lipD Resolved · high auto-curated
H37Rv Rv1923 · MTBC0 - ·
446 aa · 2175173–2176513 (+) ·
RefSeq NP_216439.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipase LipD |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Lipase LipD. 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.
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 |
P95290
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable lipase LipD |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| Preferred name | lipD |
| 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 | 0.86 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 11 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.55% of strains (796) · 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 |
|---|---|---|---|---|
Beta-lactamase | PF00144.30 | 1.7e-65 | 59–394 | Beta-lactamase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1922 (lipoprotein), high confidence from genomic context alone (score 880 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1922 |
lipoprotein | 880 | 880 ctx | neighborhood:773 cooccurence:491 |
Rv1367c hyp |
hypothetical protein | 616 | 616 ctx | cooccurence:616 |
Rv3633 hyp |
hypothetical protein | 530 | 531 ctx | cooccurence:524 |
Rv1730c |
penicillin-binding protein | 496 | 497 ctx | cooccurence:495 |
Rv1921c lppF |
lipoprotein LppF | 433 | 433 ctx | neighborhood:433 |
Rv2913c |
D-amino acid aminohydrolase | 417 | 417 | |
Rv3775 lipE |
lipase LipE | 538 | 326 | |
Rv2463 lipP |
esterase/lipase LipP | 459 | 268 | |
Rv2068c blaC |
beta-lactamase | 705 | 182 | textmining:655 |
Rv1075c hyp |
hypothetical protein | 649 | 57 | textmining:644 |
Rv3203 lipV |
lipase LipV | 643 | 48 | textmining:640 |
Rv1834 lipZ |
hydrolase | 655 | 46 | textmining:654 |
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): lipase LipD
- Pfam (hmmscan --cut_ga): Beta-lactamase PF00144.30 (E=2e-65)
- (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_216439.1)
- 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 P95290 (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 —
12 functional partner(s); context anchor
Rv1922 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1923|lipD MDVAGLPRLAAGTQAAIIHGMAQPPSLLTTDNGLPFGVQGACDSRFTGVIRAFAGLYPGRKFGGGALSVYIDGRQVVDVWTGWSDRQGKVPWTADTGAMVFSATKGLAATVIHRLVDRGLLSYDAPVAEYWPEFGANGKSEVTVSDVLRHRSGLAHLKGVDKDEVMDHLLMEQKLAAAPLDRQHGKLAYHAVTYGWLLSGLARAVTGKGMRELFREELARPLNTDGIHLGRPPADSPTKAAQTLLPQAKVPTPLLDFIAPKVAGLSFSGLLGAVYFPGILSLLQDDMPFLDGEVPAVNGVVTARALAKTYGALANDGVIDGTRLLSSQAVRGLTGKSELWPDLNLGLPFTYHQGYQSSPVPGLLEGYGHIGLGGTIGWADPETGSAFGYVHNRLLTLLLFDIGSFAGLAALLNSAVVAARRDDPLEVPHFGAPYSEPRHEQAASGA