glpQ1 Resolved · high auto-curated
H37Rv Rv3842c · MTBC0 mtbc0_004072 ·
274 aa · 4338849–4339673 (-) ·
RefSeq NP_218359.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycerophosphoryl diester phosphodiesterase |
|---|---|
| MTBC0 PGAP re-annotation | glycerophosphodiester phosphodiesterase |
| Revised (this work) | Glycerophosphodiester phosphodiesterase. Pfam: GDPD (PF03009.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMU3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable glycerophosphodiester phosphodiesterase 1 |
| EC (curated) |
EC 3.1.4.46
|
| Curated function | Glycerophosphodiester phosphodiesterase hydrolyzes glycerophosphodiesters into glycerol-3-phosphate (G3P) and the corresponding alcohol. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | glpQ |
| eggNOG description | glycerophosphoryl diester phosphodiesterase |
| Orthologous group | COG0584 |
| EC number |
EC 3.1.4.46
|
| KEGG orthology |
K01126
|
| KEGG pathways |
map00564
|
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 | 0.729 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 7 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (191) · 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 |
|---|---|---|---|---|
GDPD | PF03009.24 | 4.4e-61 | 17–258 | Glycerophosphoryl diester phosphodiesterase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2277c (glycerolphosphodiesterase), high confidence from genomic context alone (score 953 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2277c |
glycerolphosphodiesterase | 952 | 953 ctx | cooccurence:546 database:900 |
Rv0317c glpQ2 |
glycerophosphoryl diester phosphodiesterase GlpQ | 952 | 952 ctx | cooccurence:543 database:900 |
Rv3843c |
transmembrane protein | 889 | 889 ctx | neighborhood:882 |
Rv2249c glpD1 |
glycerol-3-phosphate dehydrogenase | 759 | 744 | database:500 |
Rv3302c glpD2 |
glycerol-3-phosphate dehydrogenase | 750 | 735 | database:500 |
Rv3696c glpK |
glycerol kinase | 668 | 551 | coexpression:445 |
Rv0178 |
Mce associated membrane protein | 427 | 407 | database:401 |
Rv0200 |
transmembrane protein | 425 | 405 | database:401 |
Rv3492c |
Mce associated protein | 424 | 403 | database:401 |
Rv2390c hyp |
hypothetical protein | 424 | 403 | database:401 |
Rv1362c |
membrane protein | 424 | 403 | database:401 |
Rv1363c |
membrane protein | 424 | 403 | database:401 |
Rv0199 |
membrane protein | 424 | 403 | database:401 |
Rv1973 |
Mce associated membrane protein | 422 | 401 | database:401 |
Rv0177 |
Mce associated protein | 422 | 401 | database:401 |
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: glycerophosphoryl diester phosphodiesterase
- MTBC0 PGAP product: glycerophosphodiester phosphodiesterase
- Pfam (hmmscan --cut_ga): GDPD PF03009.24 (E=4e-61)
- (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_218359.1)
- Domains: Pfam-A via hmmscan --cut_ga — GDPD (PF03009.24)
- 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
COG0584 - Curated reference: UniProt P9WMU3 (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
Rv2277c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004072|Rv3842c|glpQ1 MTWADEVLAGHPFVVAHRGASAARPEHTLAAYDLALKEGADGVECDVRLTRDGHLVCVHDRRLDRTSTGAGLVSTMTLAQLRELEYGAWHDSWRPDGSHGDTSLLTLDALVSLVLDWHRPVKIFVETKHPVRYGSLVENKLLALLHRFGIAAPASADRSRAVVMSFSAAAVWRIRRAAPLLPTVLLGKTPRYLTSSAATAVGATAVGPSLPALKEYPQLVDRSAAQGRAVYCWNVDEYEDIDFCREVGVAWIGTHHPGRTKAWLEDGRANGTTR