lpqX Still unknown · low auto-curated
H37Rv Rv1228 · MTBC0 mtbc0_001316 ·
185 aa · 1379364–1379921 (+) ·
RefSeq NP_215744.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqX |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33224
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable lipoprotein LpqX |
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 6 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: Rv1227c (transmembrane protein), medium confidence from genomic context alone (score 550 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1227c |
transmembrane protein | 549 | 550 ctx | neighborhood:547 |
Rv1226c |
transmembrane protein | 549 | 549 ctx | neighborhood:547 |
Rv2403c lppR |
lipoprotein LppR | 655 | 46 | textmining:654 |
Rv2138 lppL |
lipoprotein LppL | 545 | 46 | textmining:543 |
Rv0399c lpqK |
lipoprotein LpqK | 655 | 45 | textmining:654 |
Rv0419 lpqM |
lipoprotein peptidase LpqM | 615 | 44 | textmining:614 |
Rv3576 lppH |
lipoprotein LppH | 517 | 44 | textmining:516 |
Rv3044 fecB |
FeIII-dicitrate-binding periplasmic lipoprotein | 440 | 44 | textmining:439 |
Rv0237 lpqI |
lipoprotein LpqI | 630 | 42 | textmining:630 |
Rv1857 modA |
molybdate ABC transporter substrate-binding lipoprotein ModA | 514 | 42 | textmining:514 |
Rv3244c lpqB |
lipoprotein LpqB | 630 | 41 | textmining:630 |
Rv1016c lpqT |
lipoprotein LpqT | 542 | 41 | textmining:542 |
Rv0418 lpqL |
lipoprotein aminopeptidase LpqL | 475 | 41 | textmining:475 |
Rv1166 lpqW |
monoacyl phosphatidylinositol tetramannoside-binding protein LpqW | 433 | 41 | textmining:433 |
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 LpqX
- MTBC0 PGAP product: hypothetical protein
- (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_215744.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt O33224 (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 —
14 functional partner(s); context anchor
Rv1227c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001316|Rv1228|lpqX MSRQWHWLAATLLLITTAACSRPGTEEPDCPTKITLPPGATPTTTLDPRCIVRATTTGTADGDAASRWTGTVRIAGFYASICNAVWDGNVSLAGKDELTGKATLILVETSCPGKVVAGELVLKGNVGSDSLAITWAHPELPQRAFDLGAGQGTIRRSGDRAEGTFNSDMGGGTEFFLTWSLTMRN