lprJ Resolved · medium auto-curated
H37Rv Rv1690 · MTBC0 mtbc0_001798 ·
127 aa · 1927542–1927925 (+) ·
RefSeq NP_216206.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LprJ |
|---|---|
| MTBC0 PGAP re-annotation | lipoprotein LprJ |
| Revised (this work) | Lipoprotein LprJ. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33192
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative lipoprotein LprJ |
| Curated function | Overexpression induces expression of sensor protein kdpD gene at low K(+) concentrations (0 and 250 uM, tested in M.smegatis). |
UniProt still lists this protein as Putative lipoprotein LprJ; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lprJ |
| eggNOG description | Protein of unknown function (DUF732) |
| Orthologous group | 2EPYI |
| Gene Ontology (6) |
GO:0005575, 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 0 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 7.89% of strains (11457) · 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 |
|---|---|---|---|---|
DUF732 | PF05305.20 | 3.3e-12 | 47–114 | Protein of unknown function (DUF732) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1692 (phosphatase), high confidence from genomic context alone (score 741 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1691 hyp |
hypothetical protein | 744 | 744 ctx | neighborhood:740 |
Rv1692 |
phosphatase | 741 | 741 ctx | neighborhood:741 |
Rv1693 hyp |
hypothetical protein | 735 | 735 ctx | neighborhood:732 |
Rv1695 ppnK |
inorganic polyphosphate/ATP-NAD kinase | 734 | 734 ctx | neighborhood:732 |
Rv1694 tlyA |
16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA | 732 | 733 ctx | neighborhood:732 |
Rv0888 spmT hyp |
hypothetical protein | 687 | 687 | coexpression:687 |
Rv1696 recN |
DNA repair protein RecN | 668 | 668 ctx | neighborhood:668 |
Rv1689 tyrS |
tyrosine--tRNA ligase | 543 | 512 ctx | neighborhood:509 |
Rv1469 ctpD |
cobalt/nickel-exporting P-type ATPase | 457 | 458 | coexpression:458 |
Rv1697 steA hyp |
hypothetical protein | 441 | 440 ctx | neighborhood:435 |
Rv1698 mctB |
copper transporter MctB | 409 | 409 ctx | neighborhood:403 |
Rv3675 |
membrane protein | 535 | 212 | textmining:435 |
Rv3717 hyp |
hypothetical protein | 541 | 53 | textmining:536 |
Rv1028A kdpF |
membrane protein KdpF | 545 | 50 | textmining:541 |
Rv1368 lprF |
lipoprotein LprF | 652 | 49 | textmining:649 |
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 LprJ
- MTBC0 PGAP product: lipoprotein LprJ
- Pfam (hmmscan --cut_ga): DUF732 PF05305.20 (E=3e-12)
- (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_216206.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF732 (PF05305.20)
- 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
2EPYI - Curated reference: UniProt O33192 (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 —
17 functional partner(s); context anchor
Rv1692 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001798|Rv1690|lprJ MTAHTHDGTRTWRTGRQATTLLALLAGVFGGAASCAAPIQADMMGNAFLTALTNAGIAYDQPATTVALGRSVCPMVVAPGGTFESITSRMAEINGMSRDMASTFTIVAIGTYCPAVIAPLMPNRLQA