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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).

Superfamily domains annotated to this GO term (SDFO level: Informative)
Highlighted in gray are those with either FDR_singleton>0.001 or FDR_all>0.001

SCOP term	FDR (singleton)	FDR (all)	Annotation (direct or inherited)
Cysteine proteinases	1.129e-10	5.379e-08	DIRECT
eIF4e-like	2.041e-09	1.131e-06	DIRECT
Metallothionein	8.793e-10	4.854e-07	DIRECT
PIN domain-like	7.286e-05	0.0002497	DIRECT
Ribosome inactivating proteins (RIP)	2.72e-08	1.539e-09	DIRECT
RNA-binding domain, RBD	0.0008744	0	DIRECT
Nucleic acid-binding proteins	0.01512	4.395e-10	INHERITED FROM: regulation of RNA stability || regulation of mRNA stability
Class I glutamine amidotransferase-like	3.355e-07	0.01514	INHERITED FROM: regulation of protein stability || protein stabilization
NagB/RpiA/CoA transferase-like	0.007333	0.002942	INHERITED FROM: regulation of translation || regulation of translational initiation

Family domains annotated to this GO term (Not in SDFO)
Highlighted in gray are those with either FDR_singleton>0.001 or FDR_all>0.001

SCOP term	FDR (singleton)	FDR (all)	Annotation (direct or inherited)
Canonical RBD	0.000751	0	DIRECT
DJ-1/PfpI	3.531e-09	3.428e-06	DIRECT
IF2B-like	3.486e-05	3.387e-08	DIRECT
Metallothionein	1.471e-09	9.242e-07	DIRECT
MIF4G domain-like	1.4e-05	0	DIRECT
Papain-like	4.485e-11	9.799e-07	DIRECT
Plant cytotoxins	6.485e-09	8.295e-10	DIRECT
Translation initiation factor eIF4e	2.668e-09	1.504e-06	DIRECT
Cold shock DNA-binding domain-like	0.009106	3.255e-15	INHERITED FROM: regulation of RNA stability
Calmodulin-like	0.0009368	0.336	INHERITED FROM: regulation of protein stability || protein stabilization

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 GO term (SPFO level: Informative)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
PAZ domain	0	DIRECT
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	0	DIRECT
Ribonuclease H-like	0	DIRECT
RNA-binding domain, RBD	0	DIRECT
Amyloid beta a4 protein copper binding domain (domain 2)	0	DIRECT
RNase III domain-like	0	DIRECT
dsRNA-binding domain-like	0	DIRECT
CAPPD, an extracellular domain of amyloid beta A4 protein	0	DIRECT
A heparin-binding domain	0	DIRECT
Translation proteins	1.768e-12	DIRECT
ThrRS/AlaRS common domain	1.153e-11	DIRECT
Eukaryotic type KH-domain (KH-domain type I)	1.864e-11	DIRECT
Nucleic acid-binding proteins	2.833e-10	DIRECT
BPTI-like	4.615e-10	DIRECT
Ribosome inactivating proteins (RIP)	9.936e-10	DIRECT
ARM repeat	2.385e-09	DIRECT
Retrovirus zinc finger-like domains	3.207e-09	DIRECT
Initiation factor IF2/eIF5b, domain 3	6.466e-09	DIRECT
P-domain of calnexin/calreticulin	9.326e-09	DIRECT
Class II aaRS and biotin synthetases	1.909e-08	DIRECT
Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain	2.735e-08	DIRECT
Cysteine proteinases	3.542e-08	DIRECT
Ribosomal protein L13	8.044e-08	DIRECT
DPP6 N-terminal domain-like	8.201e-08	DIRECT
P-loop containing nucleoside triphosphate hydrolases	1.877e-07	DIRECT
Tricorn protease domain 2	2.929e-07	DIRECT
eIF-2-alpha, C-terminal domain	3.244e-07	DIRECT
Metallothionein	3.253e-07	DIRECT
Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	6.8e-07	DIRECT
eIF4e-like	7.611e-07	DIRECT
Dcp2 domain-like	8.289e-07	DIRECT
Mitochondrial glycoprotein MAM33-like	8.821e-07	DIRECT
Signal peptide-binding domain	6.127e-06	DIRECT
Cell growth inhibitor/plasmid maintenance toxic component	7.94e-06	DIRECT
LeuD/IlvD-like	8.062e-06	DIRECT
PABC (PABP) domain	8.27e-06	DIRECT
eIF2alpha middle domain-like	1.021e-05	DIRECT
Domain of the SRP/SRP receptor G-proteins	1.277e-05	DIRECT
RING/U-box	5.367e-05	DIRECT
CCCH zinc finger	6.036e-05	DIRECT
Translation initiation factor IF3, C-terminal domain	7.162e-05	DIRECT
HSP20-like chaperones	9.655e-05	DIRECT
Aconitase iron-sulfur domain	0.0001192	DIRECT
WWE domain	0.0001705	DIRECT
Protein kinase-like (PK-like)	0.0001721	DIRECT
PIN domain-like	0.0001779	DIRECT
BTG domain-like	0.0001811	DIRECT
NHL repeat	0.0002423	DIRECT
UBC-like	0.000482	DIRECT
Translation initiation factor IF3, N-terminal domain	0.0005034	DIRECT
Sm-like ribonucleoproteins	0.0005162	DIRECT
Zinc-binding domain of translation initiation factor 2 beta	0.0006097	DIRECT
Translation initiation factor 2 beta, aIF2beta, N-terminal domain	0.0006933	DIRECT
DUSP-like	0.0009522	DIRECT
beta-beta-alpha zinc fingers	1	INHERITED FROM: regulation of cytoplasmic translation || mRNA localization resulting in posttranscriptional regulation of gene expression
Toll/Interleukin receptor TIR domain	0.5136	INHERITED FROM: 3'-UTR-mediated mRNA stabilization || RNA stabilization || regulation of mRNA stability || mRNA stabilization
Ran binding protein zinc finger-like	0.369	INHERITED FROM: 3'-UTR-mediated mRNA stabilization || regulation of RNA stability || RNA stabilization || regulation of mRNA stability || mRNA stabilization
L domain-like	0.751	INHERITED FROM: mRNA destabilization || RNA destabilization
Formin homology 2 domain (FH2 domain)	0.2262	INHERITED FROM: protein stabilization
Frizzled cysteine-rich domain	0.3843	INHERITED FROM: protein stabilization
WW domain	0.4232	INHERITED FROM: protein stabilization
Calponin-homology domain, CH-domain	0.4286	INHERITED FROM: protein stabilization
HMG-box	1	INHERITED FROM: protein stabilization
EF-hand	1	INHERITED FROM: protein stabilization
Tudor/PWWP/MBT	0.1389	INHERITED FROM: regulation of oskar mRNA translation || negative regulation of oskar mRNA translation
E set domains	0.7357	INHERITED FROM: regulation of translation, ncRNA-mediated || negative regulation of translation involved in gene silencing by miRNA || negative regulation of translation, ncRNA-mediated
Trimeric LpxA-like enzymes	0.001365	INHERITED FROM: positive regulation of translation || regulation of translation || regulation of translational initiation || positive regulation of translational initiation
FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)	0.002018	INHERITED FROM: positive regulation of translation || regulation of translation
Nucleoplasmin-like core domain	0.01701	INHERITED FROM: positive regulation of translation
TNF receptor-like	0.4174	INHERITED FROM: regulation of RNA stability || RNA destabilization
Cystine-knot cytokines	1	INHERITED FROM: regulation of RNA stability || RNA stabilization || regulation of mRNA stability || mRNA stabilization
Hormone receptor domain	0.01055	INHERITED FROM: regulation of RNA stability || regulation of mRNA stability
DNase I-like	0.02725	INHERITED FROM: regulation of RNA stability
SMAD/FHA domain	0.1963	INHERITED FROM: production of miRNAs involved in gene silencing by miRNA || negative regulation of translation || negative regulation of translational elongation || regulation of translational elongation
Nudix	0.04442	INHERITED FROM: posttranscriptional gene silencing by RNA || gene silencing by miRNA || posttranscriptional gene silencing
Nucleotide-diphospho-sugar transferases	0.6366	INHERITED FROM: negative regulation of translational initiation in response to stress || negative regulation of translation in response to stress || regulation of translation in response to stress || regulation of translational initiation || positive regulation of translational initiation
NagB/RpiA/CoA transferase-like	0.00217	INHERITED FROM: negative regulation of translational initiation in response to stress || negative regulation of translation in response to stress || regulation of translation || regulation of translation in response to stress || regulation of translational initiation
BAG domain	0.005048	INHERITED FROM: regulation of protein stability || protein stabilization
Class I glutamine amidotransferase-like	0.0115	INHERITED FROM: regulation of protein stability || protein stabilization
UBA-like	0.1265	INHERITED FROM: regulation of protein stability || protein stabilization
NAD(P)-binding Rossmann-fold domains	0.8416	INHERITED FROM: regulation of protein stability || protein stabilization
Leucine zipper domain	1	INHERITED FROM: regulation of protein stability || protein stabilization
B-box zinc-binding domain	0.06406	INHERITED FROM: regulation of protein stability || regulation of translation, ncRNA-mediated || posttranscriptional gene silencing by RNA || negative regulation of translation involved in gene silencing by miRNA || negative regulation of translation || posttranscriptional gene silencing || negative regulation of translation, ncRNA-mediated
Ubiquitin-like	0.002633	INHERITED FROM: regulation of protein stability
F-box domain	0.08587	INHERITED FROM: regulation of protein stability
HIT/MYND zinc finger-like	0.7179	INHERITED FROM: regulation of protein stability
HLH, helix-loop-helix DNA-binding domain	1	INHERITED FROM: regulation of protein stability
Quinoprotein alcohol dehydrogenase-like	0.00864	INHERITED FROM: negative regulation of translation || regulation of translation
PAP/OAS1 substrate-binding domain	0.05164	INHERITED FROM: posttranscriptional gene silencing
Translation proteins SH3-like domain	0.004084	INHERITED FROM: RNA interference || production of miRNAs involved in gene silencing by miRNA || production of ta-siRNAs involved in RNA interference || positive regulation of translation || production of siRNA involved in RNA interference || gene silencing by miRNA
Smc hinge domain	0.007201	INHERITED FROM: RNA interference || production of miRNAs involved in gene silencing by miRNA || production of ta-siRNAs involved in RNA interference || production of siRNA involved in RNA interference || gene silencing by miRNA
ACP-like	0.04733	INHERITED FROM: RNA interference || posttranscriptional gene silencing by RNA || production of miRNAs involved in gene silencing by miRNA || production of ta-siRNAs involved in RNA interference || production of siRNA involved in RNA interference || gene silencing by miRNA || posttranscriptional gene silencing
beta and beta-prime subunits of DNA dependent RNA-polymerase	0.0343	INHERITED FROM: RNA interference || production of siRNA involved in RNA interference
TPR-like	0.4206	INHERITED FROM: RNA interference || posttranscriptional gene silencing
SET domain	1	INHERITED FROM: production of ta-siRNAs involved in RNA interference
Heat shock protein 70kD (HSP70), peptide-binding domain	0.02785	INHERITED FROM: regulation of translational fidelity || regulation of translational elongation
Actin-like ATPase domain	0.9018	INHERITED FROM: regulation of translational fidelity
Sec63 N-terminal domain-like	0.007324	INHERITED FROM: regulation of translation

Supra-domains annotated to this GO term (SPFO level: 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)
69065,54768 69065 - RNase III domain-like 54768 - dsRNA-binding domain-like	0	DIRECT
54928,69322 54928 - RNA-binding domain, RBD 69322 - Tricorn protease domain 2	0	DIRECT
51735,55347 51735 - NAD(P)-binding Rossmann-fold domains 55347 - Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	0	DIRECT
56491,89811 56491 - A heparin-binding domain 89811 - Amyloid beta a4 protein copper binding domain (domain 2)	0	DIRECT
56112,55681 56112 - Protein kinase-like (PK-like) 55681 - Class II aaRS and biotin synthetases	0	DIRECT
69065,69065 69065 - RNase III domain-like 69065 - RNase III domain-like	0	DIRECT
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD	0	DIRECT
57362,109843 57362 - BPTI-like 109843 - CAPPD, an extracellular domain of amyloid beta A4 protein	0	DIRECT
54768,54768 54768 - dsRNA-binding domain-like 54768 - dsRNA-binding domain-like	0	DIRECT
47769,48371 47769 - SAM/Pointed domain 48371 - ARM repeat	0	DIRECT
101690,53098 101690 - PAZ domain 53098 - Ribonuclease H-like	2.417e-15	DIRECT
48371,48371 48371 - ARM repeat 48371 - ARM repeat	6.873e-13	DIRECT
50447,55186 50447 - Translation proteins 55186 - ThrRS/AlaRS common domain	1.056e-12	DIRECT
54791,54791 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I)	6.476e-12	DIRECT
50249,57756 50249 - Nucleic acid-binding proteins 57756 - Retrovirus zinc finger-like domains	5.156e-10	DIRECT
90229,90229 90229 - CCCH zinc finger 90229 - CCCH zinc finger	7.694e-10	DIRECT
81296,101898 81296 - E set domains 101898 - NHL repeat	1.385e-09	DIRECT
51161,48371 51161 - Trimeric LpxA-like enzymes 48371 - ARM repeat	2.335e-09	DIRECT
52156,50447 52156 - Initiation factor IF2/eIF5b, domain 3 50447 - Translation proteins	3.633e-09	DIRECT
49899,63887 49899 - Concanavalin A-like lectins/glucanases 63887 - P-domain of calnexin/calreticulin	9.326e-09	DIRECT
54928,82171 54928 - RNA-binding domain, RBD 82171 - DPP6 N-terminal domain-like	7.295e-08	DIRECT
54001,144232 54001 - Cysteine proteinases 144232 - HIT/MYND zinc finger-like	7.295e-08	DIRECT
57850,117839 57850 - RING/U-box 117839 - WWE domain	1.011e-07	DIRECT
53448,51161 53448 - Nucleotide-diphospho-sugar transferases 51161 - Trimeric LpxA-like enzymes	1.611e-07	DIRECT
101690,69065 101690 - PAZ domain 69065 - RNase III domain-like	3.263e-07	DIRECT
55681,101353 55681 - Class II aaRS and biotin synthetases 101353 - Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	6.8e-07	DIRECT
101353,50447 101353 - Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) 50447 - Translation proteins	6.8e-07	DIRECT
140586,55811 140586 - Dcp2 domain-like 55811 - Nudix	8.289e-07	DIRECT
64593,46579 64593 - Intermediate filament protein, coiled coil region 46579 - Prefoldin	1.971e-06	DIRECT
50447,52156 50447 - Translation proteins 52156 - Initiation factor IF2/eIF5b, domain 3	2.526e-06	DIRECT
52540,47446 52540 - P-loop containing nucleoside triphosphate hydrolases 47446 - Signal peptide-binding domain	6.127e-06	DIRECT
52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	6.244e-06	DIRECT
52540,50447 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins	6.876e-06	DIRECT
54001,46934 54001 - Cysteine proteinases 46934 - UBA-like	1.012e-05	DIRECT
50249,116742 50249 - Nucleic acid-binding proteins 116742 - eIF2alpha middle domain-like	1.021e-05	DIRECT
116742,110993 116742 - eIF2alpha middle domain-like 110993 - eIF-2-alpha, C-terminal domain	1.021e-05	DIRECT
47364,52540 47364 - Domain of the SRP/SRP receptor G-proteins 52540 - P-loop containing nucleoside triphosphate hydrolases	1.277e-05	DIRECT
52540,52156 52540 - P-loop containing nucleoside triphosphate hydrolases 52156 - Initiation factor IF2/eIF5b, domain 3	1.539e-05	DIRECT
75689,48371 75689 - Zinc-binding domain of translation initiation factor 2 beta 48371 - ARM repeat	2.224e-05	DIRECT
46579,64593 46579 - Prefoldin 64593 - Intermediate filament protein, coiled coil region	2.385e-05	DIRECT
54236,50729 54236 - Ubiquitin-like 50729 - PH domain-like	2.882e-05	DIRECT
64593,64593 64593 - Intermediate filament protein, coiled coil region 64593 - Intermediate filament protein, coiled coil region	5.303e-05	DIRECT
50104,50249 50104 - Translation proteins SH3-like domain 50249 - Nucleic acid-binding proteins	0.0002475	DIRECT
53732,52016 53732 - Aconitase iron-sulfur domain 52016 - LeuD/IlvD-like	0.0004865	DIRECT
54364,55200 54364 - Translation initiation factor IF3, N-terminal domain 55200 - Translation initiation factor IF3, C-terminal domain	0.0005034	DIRECT
100966,75689 100966 - Translation initiation factor 2 beta, aIF2beta, N-terminal domain 75689 - Zinc-binding domain of translation initiation factor 2 beta	0.0006097	DIRECT
52799,49562 52799 - (Phosphotyrosine protein) phosphatases II 49562 - C2 domain (Calcium/lipid-binding domain, CaLB)	0.0006341	DIRECT
81383,50978 81383 - F-box domain 50978 - WD40 repeat-like	0.0007301	DIRECT
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0.0009522	DIRECT
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0.0009522	DIRECT
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	1	INHERITED FROM: regulation of cytoplasmic translation || mRNA localization resulting in posttranscriptional regulation of gene expression
90209,54928 90209 - Ran binding protein zinc finger-like 54928 - RNA-binding domain, RBD	0.03929	INHERITED FROM: 3'-UTR-mediated mRNA stabilization || regulation of RNA stability || RNA stabilization || regulation of mRNA stability || mRNA stabilization
54928,90209 54928 - RNA-binding domain, RBD 90209 - Ran binding protein zinc finger-like	0.05431	INHERITED FROM: 3'-UTR-mediated mRNA stabilization || regulation of RNA stability || RNA stabilization || regulation of mRNA stability || mRNA stabilization
47212,56112 47212 - FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) 56112 - Protein kinase-like (PK-like)	0.002018	INHERITED FROM: positive regulation of translation || regulation of translation
111418,81321 111418 - Hormone receptor domain 81321 - Family A G protein-coupled receptor-like	0.01852	INHERITED FROM: regulation of RNA stability || regulation of mRNA stability
57850,57845 57850 - RING/U-box 57845 - B-box zinc-binding domain	0.9288	INHERITED FROM: protein destabilization
81296,81296 81296 - E set domains 81296 - E set domains	0.02	INHERITED FROM: regulation of protein stability || protein stabilization
47986,47986 47986 - DEATH domain 47986 - DEATH domain	0.07193	INHERITED FROM: regulation of protein stability
50249,50249 50249 - Nucleic acid-binding proteins 50249 - Nucleic acid-binding proteins	0.01141	INHERITED FROM: negative regulation of translation
55681,52954 55681 - Class II aaRS and biotin synthetases 52954 - Class II aaRS ABD-related	0.08867	INHERITED FROM: negative regulation of translation
81301,81631 81301 - Nucleotidyltransferase 81631 - PAP/OAS1 substrate-binding domain	0.04229	INHERITED FROM: posttranscriptional gene silencing
53067,100920 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain	0.02724	INHERITED FROM: regulation of translational fidelity || regulation of translational elongation
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain	0.6645	INHERITED FROM: regulation of translational fidelity || regulation of translational elongation

Supra-domains annotated to this GO term (SPFO level: 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)
69065,69065,54768 69065 - RNase III domain-like 69065 - RNase III domain-like 54768 - dsRNA-binding domain-like	0	DIRECT
48371,48371,48371 48371 - ARM repeat 48371 - ARM repeat 48371 - ARM repeat	0	DIRECT
54768,54768,54768 54768 - dsRNA-binding domain-like 54768 - dsRNA-binding domain-like 54768 - dsRNA-binding domain-like	1.708e-13	DIRECT
69065,54768,54768 69065 - RNase III domain-like 54768 - dsRNA-binding domain-like 54768 - dsRNA-binding domain-like	1.075e-09	DIRECT
53448,51161,48371 53448 - Nucleotide-diphospho-sugar transferases 51161 - Trimeric LpxA-like enzymes 48371 - ARM repeat	2.335e-09	DIRECT
52540,50447,52156 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins 52156 - Initiation factor IF2/eIF5b, domain 3	5.324e-07	DIRECT
101353,50447,55186 101353 - Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) 50447 - Translation proteins 55186 - ThrRS/AlaRS common domain	6.8e-07	DIRECT
55681,101353,50447 55681 - Class II aaRS and biotin synthetases 101353 - Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) 50447 - Translation proteins	6.8e-07	DIRECT
64593,64593,46579 64593 - Intermediate filament protein, coiled coil region 64593 - Intermediate filament protein, coiled coil region 46579 - Prefoldin	9.021e-07	DIRECT
64593,46579,64593 64593 - Intermediate filament protein, coiled coil region 46579 - Prefoldin 64593 - Intermediate filament protein, coiled coil region	9.021e-07	DIRECT
50447,52156,50447 50447 - Translation proteins 52156 - Initiation factor IF2/eIF5b, domain 3 50447 - Translation proteins	2.526e-06	DIRECT
47364,52540,47446 47364 - Domain of the SRP/SRP receptor G-proteins 52540 - P-loop containing nucleoside triphosphate hydrolases 47446 - Signal peptide-binding domain	3.731e-06	DIRECT
50249,116742,110993 50249 - Nucleic acid-binding proteins 116742 - eIF2alpha middle domain-like 110993 - eIF-2-alpha, C-terminal domain	1.021e-05	DIRECT
52540,52156,50447 52540 - P-loop containing nucleoside triphosphate hydrolases 52156 - Initiation factor IF2/eIF5b, domain 3 50447 - Translation proteins	1.539e-05	DIRECT
54791,54791,54791 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I)	1.804e-05	DIRECT
100966,75689,48371 100966 - Translation initiation factor 2 beta, aIF2beta, N-terminal domain 75689 - Zinc-binding domain of translation initiation factor 2 beta 48371 - ARM repeat	2.224e-05	DIRECT
54928,54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD	8.113e-05	DIRECT
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain	0.0001811	DIRECT
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0.0009522	DIRECT
54928,90209,54928 54928 - RNA-binding domain, RBD 90209 - Ran binding protein zinc finger-like 54928 - RNA-binding domain, RBD	0.03929	INHERITED FROM: 3'-UTR-mediated mRNA stabilization || regulation of RNA stability || RNA stabilization || regulation of mRNA stability || mRNA stabilization
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains	0.00247	INHERITED FROM: regulation of protein stability || protein stabilization
50249,50249,50249 50249 - Nucleic acid-binding proteins 50249 - Nucleic acid-binding proteins 50249 - Nucleic acid-binding proteins	0.005048	INHERITED FROM: negative regulation of translation || regulation of translation
53067,53067,100920 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain	0.02602	INHERITED FROM: regulation of translational fidelity || regulation of translational elongation

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.