gnd1 Resolved · high auto-curated
H37Rv Rv1844c · MTBC0 - ·
485 aa · 2093731–2095188 (-) ·
RefSeq YP_177848.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 6-phosphogluconate dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 6-phosphogluconate dehydrogenase. Pfam: NAD_binding_2 (PF03446.22), 6PGD (PF00393.25). |
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 |
Q79FJ2
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 6-phosphogluconate dehydrogenase, decarboxylating |
| EC (curated) |
EC 1.1.1.44
|
| Curated function | Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | gnd |
| eggNOG description | Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH |
| Orthologous group | COG0362 |
| EC number |
EC 1.1.1.343, EC 1.1.1.44
|
| KEGG orthology |
K00033
|
| KEGG pathways |
map00030, map00480, map01100, map01110, map01120, map01130, map01200
|
| KEGG modules |
M00004, M00006
|
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) pseudogene candidate
| pN/pS | 0.605 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 9 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 10.18% of strains (14784) · clonal |
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 |
|---|---|---|---|---|
NAD_binding_2 | PF03446.22 | 2.0e-46 | 12–183 | NAD binding domain of 6-phosphogluconate dehydrogenase |
6PGD | PF00393.25 | 3.2e-125 | 188–476 | 6-phosphogluconate dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: zwf1 (glucose-6-phosphate 1-dehydrogenase), high confidence from genomic context alone (score 928 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1445c devB |
6-phosphogluconolactonase | 958 | 942 | database:900 |
Rv1121 zwf1 |
glucose-6-phosphate 1-dehydrogenase | 973 | 928 ctx | cooccurence:733 coexpression:658 textmining:650 |
Rv1408 rpe |
ribulose-phosphate 3-epimerase | 951 | 928 | database:900 |
Rv1447c zwf2 |
glucose-6-phosphate 1-dehydrogenase | 962 | 927 ctx | cooccurence:723 coexpression:659 textmining:505 |
Rv1122 gnd2 |
6-phosphogluconate dehydrogenase (decarboxylating) | 916 | 916 | database:900 |
Rv2465c rpiB |
ribose-5-phosphate isomerase B | 919 | 908 | database:900 |
Rv1449c tkt |
transketolase | 897 | 855 | coexpression:780 |
Rv1845c blaR |
sensor-transducer protein BlaR | 848 | 848 ctx | neighborhood:841 |
Rv1843c guaB1 |
inosine-5'-monophosphate dehydrogenase | 847 | 846 ctx | neighborhood:836 |
Rv1448c tal |
transaldolase | 887 | 811 | coexpression:757 textmining:430 |
Rv1846c blaI |
transcriptional repressor BlaI | 760 | 761 ctx | neighborhood:748 |
Rv1841c hyp |
hypothetical protein | 733 | 734 ctx | neighborhood:719 |
Rv1842c hyp |
hypothetical protein | 731 | 732 ctx | neighborhood:719 |
Rv1837c glcB |
malate synthase | 668 | 620 ctx | neighborhood:610 |
Rv1836c hyp |
hypothetical protein | 570 | 570 ctx | neighborhood:563 |
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): 6-phosphogluconate dehydrogenase
- Pfam (hmmscan --cut_ga): NAD_binding_2 PF03446.22 (E=2e-46), 6PGD PF00393.25 (E=3e-125)
- (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_177848.1)
- Domains: Pfam-A via hmmscan --cut_ga — NAD_binding_2 (PF03446.22), 6PGD (PF00393.25)
- 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
COG0362 - Curated reference: UniProt Q79FJ2 (TrEMBL, unreviewed; 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 —
70 functional partner(s); context anchor
zwf1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1844c|gnd1 MSSSESPAGIAQIGVTGLAVMGSNIARNFARHGYTVAVHNRSVAKTDALLKEHSSDGKFVRSETIPEFLAALEKPRRVLIMVKAGEATDADAVINELADAMEPGDIIIDGGNALYTDTMRREKAMRERGLHFVGAGISGGEEGALNGPSIMPGGPAESYQSLGPLLEEISAHVDGVPCCTHIGPDGSGHFVKMVHNGIEYSDMQLIGEAYQLMRDGLGLTAPAIADVFTEWNNGDLDSYLVEITAEVLRQTDAKTGKPLVDVIVDRAEQKGTGRWTVKSALDLGVPVTGIAEAVFARALSGSVGQRSAASGLASGKLGEQPADPATFTEDVRQALYASKIVAYAQGFNQIQAGSAEFGWDITPGDLATIWRGGCIIRAKFLNHIKEAFDASPNLASLIVAPYFRGAVESAIDSWRRVVSTAAQLGIPTPGFSSALSYYDALRTARLPAALTQAQRDFFGAHTYGRIDEPGKFHTLWSSDRTEVPV