lpqS Resolved · high auto-curated
H37Rv Rv0847 · MTBC0 mtbc0_000902 ·
130 aa · 947494–947886 (+) ·
RefSeq NP_215362.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqS |
|---|---|
| MTBC0 PGAP re-annotation | lipoprotein LpqS |
| Revised (this work) | Lipoprotein LpqS. Pfam: LpqS (PF26327.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53859
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | Lipoprotein LpqS |
| Curated function | May play an essential role in M.tuberculosis replication and survival inside the host cell. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Preferred name | lpqS |
|---|---|
| Orthologous group | 2BG8G |
| KEGG orthology |
K21608
|
| Gene Ontology (6) |
GO:0008150, GO:0010035, GO:0010038, GO:0042221, GO:0046688, GO:0050896
|
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 | 0.194 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
LpqS | PF26327.1 | 9.2e-46 | 4–130 | Lipoprotein LpqS family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cysK2 (cysteine synthase CysK), high confidence from genomic context alone (score 901 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0848 cysK2 |
cysteine synthase CysK | 964 | 901 ctx | neighborhood:512 coexpression:806 textmining:652 |
Rv0849 |
MFS-type transporter | 969 | 854 ctx | neighborhood:472 coexpression:734 textmining:803 |
Rv0846c mmcO |
oxidase | 980 | 853 ctx | neighborhood:772 textmining:870 |
Rv2963 |
integral membrane protein | 974 | 813 | coexpression:813 textmining:870 |
Rv0850 |
Rv0850, (MTV043.43), len: 110 aa. Putative transposase (fragment), similar in part to others e.g. Q45144|Q4514 transposable element IS31831 | 909 | 553 ctx | neighborhood:473 textmining:805 |
Rv0190 ricR hyp |
hypothetical protein | 883 | 144 | textmining:870 |
Rv0968 hyp |
hypothetical protein | 429 | 83 | textmining:403 |
Rv0967 csoR |
copper-sensing transcriptional repressor CsoR | 663 | 56 | textmining:658 |
Rv2641 cadI |
cadmium inducible protein CadI | 447 | 55 | textmining:439 |
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 517 | 54 | textmining:511 |
Rv0970 |
integral membrane protein | 418 | 54 | textmining:411 |
Rv2115c mpa |
proteasome-associated ATPase | 544 | 47 | textmining:542 |
Rv1946c lppG |
lipoprotein | 531 | 44 | textmining:530 |
Rv0604 lpqO |
lipoprotein LpqO | 465 | 44 | textmining:464 |
Rv1049 |
transcriptional repressor | 433 | 42 | 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 LpqS
- MTBC0 PGAP product: lipoprotein LpqS
- Pfam (hmmscan --cut_ga): LpqS PF26327.1 (E=9e-46)
- (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_215362.1)
- Domains: Pfam-A via hmmscan --cut_ga — LpqS (PF26327.1)
- 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
2BG8G - Curated reference: UniProt O53859 (SwissProt, reviewed; Evidence at transcript 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
cysK2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000902|Rv0847|lpqS MVWMRSAIVAVALGVTVAAVAAACWLPQLHRHVAHPNHPLTTSVGSEFVINTDHGHLVDNSMPPCPERLATAVLPRSATPVLLPDVVAAAPGMTAALTDPVAPAARGPPAAQGSVRTGQDLLTRFCLARR