lppX Resolved · high auto-curated
H37Rv Rv2945c · MTBC0 mtbc0_003128 ·
233 aa · 3311621–3312322 (-) ·
RefSeq NP_217461.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LppX |
|---|---|
| MTBC0 PGAP re-annotation | LppX_LprAFG lipoprotein |
| Revised (this work) | LppX_LprAFG lipoprotein. Pfam: LppX_LprAFG (PF07161.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WK65
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative phthiocerol dimycocerosate transporter LppX |
| Curated function | Might be involved in translocating phthiocerol dimycocerosates (PDIM) from the cell membrane to the outer membrane; PDIM forms part of the cell wall. |
UniProt still lists this protein as Putative phthiocerol dimycocerosate transporter LppX; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | lppX |
| eggNOG description | Might be involved in translocating phthiocerol dimycocerosates (PDIM) from the cell membrane to the outer membrane |
| Orthologous group | 2BPGV |
| Gene Ontology (40) |
GO:0003674, GO:0005215, GO:0005319, GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0005886, GO:0006810, GO:0006869, GO:0008150, GO:0009273 +28 more
|
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 | 0.347 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
LppX_LprAFG | PF07161.20 | 5.5e-64 | 48–232 | LppX_LprAFG lipoprotein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pks1 (polyketide synthase), high confidence from genomic context alone (score 880 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2946c pks1 |
polyketide synthase | 911 | 880 ctx | neighborhood:469 coexpression:783 |
Rv2942 mmpL7 |
transmembrane transport protein MmpL7 | 953 | 764 ctx | cooccurence:760 textmining:812 |
Rv2608 PPE42 |
PPE family protein PPE42 | 747 | 747 ctx | cooccurence:747 |
Rv0878c PPE13 |
PPE family protein PPE13 | 737 | 738 ctx | cooccurence:734 |
Rv2939 papA5 |
phthiocerol/phthiodiolone dimycocerosyl transferase | 785 | 731 ctx | cooccurence:587 |
Rv0442c PPE10 |
PPE family protein PPE10 | 720 | 721 ctx | cooccurence:720 |
Rv0305c PPE6 |
PPE family protein PPE6 | 707 | 708 ctx | cooccurence:707 |
Rv2932 ppsB |
phthiocerol synthesis polyketide synthase type I PpsB | 717 | 705 | coexpression:703 |
Rv3343c PPE54 |
PPE family protein PPE54 | 704 | 705 ctx | cooccurence:699 |
Rv0256c PPE2 |
PPE family protein PPE2 | 702 | 703 ctx | cooccurence:702 |
Rv0755c PPE12 |
PPE family protein PPE12 | 696 | 697 ctx | cooccurence:696 |
Rv1548c PPE21 |
PPE family protein PPE21 | 695 | 696 ctx | cooccurence:694 |
Rv1917c PPE34 |
PPE family protein PPE34 | 694 | 695 ctx | cooccurence:694 |
Rv2356c PPE40 |
Rv2356c, (MTCY98.25), len: 615 aa. PPE40, Member of Mycobacterium tuberculosis PPE_family, highly similar to others e.g. Q10778|MTCY48.17|YF | 679 | 680 ctx | cooccurence:676 |
Rv0355c PPE8 |
PPE family protein PPE8 | 675 | 675 ctx | cooccurence:674 |
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 LppX
- MTBC0 PGAP product: LppX_LprAFG lipoprotein
- Pfam (hmmscan --cut_ga): LppX_LprAFG PF07161.20 (E=5e-64)
- (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_217461.1)
- Domains: Pfam-A via hmmscan --cut_ga — LppX_LprAFG (PF07161.20)
- 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
2BPGV - Curated reference: UniProt P9WK65 (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 —
91 functional partner(s); context anchor
pks1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003128|Rv2945c|lppX MNDGKRAVTSAVLVVLGACLALWLSGCSSPKPDAEEQGVPVSPTASDPALLAEIRQSLDATKGLTSVHVAVRTTGKVDSLLGITSADVDVRANPLAAKGVCTYNDEQGVPFRVQGDNISVKLFDDWSNLGSISELSTSRVLDPAAGVTQLLSGVTNLQAQGTEVIDGISTTKITGTIPASSVKMLDPGAKSARPATVWIAQDGSHHLVRASIDLGSGSIQLTQSKWNEPVNVD