lpqJ Family assigned · low
H37Rv Rv0344c · MTBC0 mtbc0_000364 ·
186 aa · 417704–418264 (-) ·
RefSeq NP_214858.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqJ |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Lipoprotein LpqJ with an LpqN/LpqE-like lipid-binding fold; possible association with the respiratory supercomplex RefSeq leaves this locus uncharacterised. |
Curated reference (UniProt)
| UniProt |
O06295
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable lipoprotein LpqJ |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Preferred name | lpqJ |
|---|---|
| Orthologous group | 2B7Q4 |
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 | 0.06 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 1 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0373c (carbon monoxyde dehydrogenase large subunit), medium confidence from genomic context alone (score 483 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0345 hyp |
hypothetical protein | 594 | 594 ctx | neighborhood:594 |
Rv0373c |
carbon monoxyde dehydrogenase large subunit | 482 | 483 ctx | neighborhood:480 |
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
- HHpred (Neff 8.0, signal peptide): hits to M.tb lipoproteins LpqN (6E5F, lipid-binding, 89%) and LpqE (6ADQ, respiratory supercomplex, 86%) + 7Q21 supercomplex (83%) + LPS-assembly lipoprotein folds (LptM/YifL); already named LpqJ
- HHpred web (MPI Bioinformatics Toolkit, profile-profile remote homology), interpreted in project 'Still unknown gene function', 2026-06-10. A fold/family-level assignment, not a demonstrated function.
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_214858.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2B7Q4 - Curated reference: UniProt O06295 (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 —
2 functional partner(s); context anchor
Rv0373c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000364|Rv0344c|lpqJ MRLSLIARGMAALLAATALVAGCNTTIDGRPVASPGSGPTEPTFPTPRPTTAPPGTTAPTLPTTPVSPTAPAGAIPLPPDSNGYVFIETKSGMTRCQINRDSVGCEAPFTNSPLRDGEHANGIHITAGGSVQWVLGNLGAIPTVSIDYRTYEAQGWTIDATTDGTRFTNNRTGHGMFVSIEKVDTF