lpqP Family assigned · medium auto-curated
H37Rv Rv0671 · MTBC0 mtbc0_000710 ·
280 aa · 774668–775510 (+) ·
RefSeq NP_215185.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqP |
|---|---|
| MTBC0 PGAP re-annotation | PHB depolymerase family esterase |
| Revised (this work) | PHB depolymerase family esterase. Pfam: Esterase_PHB (PF10503.15). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XVY0
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible conserved lipoprotein LpqP |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | lpqP |
| eggNOG description | Esterase PHB depolymerase |
| Orthologous group | COG3509 |
| KEGG orthology |
K03932
|
| CAZy family |
CE1
|
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 | 0.342 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 4 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.47% of strains (689) · 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 |
|---|---|---|---|---|
Esterase_PHB | PF10503.15 | 1.9e-12 | 45–177 | Esterase PHB depolymerase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: end (endonuclease IV), high confidence from genomic context alone (score 844 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0670 end |
endonuclease IV | 844 | 844 ctx | neighborhood:835 |
Rv0672 fadE8 |
acyl-CoA dehydrogenase FadE8 | 646 | 646 ctx | neighborhood:641 |
Rv0673 echA4 |
enoyl-CoA hydratase EchA4 | 641 | 639 ctx | neighborhood:629 |
Rv0674 hyp |
hypothetical protein | 634 | 634 ctx | neighborhood:629 |
Rv0675 echA5 |
enoyl-CoA hydratase EchA5 | 623 | 622 ctx | neighborhood:617 |
Rv0669c |
neutral ceramidase | 440 | 440 ctx | neighborhood:440 |
Rv2305 hyp |
hypothetical protein | 439 | 439 ctx | cooccurence:439 |
Rv0519c |
membrane protein | 438 | 438 | experimental:420 |
Rv1498c |
methyltransferase | 409 | 409 ctx | cooccurence:401 |
Rv2601 speE |
spermidine synthase | 608 | 190 | textmining:537 |
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: lipoprotein LpqP
- MTBC0 PGAP product: PHB depolymerase family esterase
- Pfam (hmmscan --cut_ga): Esterase_PHB PF10503.15 (E=2e-12)
- (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_215185.1)
- Domains: Pfam-A via hmmscan --cut_ga — Esterase_PHB (PF10503.15)
- 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
COG3509 - Curated reference: UniProt I6XVY0 (TrEMBL, unreviewed; Predicted)
- 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 —
10 functional partner(s); context anchor
end - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000710|Rv0671|lpqP MLRRVAILLAAVLAFAGCSGGTRLAAGFGNGNSVHTLDVDGAGRSYRLYKPVGLPSSAPLVVMLHGGFGSAKQAERSYGWDELADSEKFLVAYPDGYHRAWNANGGGCCGRPAREGVDDIGFVRAVVADIANNVSIDPARVYVTGMSNGAIMSYTLACNTSIFAAIGVVSGTQLDPCQSPRPVSVIHIHGTADPLVRYHGGPGAGFARIDGPPVPDLNAFWREVNRCGALDTTTEGPVTTSGATCADNRRVVLLTVDDAGHRWPSFATQTLWRFFAAHFR