHERITED FROM: [Acyl-carrier-protein] S-malonyltransferase
Glutamine synthetase/guanido kinase	1	INHERITED FROM: Protein S-acyltransferase
"Winged helix" DNA-binding domain	1	INHERITED FROM: Histone acetyltransferase
P-loop containing nucleoside triphosphate hydrolases	1	INHERITED FROM: tRNA(Met) cytidine acetyltransferase || Phosphate acetyltransferase
PUA domain-like	1	INHERITED FROM: RING-type E3 ubiquitin transferase
BRCT domain	1	INHERITED FROM: RING-type E3 ubiquitin transferase
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	1	INHERITED FROM: Aminoacyltransferases || Gamma-glutamyltransferase
tRNA-binding arm	1	INHERITED FROM: glycyltransferase
Succinyl-CoA synthetase domains	1	INHERITED FROM: Acyl groups converted into alkyl groups on transfer || ATP citrate synthase
Glutathione synthetase ATP-binding domain-like	1	INHERITED FROM: ATP citrate synthase
Clavaminate synthase-like	1	INHERITED FROM: methoxycarbonyltransferase
S-adenosyl-L-methionine-dependent methyltransferases	1	INHERITED FROM: [Acyl-carrier-protein] S-acetyltransferase || Fatty-acid synthase system || Lovastatin nonaketide synthase || 2-methylbutanoate polyketide synthase || methoxycarbonyltransferase
L domain-like	1	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases

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)
57903,57850 57903 - FYVE/PHD zinc finger 57850 - RING/U-box	0	DIRECT
57850,57933 57850 - RING/U-box 57933 - TAZ domain	0	DIRECT
63570,56204 63570 - PABC (PABP) domain 56204 - Hect, E3 ligase catalytic domain	0	DIRECT
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0	DIRECT
49879,57850 49879 - SMAD/FHA domain 57850 - RING/U-box	0	DIRECT
53300,57850 53300 - vWA-like 57850 - RING/U-box	0	DIRECT
69593,47473 69593 - Glycerol-3-phosphate (1)-acyltransferase 47473 - EF-hand	0	DIRECT
54160,55729 54160 - Chromo domain-like 55729 - Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
69593,56801 69593 - Glycerol-3-phosphate (1)-acyltransferase 56801 - Acetyl-CoA synthetase-like	0	DIRECT
53633,55729 53633 - Carbamate kinase-like 55729 - Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
49599,57953 49599 - TRAF domain-like 57953 - Trimerization domain of TRAF	0	DIRECT
57850,48371 57850 - RING/U-box 48371 - ARM repeat	0	DIRECT
47473,55550 47473 - EF-hand 55550 - SH2 domain	0	DIRECT
81296,54001 81296 - E set domains 54001 - Cysteine proteinases	0	DIRECT
55729,47370 55729 - Acyl-CoA N-acyltransferases (Nat) 47370 - Bromodomain	0	DIRECT
55112,55112 55112 - Formylmethanofuran:tetrahydromethanopterin formyltransferase 55112 - Formylmethanofuran:tetrahydromethanopterin formyltransferase	0	DIRECT
47668,47473 47668 - N-terminal domain of cbl (N-cbl) 47473 - EF-hand	0	DIRECT
57850,52540 57850 - RING/U-box 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
51045,56204 51045 - WW domain 56204 - Hect, E3 ligase catalytic domain	0	DIRECT
55729,46589 55729 - Acyl-CoA N-acyltransferases (Nat) 46589 - tRNA-binding arm	0	DIRECT
54495,57850 54495 - UBC-like 57850 - RING/U-box	0	DIRECT
51230,51230 51230 - Single hybrid motif 51230 - Single hybrid motif	0	DIRECT
117839,117839 117839 - WWE domain 117839 - WWE domain	0	DIRECT
49599,49599 49599 - TRAF domain-like 49599 - TRAF domain-like	0	DIRECT
57850,50978 57850 - RING/U-box 50978 - WD40 repeat-like	0	DIRECT
47005,52777 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases	0	DIRECT
161219,161245 161219 - CHY zinc finger-like 161245 - Zinc hairpin stack	0	DIRECT
49265,49899 49265 - Fibronectin type III 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
90229,90229 90229 - CCCH zinc finger 90229 - CCCH zinc finger	0	DIRECT
53335,50965 53335 - S-adenosyl-L-methionine-dependent methyltransferases 50965 - Galactose oxidase, central domain	0	DIRECT
57850,159034 57850 - RING/U-box 159034 - Mib/herc2 domain-like	0	DIRECT
57783,47954 57783 - Zinc beta-ribbon 47954 - Cyclin-like	0	DIRECT
57850,101898 57850 - RING/U-box 101898 - NHL repeat	0	DIRECT
53901,53901 53901 - Thiolase-like 53901 - Thiolase-like	0	DIRECT
52540,55729 52540 - P-loop containing nucleoside triphosphate hydrolases 55729 - Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
54001,49309 54001 - Cysteine proteinases 49309 - Transglutaminase, two C-terminal domains	0	DIRECT
49599,50156 49599 - TRAF domain-like 50156 - PDZ domain-like	0	DIRECT
48403,57850 48403 - Ankyrin repeat 57850 - RING/U-box	0	DIRECT
57850,117839 57850 - RING/U-box 117839 - WWE domain	0	DIRECT
48371,117839 48371 - ARM repeat 117839 - WWE domain	0	DIRECT
50965,51197 50965 - Galactose oxidase, central domain 51197 - Clavaminate synthase-like	0	DIRECT
161245,57850 161245 - Zinc hairpin stack 57850 - RING/U-box	0	DIRECT
54236,90209 54236 - Ubiquitin-like 90209 - Ran binding protein zinc finger-like	0	DIRECT
68906,57850 68906 - SAP domain 57850 - RING/U-box	0	DIRECT
57953,49599 57953 - Trimerization domain of TRAF 49599 - TRAF domain-like	0	DIRECT
53474,54631 53474 - alpha/beta-Hydrolases 54631 - CBS-domain pair	0	DIRECT
90209,57850 90209 - Ran binding protein zinc finger-like 57850 - RING/U-box	0	DIRECT
51735,48256 51735 - NAD(P)-binding Rossmann-fold domains 48256 - Citrate synthase	0	DIRECT
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain	0	DIRECT
51569,89000 51569 - Aldolase 89000 - post-HMGL domain-like	0	DIRECT
57850,57667 57850 - RING/U-box 57667 - beta-beta-alpha zinc fingers	0	DIRECT
46589,55729 46589 - tRNA-binding arm 55729 - Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
51735,47336 51735 - NAD(P)-binding Rossmann-fold domains 47336 - ACP-like	0	DIRECT
49785,50985 49785 - Galactose-binding domain-like 50985 - RCC1/BLIP-II	0	DIRECT
50044,50044 50044 - SH3-domain 50044 - SH3-domain	0	DIRECT
52151,55048 52151 - FabD/lysophospholipase-like 55048 - Probable ACP-binding domain of malonyl-CoA ACP transacylase	0	DIRECT
55729,55729 55729 - Acyl-CoA N-acyltransferases (Nat) 55729 - Acyl-CoA N-acyltransferases (Nat)	0	DIRECT
53901,55718 53901 - Thiolase-like 55718 - SCP-like	0	DIRECT
51045,51045 51045 - WW domain 51045 - WW domain	0	DIRECT
52025,57850 52025 - PA domain 57850 - RING/U-box	0	DIRECT
117281,51197 117281 - Kelch motif 51197 - Clavaminate synthase-like	0	DIRECT
159034,57850 159034 - Mib/herc2 domain-like 57850 - RING/U-box	0	DIRECT
54495,46934 54495 - UBC-like 46934 - UBA-like	0	DIRECT
52210,51735 52210 - Succinyl-CoA synthetase domains 51735 - NAD(P)-binding Rossmann-fold domains	0	DIRECT
90229,57850 90229 - CCCH zinc finger 57850 - RING/U-box	0	DIRECT
54637,52151 54637 - Thioesterase/thiol ester dehydrase-isomerase 52151 - FabD/lysophospholipase-like	0	DIRECT
47592,90209 47592 - SWIB/MDM2 domain 90209 - Ran binding protein zinc finger-like	0	DIRECT
57850,49599 57850 - RING/U-box 49599 - TRAF domain-like	0	DIRECT
52540,75138 52540 - P-loop containing nucleoside triphosphate hydrolases 75138 - HprK N-terminal domain-like	0	DIRECT
49785,159034 49785 - Galactose-binding domain-like 159034 - Mib/herc2 domain-like	0	DIRECT
48403,52113 48403 - Ankyrin repeat 52113 - BRCT domain	0	DIRECT
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0	DIRECT
53448,51161 53448 - Nucleotide-diphospho-sugar transferases 51161 - Trimeric LpxA-like enzymes	0	DIRECT
49562,51045 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 51045 - WW domain	0	DIRECT
89000,110921 89000 - post-HMGL domain-like 110921 - 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain	0	DIRECT
57850,57850 57850 - RING/U-box 57850 - RING/U-box	0	DIRECT
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain)	0	DIRECT
52777,52777 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases	0	DIRECT
56112,57850 56112 - Protein kinase-like (PK-like) 57850 - RING/U-box	0	DIRECT
51230,47005 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
49599,160088 49599 - TRAF domain-like 160088 - NRDP1 C-terminal domain-like	0	DIRECT
81296,101898 81296 - E set domains 101898 - NHL repeat	0	DIRECT
57850,57845 57850 - RING/U-box 57845 - B-box zinc-binding domain	0	DIRECT
52151,51412 52151 - FabD/lysophospholipase-like 51412 - Inosine monophosphate dehydrogenase (IMPDH)	0	DIRECT
53067,56112 53067 - Actin-like ATPase domain 56112 - Protein kinase-like (PK-like)	0	DIRECT
49309,49309 49309 - Transglutaminase, two C-terminal domains 49309 - Transglutaminase, two C-terminal domains	0	DIRECT
46785,57903 46785 - "Winged helix" DNA-binding domain 57903 - FYVE/PHD zinc finger	0	DIRECT
51230,52777 51230 - Single hybrid motif 52777 - CoA-dependent acyltransferases	0	DIRECT
75138,53659 75138 - HprK N-terminal domain-like 53659 - Isocitrate/Isopropylmalate dehydrogenase-like	0	DIRECT
48452,57850 48452 - TPR-like 57850 - RING/U-box	0	DIRECT
51569,54909 51569 - Aldolase 54909 - Dimeric alpha+beta barrel	0	DIRECT
51735,51735 51735 - NAD(P)-binding Rossmann-fold domains 51735 - NAD(P)-binding Rossmann-fold domains	0	DIRECT
55550,57850 55550 - SH2 domain 57850 - RING/U-box	0	DIRECT
47336,53474 47336 - ACP-like 53474 - alpha/beta-Hydrolases	0.0000000000001121	DIRECT
52113,52113 52113 - BRCT domain 52113 - BRCT domain	0.0000000000001372	DIRECT
49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0.000000001867	DIRECT
53335,51735 53335 - S-adenosyl-L-methionine-dependent methyltransferases 51735 - NAD(P)-binding Rossmann-fold domains	0.0000003632	DIRECT
57903,47370 57903 - FYVE/PHD zinc finger 47370 - Bromodomain	0.000022	DIRECT
48371,48403 48371 - ARM repeat 48403 - Ankyrin repeat	0.000046	DIRECT
47336,52777 47336 - ACP-like 52777 - CoA-dependent acyltransferases	0.0001274	DIRECT
47370,47370 47370 - Bromodomain 47370 - Bromodomain	0.0003459	DIRECT
54236,47031 54236 - Ubiquitin-like 47031 - Second domain of FERM	0.004246	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.01895	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
47031,50729 47031 - Second domain of FERM 50729 - PH domain-like	0.03285	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
48371,48371 48371 - ARM repeat 48371 - ARM repeat	0.04924	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
55785,55785 55785 - PYP-like sensor domain (PAS domain) 55785 - PYP-like sensor domain (PAS domain)	0.0702	INHERITED FROM: Transferring groups other than amino-acyl groups || Histone acetyltransferase
57903,57903 57903 - FYVE/PHD zinc finger 57903 - FYVE/PHD zinc finger	0.08723	INHERITED FROM: Histone acetyltransferase
51735,50129 51735 - NAD(P)-binding Rossmann-fold domains 50129 - GroES-like	0.2093	INHERITED FROM: Beta-ketoacyl-[acyl-carrier-protein] synthase I
54368,55931 54368 - Glutamine synthetase, N-terminal domain 55931 - Glutamine synthetase/guanido kinase	0.2466	INHERITED FROM: Protein S-acyltransferase
48452,48452 48452 - TPR-like 48452 - TPR-like	0.446	INHERITED FROM: RING-type E3 ubiquitin transferase || Aminoacyltransferases
50129,51735 50129 - GroES-like 51735 - NAD(P)-binding Rossmann-fold domains	0.9679	INHERITED FROM: [Acyl-carrier-protein] S-acetyltransferase || Fatty-acid synthase system || [Acyl-carrier-protein] S-malonyltransferase || 2-methylbutanoate polyketide synthase || 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
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
56059,52210 56059 - Glutathione synthetase ATP-binding domain-like 52210 - Succinyl-CoA synthetase domains	1	INHERITED FROM: Acyl groups converted into alkyl groups on transfer || ATP citrate synthase
50249,55681 50249 - Nucleic acid-binding proteins 55681 - Class II aaRS and biotin synthetases	1	INHERITED FROM: Lysyltransferase
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