lipW Family assigned · medium auto-curated
H37Rv Rv0217c · MTBC0 mtbc0_000231 ·
302 aa · 260304–261212 (-) ·
RefSeq NP_214731.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | esterase LipW |
|---|---|
| MTBC0 PGAP re-annotation | alpha/beta hydrolase |
| Revised (this work) | Alpha/beta hydrolase. Pfam: BD-FAE (PF20434.6), Abhydrolase_3 (PF07859.20), AXE1 (PF05448.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96399
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible esterase LipW |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | lipW |
| eggNOG description | Alpha beta hydrolase |
| 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 | 0.567 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 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 | 4.5e-17 | 61–163 | BD-FAE |
Abhydrolase_3 | PF07859.20 | 5.0e-62 | 74–271 | alpha/beta hydrolase fold |
AXE1 | PF05448.19 | 4.4e-05 | 124–171 | Acetyl xylan esterase (AXE1) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lipC (esterase LipC), high confidence from genomic context alone (score 848 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0220 lipC |
esterase LipC | 972 | 848 ctx | neighborhood:623 cooccurence:614 textmining:825 |
Rv0218 |
transmembrane protein | 641 | 641 ctx | neighborhood:636 |
Rv0219 |
transmembrane protein | 602 | 602 ctx | neighborhood:600 |
Rv3097c lipY |
triacylglycerol lipase Lip | 791 | 591 ctx | cooccurence:591 textmining:511 |
Rv0221 |
diacyglycerol O-acyltransferase | 822 | 513 ctx | neighborhood:513 textmining:651 |
Rv2903c lepB |
signal peptidase | 500 | 481 | database:464 |
Rv0310c hyp |
hypothetical protein | 480 | 477 | experimental:439 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 451 | 452 | experimental:440 |
Rv3151 nuoG |
NADH-quinone oxidoreductase subunit G | 471 | 447 | experimental:441 |
Rv0222 echA1 |
enoyl-CoA hydratase EchA1 | 466 | 445 ctx | neighborhood:436 |
Rv3149 nuoE |
NADH-quinone oxidoreductase subunit E | 443 | 444 | experimental:440 |
Rv3150 nuoF |
NADH-quinone oxidoreductase subunit F | 442 | 443 | experimental:441 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 429 | 430 | experimental:426 |
Rv2946c pks1 |
polyketide synthase | 473 | 421 | |
Rv2782c pepR |
zinc protease | 439 | 414 | experimental:413 |
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 LipW
- MTBC0 PGAP product: alpha/beta hydrolase
- Pfam (hmmscan --cut_ga): BD-FAE PF20434.6 (E=4e-17), Abhydrolase_3 PF07859.20 (E=5e-62), AXE1 PF05448.19 (E=4e-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_214731.1)
- Domains: Pfam-A via hmmscan --cut_ga — BD-FAE (PF20434.6), Abhydrolase_3 (PF07859.20), AXE1 (PF05448.19)
- 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 P96399 (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 —
43 functional partner(s); context anchor
lipC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000231|Rv0217c|lipW MSGNEVHPDLRRIAVVTPRQLVGPRTLPVMRALIVVAGLRMSRTPPDIEVLTLESGVGVRLYRPAGSNEPAPALLWIHAGGYVMGTAQQDDRLCLRFSSRLGITVASVDYRLAPENPYPAALGDCYSALTWLASLPAVDPARVAIGGASAGGGLAAALALLARDRGGITPAFQLLVYPMLDDRTSIAPANPHYRLWNGRANRFGWRAYLGDADARVAVPGRRDDLGGLAPAWIGVGTHDLLHDEDLAYAERLTAAGVPCQVEVVEGAFHGFDRVAPNVGVSQRFFTSQCNSLRAALALSNRT