fgd1 Resolved · high auto-curated
H37Rv Rv0407 · MTBC0 mtbc0_000427 ·
336 aa · 494148–495158 (+) ·
RefSeq NP_214921.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | F420-dependent glucose-6-phosphate dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | glucose-6-phosphate dehydrogenase (coenzyme-F420) |
| Revised (this work) | Glucose-6-phosphate dehydrogenase (coenzyme-F420). Pfam: Bac_luciferase (PF00296.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNE1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | F420-dependent glucose-6-phosphate dehydrogenase |
| EC (curated) |
EC 1.1.98.2
|
| Curated function | Catalyzes the coenzyme F420-dependent oxidation of glucose 6-phosphate to 6-phosphogluconolactone. Appears to have a role in resistance to oxidative stress, via its consumption of G6P that serves as a source of reducing power to combat oxidative stress in mycobacteria. More precisely, is likely involved in a F420-dependent anti-oxidant mechanism that protects M.tuberculosis against oxidative stress and bactericidal agents..; FUNCTION: Is essential for the bioreductive activation of the bicyclic 4-nitroimidazole prodrug PA-824 (a nitroimidazo-oxazine) developed for anti-tuberculosis therapy aga. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | fgd |
| eggNOG description | Catalyzes the coenzyme F420-dependent oxidation of glucose 6-phosphate (G6P) to 6-phosphogluconolactone. Appears to have a role in resistance to oxidative stress, via its consumption of G6P that serves as a source of reducing power to combat oxidative stress in mycobacteria |
| Orthologous group | COG2141 |
| EC number |
EC 1.1.98.2
|
| KEGG orthology |
K15510
|
| Gene Ontology (44) |
GO:0003674, GO:0003824, GO:0005488, GO:0005515, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150 +32 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 | 0.656 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 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 |
|---|---|---|---|---|
Bac_luciferase | PF00296.27 | 4.6e-67 | 11–306 | Luciferase-like monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pta (phosphate acetyltransferase), high confidence from genomic context alone (score 889 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0408 pta |
phosphate acetyltransferase | 903 | 889 ctx | neighborhood:882 |
Rv0409 ackA |
acetate kinase | 889 | 889 ctx | neighborhood:882 |
Rv0406c |
beta lactamase-like protein | 787 | 787 ctx | neighborhood:784 |
Rv0044c |
oxidoreductase | 804 | 777 ctx | cooccurence:771 |
Rv3261 fbiA |
2-phospho-L-lactate transferase | 990 | 747 ctx | cooccurence:728 textmining:965 |
Rv3547 ddn |
deazaflavin-dependent nitroreductase | 983 | 745 ctx | cooccurence:745 textmining:936 |
Rv3178 |
nitroreductase | 953 | 745 ctx | cooccurence:745 textmining:824 |
Rv1558 hyp |
hypothetical protein | 949 | 745 ctx | cooccurence:745 textmining:812 |
Rv1261c hyp |
hypothetical protein | 845 | 741 ctx | cooccurence:739 textmining:430 |
Rv2983 cofC |
2-phospho-L-lactate guanylyltransferase | 970 | 689 ctx | cooccurence:677 textmining:909 |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 988 | 685 ctx | cooccurence:641 textmining:965 |
Rv2161c hyp |
hypothetical protein | 645 | 645 ctx | cooccurence:641 |
Rv3093c |
oxidoreductase | 604 | 604 ctx | cooccurence:602 |
Rv3079c hyp |
hypothetical protein | 594 | 595 ctx | cooccurence:585 |
Rv3072c hyp |
hypothetical protein | 591 | 568 ctx | cooccurence:567 |
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: F420-dependent glucose-6-phosphate dehydrogenase
- MTBC0 PGAP product: glucose-6-phosphate dehydrogenase (coenzyme-F420)
- Pfam (hmmscan --cut_ga): Bac_luciferase PF00296.27 (E=5e-67)
- (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_214921.1)
- Domains: Pfam-A via hmmscan --cut_ga — Bac_luciferase (PF00296.27)
- 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
COG2141 - Curated reference: UniProt P9WNE1 (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 —
34 functional partner(s); context anchor
pta - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000427|Rv0407|fgd1 MAELKLGYKASAEQFAPRELVELAVAAEAHGMDSATVSDHFQPWRHQGGHAPFSLSWMTAVGERTNRLLLGTSVLTPTFRYNPAVIAQAFATMGCLYPNRVFLGVGTGEALNEIATGYEGAWPEFKERFARLRESVGLMRQLWSGDRVDFDGDYYRLKGASIYDVPDGGVPVYIAAGGPAVAKYAGRAGDGFICTSGKGEELYTEKLMPAVREGAAAADRSVDGIDKMIEIKISYDPDPELALNNTRFWAPLSLTAEQKHSIDDPIEMEKAADALPIEQIAKRWIVASDPDEAVEKVGQYVTWGLNHLVFHAPGHDQRRFLELFQSDLAPRLRRLG