MTBC Gene Atlas

lipM Family assigned · medium auto-curated

H37Rv Rv2284 · MTBC0 mtbc0_002425 · 431 aa · 2580892–2582187 (+) · RefSeq NP_216800.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)esterase LipM
MTBC0 PGAP re-annotationalpha/beta hydrolase
Revised (this work)Alpha/beta hydrolase. Pfam: COesterase (PF00135.35), BD-FAE (PF20434.6), Abhydrolase_3 (PF07859.20), Peptidase_S9 (PF00326.28).

Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.

Curated reference (UniProt)

UniProt Q50681 SwissProt · reviewed · Evidence at protein level
UniProt nameProbable carboxylic ester hydrolase LipM
EC (curated) EC 3.1.1.-

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category I Lipid transport and metabolism
Preferred namelipM
eggNOG descriptionesterase
Orthologous groupCOG0657

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 0.354 · purifying
Polymorphic sites (≥ 0.1% of strains) 4 synonymous, 4 missense, 0 nonsense, 1 frameshift
Disruption 1 distinct premature-stop/frameshift site(s); most common in 0.53% of strains (771) · 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)

PfamAccessioni-EvalueResiduesDescription
COesterasePF00135.35 1.5e-11166–275 Carboxylesterase family
BD-FAEPF20434.6 8.0e-47177–372 BD-FAE
Abhydrolase_3PF07859.20 8.1e-20186–392 alpha/beta hydrolase fold
Peptidase_S9PF00326.28 3.5e-13208–392 Prolyl oligopeptidase family

Functional interaction network (STRING v12, guilt-by-association)

Closest characterised functional partner: Rv2285 (diacylglycerol acyltransferase), high confidence from genomic context alone (score 760 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv2283 hyp hypothetical protein 763 763 ctx neighborhood:762
Rv2285 diacylglycerol acyltransferase 760 760 ctx neighborhood:712
Rv0310c hyp hypothetical protein 571 568 experimental:439
Rv2282c LysR family HTH-type transcriptional regulator 558 552 ctx neighborhood:549
Rv0722 rpmD 50S ribosomal protein L30 492 493 database:490
Rv1400c lipI lipase 895 491 ctx cooccurence:483 textmining:803
Rv2970c lipN lipase/esterase LipN 892 480 ctx cooccurence:475 textmining:802
Rv2903c lepB signal peptidase 499 480 database:464
Rv3153 nuoI NADH-quinone oxidoreductase subunit I 451 452 experimental:440
Rv3151 nuoG NADH-quinone oxidoreductase subunit G 472 449 experimental:441
Rv3150 nuoF NADH-quinone oxidoreductase subunit F 444 444 experimental:441
Rv3149 nuoE NADH-quinone oxidoreductase subunit E 441 442 experimental:440
Rv2195 qcrA ubiquinol-cytochrome C reductase rieske iron-sulfur subunit 431 431 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 LipM
  • MTBC0 PGAP product: alpha/beta hydrolase
  • Pfam (hmmscan --cut_ga): COesterase PF00135.35 (E=1e-11), BD-FAE PF20434.6 (E=8e-47), Abhydrolase_3 PF07859.20 (E=8e-20), Peptidase_S9 PF00326.28 (E=4e-13)
  • (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_216800.1)
  • Domains: Pfam-A via hmmscan --cut_ga — COesterase (PF00135.35), BD-FAE (PF20434.6), Abhydrolase_3 (PF07859.20), Peptidase_S9 (PF00326.28)
  • 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 Q50681 (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 — 44 functional partner(s); context anchor Rv2285
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_002425|Rv2284|lipM
MGAPRLIHVIRQIGALVVAAVTAAATINAYRPLARNGFASLWSWFIGLVVTEFPLPTLASQLGGLVLTAQRLTRPVRAVSWLVAAFSALGLLNLSRAGRQADAQLTAALDSGLGPDRRTASAGLWRRPAGGGTAKTPGPLRMLRIYRDYAHDGDISYGEYGRANHLDIWRRPDLDLTGTAPVLFQIPGGAWTTGNKRGQAHPLMSHLAELGWICVAINYRHSPRNTWPDHIIDVKRALAWVKAHISEYGGDPDFIAITGGSAGGHLSSLAALTPNDPRFQPGFEEADTRVQAAVPFYGVYDFTRLQDAMHPMMLPLLERMVVKQPRTANMQSYLDASPVTHISADAPPFFVLHGRNDSLVPVQQARGFVDQLRQVSKQPVVYAELPFTQHAFDLLGSARAAHTAIAVEQFLAEVYATQHAGSEPGPAVAIP