lpqT Resolved · high auto-curated
H37Rv Rv1016c · MTBC0 - ·
226 aa · 1134785–1135465 (-) ·
RefSeq NP_215532.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqT |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Lipoprotein LpqT. Pfam: Lpp-LpqN (PF10738.16). |
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 |
P9WK59
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative lipoprotein LpqT |
UniProt still lists this protein as Putative lipoprotein LpqT; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lpqT |
| eggNOG description | Probable lipoprotein LpqN |
| Orthologous group | 2APGE |
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 10.41% of strains (15110) · 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 |
|---|---|---|---|---|
Lpp-LpqN | PF10738.16 | 1.2e-64 | 57–224 | Probable lipoprotein LpqN |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: prsA (ribose-phosphate pyrophosphokinase), high confidence from genomic context alone (score 834 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 833 | 834 ctx | neighborhood:832 |
Rv1018c glmU |
bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase | 748 | 749 ctx | neighborhood:747 |
Rv1015c rplY |
50S ribosomal protein L25/general stress protein Ctc | 735 | 735 ctx | neighborhood:732 |
Rv1014c pth |
peptidyl-tRNA hydrolase | 730 | 729 ctx | neighborhood:728 |
Rv1019 |
transcriptional regulator | 667 | 668 ctx | neighborhood:667 |
Rv0418 lpqL |
lipoprotein aminopeptidase LpqL | 414 | 52 | textmining:408 |
Rv0237 lpqI |
lipoprotein LpqI | 551 | 51 | textmining:547 |
Rv3044 fecB |
FeIII-dicitrate-binding periplasmic lipoprotein | 529 | 50 | textmining:525 |
Rv2945c lppX |
lipoprotein LppX | 468 | 50 | textmining:463 |
Rv3244c lpqB |
lipoprotein LpqB | 700 | 47 | textmining:698 |
Rv1368 lprF |
lipoprotein LprF | 598 | 47 | textmining:596 |
Rv2403c lppR |
lipoprotein LppR | 561 | 47 | textmining:559 |
Rv0419 lpqM |
lipoprotein peptidase LpqM | 543 | 47 | textmining:541 |
Rv2138 lppL |
lipoprotein LppL | 437 | 47 | textmining:434 |
Rv3576 lppH |
lipoprotein LppH | 437 | 47 | textmining:434 |
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 LpqT
- Pfam (hmmscan --cut_ga): Lpp-LpqN PF10738.16 (E=1e-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_215532.1)
- Domains: Pfam-A via hmmscan --cut_ga — Lpp-LpqN (PF10738.16)
- 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
2APGE - Curated reference: UniProt P9WK59 (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 —
21 functional partner(s); context anchor
prsA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1016c|lpqT MAGRRCPQDSVRPLAVAVAVATLAMSAVACGPKSPDFQSILSTSPTTSAVSTTTEVPVPLWKYLESVGVTGEPVAPSSLTDLTVSIPTPPGWAPMKNPNITPNTEMIAKGESYPTAMLMVFKLHRDFDIAEALKHGTADARLSTNFTELDSSTADFNGFPSSMIQGSYDLHGRRLHTWNRIVFPTGAPPAKQRYLVQLTITSLANEAVKHASDIEAIIAGFVVAAK