lppD Resolved · high auto-curated
H37Rv Rv1899c · MTBC0 - ·
343 aa · 2145214–2146245 (-) ·
RefSeq NP_216415.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LppD |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Lipoprotein LppD. Pfam: Macro (PF01661.28). |
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 |
P9WK29
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1899c |
UniProt still lists this protein as Uncharacterized protein Rv1899c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lppD |
| eggNOG description | Appr-1'-p processing enzyme |
| Orthologous group | COG2110 |
| Gene Ontology (7) |
GO:0005575, GO:0005576, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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) pseudogene candidate
| pN/pS | 0.45 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 1.06% of strains (1544) · 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 |
|---|---|---|---|---|
Macro | PF01661.28 | 1.4e-29 | 193–302 | Macro domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lipJ (lignin peroxidase LipJ), high confidence from genomic context alone (score 788 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1900c lipJ |
lignin peroxidase LipJ | 789 | 788 ctx | neighborhood:780 |
Rv1151c cobB |
NAD-dependent protein deacylase | 775 | 765 ctx | cooccurence:586 |
Rv1901 cinA |
competence damage-inducible protein CinA | 592 | 593 ctx | neighborhood:580 |
Rv2972c hyp |
hypothetical protein | 423 | 419 | |
Rv0143c |
transmembrane protein | 403 | 403 | |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 426 | 384 | |
Rv2116 lppK |
lipoprotein LppK | 690 | 151 | textmining:650 |
Rv0805 cpdA |
3',5'-cyclic adenosine monophosphate phosphodiesterase CpdA | 462 | 91 | textmining:433 |
Rv3623 lpqG |
lipoprotein LpqG | 529 | 75 | textmining:512 |
Rv0619 galTb |
Rv0619, (MTCY19H5.02c), len: 181 aa (probable partial CDS). Probable galTb, second part of galactose-1-phosphate uridylyltransferase, highly | 452 | 75 | textmining:433 |
Rv3390 lpqD |
lipoprotein LpqD | 534 | 62 | textmining:524 |
Rv2080 lppJ |
lipoprotein LppJ | 486 | 55 | textmining:479 |
Rv3905c esxF |
ESAT-6 like protein EsxF | 478 | 52 | textmining:473 |
Rv0604 lpqO |
lipoprotein LpqO | 653 | 51 | textmining:650 |
Rv3904c esxE |
ESAT-6 like protein EsxE | 404 | 50 |
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): lipoprotein LppD
- Pfam (hmmscan --cut_ga): Macro PF01661.28 (E=1e-29)
- (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_216415.1)
- Domains: Pfam-A via hmmscan --cut_ga — Macro (PF01661.28)
- 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
COG2110 - Curated reference: UniProt P9WK29 (SwissProt, reviewed; 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
lipJ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1899c|lppD MSRAAGLPRLSWFAGLTWFAGGSTGAGCAAHPALAGLTAGARCPAYAAISASTARPAATAGTTPATGASGSARPTDAAGMADLARPGVVATHAVRTLGTTGSRAIGLCPCQPLDCPRSPQATLNLGSMGRSLDGPQWRRARVRLCGRWWRRSNTTRGASPRPPSTCRGDNVSMIELEVHQADVTKLELDAITNAANTRLRHAGGVAAAIARAGGPELQRESTEKAPIGLGEAVETTAGDMPARYVIHAATMELGGPTSGEIITAATAATLRKADELGCRSLALVAFGTGVGGFPLDDAARLMVGAVRRHRPGSLQRVVFAVHGDAAERAFSAAIQAGEDTARR