gpm2 Resolved · high auto-curated
H37Rv Rv3214 · MTBC0 - ·
203 aa · 3591646–3592257 (+) ·
RefSeq YP_177944.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphoglycerate mutase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Phosphoglycerate mutase. 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.
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 |
Q6MWZ7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Acid phosphatase |
| EC (curated) |
EC 3.1.3.11, EC 3.1.3.2
|
| Curated function | Phosphatase with a broad specificity. Can dephosphorylate a variety of substrates including phosphorylated sugars like fructose-6-phosphate (F6P). Is able to function in vivo as a fructose-1,6-bisphosphatase (FBPase) and to maintain gluconeogenesis when the classical FBPase GlpX is absent. Shows negligible phosphoglycerate mutase activity. Has no phosphatase activity against 3-phosphoglycerate, 2,3-bisphosphoglycerate, or hydrophobic substrates such as alpha-napthyl phosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | gpm2 |
| eggNOG description | phosphoglycerate mutase |
| Orthologous group | COG0406 |
| EC number |
EC 3.1.3.73
|
| KEGG orthology |
K02226
|
| KEGG pathways |
map00860, map01100
|
| KEGG modules |
M00122
|
| Gene Ontology (19) |
GO:0003674, GO:0003824, GO:0003993, GO:0005488, GO:0005515, GO:0006793, GO:0006796, GO:0008150, GO:0008152, GO:0009987, GO:0016311, GO:0016787 +7 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 | 0.351 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
His_Phos_1 | PF00300.28 | 7.6e-45 | 8–191 | Histidine phosphatase superfamily (branch 1) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: thyA (thymidylate synthase ThyA), high confidence from genomic context alone (score 895 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2764c thyA |
thymidylate synthase ThyA | 895 | 895 ctx | fusion:890 |
Rv3215 entC |
isochorismate synthase | 888 | 882 ctx | neighborhood:881 |
Rv3213c |
SOJ/ParA-like protein | 748 | 748 ctx | neighborhood:744 |
Rv3010c pfkA |
6-phosphofructokinase | 636 | 614 | database:500 |
Rv0946c pgi |
glucose-6-phosphate isomerase | 627 | 571 | database:500 |
Rv0363c fba |
fructose-bisphosphate aldolase | 623 | 569 | database:500 |
Rv1695 ppnK |
inorganic polyphosphate/ATP-NAD kinase | 528 | 529 | database:500 |
Rv2066 cobIJ |
bifunctional S-adenosyl-L-methionine-precorrin-2 methyl transferase/precorrin-3 methylase | 541 | 521 | coexpression:460 |
Rv2029c pfkB |
6-phosphofructokinase PfkB | 536 | 512 | database:500 |
Rv3199c nudC |
NADH pyrophosphatase | 510 | 510 | database:500 |
Rv2135c hyp |
hypothetical protein | 926 | 457 ctx | cooccurence:452 textmining:870 |
Rv0255c cobQ1 |
cobyric acid synthase | 457 | 432 | coexpression:413 |
Rv3837c |
phosphoglycerate mutase | 693 | 361 | textmining:540 |
Rv2419c gpgP |
glucosyl-3-phosphoglycerate phosphatase | 518 | 295 | |
Rv0489 gpm1 |
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | 525 | 264 |
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): phosphoglycerate mutase
- Pfam (hmmscan --cut_ga): His_Phos_1 PF00300.28 (E=8e-45)
- (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_177944.1)
- 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 Q6MWZ7 (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 —
22 functional partner(s); context anchor
thyA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3214|gpm2 MGVRNHRLLLLRHGETAWSTLGRHTGGTEVELTDTGRTQAELAGQLLGELELDDPIVICSPRRRTLDTAKLAGLTVNEVTGLLAEWDYGSYEGLTTPQIRESEPDWLVWTHGCPAGESVAQVNDRADSAVALALEHMSSRDVLFVSHGHFSRAVITRWVQLPLAEGSRFAMPTASIGICGFEHGVRQLAVLGLTGHPQPIAAG