Gene Ontology (GO)
GO depicts three complementary biological concepts including Biological Process (BP), Molecular Function (MF) and Cellular Component (CC). The hierarchical structure of GO is organized as a 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 GO terms to the current GO term of interest ordered by their shortest distances to the current term. Also, only direct children GO terms of the current GO 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 GO annotations for each of the three concepts at each of the two domain levels.
Structural Domain Functional Ontology (SDFO)
As domain-centric ontology, SDFO only refers to those GO terms which are the most informative to annotate SCOP domains.
GO annotations for SCOP domains
For details, please visit
Documentation: GO annotations for SCOP domains. Therein, we provide several relevant files (
Data Availability) for the download. It includes two mapping results: Domain2GO supported by both, and Domain2GO supported only by all. For each mapping result, the ontology and annotation files are available. The annotation (i.e.,
Domain2GO_supported_by_both.txt) and the corresponding ontology (i.e.,
SDFO.both.txt) are suitable for small-scale studies (high-quality, and
BROWSABLE BELOW), while the annotation (i.e.,
Domain2GO_supported_only_by_all.txt) and the corresponding ontology (i.e.,
SDFO.all.txt) for large-scale studies (high-coverage, like functional enrichment analysis).
Supra-domain Functional Ontology (SPFO)
As an extension, SPFO includes those GO terms which are the most informative to annotate supra-domains and individual SCOP domains at the
Superfamily level.
GO annotations for Supra-domains
For details, please visit
Documentation: GO annotations for Supra-domains. Therein, we provide several relevant files (
Data Availability) for the download, including a annotation file (i.e.,
SP2GO.txt) and an ontology (i.e.,
SPFO.txt). For the sake of being browsable, listed below are those supra-domains (single, dual, triple, quad).
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-domain (Single) |
FDR (all) |
Annotation (direct or inherited) |
| HemD-like | 0 | Direct |
| Chelatase | 0 | Direct |
| Molybdopterin synthase subunit MoaE | 0 | Direct |
| Activating enzymes of the ubiquitin-like proteins | 0 | Direct |
| Radical SAM enzymes | 0 | Direct |
| MoaD/ThiS | 0 | Direct |
| Acetyl-CoA synthetase-like | 0 | Direct |
| Thiamin diphosphate-binding fold (THDP-binding) | 0 | Direct |
| Molybdenum cofactor biosynthesis protein C, MoaC | 0 | Direct |
| MoeA N-terminal region -like | 9.306e-15 | Direct |
| F1 ATPase inhibitor, IF1, C-terminal domain | 9.306e-15 | Direct |
| MoeA C-terminal domain-like | 9.306e-15 | Direct |
| Citrate synthase | 3.02e-14 | Direct |
| Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 4.187e-14 | Direct |
| CoA-dependent acyltransferases | 5.455e-14 | Direct |
| CoaB-like | 1.986e-12 | Direct |
| S-adenosylmethionine synthetase | 1.419e-11 | Direct |
| Homo-oligomeric flavin-containing Cys decarboxylases, HFCD | 3.051e-11 | Direct |
| Nicotinate/Quinolinate PRTase C-terminal domain-like | 5.214e-11 | Direct |
| Molybdenum cofactor biosynthesis proteins | 6.099e-11 | Direct |
| Glutamyl tRNA-reductase dimerization domain | 1.134e-10 | Direct |
| Glutamyl tRNA-reductase catalytic, N-terminal domain | 1.134e-10 | Direct |
| TK C-terminal domain-like | 3.239e-10 | Direct |
| Tetrahydrobiopterin biosynthesis enzymes-like | 3.629e-10 | Direct |
| Nicotinate/Quinolinate PRTase N-terminal domain-like | 1.169e-09 | Direct |
| FAD/NAD(P)-binding domain | 7.418e-09 | Direct |
| Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain | 7.429e-09 | Direct |
| FMN-binding split barrel | 2.817e-08 | Direct |
| FAD-linked reductases, C-terminal domain | 8.211e-08 | Direct |
| Aldolase | 1.657e-07 | Direct |
| MurD-like peptide ligases, peptide-binding domain | 4.227e-07 | Direct |
| MurD-like peptide ligases, catalytic domain | 4.227e-07 | Direct |
| Succinyl-CoA synthetase domains | 5.506e-07 | Direct |
| Single hybrid motif | 1.072e-06 | Direct |
| UROD/MetE-like | 2.68e-06 | Direct |
| Phosphoenolpyruvate/pyruvate domain | 2.68e-06 | Direct |
| Dihydropteroate synthetase-like | 4.323e-06 | Direct |
| Coproporphyrinogen III oxidase | 5.062e-06 | Direct |
| ACP-like | 8.75e-06 | Direct |
| Siroheme synthase middle domains-like | 9.439e-06 | Direct |
| Dimerization cofactor of HNF-1 alpha | 9.439e-06 | Direct |
| Ferritin-like | 1.1e-05 | Direct |
| Tetrapyrrole methylase | 1.687e-05 | Direct |
| FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 3.006e-05 | Direct |
| 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK | 4.673e-05 | Direct |
| Peptidyl-tRNA hydrolase-like | 4.673e-05 | Direct |
| ADC synthase | 5.076e-05 | Direct |
| NAD(P)-binding Rossmann-fold domains | 9.064e-05 | Direct |
| NadA-like | 0.0001 | Direct |
| Isochorismatase-like hydrolases | 0.0001399 | Direct |
| Spectrin repeat | 0.000185 | Direct |
| S-adenosyl-L-methionine-dependent methyltransferases | 0.0002799 | Direct |
| alpha-ketoacid dehydrogenase kinase, N-terminal domain | 0.0003181 | Direct |
| Riboflavin kinase-like | 0.000417 | Direct |
| NAD kinase/diacylglycerol kinase-like | 0.0007477 | Direct |
| Nucleotidylyl transferase | 0.0007504 | Direct |
| DEATH domain | 0.0009735 | Direct |
| Adenine nucleotide alpha hydrolases-like | 0.08738 | Inherited |
| Glutathione synthetase ATP-binding domain-like | 0.01592 | Inherited |
| Ribokinase-like | 0.01295 | Inherited |
| Thioesterase/thiol ester dehydrase-isomerase | 0.06535 | Inherited |
| PLP-dependent transferases | 0.123 | Inherited |
| 4'-phosphopantetheinyl transferase | 0.004306 | Inherited |
| alpha/beta-Hydrolases | 0.8178 | Inherited |
| Nucleic acid-binding proteins | 1 | Inherited |
| 6-phosphogluconate dehydrogenase C-terminal domain-like | 0.6169 | Inherited |
| Actin-like ATPase domain | 0.2662 | Inherited |
| P-loop containing nucleoside triphosphate hydrolases | 1 | Inherited |
| Aminoacid dehydrogenase-like, N-terminal domain | 0.00718 | Inherited |
| Formyltransferase | 0.06345 | Inherited |
| Dihydrofolate reductase-like | 0.001 | Inherited |
| Cytochrome P450 | 0.3595 | Inherited |
| Terpenoid synthases | 0.001736 | Inherited |
| PurM N-terminal domain-like | 0.1109 | Inherited |
| PurM C-terminal domain-like | 0.1109 | Inherited |
| Class II aaRS and biotin synthetases | 1 | Inherited |
| Mitochondrial carrier | 0.05691 | Inherited |
| Periplasmic binding protein-like II | 0.0642 | Inherited |
| LeuD/IlvD-like | 0.1259 | Inherited |
| Ankyrin repeat | 0.2936 | Inherited |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 0.4811 | Inherited |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
51735,48256
51735 - NAD(P)-binding Rossmann-fold domains
48256 - Citrate synthase | 0 | Direct |
51230,47005
51230 - Single hybrid motif
47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 0 | Direct |
63882,53218
63882 - MoeA N-terminal region -like
53218 - Molybdenum cofactor biosynthesis proteins | 9.306e-15 | Direct |
53218,63867
53218 - Molybdenum cofactor biosynthesis proteins
63867 - MoeA C-terminal domain-like | 9.306e-15 | Direct |
52210,51735
52210 - Succinyl-CoA synthetase domains
51735 - NAD(P)-binding Rossmann-fold domains | 2.698e-13 | Direct |
51230,51230
51230 - Single hybrid motif
51230 - Single hybrid motif | 8.49e-13 | Direct |
55973,55973
55973 - S-adenosylmethionine synthetase
55973 - S-adenosylmethionine synthetase | 3.118e-12 | Direct |
47005,52777
47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
52777 - CoA-dependent acyltransferases | 5.457e-12 | Direct |
52518,52922
52518 - Thiamin diphosphate-binding fold (THDP-binding)
52922 - TK C-terminal domain-like | 1.035e-10 | Direct |
51735,69075
51735 - NAD(P)-binding Rossmann-fold domains
69075 - Glutamyl tRNA-reductase dimerization domain | 1.134e-10 | Direct |
69742,51735
69742 - Glutamyl tRNA-reductase catalytic, N-terminal domain
51735 - NAD(P)-binding Rossmann-fold domains | 1.134e-10 | Direct |
52777,56801
52777 - CoA-dependent acyltransferases
56801 - Acetyl-CoA synthetase-like | 8.163e-10 | Direct |
46966,50729
46966 - Spectrin repeat
50729 - PH domain-like | 1.915e-09 | Direct |
54675,51690
54675 - Nicotinate/Quinolinate PRTase N-terminal domain-like
51690 - Nicotinate/Quinolinate PRTase C-terminal domain-like | 2.768e-09 | Direct |
53850,54782
53850 - Periplasmic binding protein-like II
54782 - Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain | 7.429e-09 | Direct |
52777,52777
52777 - CoA-dependent acyltransferases
52777 - CoA-dependent acyltransferases | 9.882e-09 | Direct |
56059,52210
56059 - Glutathione synthetase ATP-binding domain-like
52210 - Succinyl-CoA synthetase domains | 1.832e-08 | Direct |
51905,54373
51905 - FAD/NAD(P)-binding domain
54373 - FAD-linked reductases, C-terminal domain | 5.214e-08 | Direct |
47336,52777
47336 - ACP-like
52777 - CoA-dependent acyltransferases | 5.926e-08 | Direct |
56801,47336
56801 - Acetyl-CoA synthetase-like
47336 - ACP-like | 4.227e-07 | Direct |
52374,52540
52374 - Nucleotidylyl transferase
52540 - P-loop containing nucleoside triphosphate hydrolases | 2.668e-06 | Direct |
47336,53474
47336 - ACP-like
53474 - alpha/beta-Hydrolases | 5.827e-06 | Direct |
53623,53244
53623 - MurD-like peptide ligases, catalytic domain
53244 - MurD-like peptide ligases, peptide-binding domain | 7.58e-06 | Direct |
46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat | 1.056e-05 | Direct |
51905,55424
51905 - FAD/NAD(P)-binding domain
55424 - FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 3.006e-05 | Direct |
51735,48179
51735 - NAD(P)-binding Rossmann-fold domains
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like | 0.5726 | Inherited |
53067,53067
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain | 0.1094 | Inherited |
53223,51735
53223 - Aminoacid dehydrogenase-like, N-terminal domain
51735 - NAD(P)-binding Rossmann-fold domains | 0.01434 | Inherited |
55326,56042
55326 - PurM N-terminal domain-like
56042 - PurM C-terminal domain-like | 0.1109 | Inherited |
47413,46689
47413 - lambda repressor-like DNA-binding domains
46689 - Homeodomain-like | 0.03215 | Inherited |
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.
