lipQ Family assigned · medium auto-curated
H37Rv Rv2485c · MTBC0 mtbc0_002645 ·
421 aa · 2815613–2816878 (-) ·
RefSeq NP_217001.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | carboxylesterase LipQ |
|---|---|
| MTBC0 PGAP re-annotation | alpha/beta hydrolase |
| Revised (this work) | Alpha/beta hydrolase. Pfam: COesterase (PF00135.35), BD-FAE (PF20434.6), Abhydrolase_3 (PF07859.20), 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 |
I6Y9F7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Esterase LipQ |
| EC (curated) |
EC 3.1.1.-
|
| Curated function | Shows lipase activity. Is highly immunogenic and may play an important role in the virulence and pathogenesis of M.tuberculosis infection, by altering the balance of cytokines. Significantly down-regulates the expression level of pro-inflammatory cytokines (TNF and IFN-gamma) and up-regulates the level of anti-inflammatory cytokines such as IL-4 and IL-10 as compared to LPS stimulated macrophages. Also inhibits the expression of iNOS, TLR2 and transcription factor NF-kappa-B in LPS stimulated macrophages whereas the expression of TLR-4 remains unchanged. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | lipQ |
| eggNOG description | Prolyl oligopeptidase family |
| Orthologous group | COG0657 |
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 | 0.798 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 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 |
|---|---|---|---|---|
COesterase | PF00135.35 | 7.7e-12 | 154–262 | Carboxylesterase family |
BD-FAE | PF20434.6 | 2.2e-47 | 166–359 | BD-FAE |
Abhydrolase_3 | PF07859.20 | 2.4e-21 | 176–379 | alpha/beta hydrolase fold |
Peptidase_S9 | PF00326.28 | 2.1e-13 | 221–380 | Prolyl oligopeptidase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2484c (diacyglycerol O-acyltransferase), medium confidence from genomic context alone (score 558 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1549 fadD11.1 |
Possible fatty-acid-CoA ligase FadD11.1 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase); Rv1549, (MTCY48.16c), len: 175 aa. Possible f | 884 | 839 | coexpression:838 |
Rv1550 fadD11 |
fatty-acid--CoA ligase FadD11 | 807 | 800 | coexpression:799 |
Rv0458 |
aldehyde dehydrogenase | 748 | 740 | coexpression:739 |
Rv0166 fadD5 |
fatty-acid--CoA ligase FadD5 | 582 | 581 | coexpression:517 |
Rv0310c hyp |
hypothetical protein | 567 | 564 | experimental:439 |
Rv2484c |
diacyglycerol O-acyltransferase | 740 | 558 ctx | neighborhood:449 textmining:435 |
Rv1400c lipI |
lipase | 794 | 493 ctx | cooccurence:490 textmining:612 |
Rv0722 rpmD |
50S ribosomal protein L30 | 493 | 493 | database:490 |
Rv2482c plsB2 |
glycerol-3-phosphate acyltransferase | 502 | 486 ctx | neighborhood:458 |
Rv2903c lepB |
signal peptidase | 502 | 483 | database:464 |
Rv2970c lipN |
lipase/esterase LipN | 743 | 473 ctx | cooccurence:470 textmining:534 |
Rv3151 nuoG |
NADH-quinone oxidoreductase subunit G | 493 | 471 | experimental:441 |
Rv2483c plsC |
bifunctional L-3-phosphoserine phosphatase/1-acyl-sn-glycerol-3-phosphate acyltransferase | 632 | 469 ctx | neighborhood:449 |
Rv3150 nuoF |
NADH-quinone oxidoreductase subunit F | 466 | 466 | experimental:441 |
Rv3149 nuoE |
NADH-quinone oxidoreductase subunit E | 465 | 466 | experimental:440 |
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: carboxylesterase LipQ
- MTBC0 PGAP product: alpha/beta hydrolase
- Pfam (hmmscan --cut_ga): COesterase PF00135.35 (E=8e-12), BD-FAE PF20434.6 (E=2e-47), Abhydrolase_3 PF07859.20 (E=2e-21), Peptidase_S9 PF00326.28 (E=2e-13)
- (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_217001.1)
- Domains: Pfam-A via hmmscan --cut_ga — COesterase (PF00135.35), BD-FAE (PF20434.6), Abhydrolase_3 (PF07859.20), 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
COG0657 - Curated reference: UniProt I6Y9F7 (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 —
63 functional partner(s); context anchor
Rv2484c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002645|Rv2485c|lipQ MHIASVTSRCSRAGAEALRQGAQLAADARDTCRAGALLLRGSPCAIGWVAGWLSAEFPARVVTGHALSRISPRSIGRFGTSWAAQRADQILHAALVDAFGPDFRDLVWHPTGEQSEAARRSGLLNLPHIPGPHRRYAAQTSDIPYGPGGRENLLDIWRRPDLAPGRRAPVLIQVPGGAWTINGKRPQAYPLMSRMVELGWICVSINYSKSPRCTWPAHIVDVKRAIAWVRENIADYGGDPDFITITGGSAGAHLAALAALSANDPALQPGFESADTAVQAAAPYYGVYDLTNAENMHEMMMPFLEHFVMRSRYVDNPGLFKAASPISYVHSEAPPFFVLHGEKDPMVPSAQSRAFSAALRDAGAATVSYAELPNAHHAFDLAATVRSRMVAEAVSDFLGVIYGRRMGARKGSLALSSPPAS