lipV Resolved · high auto-curated
H37Rv Rv3203 · MTBC0 - ·
224 aa · 3580638–3581312 (+) ·
RefSeq NP_217719.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipase LipV |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Lipase LipV. Pfam: Hydrolase_4 (PF12146.16), Abhydrolase_6 (PF12697.14), Abhydrolase_1 (PF00561.27), Ser_hydrolase (PF06821.20), Thioesterase (PF00975.27). |
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 |
L0TC47
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Lipase LipV |
| EC (curated) |
EC 3.1.1.1
|
| Curated function | Lipase that displays broad substrate specificity and preferentially hydrolyzes p-nitrophenyl myristate in vitro. Also shows significant activity with pNP-butyrate (68%), pNP-octanoate (82%), pNP-decanoate (90%), and pNP-laurate (74%). Is probably involved in lipid catabolism. Is active at low pH, and might play some important role in mycobacterial biology in macrophages where the bacteria encounters acidic stress. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lipV |
| eggNOG description | Alpha beta hydrolase |
| Orthologous group | COG0596 |
| KEGG orthology |
K19311
|
| Gene Ontology (47) |
GO:0003674, GO:0003824, GO:0005488, GO:0005504, GO:0006082, GO:0006629, GO:0006631, GO:0008150, GO:0008152, GO:0008289, GO:0009056, GO:0009062 +35 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
Hydrolase_4 | PF12146.16 | 3.8e-10 | 6–122 | Serine aminopeptidase, S33 |
Abhydrolase_6 | PF12697.14 | 2.0e-17 | 7–216 | Alpha/beta hydrolase family |
Abhydrolase_1 | PF00561.27 | 4.1e-13 | 7–78 | alpha/beta hydrolase fold |
Ser_hydrolase | PF06821.20 | 1.7e-04 | 27–79 | Serine hydrolase |
Thioesterase | PF00975.27 | 1.6e-06 | 32–74 | Thioesterase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3204 (DNA-methyltransferase), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3204 |
DNA-methyltransferase | 884 | 884 ctx | neighborhood:882 |
Rv3591c |
hydrolase | 626 | 627 ctx | cooccurence:625 |
Rv3201c adnB |
ATP-dependent DNA helicase | 544 | 544 ctx | neighborhood:544 |
Rv2001 hyp |
hypothetical protein | 499 | 500 ctx | cooccurence:498 |
Rv1527c pks5 |
polyketide synthase | 526 | 499 | experimental:441 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 526 | 499 | experimental:441 |
Rv2048c pks12 |
polyketide synthase | 526 | 498 | experimental:441 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 526 | 498 | experimental:441 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 526 | 498 | experimental:441 |
Rv1683 |
bifunctional long-chain acyl-CoA synthase/lipase | 515 | 491 ctx | cooccurence:412 |
Rv2946c pks1 |
polyketide synthase | 486 | 455 | |
Rv1274 lprB |
lipoprotein LprB | 454 | 455 ctx | cooccurence:453 |
Rv2390c hyp |
hypothetical protein | 448 | 448 | |
Rv1972 |
Mce associated membrane protein | 442 | 442 | |
Rv1661 pks7 |
polyketide synthase | 452 | 427 |
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): lipase LipV
- Pfam (hmmscan --cut_ga): Hydrolase_4 PF12146.16 (E=4e-10), Abhydrolase_6 PF12697.14 (E=2e-17), Abhydrolase_1 PF00561.27 (E=4e-13), Ser_hydrolase PF06821.20 (E=2e-04), Thioesterase PF00975.27 (E=2e-06)
- (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_217719.1)
- Domains: Pfam-A via hmmscan --cut_ga — Hydrolase_4 (PF12146.16), Abhydrolase_6 (PF12697.14), Abhydrolase_1 (PF00561.27), Ser_hydrolase (PF06821.20), Thioesterase (PF00975.27)
- 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
COG0596 - Curated reference: UniProt L0TC47 (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 —
42 functional partner(s); context anchor
Rv3204 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3203|lipV MPEIPIAAPDLLGHGRSPWAAPWTIDANVSALAALLDNQGDGPVVVVGHSFGGAVAMHLAAARPDQVAALVLLDPAVALDGSRVREVVDAMLASPDYLDPAEARAEKATGAWADVDPPVLDAELDEHLVALPNGRYGWRISLPAMVCYWSELARDIVLPPVGTATTLVRAVRASPAYVSDQLLAALDKRLGADFELLDFDCGHMVPQAKPTEVAAVIRSRLGPR