gpgP Resolved · high auto-curated
H37Rv Rv2419c · MTBC0 mtbc0_002575 ·
223 aa · 2741396–2742067 (-) ·
RefSeq NP_216935.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glucosyl-3-phosphoglycerate phosphatase |
|---|---|
| MTBC0 PGAP re-annotation | glucosyl-3-phosphoglycerate phosphatase |
| Revised (this work) | Glucosyl-3-phosphoglycerate phosphatase. Pfam: His_Phos_1 (PF00300.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIC7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glucosyl-3-phosphoglycerate phosphatase |
| EC (curated) |
EC 3.1.3.70, EC 3.1.3.85
|
| Curated function | Involved in the biosynthesis of mycobacterial methylglucose lipopolysaccharides (MGLPs). Catalyzes the dephosphorylation of glucosyl-3-phosphoglycerate (GPG) to glucosylglycerate (GG). GPG is the preferred substrate, but GpgP also exhibits low dephosphorylation activity on mannosyl-3-phosphoglycerate (MPG) and mannosylglucosyl-3-phosphoglycerate (MGPG) in vitro. Shows only trace of phosphoglycerate mutase (PGM) activity. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | gpmB |
| eggNOG description | Belongs to the phosphoglycerate mutase family |
| Orthologous group | COG0406 |
| EC number |
EC 3.1.3.85, EC 5.4.2.11
|
| KEGG orthology |
K01834, K22306
|
| KEGG pathways |
map00010, map00260, map00680, map01100, map01110, map01120, map01130, map01200, map01230, map04922, map05230
|
| KEGG modules |
M00001, M00002, M00003
|
| Gene Ontology (13) |
GO:0003674, GO:0003824, GO:0006793, GO:0006796, GO:0008150, GO:0008152, GO:0009987, GO:0016311, GO:0016787, GO:0016788, GO:0016791, GO:0042578 +1 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 | 0.347 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
His_Phos_1 | PF00300.28 | 6.3e-49 | 6–193 | Histidine phosphatase superfamily (branch 1) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nadD (nicotinate-nucleotide adenylyltransferase), high confidence from genomic context alone (score 910 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2420c rsfS hyp |
hypothetical protein | 914 | 914 ctx | neighborhood:882 |
Rv2421c nadD |
nicotinate-nucleotide adenylyltransferase | 910 | 910 ctx | neighborhood:882 |
Rv2418c octT hyp |
hypothetical protein | 982 | 901 ctx | neighborhood:882 textmining:828 |
Rv2417c |
DegV domain-containing protein | 976 | 825 ctx | neighborhood:786 textmining:870 |
Rv2135c hyp |
hypothetical protein | 944 | 592 ctx | cooccurence:591 textmining:870 |
Rv1208 gpgS |
glucosyl-3-phosphoglycerate synthase | 938 | 550 | database:500 textmining:870 |
Rv2066 cobIJ |
bifunctional S-adenosyl-L-methionine-precorrin-2 methyl transferase/precorrin-3 methylase | 546 | 526 | coexpression:465 |
Rv0255c cobQ1 |
cobyric acid synthase | 539 | 517 | coexpression:417 |
Rv2208 cobS |
adenosylcobinamide-GDP ribazoletransferase | 509 | 480 | |
Rv2422 hyp |
hypothetical protein | 477 | 477 ctx | neighborhood:477 |
Rv0254c cobU |
bifunctional cobinamide kinase/cobinamide phosphate guanylyltransferase | 483 | 453 | |
Rv2207 cobT |
nicotinate-nucleotide-dimethylbenzimidazol phosphoribosyltransferase | 472 | 440 | |
Rv2416c eis |
enhanced intracellular survival protein | 496 | 390 | |
Rv0525 hyp |
hypothetical protein | 609 | 335 | textmining:437 |
Rv2228c |
multifunctional RNASE H/alpha-ribazole phosphatase/acid phosphatase | 443 | 307 |
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 phosphatase
- MTBC0 PGAP product: glucosyl-3-phosphoglycerate phosphatase
- Pfam (hmmscan --cut_ga): His_Phos_1 PF00300.28 (E=6e-49)
- (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_216935.1)
- Domains: Pfam-A via hmmscan --cut_ga — His_Phos_1 (PF00300.28)
- 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
COG0406 - Curated reference: UniProt P9WIC7 (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 —
25 functional partner(s); context anchor
nadD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002575|Rv2419c|gpgP MRARRLVMLRHGQTDYNVGSRMQGQLDTELSELGRTQAVAAAEVLGKRQPLLIVSSDLRRAYDTAVKLGERTGLVVRVDTRLRETHLGDWQGLTHAQIDADAPGARLAWREDATWAPHGGESRVDVAARSRPLVAELVASEPEWGGADEPDRPVVLVAHGGLIAALSAALLKLPVANWPALGGMGNASWTQLSGHWAPGSDFESIRWRLDVWNASAQVSSDVL