lipO Family assigned · medium auto-curated
H37Rv Rv1426c · MTBC0 mtbc0_001526 ·
420 aa · 1610403–1611665 (-) ·
RefSeq NP_215942.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | esterase LipO |
|---|---|
| MTBC0 PGAP re-annotation | alpha/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 |
O06832
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable esterase LipO |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | lipO |
| eggNOG description | esterase |
| 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 | 0.271 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 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 |
|---|---|---|---|---|
COesterase | PF00135.35 | 1.2e-13 | 174–273 | Carboxylesterase family |
BD-FAE | PF20434.6 | 1.4e-40 | 175–370 | BD-FAE |
Abhydrolase_3 | PF07859.20 | 1.4e-18 | 182–390 | alpha/beta hydrolase fold |
Peptidase_S9 | PF00326.28 | 3.1e-12 | 205–412 | Prolyl oligopeptidase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadD12 (acyl-CoA synthetase), high confidence from genomic context alone (score 986 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1427c fadD12 |
acyl-CoA synthetase | 996 | 986 ctx | neighborhood:882 coexpression:866 textmining:755 |
Rv1428c hyp |
hypothetical protein | 928 | 927 ctx | neighborhood:882 coexpression:409 |
Rv1429 hyp |
hypothetical protein | 589 | 590 ctx | neighborhood:587 |
Rv0310c hyp |
hypothetical protein | 580 | 578 | experimental:439 |
Rv0722 rpmD |
50S ribosomal protein L30 | 495 | 496 | database:490 |
Rv2903c lepB |
signal peptidase | 504 | 485 | database:464 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 465 | 466 | experimental:440 |
Rv3151 nuoG |
NADH-quinone oxidoreductase subunit G | 485 | 463 | experimental:441 |
Rv3149 nuoE |
NADH-quinone oxidoreductase subunit E | 456 | 457 | experimental:440 |
Rv3150 nuoF |
NADH-quinone oxidoreductase subunit F | 456 | 456 | experimental:441 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 435 | 436 | experimental:426 |
Rv2946c pks1 |
polyketide synthase | 473 | 421 | |
Rv2782c pepR |
zinc protease | 444 | 419 | experimental:413 |
Rv1385 pyrF |
orotidine 5'-phosphate decarboxylase | 436 | 416 | |
Rv3152 nuoH |
NADH-quinone oxidoreductase subunit H | 411 | 411 |
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 LipO
- MTBC0 PGAP product: alpha/beta hydrolase
- Pfam (hmmscan --cut_ga): COesterase PF00135.35 (E=1e-13), BD-FAE PF20434.6 (E=1e-40), Abhydrolase_3 PF07859.20 (E=1e-18), Peptidase_S9 PF00326.28 (E=3e-12)
- (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_215942.1)
- 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 O06832 (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 —
47 functional partner(s); context anchor
fadD12 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001526|Rv1426c|lipO MRFRRMARPRPLTRAAVELLNAANGLRPLSGSGYSTVLAFWLGWPTSEVPGVYLGASVLDALRRGRRGDFGGLKGKAALALTAAAWVILAVIRYRGATTPGPVLEAGLTEQLGPDYAKELATLPTEPMRSRGRNLPLRTAMARRRYVETTNVVCYGPYGRANLADIWRRRDLPRDAKAPVLVQVPGGAWVLGWRRPQAYPLMSHLAARGWVCVSLNYRVSPRHTWPDHIVDVKRALAWVKENIAAYGGDPNFVAISGGSAGGHLCALAALTPNDPRFQPGFEQVDTSVAAAVPVYGRYDWFTTDAPGRREFVGLLETFVVKRKFSTHRDIFVDASPIHHVRADAPPFFVLHGRHDSLIPVAEAHAFVEELRAVSKSPVAYADLPHAQHAFDVFGSPRAHHTAEAVARFLSWVYATNPPAT