lipT Resolved · high auto-curated
H37Rv Rv2045c · MTBC0 - ·
511 aa · 2289685–2291220 (-) ·
RefSeq NP_216561.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | carboxylesterase LipT |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Carboxylesterase LipT. Pfam: COesterase (PF00135.35), 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.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O53488
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Carboxylic ester hydrolase |
| EC (curated) |
EC 3.1.1.-
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | lipT |
| eggNOG description | Belongs to the type-B carboxylesterase lipase family |
| Orthologous group | COG2272 |
| KEGG orthology |
K03929
|
| CAZy family |
CE10
|
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 | 0.57 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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 | 3.4e-95 | 19–490 | Carboxylesterase family |
BD-FAE | PF20434.6 | 2.1e-12 | 99–227 | BD-FAE |
Abhydrolase_3 | PF07859.20 | 2.4e-06 | 174–231 | alpha/beta hydrolase fold |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lppI (lipoprotein LppI), medium confidence from genomic context alone (score 679 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2044c hyp |
hypothetical protein | 785 | 785 ctx | neighborhood:782 |
Rv1389 gmk |
guanylate kinase | 745 | 735 | database:608 |
Rv2681 hyp |
hypothetical protein | 732 | 733 | experimental:417 database:558 |
Rv1770 hyp |
hypothetical protein | 715 | 700 | database:587 |
Rv3458c rpsD |
30S ribosomal protein S4 | 700 | 700 | database:632 |
Rv0418 lpqL |
lipoprotein aminopeptidase LpqL | 711 | 696 | database:587 |
Rv3459c rpsK |
30S ribosomal protein S11 | 684 | 684 | database:624 |
Rv2046 lppI |
lipoprotein LppI | 678 | 679 ctx | neighborhood:674 |
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 669 | 653 | database:594 |
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 668 | 652 | database:594 |
Rv1630 rpsA |
30S ribosomal protein S1 | 640 | 641 | database:636 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 634 | 635 | database:516 |
Rv1340 rphA |
ribonuclease PH | 600 | 596 | database:543 |
Rv0718 rpsH |
30S ribosomal protein S8 | 593 | 594 | database:516 |
Rv0682 rpsL |
30S ribosomal protein S12 | 592 | 592 | database:491 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): carboxylesterase LipT
- Pfam (hmmscan --cut_ga): COesterase PF00135.35 (E=3e-95), BD-FAE PF20434.6 (E=2e-12), Abhydrolase_3 PF07859.20 (E=2e-06)
- (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_216561.1)
- Domains: Pfam-A via hmmscan --cut_ga — COesterase (PF00135.35), 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
COG2272 - Curated reference: UniProt O53488 (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 —
61 functional partner(s); context anchor
lppI - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2045c|lipT MALESATVGSMHERTVRARTATGIVEGFTRDGVHRWRSIPYARAPVGSLRFRAPQPAQPWPGVRHCHTFANCAPQQRRYTVMGIGRYQTRSEDCLTLNVVTPEEPATQPLPVMVFIHGGGYILGSSATPIYDGAALARRGCVYVSVNYRLGALGCLDLSSLSTPQITLDSNVYLRDLVLALRWVHDNIAEFGGDPGNVTIFGESAGAHITATLLAVPAAKGLFARAISESPAAGMVRSREVAAEFAARFANLIGARTQDAANALMQASPAQLVEAQHHLIRQGMRKRLGAFPIGPVFGDDYLPMDPVEAMRSGRVHAVPLIVGTNAEEGRLFTRFLGMLPTNEPMVEELLSGMKPADRERITAAYPNYPAPSACIQLGGDFAFSSAAWQIAEAHGANAPTYLYRYDYAPRTLRWSGFGATHATELFAVFDIYRTRFGALLTAAADRRAALRVSNEVQRRWRCFSQIGVPGDDWPAYTQDDRAVLVFDRRCRIEFDPHQHRRIAWDGFSLAN