gpgS Resolved · high auto-curated
H37Rv Rv1208 · MTBC0 mtbc0_001296 ·
324 aa · 1360586–1361560 (+) ·
RefSeq NP_215724.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glucosyl-3-phosphoglycerate synthase |
|---|---|
| MTBC0 PGAP re-annotation | glucosyl-3-phosphoglycerate synthase |
| Revised (this work) | Glucosyl-3-phosphoglycerate synthase. Pfam: Glycos_transf_2 (PF00535.33). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMW9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glucosyl-3-phosphoglycerate synthase |
| EC (curated) |
EC 2.4.1.266
|
| Curated function | Involved in the biosynthesis of 6-O-methylglucose lipopolysaccarides (MGLPs). Catalyzes the transfer of the glucose moiety from UDP-alpha-D-glucose (UDP-Glc) to the position 2 of 3-phospho-D-glycerate (3-PGA) to form glucosyl-3-phosphoglycerate (GPG). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | gpgS |
| eggNOG description | glucosyl-3-phosphoglycerate synthase |
| Orthologous group | COG0463 |
| EC number |
EC 2.4.1.266
|
| KEGG orthology |
K13693
|
| CAZy family |
GT81
|
| Gene Ontology (33) |
GO:0000287, GO:0003674, GO:0003824, GO:0005488, GO:0005515, GO:0006011, GO:0006139, GO:0006725, GO:0006793, GO:0006807, GO:0008150, GO:0008152 +21 more
|
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 | 0.062 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 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 |
|---|---|---|---|---|
Glycos_transf_2 | PF00535.33 | 1.1e-11 | 46–150 | Glycosyl transferase family 2 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: folP2 (dihydropteroate synthase), high confidence from genomic context alone (score 889 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1207 folP2 |
dihydropteroate synthase | 915 | 889 ctx | neighborhood:881 |
Rv1210 tagA |
DNA-3-methyladenine glycosylase I TagA | 826 | 827 ctx | neighborhood:825 |
Rv1209 hyp |
hypothetical protein | 825 | 826 ctx | neighborhood:825 |
Rv1206 fadD6 |
fatty-acid--CoA ligase FadD6 | 818 | 818 ctx | neighborhood:796 |
Rv1205 log hyp |
hypothetical protein | 845 | 785 ctx | neighborhood:748 |
Rv1211 hyp |
hypothetical protein | 552 | 551 ctx | neighborhood:549 |
Rv2419c gpgP |
glucosyl-3-phosphoglycerate phosphatase | 938 | 550 | database:500 textmining:870 |
Rv1204c hyp |
hypothetical protein | 430 | 430 | |
Rv1203c hyp |
hypothetical protein | 401 | 401 ctx | neighborhood:401 |
Rv3781 rfbE |
O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE | 411 | 379 | |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 401 | 374 | |
Rv1202 dapE |
succinyl-diaminopimelate desuccinylase DapE | 713 | 323 | textmining:595 |
Rv0236c aftD |
alpha-(1->3)-arabinofuranosyltransferase | 445 | 298 | |
Rv3032 |
glycogen synthase | 895 | 197 | textmining:875 |
Rv3030 |
S-adenosylmethionine-dependent methyltransferase | 919 | 185 | textmining:906 |
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: glucosyl-3-phosphoglycerate synthase
- MTBC0 PGAP product: glucosyl-3-phosphoglycerate synthase
- Pfam (hmmscan --cut_ga): Glycos_transf_2 PF00535.33 (E=1e-11)
- (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_215724.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glycos_transf_2 (PF00535.33)
- 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
COG0463 - Curated reference: UniProt P9WMW9 (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 —
31 functional partner(s); context anchor
folP2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001296|Rv1208|gpgS MTASELVAGDLAGGRAPGALPLDTTWHRPGWTIGELEAAKAGRTISVVLPALNEEATIESVIDSISPLVDGLVDELIVLDSGSTDDTEIRAIASGARVVSREQALPEVPVRPGKGEALWRSLAATSGDIVVFIDSDLINPHPLFVPWLVGPLLTGEGIQLVKSFYRRPLQVSDVTSGVCATGGGRVTELVARPLLAALRPELGCVLQPLSGEYAASRELLTSLPFAPGYGVEIGLLIDTFDRLGLDAIAQVNLGVRAHRNRPLDELGAMSRQVIATLLSRCGIPDSGVGLTQFLPGGPDDSDYTRHTWPVSLVDRPPMKVMRPR