galE1 Resolved · high auto-curated
H37Rv Rv3634c · MTBC0 mtbc0_003851 ·
314 aa · 4096371–4097315 (-) ·
RefSeq NP_215015.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | UDP-glucose 4-epimerase |
|---|---|
| MTBC0 PGAP re-annotation | UDP-glucose 4-epimerase |
| Revised (this work) | UDP-glucose 4-epimerase. Pfam: RmlD_sub_bind (PF04321.24), Epimerase (PF01370.28), GDP_Man_Dehyd (PF16363.12), 3Beta_HSD (PF01073.26), Polysacc_synt_2 (PF02719.22), NAD_binding_10 (PF13460.13), NAD_binding_4 (PF07993.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN67
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | UDP-glucose 4-epimerase |
| EC (curated) |
EC 5.1.3.2
|
| Curated function | Involved in the metabolism of galactose. Catalyzes the conversion of UDP-galactose (UDP-Gal) to UDP-glucose (UDP-Glc) through a mechanism involving the transient reduction of NAD (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | galE1 |
| eggNOG description | UDP-glucose 4-epimerase |
| Orthologous group | COG0451 |
| EC number |
EC 4.2.1.46, EC 5.1.3.2
|
| KEGG orthology |
K01710, K01784
|
| KEGG pathways |
map00052, map00520, map00521, map00523, map00525, map01055, map01100, map01130
|
| KEGG modules |
M00361, M00362, M00632, M00793
|
| Gene Ontology (8) |
GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040007, GO:0044464, GO:0071944
|
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 | 0.119 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 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 |
|---|---|---|---|---|
RmlD_sub_bind | PF04321.24 | 1.1e-15 | 1–156 | RmlD substrate binding domain |
Epimerase | PF01370.28 | 6.6e-60 | 3–241 | NAD dependent epimerase/dehydratase family |
GDP_Man_Dehyd | PF16363.12 | 5.6e-57 | 4–304 | GDP-mannose 4,6 dehydratase |
3Beta_HSD | PF01073.26 | 1.2e-16 | 4–226 | 3-beta hydroxysteroid dehydrogenase/isomerase family |
Polysacc_synt_2 | PF02719.22 | 4.7e-10 | 4–121 | Polysaccharide biosynthesis protein |
NAD_binding_10 | PF13460.13 | 2.3e-08 | 7–132 | NAD(P)H-binding |
NAD_binding_4 | PF07993.19 | 1.8e-05 | 72–224 | Male sterility protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3635 (transmembrane protein), high confidence from genomic context alone (score 795 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0322 udgA |
UDP-glucose 6-dehydrogenase UdgA | 969 | 967 | coexpression:412 database:900 |
Rv3468c |
dTDP-glucose 4,6-dehydratase | 991 | 935 | database:900 textmining:870 |
Rv3809c glf |
UDP-galactopyranose mutase | 969 | 927 | database:900 textmining:600 |
Rv0993 galU |
UTP--glucose-1-phosphate uridylyltransferase | 934 | 922 | database:900 |
Rv0501 galE2 |
UDP-glucose 4-epimerase GalE | 920 | 921 | database:900 |
Rv0618 galTa |
Rv0618, (MTCY19H5.03c), len: 231 aa (probable partial CDS). Probable galTa, first part of galactose-1-phosphate uridylyltransferase, highly | 907 | 903 | database:900 |
Rv0705 rpsS |
30S ribosomal protein S19 | 823 | 824 | experimental:463 database:574 |
Rv0682 rpsL |
30S ribosomal protein S12 | 818 | 810 | experimental:463 database:573 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 808 | 803 | experimental:463 database:578 |
Rv0707 rpsC |
30S ribosomal protein S3 | 808 | 801 | experimental:463 database:578 |
Rv0721 rpsE |
30S ribosomal protein S5 | 806 | 799 | experimental:463 database:575 |
Rv0718 rpsH |
30S ribosomal protein S8 | 802 | 795 | experimental:463 database:578 |
Rv3635 |
transmembrane protein | 796 | 795 ctx | neighborhood:790 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 798 | 794 | experimental:463 database:557 |
Rv0717 rpsN1 |
30S ribosomal protein S14 | 793 | 793 | experimental:436 database:548 |
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
- Legacy H37Rv annotation: UDP-glucose 4-epimerase
- MTBC0 PGAP product: UDP-glucose 4-epimerase
- Pfam (hmmscan --cut_ga): RmlD_sub_bind PF04321.24 (E=1e-15), Epimerase PF01370.28 (E=7e-60), GDP_Man_Dehyd PF16363.12 (E=6e-57), 3Beta_HSD PF01073.26 (E=1e-16), Polysacc_synt_2 PF02719.22 (E=5e-10), NAD_binding_10 PF13460.13 (E=2e-08), NAD_binding_4 PF07993.19 (E=2e-05)
- (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 NP_215015.2)
- Domains: Pfam-A via hmmscan --cut_ga — RmlD_sub_bind (PF04321.24), Epimerase (PF01370.28), GDP_Man_Dehyd (PF16363.12), 3Beta_HSD (PF01073.26), Polysacc_synt_2 (PF02719.22), NAD_binding_10 (PF13460.13), NAD_binding_4 (PF07993.19)
- 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 P9WN67 (SwissProt, reviewed; 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 —
104 functional partner(s); context anchor
Rv3635 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003851|Rv3634c|galE1 MRALVTGAAGFIGSTLVDRLLADGHSVVGLDNFATGRATNLEHLADNSAHVFVEADIVTADLHAILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGVRKIVHTSSGGSIYGTPPEYPTPETAPTDPASPYAAGKVAGEIYLNTFRHLYGLDCSHIAPANVYGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRVSADVGGGLRFNIGTGKETSDRQLHSAVAAAVGGPDDPEFHPPRLGDLKRSCLDIGLAERVLGWRPQIELADGVRRTVEYFRHKHTD