glpX Resolved · high auto-curated
H37Rv Rv1099c · MTBC0 mtbc0_001182 ·
362 aa · 1236036–1237124 (-) ·
RefSeq NP_215615.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | fructose 1,6-bisphosphatase |
|---|---|
| MTBC0 PGAP re-annotation | class II fructose-bisphosphatase |
| Revised (this work) | Class II fructose-bisphosphatase. Pfam: FBPase_glpX (PF03320.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN21
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Fructose-1,6-bisphosphatase class 2 |
| EC (curated) |
EC 3.1.3.11
|
| Curated function | Catalyzes the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate. Seems to be the major FBPase of M.tuberculosis and to play a key role in gluconeogenesis for conversion of lipid carbon into cell wall glycans. Does not display activity against inositol 1-phosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | glpX |
| eggNOG description | fructose-1,6-bisphosphatase |
| Orthologous group | COG1494 |
| EC number |
EC 3.1.3.11
|
| KEGG orthology |
K02446
|
| KEGG pathways |
map00010, map00030, map00051, map00680, map00710, map01100, map01110, map01120, map01130, map01200
|
| KEGG modules |
M00003, M00165, M00167
|
| Gene Ontology (48) |
GO:0000287, GO:0003674, GO:0003824, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005975, GO:0005996, GO:0006006 +36 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 | 0.114 · 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 |
|---|---|---|---|---|
FBPase_glpX | PF03320.19 | 4.5e-143 | 31–338 | Bacterial fructose-1,6-bisphosphatase, glpX-encoded |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tkt (transketolase), high confidence from genomic context alone (score 945 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1449c tkt |
transketolase | 974 | 945 ctx | fusion:418 database:900 textmining:562 |
Rv0363c fba |
fructose-bisphosphate aldolase | 947 | 915 | database:900 textmining:414 |
Rv1448c tal |
transaldolase | 950 | 908 | database:900 textmining:484 |
Rv3010c pfkA |
6-phosphofructokinase | 960 | 903 | database:900 textmining:607 |
Rv0946c pgi |
glucose-6-phosphate isomerase | 954 | 903 | database:900 textmining:549 |
Rv3255c manA |
mannose-6-phosphate isomerase | 904 | 901 | database:900 |
Rv2029c pfkB |
6-phosphofructokinase PfkB | 906 | 900 | database:900 |
Rv1098c fum |
fumarate hydratase | 894 | 856 ctx | neighborhood:839 |
Rv1097c hyp |
hypothetical protein | 821 | 821 ctx | neighborhood:816 |
Rv1100 hyp |
hypothetical protein | 874 | 655 ctx | neighborhood:655 textmining:652 |
Rv2299c htpG |
chaperone protein HtpG | 452 | 452 | experimental:444 |
Rv2773c dapB |
4-hydroxy-tetrahydrodipicolinate reductase | 570 | 416 | coexpression:416 |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 574 | 277 | textmining:436 |
Rv1659 argH |
argininosuccinate lyase | 419 | 275 | |
Rv1240 mdh |
malate dehydrogenase | 466 | 188 |
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: fructose 1,6-bisphosphatase
- MTBC0 PGAP product: class II fructose-bisphosphatase
- Pfam (hmmscan --cut_ga): FBPase_glpX PF03320.19 (E=5e-143)
- (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_215615.3)
- Domains: Pfam-A via hmmscan --cut_ga — FBPase_glpX (PF03320.19)
- 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
COG1494 - Curated reference: UniProt P9WN21 (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 —
32 functional partner(s); context anchor
tkt - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001182|Rv1099c|glpX MTAEGSGSSTAAVASHDPSHTRPSRREAPDRNLAMELVRVTEAGAMAAGRWVGRGDKEGGDGAAVDAMRELVNSVSMRGVVVIGEGEKDHAPMLYNGEEVGNGDGPECDFAVDPIDGTTLMSKGMTNAISVLAVADRGTMFDPSAVFYMNKIAVGPDAAHVLDITAPISENIRAVAKVKDLSVRDMTVCILDRPRHAQLIHDVRATGARIRLITDGDVAGAISACRPHSGTDLLAGIGGTPEGIIAAAAIRCMGGAIQAQLAPRDDAERRKALEAGYDLNQVLTTEDLVSGENVFFCATGVTDGDLLKGVRYYPGGCTTHSIVMRSKSGTVRMIEAYHRLSKLNEYSAIDFTGDSSAVYPLP