glpQ2 Resolved · high auto-curated
H37Rv Rv0317c · MTBC0 mtbc0_000337 ·
256 aa · 388496–389266 (-) ·
RefSeq NP_214831.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycerophosphoryl diester phosphodiesterase GlpQ |
|---|---|
| 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 |
O07244
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable glycerophosphodiester phosphodiesterase 2 |
| 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 | glpQ2 |
| 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 | 0.715 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.73% of strains (1054) · 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 | 1.2e-52 | 14–241 | Glycerophosphoryl diester phosphodiesterase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glpQ1 (glycerophosphoryl diester phosphodiesterase), high confidence from genomic context alone (score 952 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3842c glpQ1 |
glycerophosphoryl diester phosphodiesterase | 952 | 952 ctx | cooccurence:543 database:900 |
Rv2277c |
glycerolphosphodiesterase | 943 | 943 ctx | cooccurence:455 database:900 |
Rv3302c glpD2 |
glycerol-3-phosphate dehydrogenase | 697 | 678 | database:500 |
Rv2249c glpD1 |
glycerol-3-phosphate dehydrogenase | 695 | 676 | database:500 |
Rv3696c glpK |
glycerol kinase | 672 | 539 | coexpression:444 |
Rv0318c |
integral membrane protein | 413 | 412 ctx | neighborhood:402 |
Rv0200 |
transmembrane protein | 425 | 405 | database:401 |
Rv3492c |
Mce associated protein | 425 | 405 | database:401 |
Rv0199 |
membrane protein | 425 | 404 | database:401 |
Rv0178 |
Mce associated membrane protein | 425 | 404 | database:401 |
Rv1362c |
membrane protein | 424 | 403 | database:401 |
Rv1363c |
membrane protein | 422 | 402 | database:401 |
Rv2508c |
integral membrane protein | 401 | 402 | |
Rv1972 |
Mce associated membrane protein | 422 | 401 | database:401 |
Rv2390c hyp |
hypothetical 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 GlpQ
- MTBC0 PGAP product: glycerophosphodiester phosphodiesterase
- Pfam (hmmscan --cut_ga): GDPD PF03009.24 (E=1e-52)
- (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_214831.1)
- 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 O07244 (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 —
20 functional partner(s); context anchor
glpQ1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000337|Rv0317c|glpQ2 MEFLRHGGRIAMAHRGFTSFRLPMNSMGAFQEAAKLGFRYIETDVRATRDGVAVILHDRRLAPGVGLSGAVDRLDWRDVRKAQLGAGQSIPTLEDLLTALPDMRVNIDIKAASAIEPTVNVIERCNAHNRVLIGSFSERRRRRALRLLTKRVASSAGTGALLAWLTARPLGSRAYAWRMMRDIDCVQLPSRLGGVPVITPARVRGFHAAGRQVHAWTVDEPDVMHTLLDMDVDGIITDRADLLRDVLIARGEWDGA