glpD2 Resolved · high auto-curated
H37Rv Rv3302c · MTBC0 mtbc0_003510 ·
585 aa · 3709765–3711522 (-) ·
RefSeq NP_217819.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycerol-3-phosphate dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | glycerol-3-phosphate dehydrogenase/oxidase |
| Revised (this work) | Glycerol-3-phosphate dehydrogenase/oxidase. Pfam: FAD_binding_3 (PF01494.26), DAO (PF01266.31), FAD_oxidored (PF12831.14), FAD_binding_2 (PF00890.31), DAO_C (PF16901.11). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN79
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glycerol-3-phosphate dehydrogenase 2 |
| EC (curated) |
EC 1.1.5.3
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | glpD |
| eggNOG description | Belongs to the FAD-dependent glycerol-3-phosphate dehydrogenase family |
| Orthologous group | COG0578 |
| EC number |
EC 1.1.5.3
|
| KEGG orthology |
K00111
|
| KEGG pathways |
map00564, map01110
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.712 · 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 |
|---|---|---|---|---|
FAD_binding_3 | PF01494.26 | 2.5e-06 | 36–304 | FAD binding domain |
DAO | PF01266.31 | 8.2e-54 | 37–390 | FAD dependent oxidoreductase |
FAD_oxidored | PF12831.14 | 5.6e-07 | 37–98 | FAD dependent oxidoreductase |
FAD_binding_2 | PF00890.31 | 6.3e-06 | 37–78 | FAD binding domain |
DAO_C | PF16901.11 | 1.5e-31 | 413–536 | C-terminal domain of alpha-glycerophosphate oxidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glpK (glycerol kinase), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3696c glpK |
glycerol kinase | 998 | 994 ctx | fusion:796 cooccurence:741 coexpression:726 database:500 textmining:691 |
Rv3303c lpdA |
NAD(P)H quinone reductase LpdA | 983 | 971 ctx | neighborhood:869 coexpression:791 textmining:447 |
Rv2249c glpD1 |
glycerol-3-phosphate dehydrogenase | 935 | 921 | database:900 |
Rv2982c gpdA2 |
glycerol-3-phosphate dehydrogenase | 961 | 916 | database:900 textmining:557 |
Rv0564c gpdA1 |
glycerol-3-phosphate dehydrogenase | 945 | 916 | database:900 |
Rv2482c plsB2 |
glycerol-3-phosphate acyltransferase | 930 | 903 | database:900 |
Rv1551 plsB1 |
acyltransferase PlsB | 915 | 902 | database:900 |
Rv2182c |
1-acylglycerol-3-phosphate O-acyltransferase | 818 | 809 | database:800 |
Rv2252 dagK |
diacylglycerol kinase | 819 | 808 | database:800 |
Rv3300c hyp |
hypothetical protein | 895 | 779 ctx | neighborhood:766 textmining:547 |
Rv3304 hyp |
hypothetical protein | 909 | 753 ctx | neighborhood:751 textmining:650 |
Rv3842c glpQ1 |
glycerophosphoryl diester phosphodiesterase | 750 | 735 | database:500 |
Rv0317c glpQ2 |
glycerophosphoryl diester phosphodiesterase GlpQ | 697 | 678 | database:500 |
Rv2277c |
glycerolphosphodiesterase | 696 | 677 | database:500 |
Rv3299c atsB |
arylsulfatase AtsB | 611 | 611 ctx | neighborhood:541 |
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: glycerol-3-phosphate dehydrogenase/oxidase
- Pfam (hmmscan --cut_ga): FAD_binding_3 PF01494.26 (E=3e-06), DAO PF01266.31 (E=8e-54), FAD_oxidored PF12831.14 (E=6e-07), FAD_binding_2 PF00890.31 (E=6e-06), DAO_C PF16901.11 (E=1e-31)
- (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_217819.1)
- Domains: Pfam-A via hmmscan --cut_ga — FAD_binding_3 (PF01494.26), DAO (PF01266.31), FAD_oxidored (PF12831.14), FAD_binding_2 (PF00890.31), DAO_C (PF16901.11)
- 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
COG0578 - Curated reference: UniProt P9WN79 (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
glpK - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003510|Rv3302c|glpD2 MSNPIQAPDGGQGWPAAALGPAQRAVAWKRLGTEQFDVVVIGGGVVGSGCALDAATRGLKVALVEARDLASGTSSRSSKMFHGGLRYLEQLEFGLVREALYERELSLTTLAPHLVKPLPFLFPLTKRWWERPYIAAGIFLYDRLGGAKSVPAQRHFTRAGALRLSPGLKRSSLIGGIRYYDTVVDDARHTMTVARTAAHYGAVVRCSTQVVALLREGDRVIGVGVRDSENGAVAEVRGHVVVNATGVWTDEIQALSKQRGRFQVRASKGVHVVVPRDRIVSDVAMILRTEKSVMFVIPWGSHWIIGTTDTDWNLDLAHPAATKADIDYILGTVNAVLATPLTHADIDGVYAGLRPLLAGESDDTSKLSREHAVAVPAAGLVAIAGGKYTTYRVMAADAIDAAVQFIPARVAPSITEKVSLLGADGYFALVNQAEHVGALQGLHPYRVRHLLDRYGSLISDVLAMAASDPSLLSPITEAPGYLKVEAAYAAAAEGALHLEDILARRMRISIEYPHRGVDCAREVAEVVAPVLGWTAADIDREVANYMARVEAEVLSQAQPDDVSADMLRASAPEARAEILEPVPLD