lipF Resolved · high auto-curated
H37Rv Rv3487c · MTBC0 - ·
277 aa · 3906174–3907007 (-) ·
RefSeq NP_218004.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | carboxylesterase LipF |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Carboxylesterase LipF. Pfam: BD-FAE (PF20434.6), Say1_Mug180 (PF10340.16), Abhydrolase_3 (PF07859.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O06350
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Carboxylesterase/phospholipase LipF |
| EC (curated) |
EC 3.1.1.1, EC 3.1.4.3
|
| Curated function | Hydrolyzes short-chain esters. Shows maximal activity with triacetin and p-nitrophenyl acetate. Has no enzyme activity on triacylglycerides or p-nitrophenyl esters (p-NP) with long fatty acids (tricaprin, p-NP caprylate, or p-NP caprate); experiments performed with enzyme missing the first 97 residues. Has phospholipase C activity, making 1,2-DAG phosphocholine; experiments performed with enzyme missing the first 97 residues. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | lipF |
| eggNOG description | Alpha beta hydrolase |
| Orthologous group | COG0657 |
| Gene Ontology (33) |
GO:0003674, GO:0003824, GO:0004620, GO:0004629, GO:0008081, GO:0008150, GO:0009268, GO:0009605, GO:0009607, GO:0009628, GO:0010447, GO:0016298 +21 more
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 7 missense, 2 nonsense, 2 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 6.00% of strains (8711) · convergent |
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 |
|---|---|---|---|---|
BD-FAE | PF20434.6 | 4.9e-09 | 13–100 | BD-FAE |
Say1_Mug180 | PF10340.16 | 3.3e-09 | 14–124 | Steryl acetyl hydrolase |
Abhydrolase_3 | PF07859.20 | 5.9e-45 | 16–222 | alpha/beta hydrolase fold |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lipY (triacylglycerol lipase Lip), high confidence from genomic context alone (score 758 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3097c lipY |
triacylglycerol lipase Lip | 856 | 758 ctx | cooccurence:758 textmining:433 |
Rv0722 rpmD |
50S ribosomal protein L30 | 497 | 497 | database:490 |
Rv2903c lepB |
signal peptidase | 513 | 494 | database:464 |
Rv0310c hyp |
hypothetical protein | 479 | 475 | experimental:439 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 556 | 464 | experimental:440 |
Rv3151 nuoG |
NADH-quinone oxidoreductase subunit G | 485 | 463 | experimental:441 |
Rv3150 nuoF |
NADH-quinone oxidoreductase subunit F | 461 | 461 | experimental:441 |
Rv3149 nuoE |
NADH-quinone oxidoreductase subunit E | 456 | 457 | experimental:440 |
Rv0220 lipC |
esterase LipC | 796 | 440 ctx | cooccurence:432 textmining:652 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 442 | 436 | experimental:426 |
Rv2946c pks1 |
polyketide synthase | 478 | 427 | |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 629 | 420 | |
Rv2782c pepR |
zinc protease | 442 | 417 | experimental:413 |
Rv1181 pks4 |
polyketide beta-ketoacyl synthase | 607 | 410 | |
Rv3152 nuoH |
NADH-quinone oxidoreductase subunit H | 472 | 409 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): carboxylesterase LipF
- Pfam (hmmscan --cut_ga): BD-FAE PF20434.6 (E=5e-09), Say1_Mug180 PF10340.16 (E=3e-09), Abhydrolase_3 PF07859.20 (E=6e-45)
- (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_218004.3)
- Domains: Pfam-A via hmmscan --cut_ga — BD-FAE (PF20434.6), Say1_Mug180 (PF10340.16), Abhydrolase_3 (PF07859.20)
- 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 O06350 (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 —
48 functional partner(s); context anchor
lipY - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3487c|lipF MRAPGVRAADGAGRVVLYLHGGAFVMCGPNSHSRIVNALSGFAESPVLIVDYRLIPKHSLGMALDDCHDAYQWLRARGYRPEQIVLAGDSAGGYLALALAQRLQCDDEKPAAIVAISPLLQLAKGPKQDHPNIGTDAMFPARAFDALAAWVRAAAAKNMVDGRPEDLYEPLDHIESSLPPTLIHVSGSEVLLHDAQLGAGKLAAAGVCAEVRVWPGQAHLFQLATPLVPEATRSLRQIGQFIRDATADSSLSPVHRSRYVAGSPRAASRGAFGQSPI