lppJ Family assigned · medium auto-curated
H37Rv Rv2080 · MTBC0 mtbc0_002214 ·
187 aa · 2365919–2366482 (+) ·
RefSeq NP_216596.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LppJ |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Contains LppJ (PF27220.1) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WK77
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative lipoprotein LppJ |
UniProt still lists this protein as Putative lipoprotein LppJ; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Preferred name | lppJ |
|---|---|
| Orthologous group | 29IV3 |
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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 | 1.833 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 6 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.20% of strains (285) · 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 |
|---|---|---|---|---|
LppJ | PF27220.1 | 5.3e-49 | 53–183 | Putative lipoprotein LppJ |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1885c (chorismate mutase), medium confidence from genomic context alone (score 547 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2078 hyp |
hypothetical protein | 885 | 885 ctx | neighborhood:882 |
Rv2079 hyp |
hypothetical protein | 814 | 813 ctx | neighborhood:801 |
Rv1885c |
chorismate mutase | 546 | 547 ctx | neighborhood:544 |
Rv0604 lpqO |
lipoprotein LpqO | 662 | 55 | textmining:657 |
Rv1899c lppD |
lipoprotein LppD | 486 | 55 | textmining:479 |
Rv0404 fadD30 |
long-chain-fatty-acid--AMP ligase FadD30 | 441 | 53 | textmining:434 |
Rv0565c |
monooxygenase | 515 | 50 | textmining:511 |
Rv0323c hyp |
hypothetical protein | 651 | 44 | textmining:650 |
Rv3756c proZ |
glycine betaine/carnitine/choline/L-proline ABC transporter permease ProZ | 517 | 44 | textmining:516 |
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 LppJ
- MTBC0 PGAP product: hypothetical protein
- Pfam (hmmscan --cut_ga): LppJ PF27220.1 (E=5e-49)
- (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_216596.1)
- Domains: Pfam-A via hmmscan --cut_ga — LppJ (PF27220.1)
- 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
29IV3 - Curated reference: UniProt P9WK77 (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 —
9 functional partner(s); context anchor
Rv1885c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002214|Rv2080|lppJ MPHSTADRRLRLTRQALLAAAVVPLLAGCALVMHKPHSAGSSNPWDDSAHPLTDDQAMAQVVEPAKQIVAAADLQAVRAGFSFTSCNDQGDPPYQGTVRMAFLLQGDHDAYFQHVRAAMLSHGWIDGPPPGQYFHGITLHKNGVTANMSLALDHSYGEMILDGECRNTTDHHHDDETTNITNQLVQP