lipN Resolved · high auto-curated
H37Rv Rv2970c · MTBC0 mtbc0_003154 ·
376 aa · 3345748–3346878 (-) ·
RefSeq NP_217486.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipase/esterase LipN |
|---|---|
| MTBC0 PGAP re-annotation | lipase/esterase LipN |
| Revised (this work) | Lipase/esterase LipN. Pfam: BD-FAE (PF20434.6), Abhydrolase_3 (PF07859.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95125
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Carboxylic ester hydrolase LipN |
| EC (curated) |
EC 3.1.1.-
|
| Curated function | Non specific carboxylic ester hydrolase. Hydrolyzes various pNP-esters, with a preference for short carbon chain substrates. Can also hydrolyze tributyrin to di- and monobutyrin and 4-hydroxyphenylacetate to hydroquinone. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | lipN |
| eggNOG description | Alpha beta hydrolase |
| Orthologous group | COG0657 |
| KEGG orthology |
K01066
|
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 | 1.258 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
BD-FAE | PF20434.6 | 1.1e-15 | 130–230 | BD-FAE |
Abhydrolase_3 | PF07859.20 | 1.1e-71 | 137–349 | alpha/beta hydrolase fold |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2968c (integral membrane protein), high confidence from genomic context alone (score 781 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2969c hyp |
hypothetical protein | 785 | 785 ctx | neighborhood:775 |
Rv2968c |
integral membrane protein | 780 | 781 ctx | neighborhood:775 |
Rv2970A hyp |
hypothetical protein | 769 | 765 ctx | neighborhood:748 |
Rv2967c pca |
pyruvate carboxylase | 763 | 764 ctx | neighborhood:756 |
Rv2971 |
oxidoreductase | 734 | 729 ctx | neighborhood:713 |
Rv2966c rsmD |
methyltransferase | 675 | 675 ctx | neighborhood:670 |
Rv3097c lipY |
triacylglycerol lipase Lip | 751 | 576 ctx | cooccurence:576 textmining:437 |
Rv0722 rpmD |
50S ribosomal protein L30 | 495 | 496 | database:490 |
Rv2903c lepB |
signal peptidase | 506 | 488 | database:464 |
Rv2284 lipM |
esterase LipM | 892 | 480 ctx | cooccurence:475 textmining:802 |
Rv0310c hyp |
hypothetical protein | 477 | 474 | experimental:439 |
Rv2485c lipQ |
carboxylesterase LipQ | 743 | 473 ctx | cooccurence:470 textmining:534 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 456 | 456 | experimental:440 |
Rv3151 nuoG |
NADH-quinone oxidoreductase subunit G | 477 | 453 | experimental:441 |
Rv3150 nuoF |
NADH-quinone oxidoreductase subunit F | 449 | 449 | experimental:441 |
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: lipase/esterase LipN
- MTBC0 PGAP product: lipase/esterase LipN
- Pfam (hmmscan --cut_ga): BD-FAE PF20434.6 (E=1e-15), Abhydrolase_3 PF07859.20 (E=1e-71)
- (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_217486.1)
- Domains: Pfam-A via hmmscan --cut_ga — BD-FAE (PF20434.6), 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 P95125 (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 —
47 functional partner(s); context anchor
Rv2968c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003154|Rv2970c|lipN MTKSLPGVADLRLGANHPRMWTRRVQGTVVNVGVKVLPWIPTPAKRILSAGRSVIIDGNTLDPTLQLMLSTSRIFGVDGLAVDDDIVASRAHMRAICEAMPGPQIHVDVTDLSIPGPAGEIPARHYRPSGGGATPLLVFYHGGGWTLGDLDTHDALCRLTCRDADIQVLSIDYRLAPEHPAPAAVEDAYAAFVWAHEHASDEFGALPGRVAVGGDSAGGNLSAVVCQLARDKARYEGGPTPVLQWLLYPRTDFTAQTRSMGLFGNGFLLTKRDIDWFHTQYLRDSDVDPADPRLSPLLAESLSGLAPALIAVAGFDPLRDEGESYAKALRAAGTAVDLRYLGSLTHGFLNLFQLGGGSAAGTNELISALRAHLSRV