gpdA1 Resolved · high auto-curated
H37Rv Rv0564c · MTBC0 mtbc0_000593 ·
341 aa · 658475–659500 (-) ·
RefSeq NP_215078.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycerol-3-phosphate dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | NAD(P)H-dependent glycerol-3-phosphate dehydrogenase |
| Revised (this work) | NAD(P)H-dependent glycerol-3-phosphate dehydrogenase. Pfam: NAD_Gly3P_dh_N (PF01210.30), F420_oxidored (PF03807.24), NAD_Gly3P_dh_C (PF07479.20), GPD_NAD_C_bact (PF20618.4). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN75
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glycerol-3-phosphate dehydrogenase [NAD(P)+] 1 |
| EC (curated) |
EC 1.1.1.94
|
| Curated function | Catalyzes the reduction of the glycolytic intermediate dihydroxyacetone phosphate (DHAP) to sn-glycerol 3-phosphate (G3P), the key precursor for phospholipid synthesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | gpsA |
| eggNOG description | Glycerol-3-phosphate dehydrogenase |
| Orthologous group | COG0240 |
| EC number |
EC 1.1.1.94
|
| KEGG orthology |
K00057
|
| KEGG pathways |
map00564, map01110
|
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 | 1.029 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
NAD_Gly3P_dh_N | PF01210.30 | 1.5e-48 | 9–164 | NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus |
F420_oxidored | PF03807.24 | 2.6e-04 | 9–111 | NADP oxidoreductase coenzyme F420-dependent |
NAD_Gly3P_dh_C | PF07479.20 | 7.0e-50 | 184–323 | NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus |
GPD_NAD_C_bact | PF20618.4 | 4.7e-20 | 244–310 | Bacterial GPD, NAD-dependent C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0565c (monooxygenase), high confidence from genomic context alone (score 807 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2249c glpD1 |
glycerol-3-phosphate dehydrogenase | 960 | 916 | database:900 textmining:554 |
Rv3302c glpD2 |
glycerol-3-phosphate dehydrogenase | 945 | 916 | database:900 |
Rv2982c gpdA2 |
glycerol-3-phosphate dehydrogenase | 922 | 913 | database:900 |
Rv1551 plsB1 |
acyltransferase PlsB | 940 | 904 | database:900 textmining:409 |
Rv2482c plsB2 |
glycerol-3-phosphate acyltransferase | 927 | 904 | database:900 |
Rv2182c |
1-acylglycerol-3-phosphate O-acyltransferase | 878 | 852 | database:800 |
Rv0565c |
monooxygenase | 812 | 807 ctx | neighborhood:802 |
Rv2252 dagK |
diacylglycerol kinase | 808 | 802 | database:800 |
Rv1713 engA |
GTPase Der | 812 | 788 | coexpression:704 |
Rv0566c hyp |
hypothetical protein | 735 | 735 ctx | neighborhood:734 |
Rv1614 lgt |
prolipoprotein diacylglyceryl transferase | 541 | 524 | coexpression:497 |
Rv1329c dinG |
ATP-dependent helicase DinG | 518 | 519 | coexpression:502 |
Rv2043c pncA |
pyrazinamidase/nicotinamidase PncA | 522 | 504 | coexpression:411 |
Rv3068c pgmA |
phosphoglucomutase PgmA | 507 | 476 | coexpression:412 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 467 | 468 |
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: glycerol-3-phosphate dehydrogenase
- MTBC0 PGAP product: NAD(P)H-dependent glycerol-3-phosphate dehydrogenase
- Pfam (hmmscan --cut_ga): NAD_Gly3P_dh_N PF01210.30 (E=1e-48), F420_oxidored PF03807.24 (E=3e-04), NAD_Gly3P_dh_C PF07479.20 (E=7e-50), GPD_NAD_C_bact PF20618.4 (E=5e-20)
- (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_215078.1)
- Domains: Pfam-A via hmmscan --cut_ga — NAD_Gly3P_dh_N (PF01210.30), F420_oxidored (PF03807.24), NAD_Gly3P_dh_C (PF07479.20), GPD_NAD_C_bact (PF20618.4)
- 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
COG0240 - Curated reference: UniProt P9WN75 (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 —
46 functional partner(s); context anchor
Rv0565c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000593|Rv0564c|gpdA1 MAANKREPKVVVLGGGSWGTTVASICARRGPTLQWVRSAVTAQDINDNHRNSRYLGNDVVLSDTLRATTDFTEAANCADVVVMGVPSHGFRGVLVELSKELRPWVPVVSLVKGLEQGTNMRMSQIIEEVLPGHPAGILAGPNIAREVAEGYAAAAVLAMPDQHLATRLSAMFRTRRFRVYTTDDVVGVETAGALKNVFAIAVGMGYSLGIGENTRALVIARALREMTKLGVAMGGKSETFPGLAGLGDLIVTCTSQRSRNRHVGEQLGAGKPIDEIIASMSQVAEGVKAAGVVMEFANEFGLNMPIAREVDAVINHGSTVEQAYRGLIAEVPGHEVHGSGF