gpm1 Resolved · high auto-curated
H37Rv Rv0489 · MTBC0 - ·
249 aa · 578426–579175 (+) ·
RefSeq YP_177731.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 2,3-bisphosphoglycerate-dependent 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 |
P9WIC9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase |
| EC (curated) |
EC 5.4.2.11
|
| Curated function | Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | gpmA |
| eggNOG description | Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate |
| Orthologous group | COG0588 |
| EC number |
EC 5.4.2.11
|
| KEGG orthology |
K01834
|
| KEGG pathways |
map00010, map00260, map00680, map01100, map01110, map01120, map01130, map01200, map01230, map04922, map05230
|
| KEGG modules |
M00001, M00002, M00003
|
| Gene Ontology (173) |
GO:0003674, GO:0003824, GO:0004619, GO:0005488, GO:0005515, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0005975 +161 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 | 1.5e-30 | 7–206 | Histidine phosphatase superfamily (branch 1) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: senX3 (two component sensor histidine kinase SenX3), high confidence from genomic context alone (score 747 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1437 pgk |
phosphoglycerate kinase | 990 | 975 | coexpression:727 database:900 textmining:648 |
Rv1023 eno |
enolase | 987 | 971 | coexpression:665 database:900 textmining:587 |
Rv0728c serA2 |
D-3-phosphoglycerate dehydrogenase SerA | 944 | 939 | database:900 |
Rv0363c fba |
fructose-bisphosphate aldolase | 953 | 922 | coexpression:624 database:800 textmining:429 |
Rv0946c pgi |
glucose-6-phosphate isomerase | 959 | 920 | coexpression:614 database:800 textmining:511 |
Rv2996c serA1 |
D-3-phosphoglycerate dehydrogenase | 924 | 916 | database:900 |
Rv2205c hyp |
hypothetical protein | 905 | 900 | database:900 |
Rv1448c tal |
transaldolase | 885 | 839 | database:800 |
Rv1449c tkt |
transketolase | 870 | 838 | database:800 |
Rv1121 zwf1 |
glucose-6-phosphate 1-dehydrogenase | 851 | 832 | database:800 |
Rv1447c zwf2 |
glucose-6-phosphate 1-dehydrogenase | 850 | 831 | database:800 |
Rv1438 tpi |
triosephosphate isomerase | 948 | 824 | coexpression:787 textmining:720 |
Rv0478 deoC |
2-deoxyribose-5-phosphate aldolase | 807 | 802 | database:800 |
Rv0490 senX3 |
two component sensor histidine kinase SenX3 | 773 | 747 ctx | neighborhood:743 |
Rv0491 regX3 |
two component sensory transduction protein RegX | 696 | 673 ctx | neighborhood:660 |
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): 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
- Pfam (hmmscan --cut_ga): His_Phos_1 PF00300.28 (E=1e-30)
- (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_177731.1)
- 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
COG0588 - Curated reference: UniProt P9WIC9 (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 —
78 functional partner(s); context anchor
senX3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0489|gpm1 MANTGSLVLLRHGESDWNALNLFTGWVDVGLTDKGQAEAVRSGELIAEHDLLPDVLYTSLLRRAITTAHLALDSADRLWIPVRRSWRLNERHYGALQGLDKAETKARYGEEQFMAWRRSYDTPPPPIERGSQFSQDADPRYADIGGGPLTECLADVVARFLPYFTDVIVGDLRVGKTVLIVAHGNSLRALVKHLDQMSDDEIVGLNIPTGIPLRYDLDSAMRPLVRGGTYLDPEAAAAGAAAVAGQGRG