lipR Family assigned · medium auto-curated
H37Rv Rv3084 · MTBC0 mtbc0_003278 ·
308 aa · 3471361–3472287 (+) ·
RefSeq NP_217600.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acetyl-hydrolase LipR |
|---|---|
| MTBC0 PGAP re-annotation | alpha/beta hydrolase |
| Revised (this work) | Alpha/beta hydrolase. Pfam: 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.
Curated reference (UniProt)
| UniProt |
P9WK85
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative acetyl-hydrolase LipR |
| EC (curated) |
EC 3.1.1.-
|
| Curated function | Required for maintaining the appropriate mycolic acid composition and permeability of the envelope on its exposure to acidic pH. |
UniProt still lists this protein as Putative acetyl-hydrolase LipR; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | lipR |
| eggNOG description | alpha/beta hydrolase fold |
| Orthologous group | COG0657 |
| Gene Ontology (27) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0008152, GO:0009056, GO:0009268, GO:0009628, GO:0010447, GO:0016020 +15 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 | 1.027 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 10 missense, 1 nonsense, 2 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 0.37% of strains (538) · clonal |
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 |
|---|---|---|---|---|
Say1_Mug180 | PF10340.16 | 1.6e-10 | 71–191 | Steryl acetyl hydrolase |
Abhydrolase_3 | PF07859.20 | 5.2e-44 | 72–272 | alpha/beta hydrolase fold |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mymA (FAD-containing monooxygenase MymA), high confidence from genomic context alone (score 984 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3083 mymA |
FAD-containing monooxygenase MymA | 994 | 984 ctx | neighborhood:882 coexpression:869 textmining:660 |
Rv3085 sadH |
oxidoreductase SadH | 997 | 983 ctx | neighborhood:882 coexpression:860 textmining:870 |
Rv3086 adhD |
alcohol dehydrogenase D | 991 | 960 ctx | neighborhood:721 coexpression:862 textmining:803 |
Rv3089 fadD13 |
long chain-fatty-acid--CoA ligase FadD13 | 988 | 953 ctx | neighborhood:616 coexpression:866 textmining:759 |
Rv3088 tgs4 |
diacyglycerol O-acyltransferase | 974 | 944 ctx | neighborhood:616 coexpression:860 textmining:557 |
Rv3087 |
diacyglycerol O-acyltransferase | 976 | 941 ctx | neighborhood:590 coexpression:863 textmining:616 |
Rv3082c virS |
HTH-type transcriptional regulator VirS | 611 | 611 ctx | neighborhood:602 |
Rv0722 rpmD |
50S ribosomal protein L30 | 492 | 493 | database:490 |
Rv2903c lepB |
signal peptidase | 501 | 482 | database:464 |
Rv0310c hyp |
hypothetical protein | 477 | 474 | experimental:439 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 457 | 457 | experimental:440 |
Rv3151 nuoG |
NADH-quinone oxidoreductase subunit G | 476 | 453 | experimental:441 |
Rv3149 nuoE |
NADH-quinone oxidoreductase subunit E | 448 | 448 | experimental:440 |
Rv3150 nuoF |
NADH-quinone oxidoreductase subunit F | 446 | 446 | experimental:441 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 439 | 433 | experimental:426 |
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: acetyl-hydrolase LipR
- MTBC0 PGAP product: alpha/beta hydrolase
- Pfam (hmmscan --cut_ga): Say1_Mug180 PF10340.16 (E=2e-10), Abhydrolase_3 PF07859.20 (E=5e-44)
- (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_217600.1)
- Domains: Pfam-A via hmmscan --cut_ga — 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 P9WK85 (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 —
46 functional partner(s); context anchor
mymA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003278|Rv3084|lipR MNLRKNVIRSVLRGARPLFASRRLGIAGRRVLLATLTAGARAPKGTRFQRVSIAGVPVQRVQPPHAATSGTLIYLHGGAYALGSARGYRGLAAQLAAAAGMTALVPDYTRAPHAHYPVALEEMAAVYTRLLDDGLDPKTTVIAGDSAGGGLTLALAMALRDRGIQAPAALGLICPWADLAVDIEATRPALRDPLILPSMCTEWAPRYVGSSDPRLPGISPVYGDMSGLPPIVMQTAGDDPICVDADKIETACAASKTSIEHRRFAGMWHDFHLQVSLLPEARDAIADLGARLRGHLHQSQGQPRGVVK