lppV Family assigned · medium auto-curated
H37Rv Rv2796c · MTBC0 mtbc0_002975 ·
187 aa · 3127471–3128034 (-) ·
RefSeq NP_217312.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LppV |
|---|---|
| MTBC0 PGAP re-annotation | LppA family lipoprotein |
| Revised (this work) | LppA family lipoprotein. Pfam: LppA (PF16708.11). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71655
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved lipoprotein LppV |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lppV |
| eggNOG description | Lipoprotein confined to pathogenic Mycobacterium |
| Orthologous group | 2CAUG |
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 | 0.265 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 4 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (163) · 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 |
|---|---|---|---|---|
LppA | PF16708.11 | 6.9e-58 | 31–176 | Lipoprotein confined to pathogenic Mycobacterium |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2799 (membrane protein), medium confidence from genomic context alone (score 592 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2797c hyp |
hypothetical protein | 886 | 886 ctx | neighborhood:882 |
Rv2798c hyp |
hypothetical protein | 883 | 883 ctx | neighborhood:882 |
Rv2799 |
membrane protein | 592 | 592 ctx | neighborhood:589 |
Rv2794c pptT |
4'-phosphopantetheinyl transferase | 545 | 544 ctx | neighborhood:542 |
Rv2795c hyp |
hypothetical protein | 544 | 543 ctx | neighborhood:542 |
Rv2793c truB |
tRNA pseudouridine synthase B | 542 | 542 ctx | neighborhood:542 |
Rv2800 |
hydrolase | 529 | 529 ctx | neighborhood:529 |
Rv1662 pks8 |
polyketide synthase | 672 | 50 | textmining:670 |
Rv1527c pks5 |
polyketide synthase | 796 | 47 | textmining:796 |
Rv1266c pknH |
serine/threonine-protein kinase PknH | 511 | 44 | textmining:510 |
Rv1736c narX |
nitrate reductase-like protein NarX | 514 | 41 | textmining:514 |
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: lipoprotein LppV
- MTBC0 PGAP product: LppA family lipoprotein
- Pfam (hmmscan --cut_ga): LppA PF16708.11 (E=7e-58)
- (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_217312.1)
- Domains: Pfam-A via hmmscan --cut_ga — LppA (PF16708.11)
- 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
2CAUG - Curated reference: UniProt P71655 (TrEMBL, unreviewed; Predicted)
- 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 —
11 functional partner(s); context anchor
Rv2799 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002975|Rv2796c|lppV MRWPTAWLLALVCVMATGCGPSGHGTRAGEEGPLSPEKVAELENPLRAKPPLEDAKDQYRAAVTQLANAITALVPGLTWRTDMDTWTGCGGEYEWTRAKAAYFMIVFSGPIPDDKWLQAVQIVKDGVEQFGATGFGVMKNKPADHDVYFAGHGGVEFKFSTQKAAVLTAQSDCRISRTDTPKPSPTP