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Enzyme Commission (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. To navigate hierarchical structure of EC, we display all parental EC terms to the current EC term of interest ordered by their shortest distances to the current term. Also, only direct children EC terms of the current EC term are listed.

Structural Classification of Proteins (SCOP)
SCOP classifies evolutionary-related domains into Superfamily level and Family level. Accordingly, we have generated the domain-centric EC annotations for each of the three concepts at each of the two domain levels.

Structural Domain Enzyme Commission Ontology (SDEO)
As domain-centric ontology, SDEO only refers to those EC terms which are the most informative to annotate SCOP domains.

EC annotations for SCOP domains
For details, please visit Documentation: EC annotations for SCOP domains. Therein, we provide several relevant files (Data Availability) for the download, including an annotation file (i.e., Domain2EC.txt) and the corresponding ontology (i.e., SDEO.txt).

Supra-domain Enzyme Commission Ontology (SPEO)
As an extension, SPEO includes those EC terms which are the most informative to annotate supra-domains and individual SCOP domains at the Superfamily level.

EC annotations for Supra-domains
For details, please visit Documentation: EC annotations for Supra-domains. Therein, we provide several relevant files (Data Availability) for the download, including a annotation file (i.e., SP2EC.txt) and an ontology (i.e., SPEO.txt). For the sake of being browsable, listed below are those supra-domains (single, dual, triple, quad).

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

SCOP term	FDR (all)	Annotation (direct or inherited)
Phosphoglucomutase, first 3 domains	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Eukaryotic DNA topoisomerase I, dispensable insert domain	0	DIRECT
2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain	0	DIRECT
PLP-binding barrel	0	DIRECT
FKBP-like	0	DIRECT
Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment	0	DIRECT
ERP29 C domain-like	0	DIRECT
FucI/AraA C-terminal domain-like	0	DIRECT
Triger factor/SurA peptide-binding domain-like	0	DIRECT
Type II DNA topoisomerase	0	DIRECT
TPR-like	0	DIRECT
Zinc beta-ribbon	0	DIRECT
N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)	0	DIRECT
Kelch motif	0	DIRECT
Ribose/Galactose isomerase RpiB/AlsB	0	DIRECT
DNA breaking-rejoining enzymes	0	DIRECT
Alanine racemase C-terminal domain-like	0	DIRECT
GyrA/ParC C-terminal domain-like	0	DIRECT
Phosphoglycerate mutase-like	0	DIRECT
RbsD-like	0	DIRECT
RmlC-like cupins	0	DIRECT
PTPA-like	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
Alkaline phosphatase-like	0	DIRECT
NagB/RpiA/CoA transferase-like	0	DIRECT
PUA domain-like	0	DIRECT
Cyclophilin-like	0	DIRECT
Cobalamin (vitamin B12)-binding domain	0	DIRECT
DNA topoisomerase IV, alpha subunit	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
Pseudouridine synthase	0	DIRECT
Chalcone isomerase	0	DIRECT
Trigger factor ribosome-binding domain	0	DIRECT
DeoB insert domain-like	0	DIRECT
Triosephosphate isomerase (TIM)	0	DIRECT
SIS domain	0	DIRECT
Aspartate/glutamate racemase	0	DIRECT
FucI/AraA N-terminal and middle domains	0	DIRECT
Xylose isomerase-like	0	DIRECT
Nudix	0	DIRECT
PLP-dependent transferases	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	0	DIRECT
Ribulose-phoshate binding barrel	0	DIRECT
Terpenoid cyclases/Protein prenyltransferases	0	DIRECT
FMN-linked oxidoreductases	0	DIRECT
Chorismate mutase II	0	DIRECT
Cobalamin (vitamin B12)-dependent enzymes	0	DIRECT
Lipocalins	0.00000000000004383	DIRECT
Tautomerase/MIF	0.0000000000005537	DIRECT
Alpha-L RNA-binding motif	0.000000000001001	DIRECT
ClpP/crotonase	0.000000000008328	DIRECT
6-phosphogluconate dehydrogenase C-terminal domain-like	0.00000000001634	DIRECT
Thioredoxin-like	0.000000004463	DIRECT
RNA-binding domain, RBD	0.000002211	DIRECT
WW domain	0.00004689	DIRECT
ADC synthase	0.0005844	DIRECT
MAPEG domain-like	0.0006234	DIRECT
Hedgehog/intein (Hint) domain	0.0007016	DIRECT
AraD/HMP-PK domain-like	0.0009987	DIRECT
Homing endonucleases	0.001094	INHERITED FROM: DNA topoisomerase (ATP-hydrolyzing) || Other isomerases
Terpenoid synthases	0.003908	INHERITED FROM: Copalyl diphosphate synthase || Intramolecular lyases || Ent-copalyl diphosphate synthase || Lycopene beta-cyclase
Galactose mutarotase-like	0.02	INHERITED FROM: Aldose 1-epimerase || Acting on carbohydrates and derivatives || Racemases and epimerases
RING/U-box	0.0228	INHERITED FROM: Cis-trans-isomerases || Peptidylprolyl isomerase
WD40 repeat-like	0.08889	INHERITED FROM: Cis-trans-isomerases || Peptidylprolyl isomerase
Di-copper centre-containing domain	0.1491	INHERITED FROM: L-dopachrome isomerase || Transposing C==C bonds
CBS-domain pair	0.3306	INHERITED FROM: Arabinose-5-phosphate isomerase
ACP-like	0.3969	INHERITED FROM: Phenylalanine racemase (ATP-hydrolyzing) || Racemases and epimerases || Acting on amino acids and derivatives
GST C-terminal domain-like	0.6406	INHERITED FROM: Other intramolecular oxidoreductases || Cis-trans-isomerases || Maleylacetoacetate isomerase
Metallo-dependent hydrolases	0.6788	INHERITED FROM: Glucuronate isomerase || Interconverting aldoses and ketoses, and related c || Intramolecular oxidoreductases
EF-hand	0.8525	INHERITED FROM: Cis-trans-isomerases || Peptidylprolyl isomerase
UDP-Glycosyltransferase/glycogen phosphorylase	1	INHERITED FROM: Acting on carbohydrates and derivatives || UDP-N-acetylglucosamine 2-epimerase
Nucleotide-diphospho-sugar transferases	1	INHERITED FROM: UDP-arabinopyranose mutase || Mannose-6-phosphate isomerase
RuBisCO, large subunit, small (N-terminal) domain	1	INHERITED FROM: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase || Interconverting keto- and enol- groups
RuBisCo, C-terminal domain	1	INHERITED FROM: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase || Interconverting keto- and enol- groups
CoA-dependent acyltransferases	1	INHERITED FROM: Phenylalanine racemase (ATP-hydrolyzing) || Acting on amino acids and derivatives
S13-like H2TH domain	1	INHERITED FROM: DNA topoisomerase (ATP-hydrolyzing) || Other isomerases
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	1	INHERITED FROM: Intramolecular lyases || Inositol-3-phosphate synthase
Class I glutamine amidotransferase-like	1	INHERITED FROM: Phosphoribosylanthranilate isomerase
Acetyl-CoA synthetase-like	1	INHERITED FROM: Phenylalanine racemase (ATP-hydrolyzing)
Ribosomal protein S5 domain 2-like	1	INHERITED FROM: DNA topoisomerase (ATP-hydrolyzing) || Other isomerases
HAD-like	1	INHERITED FROM: Phosphomannomutase || Phosphotransferases (phosphomutases)
Tryptophan synthase beta subunit-like PLP-dependent enzymes	1	INHERITED FROM: Serine racemase
Six-hairpin glycosidases	1	INHERITED FROM: N-acylglucosamine 2-epimerase || Acting on carbohydrates and derivatives
Cytochrome P450	1	INHERITED FROM: Other intramolecular oxidoreductases || Thromboxane-A synthase
Enolase C-terminal domain-like	1	INHERITED FROM: Intramolecular lyases || Chloromuconate cycloisomerase || Muconate cycloisomerase
ACT-like	1	INHERITED FROM: Chorismate mutase
Enolase N-terminal domain-like	1	INHERITED FROM: Intramolecular lyases || Chloromuconate cycloisomerase || Muconate cycloisomerase
NAD(P)-binding Rossmann-fold domains	1	INHERITED FROM: ADP-glyceromanno-heptose 6-epimerase || Intramolecular lyases || Steroid Delta-isomerase || Acting on carbohydrates and derivatives || 3-hydroxybutyryl-CoA epimerase || Acting on hydroxy acids and derivatives || Transposing C==C bonds || Inositol-3-phosphate synthase || Racemases and epimerases || Dodecenoyl-CoA isomerase || UDP-glucose 4-epimerase
FAD/NAD(P)-binding domain	1	INHERITED FROM: Ribose 1,5-bisphosphate isomerase || Prolycopene isomerase || Lycopene beta-cyclase
Periplasmic binding protein-like II	1	INHERITED FROM: Chorismate mutase

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

SCOP term	FDR (all)	Annotation (direct or inherited)
Topoisomerase VI-B subunit middle domain	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), catalytic domain	0	DIRECT
Thi4-like	0	DIRECT
Tyrosine-dependent oxidoreductases	0	DIRECT
UDP-N-acetylglucosamine 2-epimerase	0	DIRECT
AraA N-terminal and middle domain-like	0	DIRECT
Crotonase-like	0	DIRECT
Aspartate/glutamate racemase	0	DIRECT
N-acylglucosamine (NAG) epimerase	0	DIRECT
HCDH C-domain-like	0	DIRECT
Retinol binding protein-like	0	DIRECT
PDI-like	0	DIRECT
Glucose-6-phosphate isomerase, GPI	0	DIRECT
Type I phosphomannose isomerase	0	DIRECT
Prokaryotic DNA topoisomerase I, a C-terminal fragment	0	DIRECT
DNA gyrase/MutL, second domain	0	DIRECT
PUA domain	0	DIRECT
Pseudouridine synthase RsuA N-terminal domain	0	DIRECT
Alanine racemase	0	DIRECT
dTDP-sugar isomerase	0	DIRECT
Diaminopimelate epimerase	0	DIRECT
Cobalamin (vitamin B12)-binding domain	0	DIRECT
DNA topoisomerase IV, alpha subunit	0	DIRECT
Terpene synthases	0	DIRECT
AraA C-terminal domain-like	0	DIRECT
Helicase-like "domain" of reverse gyrase	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Pseudouridine synthase II TruB	0	DIRECT
Triosephosphate isomerase (TIM)	0	DIRECT
Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment	0	DIRECT
2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, catalytic domain	0	DIRECT
PTPA-like	0	DIRECT
DeoB catalytic domain-like	0	DIRECT
KduI-like	0	DIRECT
Pseudouridine synthase RsuA/RluD	0	DIRECT
D-ribulose-5-phosphate 3-epimerase	0	DIRECT
L-fucose isomerase, C-terminal domain	0	DIRECT
Tetratricopeptide repeat (TPR)	0	DIRECT
YiiL-like	0	DIRECT
Aldose 1-epimerase (mutarotase)	0	DIRECT
ERP29 C domain-like	0	DIRECT
IF2B-like	0	DIRECT
DeoB insert domain-like	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
GyrA/ParC C-terminal domain-like	0	DIRECT
RbsD-like	0	DIRECT
Cofactor-dependent phosphoglycerate mutase	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
Proline racemase	0	DIRECT
Cyclophilin (peptidylprolyl isomerase)	0	DIRECT
Xylose isomerase	0	DIRECT
Phosphoglucose isomerase, PGI	0	DIRECT
Hypothetical protein YgbM (EC1530)	0	DIRECT
IPP isomerase-like	0	DIRECT
Histidine biosynthesis enzymes	0	DIRECT
Pseudouridine synthase I TruA	0	DIRECT
mono-SIS domain	0	DIRECT
Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain	0	DIRECT
Porin chaperone SurA, peptide-binding domain	0	DIRECT
Tryptophan biosynthesis enzymes	0	DIRECT
Alanine racemase-like, N-terminal domain	0	DIRECT
Type II DNA topoisomerase	0	DIRECT
Kelch motif	0	DIRECT
tRNA pseudouridine synthase TruD	0	DIRECT
Eukaryotic DNA topoisomerase I, catalytic core	0	DIRECT
L-rhamnose isomerase	0	DIRECT
FMN-linked oxidoreductases	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
Ribose/Galactose isomerase RpiB/AlsB	0	DIRECT
L-fucose isomerase, N-terminal and second domains	0	DIRECT
Eukaryotic DNA topoisomerase I, dispensable insert domain	0	DIRECT
Trigger factor ribosome-binding domain	0	DIRECT
TF C-terminus	0	DIRECT
N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)	0	DIRECT
DNA gyrase/MutL, N-terminal domain	0	DIRECT
Chalcone isomerase	0	DIRECT
Uronate isomerase-like	0	DIRECT
FKBP immunophilin/proline isomerase	0	DIRECT
2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain	0	DIRECT
GABA-aminotransferase-like	0	DIRECT
NanE-like	0	DIRECT
Muconalactone isomerase, MLI	0	DIRECT
6-phosphogluconate dehydrogenase-like, N-terminal domain	0.000000000000354	DIRECT
MIF-related	0.000000000008197	DIRECT
Dimeric chorismate mutase	0.0000000008732	DIRECT
Canonical RBD	0.00000001195	DIRECT
Predicted hydrolases Cof	0.0000000843	DIRECT
Peptidyl carrier domain	0.000006142	DIRECT
WW domain	0.00005875	DIRECT
mannose-1-phosphate guanylyl transferase	0.000172	DIRECT
WD40-repeat	0.000172	DIRECT
MAPEG domain	0.0007041	DIRECT
ADC synthase	0.0008387	DIRECT
AraD-like aldolase/epimerase	0.001559	INHERITED FROM: L-ribulose-5-phosphate 4-epimerase || Acting on carbohydrates and derivatives || Racemases and epimerases
Intein (protein splicing domain)	0.002635	INHERITED FROM: DNA topoisomerase (ATP-hydrolyzing) || Other isomerases
Terpenoid cyclase N-terminal domain	0.009827	INHERITED FROM: Copalyl diphosphate synthase || Intramolecular lyases || Ent-copalyl diphosphate synthase
Terpenoid cyclase C-terminal domain	0.04518	INHERITED FROM: Copalyl diphosphate synthase || Intramolecular lyases || Ent-copalyl diphosphate synthase
D-glucarate dehydratase-like	0.07305	INHERITED FROM: Intramolecular lyases || Chloromuconate cycloisomerase || Muconate cycloisomerase
CBS-domain pair	0.3327	INHERITED FROM: Arabinose-5-phosphate isomerase
Glutathione S-transferase (GST), N-terminal domain	0.5668	INHERITED FROM: Other intramolecular oxidoreductases || Cis-trans-isomerases || Maleylacetoacetate isomerase
Glutathione S-transferase (GST), C-terminal domain	0.6021	INHERITED FROM: Other intramolecular oxidoreductases || Cis-trans-isomerases || Maleylacetoacetate isomerase
ROK	0.6682	INHERITED FROM: Acting on carbohydrates and derivatives || Racemases and epimerases
double-SIS domain	0.8197	INHERITED FROM: Glucose-6-phosphate isomerase || Mannose-6-phosphate isomerase
Enolase N-terminal domain-like	1	INHERITED FROM: Intramolecular lyases || Chloromuconate cycloisomerase || Muconate cycloisomerase
Dihydrodipicolinate reductase-like	1	INHERITED FROM: Intramolecular lyases || Inositol-3-phosphate synthase
Cytochrome P450	1	INHERITED FROM: Other intramolecular oxidoreductases || Thromboxane-A synthase
Ribulose 1,5-bisphosphate carboxylase-oxygenase	1	INHERITED FROM: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase || Interconverting keto- and enol- groups
Class I glutamine amidotransferases (GAT)	1	INHERITED FROM: Phosphoribosylanthranilate isomerase
Acetyl-CoA synthetase-like	1	INHERITED FROM: Phenylalanine racemase (ATP-hydrolyzing)
Tryptophan synthase beta subunit-like PLP-dependent enzymes	1	INHERITED FROM: Serine racemase
Phosphate binding protein-like	1	INHERITED FROM: Chorismate mutase
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	1	INHERITED FROM: Intramolecular lyases || Inositol-3-phosphate synthase
RuBisCo, large subunit, C-terminal domain	1	INHERITED FROM: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase || Interconverting keto- and enol- groups

Trees by TreeVector

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

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

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
FucI/AraA C-terminal domain-like	0	DIRECT
N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)	0	DIRECT
Cobalamin (vitamin B12)-dependent enzymes	0	DIRECT
Acyl-CoA binding protein	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
TPR-like	0	DIRECT
DNA topoisomerase IV, alpha subunit	0	DIRECT
Cobalamin (vitamin B12)-binding domain	0	DIRECT
2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain	0	DIRECT
Nudix	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
Terpenoid cyclases/Protein prenyltransferases	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
Type II DNA topoisomerase	0	DIRECT
Phosphoglycerate mutase-like	0	DIRECT
NagB/RpiA/CoA transferase-like	0	DIRECT
ERP29 C domain-like	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
FMN-linked oxidoreductases	0	DIRECT
GyrA/ParC C-terminal domain-like	0	DIRECT
Alkaline phosphatase-like	0	DIRECT
PTPA-like	0	DIRECT
FKBP-like	0	DIRECT
Triger factor/SurA peptide-binding domain-like	0	DIRECT
DNA topoisomerase I domain	0	DIRECT
PUA domain-like	0	DIRECT
Ribose/Galactose isomerase RpiB/AlsB	0	DIRECT
FucI/AraA N-terminal and middle domains	0	DIRECT
Aspartate/glutamate racemase	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
SIS domain	0	DIRECT
PLP-dependent transferases	0	DIRECT
Pseudouridine synthase	0	DIRECT
Chalcone isomerase	0	DIRECT
Eukaryotic DNA topoisomerase I, dispensable insert domain	0	DIRECT
Allene oxide cyclase-like	0	DIRECT
Chorismate mutase II	0	DIRECT
DNA breaking-rejoining enzymes	0	DIRECT
DeoB insert domain-like	0	DIRECT
Oxygen-evolving enhancer protein 3,	0	DIRECT
Zinc beta-ribbon	0	DIRECT
RmlC-like cupins	0	DIRECT
Xylose isomerase-like	0	DIRECT
RbsD-like	0	DIRECT
Triosephosphate isomerase (TIM)	0	DIRECT
Trigger factor ribosome-binding domain	0	DIRECT
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Alanine racemase C-terminal domain-like	0	DIRECT
PLP-binding barrel	0	DIRECT
Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment	0	DIRECT
Precorrin-8X methylmutase CbiC/CobH	0	DIRECT
Kelch motif	0	DIRECT
Cyclophilin-like	0	DIRECT
Ribulose-phoshate binding barrel	0	DIRECT
Lipocalins	0.00000000000003221	DIRECT
Tautomerase/MIF	0.0000000000004084	DIRECT
Alpha-L RNA-binding motif	0.0000000000006881	DIRECT
ClpP/crotonase	0.000000000005401	DIRECT
6-phosphogluconate dehydrogenase C-terminal domain-like	0.00000000002505	DIRECT
Thioredoxin-like	0.000000001702	DIRECT
RNA-binding domain, RBD	0.000001754	DIRECT
WW domain	0.00003839	DIRECT
ADC synthase	0.0004859	DIRECT
MAPEG domain-like	0.0005236	DIRECT
Hedgehog/intein (Hint) domain	0.0005864	DIRECT
AraD/HMP-PK domain-like	0.0008232	DIRECT
Homing endonucleases	0.0009213	DIRECT
Terpenoid synthases	0.003269	INHERITED FROM: Copalyl diphosphate synthase || Intramolecular lyases || Ent-copalyl diphosphate synthase || Lycopene beta-cyclase
HSP20-like chaperones	0.01056	INHERITED FROM: Other intramolecular oxidoreductases || Prostaglandin-E synthase || Intramolecular oxidoreductases
Galactose mutarotase-like	0.01818	INHERITED FROM: Glucose-6-phosphate 1-epimerase || Aldose 1-epimerase || Acting on carbohydrates and derivatives || Racemases and epimerases
RING/U-box	0.02781	INHERITED FROM: Cis-trans-isomerases || Peptidylprolyl isomerase
CoA-transferase family III (CaiB/BaiF)	0.07487	INHERITED FROM: Alpha-methylacyl-CoA racemase || Acting on other compounds || Racemases and epimerases
WD40 repeat-like	0.07913	INHERITED FROM: Cis-trans-isomerases || Peptidylprolyl isomerase
Di-copper centre-containing domain	0.134	INHERITED FROM: L-dopachrome isomerase || Transposing C==C bonds
Chondroitin AC/alginate lyase	0.1454	INHERITED FROM: Acting on carbohydrates and derivatives || Racemases and epimerases || Chondroitin-glucuronate 5-epimerase
CBS-domain pair	0.3168	INHERITED FROM: Arabinose-5-phosphate isomerase
ACP-like	0.3654	INHERITED FROM: Phenylalanine racemase (ATP-hydrolyzing) || Racemases and epimerases || Acting on amino acids and derivatives
FAH	0.3997	INHERITED FROM: Transposing C==C bonds || 5-carboxymethyl-2-hydroxymuconate Delta-isomerase
GST C-terminal domain-like	0.596	INHERITED FROM: Other intramolecular oxidoreductases || Cis-trans-isomerases || Maleylacetoacetate isomerase
Metallo-dependent hydrolases	0.6279	INHERITED FROM: Glucuronate isomerase || Interconverting aldoses and ketoses, and related c || Intramolecular oxidoreductases
NTF2-like	0.7093	INHERITED FROM: Steroid Delta-isomerase || Transposing C==C bonds
Nucleotide-binding domain	0.7411	INHERITED FROM: UDP-galactopyranose mutase || Transferring other groups
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	0.7628	INHERITED FROM: Acting on other compounds || Methylmalonyl-CoA epimerase
EF-hand	0.7996	INHERITED FROM: Cis-trans-isomerases || Peptidylprolyl isomerase
Glycosyl hydrolase domain	1	INHERITED FROM: Maltose alpha-D-glucosyltransferase
Enolase C-terminal domain-like	1	INHERITED FROM: L-Ala-D/L-Glu epimerase || Intramolecular lyases || Chloromuconate cycloisomerase || Muconate cycloisomerase
NAD(P)-binding Rossmann-fold domains	1	INHERITED FROM: ADP-glyceromanno-heptose 6-epimerase || Intramolecular lyases || Steroid Delta-isomerase || Acting on carbohydrates and derivatives || 3-hydroxybutyryl-CoA epimerase || Acting on hydroxy acids and derivatives || Transposing C==C bonds || Inositol-3-phosphate synthase || Racemases and epimerases || Dodecenoyl-CoA isomerase || UDP-glucose 4-epimerase
FAD/NAD(P)-binding domain	1	INHERITED FROM: Ribose 1,5-bisphosphate isomerase || Steroid Delta-isomerase || Prolycopene isomerase || Lycopene beta-cyclase
S13-like H2TH domain	1	INHERITED FROM: DNA topoisomerase (ATP-hydrolyzing) || Other isomerases
UDP-Glycosyltransferase/glycogen phosphorylase	1	INHERITED FROM: Acting on carbohydrates and derivatives || UDP-N-acetylglucosamine 2-epimerase
Nucleotide-diphospho-sugar transferases	1	INHERITED FROM: UDP-arabinopyranose mutase || Mannose-6-phosphate isomerase
Actin-like ATPase domain	1	INHERITED FROM: UDP-N-acetylglucosamine 2-epimerase
Cytochrome P450	1	INHERITED FROM: Other intramolecular oxidoreductases || 9,12-octadecadienoate 8-hydroperoxide 8R-isomerase || Transferring hydroxy groups || Prostaglandin-I synthase || Thromboxane-A synthase
Tryptophan synthase beta subunit-like PLP-dependent enzymes	1	INHERITED FROM: Serine racemase
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	1	INHERITED FROM: Intramolecular lyases || Inositol-3-phosphate synthase
Acetyl-CoA synthetase-like	1	INHERITED FROM: Phenylalanine racemase (ATP-hydrolyzing)
L-aspartase-like	1	INHERITED FROM: Tyrosine 2,3-aminomutase || 3-carboxy-cis,cis-muconate cycloisomerase
HAD-like	1	INHERITED FROM: Beta-phosphoglucomutase || Phosphomannomutase || Phosphotransferases (phosphomutases)
Enolase N-terminal domain-like	1	INHERITED FROM: L-Ala-D/L-Glu epimerase || Intramolecular lyases || Chloromuconate cycloisomerase || Muconate cycloisomerase
ACT-like	1	INHERITED FROM: Chorismate mutase
Radical SAM enzymes	1	INHERITED FROM: Lysine 2,3-aminomutase
(Trans)glycosidases	1	INHERITED FROM: Maltose alpha-D-glucosyltransferase
RuBisCo, C-terminal domain	1	INHERITED FROM: 5.3.2.5 || Interconverting keto- and enol- groups
Phosphoenolpyruvate/pyruvate domain	1	INHERITED FROM: Phosphoenolpyruvate mutase
Heme-dependent peroxidases	1	INHERITED FROM: 9,12-octadecadienoate 8-hydroperoxide 8R-isomerase || Transferring hydroxy groups
CoA-dependent acyltransferases	1	INHERITED FROM: Phenylalanine racemase (ATP-hydrolyzing) || Acting on amino acids and derivatives
Periplasmic binding protein-like II	1	INHERITED FROM: Chorismate mutase
Class I glutamine amidotransferase-like	1	INHERITED FROM: Phosphoribosylanthranilate isomerase
Six-hairpin glycosidases	1	INHERITED FROM: N-acylglucosamine 2-epimerase || Acting on carbohydrates and derivatives
Ribosomal protein S5 domain 2-like	1	INHERITED FROM: DNA topoisomerase (ATP-hydrolyzing) || Other isomerases
FAD-linked reductases, C-terminal domain	1	INHERITED FROM: UDP-galactopyranose mutase
RuBisCO, large subunit, small (N-terminal) domain	1	INHERITED FROM: 5.3.2.5 || Interconverting keto- and enol- groups

Supra-domains annotated to this EC term (SPEO level: Least 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)
55174,55120 55174 - Alpha-L RNA-binding motif 55120 - Pseudouridine synthase	0	DIRECT
51294,56719 51294 - Hedgehog/intein (Hint) domain 56719 - Type II DNA topoisomerase	0	DIRECT
47027,52096 47027 - Acyl-CoA binding protein 52096 - ClpP/crotonase	0	DIRECT
56719,56719 56719 - Type II DNA topoisomerase 56719 - Type II DNA topoisomerase	0	DIRECT
53697,54631 53697 - SIS domain 54631 - CBS-domain pair	0	DIRECT
54534,48452 54534 - FKBP-like 48452 - TPR-like	0	DIRECT
56719,101904 56719 - Type II DNA topoisomerase 101904 - GyrA/ParC C-terminal domain-like	0	DIRECT
52833,52833 52833 - Thioredoxin-like 52833 - Thioredoxin-like	0	DIRECT
54506,54506 54506 - Diaminopimelate epimerase-like 54506 - Diaminopimelate epimerase-like	0	DIRECT
51703,52242 51703 - Cobalamin (vitamin B12)-dependent enzymes 52242 - Cobalamin (vitamin B12)-binding domain	0	DIRECT
48600,51735 48600 - Chorismate mutase II 51735 - NAD(P)-binding Rossmann-fold domains	0	DIRECT
56712,51294 56712 - Prokaryotic type I DNA topoisomerase 51294 - Hedgehog/intein (Hint) domain	0	DIRECT
48600,53850 48600 - Chorismate mutase II 53850 - Periplasmic binding protein-like II	0	DIRECT
54928,50891 54928 - RNA-binding domain, RBD 50891 - Cyclophilin-like	0	DIRECT
52540,56712 52540 - P-loop containing nucleoside triphosphate hydrolases 56712 - Prokaryotic type I DNA topoisomerase	0	DIRECT
102735,54534 102735 - Trigger factor ribosome-binding domain 54534 - FKBP-like	0	DIRECT
52833,47933 52833 - Thioredoxin-like 47933 - ERP29 C domain-like	0	DIRECT
55874,56719 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 56719 - Type II DNA topoisomerase	0	DIRECT
55120,88697 55120 - Pseudouridine synthase 88697 - PUA domain-like	0	DIRECT
50729,50891 50729 - PH domain-like 50891 - Cyclophilin-like	0	DIRECT
56719,55608 56719 - Type II DNA topoisomerase 55608 - Homing endonucleases	0	DIRECT
64158,53649 64158 - 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain 53649 - Alkaline phosphatase-like	0	DIRECT
53738,53738 53738 - Phosphoglucomutase, first 3 domains 53738 - Phosphoglucomutase, first 3 domains	0	DIRECT
55874,46946 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 46946 - S13-like H2TH domain	0	DIRECT
46946,54211 46946 - S13-like H2TH domain 54211 - Ribosomal protein S5 domain 2-like	0	DIRECT
100950,75445 100950 - NagB/RpiA/CoA transferase-like 75445 - D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
56529,56529 56529 - FAH 56529 - FAH	0	DIRECT
54534,54534 54534 - FKBP-like 54534 - FKBP-like	0	DIRECT
48239,48239 48239 - Terpenoid cyclases/Protein prenyltransferases 48239 - Terpenoid cyclases/Protein prenyltransferases	0	DIRECT
56712,57783 56712 - Prokaryotic type I DNA topoisomerase 57783 - Zinc beta-ribbon	0	DIRECT
55869,56349 55869 - DNA topoisomerase I domain 56349 - DNA breaking-rejoining enzymes	0	DIRECT
52096,51735 52096 - ClpP/crotonase 51735 - NAD(P)-binding Rossmann-fold domains	0	DIRECT
53743,50443 53743 - FucI/AraA N-terminal and middle domains 50443 - FucI/AraA C-terminal domain-like	0	DIRECT
55874,54211 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 54211 - Ribosomal protein S5 domain 2-like	0	DIRECT
56741,56349 56741 - Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment 56349 - DNA breaking-rejoining enzymes	0	DIRECT
109998,54534 109998 - Triger factor/SurA peptide-binding domain-like 54534 - FKBP-like	0	DIRECT
54534,47473 54534 - FKBP-like 47473 - EF-hand	0	DIRECT
54211,56719 54211 - Ribosomal protein S5 domain 2-like 56719 - Type II DNA topoisomerase	0	DIRECT
51419,50621 51419 - PLP-binding barrel 50621 - Alanine racemase C-terminal domain-like	0	DIRECT
56349,46596 56349 - DNA breaking-rejoining enzymes 46596 - Eukaryotic DNA topoisomerase I, dispensable insert domain	0	DIRECT
143856,53649 143856 - DeoB insert domain-like 53649 - Alkaline phosphatase-like	0	DIRECT
51366,51366 51366 - Ribulose-phoshate binding barrel 51366 - Ribulose-phoshate binding barrel	0	DIRECT
55608,56719 55608 - Homing endonucleases 56719 - Type II DNA topoisomerase	0	DIRECT
53681,53681 53681 - Aspartate/glutamate racemase 53681 - Aspartate/glutamate racemase	0	DIRECT
55608,56712 55608 - Homing endonucleases 56712 - Prokaryotic type I DNA topoisomerase	0	DIRECT
57783,57783 57783 - Zinc beta-ribbon 57783 - Zinc beta-ribbon	0	DIRECT
51735,74650 51735 - NAD(P)-binding Rossmann-fold domains 74650 - Galactose mutarotase-like	0	DIRECT
48179,48179 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
54534,109998 54534 - FKBP-like 109998 - Triger factor/SurA peptide-binding domain-like	0	DIRECT
53738,55957 53738 - Phosphoglucomutase, first 3 domains 55957 - Phosphoglucomutase, C-terminal domain	0	DIRECT
51045,54534 51045 - WW domain 54534 - FKBP-like	0	DIRECT
50891,48452 50891 - Cyclophilin-like 48452 - TPR-like	0	DIRECT
53756,53067 53756 - UDP-Glycosyltransferase/glycogen phosphorylase 53067 - Actin-like ATPase domain	0	DIRECT
52317,51366 52317 - Class I glutamine amidotransferase-like 51366 - Ribulose-phoshate binding barrel	0.00000000000001136	DIRECT
51735,48179 51735 - NAD(P)-binding Rossmann-fold domains 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	0.00000000002384	DIRECT
56801,47336 56801 - Acetyl-CoA synthetase-like 47336 - ACP-like	0.000001134	DIRECT
47336,52777 47336 - ACP-like 52777 - CoA-dependent acyltransferases	0.000004243	DIRECT
48179,52096 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like 52096 - ClpP/crotonase	0.00002601	DIRECT
53850,55021 53850 - Periplasmic binding protein-like II 55021 - ACT-like	0.00006854	DIRECT
53448,51182 53448 - Nucleotide-diphospho-sugar transferases 51182 - RmlC-like cupins	0.0001265	DIRECT
52777,56801 52777 - CoA-dependent acyltransferases 56801 - Acetyl-CoA synthetase-like	0.002796	INHERITED FROM: Racemases and epimerases || Acting on amino acids and derivatives
48239,48576 48239 - Terpenoid cyclases/Protein prenyltransferases 48576 - Terpenoid synthases	0.006188	INHERITED FROM: Copalyl diphosphate synthase || Intramolecular lyases || Ent-copalyl diphosphate synthase
52777,52777 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases	0.03814	INHERITED FROM: Phenylalanine racemase (ATP-hydrolyzing) || Racemases and epimerases || Acting on amino acids and derivatives
51971,54373 51971 - Nucleotide-binding domain 54373 - FAD-linked reductases, C-terminal domain	0.07001	INHERITED FROM: UDP-galactopyranose mutase || Intramolecular transferases (mutases) || Transferring other groups
52833,47616 52833 - Thioredoxin-like 47616 - GST C-terminal domain-like	0.4868	INHERITED FROM: Other intramolecular oxidoreductases || Cis-trans-isomerases || Maleylacetoacetate isomerase
54966,51649 54966 - RuBisCO, large subunit, small (N-terminal) domain 51649 - RuBisCo, C-terminal domain	1	INHERITED FROM: 5.3.2.5 || Interconverting keto- and enol- groups
52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	1	INHERITED FROM: Other isomerases
51445,51011 51445 - (Trans)glycosidases 51011 - Glycosyl hydrolase domain	1	INHERITED FROM: Maltose alpha-D-glucosyltransferase
51735,55347 51735 - NAD(P)-binding Rossmann-fold domains 55347 - Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	1	INHERITED FROM: Intramolecular lyases || Inositol-3-phosphate synthase
54826,51604 54826 - Enolase N-terminal domain-like 51604 - Enolase C-terminal domain-like	1	INHERITED FROM: L-Ala-D/L-Glu epimerase || Intramolecular lyases || Chloromuconate cycloisomerase || Muconate cycloisomerase

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

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
109998,54534,54534 109998 - Triger factor/SurA peptide-binding domain-like 54534 - FKBP-like 54534 - FKBP-like	0	DIRECT
54534,54534,48452 54534 - FKBP-like 54534 - FKBP-like 48452 - TPR-like	0	DIRECT
53738,53738,55957 53738 - Phosphoglucomutase, first 3 domains 53738 - Phosphoglucomutase, first 3 domains 55957 - Phosphoglucomutase, C-terminal domain	0	DIRECT
54534,54534,54534 54534 - FKBP-like 54534 - FKBP-like 54534 - FKBP-like	0	DIRECT
51735,48179,48179 51735 - NAD(P)-binding Rossmann-fold domains 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
51294,56719,55608 51294 - Hedgehog/intein (Hint) domain 56719 - Type II DNA topoisomerase 55608 - Homing endonucleases	0	DIRECT
52540,56712,51294 52540 - P-loop containing nucleoside triphosphate hydrolases 56712 - Prokaryotic type I DNA topoisomerase 51294 - Hedgehog/intein (Hint) domain	0	DIRECT
102735,54534,109998 102735 - Trigger factor ribosome-binding domain 54534 - FKBP-like 109998 - Triger factor/SurA peptide-binding domain-like	0	DIRECT
54534,54534,47473 54534 - FKBP-like 54534 - FKBP-like 47473 - EF-hand	0	DIRECT
56741,56349,46596 56741 - Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment 56349 - DNA breaking-rejoining enzymes 46596 - Eukaryotic DNA topoisomerase I, dispensable insert domain	0	DIRECT
52317,51366,51366 52317 - Class I glutamine amidotransferase-like 51366 - Ribulose-phoshate binding barrel 51366 - Ribulose-phoshate binding barrel	0	DIRECT
48600,53850,55021 48600 - Chorismate mutase II 53850 - Periplasmic binding protein-like II 55021 - ACT-like	0	DIRECT
48600,51735,48179 48600 - Chorismate mutase II 51735 - NAD(P)-binding Rossmann-fold domains 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
52096,51735,48179 52096 - ClpP/crotonase 51735 - NAD(P)-binding Rossmann-fold domains 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
55874,46946,54211 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 46946 - S13-like H2TH domain 54211 - Ribosomal protein S5 domain 2-like	0	DIRECT
52833,52833,47933 52833 - Thioredoxin-like 52833 - Thioredoxin-like 47933 - ERP29 C domain-like	0	DIRECT
53738,53738,53738 53738 - Phosphoglucomutase, first 3 domains 53738 - Phosphoglucomutase, first 3 domains 53738 - Phosphoglucomutase, first 3 domains	0	DIRECT
52833,52833,52833 52833 - Thioredoxin-like 52833 - Thioredoxin-like 52833 - Thioredoxin-like	0	DIRECT
57783,57783,57783 57783 - Zinc beta-ribbon 57783 - Zinc beta-ribbon 57783 - Zinc beta-ribbon	0	DIRECT
56719,55608,56719 56719 - Type II DNA topoisomerase 55608 - Homing endonucleases 56719 - Type II DNA topoisomerase	0	DIRECT
56712,57783,57783 56712 - Prokaryotic type I DNA topoisomerase 57783 - Zinc beta-ribbon 57783 - Zinc beta-ribbon	0	DIRECT
52540,52540,56712 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases 56712 - Prokaryotic type I DNA topoisomerase	0	DIRECT
55874,54211,56719 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 54211 - Ribosomal protein S5 domain 2-like 56719 - Type II DNA topoisomerase	0	DIRECT
48239,48239,48576 48239 - Terpenoid cyclases/Protein prenyltransferases 48239 - Terpenoid cyclases/Protein prenyltransferases 48576 - Terpenoid synthases	0.0000001203	DIRECT
56801,47336,52777 56801 - Acetyl-CoA synthetase-like 47336 - ACP-like 52777 - CoA-dependent acyltransferases	0.0000002145	DIRECT
47336,52777,52777 47336 - ACP-like 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases	0.000004243	DIRECT
48179,48179,52096 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like 52096 - ClpP/crotonase	0.00002601	DIRECT
52777,52777,56801 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases 56801 - Acetyl-CoA synthetase-like	0.0001708	DIRECT
52777,56801,47336 52777 - CoA-dependent acyltransferases 56801 - Acetyl-CoA synthetase-like 47336 - ACP-like	0.0003201	DIRECT

Trees by TreeVector

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