lpqC Family assigned · medium auto-curated
H37Rv Rv3298c · MTBC0 mtbc0_003506 ·
304 aa · 3704190–3705104 (-) ·
RefSeq NP_217815.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | esterase LpqC |
|---|---|
| MTBC0 PGAP re-annotation | PHB depolymerase family esterase |
| Revised (this work) | PHB depolymerase family esterase. Pfam: Peptidase_S9 (PF00326.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96903
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible esterase lipoprotein LpqC |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | lpqC |
| eggNOG description | esterase |
| 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 0 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 |
|---|---|---|---|---|
Peptidase_S9 | PF00326.28 | 8.7e-05 | 117–167 | Prolyl oligopeptidase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: atsB (arylsulfatase AtsB), high confidence from genomic context alone (score 762 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3299c atsB |
arylsulfatase AtsB | 762 | 762 ctx | neighborhood:703 |
Rv3300c hyp |
hypothetical protein | 953 | 677 ctx | neighborhood:660 textmining:861 |
Rv3301c phoY1 |
phosphate transport system transcriptional regulator PhoY | 874 | 650 ctx | neighborhood:640 textmining:656 |
Rv3302c glpD2 |
glycerol-3-phosphate dehydrogenase | 753 | 475 ctx | neighborhood:450 textmining:551 |
Rv0519c |
membrane protein | 441 | 442 | experimental:420 |
Rv3303c lpdA |
NAD(P)H quinone reductase LpdA | 670 | 437 ctx | neighborhood:427 textmining:437 |
Rv3304 hyp |
hypothetical protein | 751 | 313 | textmining:653 |
Rv2601 speE |
spermidine synthase | 541 | 50 | textmining:537 |
Rv3185 |
Probable transposase; Rv3185, (MTV014.29), len: 328 aa. Probable IS6110 transposase. Identical to many other M. tuberculosis IS6110 transpos | 438 | 47 | textmining:435 |
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: esterase LpqC
- MTBC0 PGAP product: PHB depolymerase family esterase
- Pfam (hmmscan --cut_ga): Peptidase_S9 PF00326.28 (E=9e-05)
- (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_217815.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_S9 (PF00326.28)
- 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 P96903 (TrEMBL, unreviewed; 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 —
9 functional partner(s); context anchor
atsB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003506|Rv3298c|lpqC MPWARMLSLIVLMVCLAGCGGDQLLARHASSVATFQFGGLTRSYRLHVPPAEPSGLVISLHGGGGTGAGQEALTDFDAVADAADLLVVYPDGYDKSWADGRGASPADRRHLDDVGFLVALAAKLVHDFDIAPGHVFATGMSNGGFMSNRLACDRADIFAAVAPVAGTLGVGVTCNPSRPVSVLEAHGTADPLVPFNGGAVRGRGGLSHSISVASLVDRWRAVDGCQGDPSAAELPDVGDGTMVHLFDSSSCAAGTEVISYQIDNGGHTWPGGRQYLPKAVIGATTRAFDGSQVIAQFFATHGRD