galE3 Resolved · high auto-curated
H37Rv Rv0536 · MTBC0 - ·
346 aa · 627248–628288 (+) ·
RefSeq YP_177737.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | UDP-glucose 4-epimerase GalE |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | UDP-glucose 4-epimerase GalE. Pfam: GDP_Man_Dehyd (PF16363.12), Epimerase (PF01370.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
L7N670
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable UDP-glucose 4-epimerase GalE3 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolismM Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | galE3 |
| eggNOG description | dehydratase |
| Orthologous group | COG0451 |
| EC number |
EC 5.1.3.25
|
| KEGG orthology |
K17947
|
| KEGG pathways |
map00523, map01130
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.285 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 4 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
GDP_Man_Dehyd | PF16363.12 | 1.2e-15 | 164–339 | GDP-mannose 4,6 dehydratase |
Epimerase | PF01370.28 | 2.8e-23 | 165–266 | NAD dependent epimerase/dehydratase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pnp (5'-methylthioadenosine phosphorylase), high confidence from genomic context alone (score 934 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3266c rmlD |
dTDP-4-dehydrorhamnose reductase | 944 | 941 | database:900 |
Rv0535 pnp |
5'-methylthioadenosine phosphorylase | 991 | 934 ctx | neighborhood:882 cooccurence:441 textmining:875 |
Rv3465 rmlC |
dTDP-4-dehydrorhamnose 3,5-epimerase | 887 | 881 | coexpression:409 database:800 |
Rv3784 |
dTDP-glucose 4,6-dehydratase | 858 | 852 | database:800 |
Rv0539 |
dolichyl-phosphate sugar synthase | 978 | 835 ctx | cooccurence:771 textmining:874 |
Rv3464 rmlB |
dTDP-glucose 4,6-dehydratase | 829 | 822 | database:800 |
Rv0540 hyp |
hypothetical protein | 975 | 817 ctx | cooccurence:770 textmining:870 |
Rv0705 rpsS |
30S ribosomal protein S19 | 816 | 816 | experimental:463 database:574 |
Rv0541c |
integral membrane protein | 974 | 809 ctx | cooccurence:767 textmining:870 |
Rv0682 rpsL |
30S ribosomal protein S12 | 813 | 805 | experimental:463 database:573 |
Rv0218 |
transmembrane protein | 804 | 805 ctx | cooccurence:769 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 803 | 797 | experimental:463 database:578 |
Rv0707 rpsC |
30S ribosomal protein S3 | 802 | 795 | experimental:463 database:578 |
Rv0534c menA |
1,4-dihydroxy-2-naphthoate octaprenyltransferase | 792 | 792 ctx | neighborhood:791 |
Rv0721 rpsE |
30S ribosomal protein S5 | 796 | 789 | experimental:463 database:575 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): UDP-glucose 4-epimerase GalE
- Pfam (hmmscan --cut_ga): GDP_Man_Dehyd PF16363.12 (E=1e-15), Epimerase PF01370.28 (E=3e-23)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq YP_177737.1)
- Domains: Pfam-A via hmmscan --cut_ga — GDP_Man_Dehyd (PF16363.12), Epimerase (PF01370.28)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG0451 - Curated reference: UniProt L7N670 (TrEMBL, unreviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
91 functional partner(s); context anchor
pnp - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0536|galE3 MRVLLTGAAGFIGSRVDAALRAAGHDVVGVDALLPAAHGPNPVLPPGCQRVDVRDASALAPLLAGVDLVCHQAAMVGAGVNAADAPAYGGHNDFATTVLLAQMFAAGVRRLVLASSMVVYGQGRYDCPQHGPVDPLPRRRADLDNGVFEHRCPGCGEPVIWQLVDEDAPLRPRSLYAASKTAQEHYALAWSEASGGSVVALRYHNVYGPGMPRDTPYSGVAAIFRSAVEKGKPPKVFEDGGQMRDFVHVDDVAAANLAAVHLGEADRDGFTAVNVCSGRPISILQVATAICDARGGSMSPAITGHYRSGDVRHIVADPARAARVLGFRAAVDPGEGLREFAFAPLR