lipE Resolved · high auto-curated
H37Rv Rv3775 · MTBC0 mtbc0_004002 ·
415 aa · 4243806–4245053 (+) ·
RefSeq NP_218292.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipase LipE |
|---|---|
| MTBC0 PGAP re-annotation | lipase LipE |
| Revised (this work) | Lipase LipE. Pfam: Beta-lactamase (PF00144.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P72041
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable lipase LipE |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| Preferred name | lipE |
| eggNOG description | beta-lactamase |
| Orthologous group | COG1680 |
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 | 0.847 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 12 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 |
|---|---|---|---|---|
Beta-lactamase | PF00144.30 | 1.3e-66 | 43–398 | Beta-lactamase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: echA21 (enoyl-CoA hydratase EchA21), high confidence from genomic context alone (score 878 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3774 echA21 |
enoyl-CoA hydratase EchA21 | 877 | 878 ctx | neighborhood:872 |
Rv3773c hyp |
hypothetical protein | 644 | 644 ctx | neighborhood:640 |
Rv1780 hyp |
hypothetical protein | 644 | 644 ctx | cooccurence:641 |
Rv0293c hyp |
hypothetical protein | 617 | 617 ctx | cooccurence:613 |
Rv2285 |
diacylglycerol acyltransferase | 521 | 522 ctx | cooccurence:507 |
Rv3480c |
diacyglycerol O-acyltransferase | 521 | 521 ctx | cooccurence:506 |
Rv2913c |
D-amino acid aminohydrolase | 497 | 498 ctx | cooccurence:481 |
Rv3776 hyp |
hypothetical protein | 488 | 488 ctx | neighborhood:470 |
Rv3777 |
oxidoreductase | 472 | 473 ctx | neighborhood:470 |
Rv2042c hyp |
hypothetical protein | 468 | 468 ctx | cooccurence:465 |
Rv2629 hyp |
hypothetical protein | 465 | 465 ctx | neighborhood:462 |
Rv0221 |
diacyglycerol O-acyltransferase | 448 | 448 ctx | cooccurence:442 |
Rv3734c tgs2 |
diacyglycerol O-acyltransferase | 442 | 443 ctx | cooccurence:438 |
Rv3740c |
diacyglycerol O-acyltransferase | 438 | 439 ctx | cooccurence:436 |
Rv2717c hyp |
hypothetical protein | 403 | 403 ctx | neighborhood:403 |
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: lipase LipE
- MTBC0 PGAP product: lipase LipE
- Pfam (hmmscan --cut_ga): Beta-lactamase PF00144.30 (E=1e-66)
- (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_218292.1)
- Domains: Pfam-A via hmmscan --cut_ga — Beta-lactamase (PF00144.30)
- 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
COG1680 - Curated reference: UniProt P72041 (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 —
29 functional partner(s); context anchor
echA21 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004002|Rv3775|lipE MRAGDGKIRVPADLDAVTATGEEDHSEIDGAAVDRIWRAARHWYRAGMHPAIQLCIRHHGRVVLNRAIGHGWGNAPTDEADAEKIPVTTDTPFCVYSAAKAITATVVHMLVERGHFALDDRVCEYLPSYTSHGKHRTTIRHVLTHSAGVPFPTGPRPDVRRADDHEYAVERLGELRPLYRPGLVHIYHALTWGPLMREIVYAATGKEIREILATEILDPLGFRWTNFGVAERDVPLVAPSHATGRQLPPVIAAVFRKAIGGTVHEIIPYTNTPFFLSTILPSSNTVSTANELSRFMEILRRGGELDGVRVLSPETLRGAVTECRRLRPDFATGLMPLRWGTGFMLGSAKYGPFGRNAPAAFGHLGLVNIAVWADPERALSGGLISSGKPGRDPEAGRYGALLNAITAEIPRASSG