lpqH Resolved · high auto-curated
H37Rv Rv3763 · MTBC0 mtbc0_003987 ·
159 aa · 4233168–4233647 (+) ·
RefSeq NP_218280.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqH |
|---|---|
| MTBC0 PGAP re-annotation | lipoprotein LpqH |
| Revised (this work) | Lipoprotein LpqH. Pfam: Myco_19_kDa (PF05481.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WK61
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Lipoprotein LpqH |
| Curated function | Based on its structure might be involved in ligand transport (By similarity) (Ref.25)..; FUNCTION: A host TLR2 agonist. Plays a complicated role in bacterial interactions with the host immune system; some effects favor the host (induces interleukin 1-beta and IL-12 p40 (IL12B), both increase the host's immune response) while others favor the bacteria (increases growth in monocyte-derived macrophages and decreases host MHC class II (MHC-II) expression and antigen processing). Induces host (human and mouse) IL-12 p40 (IL12B, a pro-inflammatory cytokine) release by monocyte cell lines via TLR2 an. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lpqH |
| eggNOG description | 19 kDa lipoprotein antigen |
| Orthologous group | 28UBJ |
| KEGG orthology |
K14953
|
| KEGG pathways |
map05152
|
| Gene Ontology (92) |
GO:0001906, GO:0001907, GO:0003674, GO:0005488, GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0009605, GO:0009607 +80 more
|
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 | 0.74 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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 |
|---|---|---|---|---|
Myco_19_kDa | PF05481.18 | 4.7e-36 | 48–158 | Mycobacterium 19 kDa lipoprotein antigen |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3762c (hydrolase), medium confidence from genomic context alone (score 532 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3762c |
hydrolase | 532 | 532 ctx | neighborhood:512 |
Rv2220 glnA1 |
glutamine synthetase | 482 | 246 | |
Rv3846 sodA |
superoxide dismutase | 472 | 99 | textmining:438 |
Rv1886c fbpB |
diacylglycerol acyltransferase/mycolyltransferase Ag85B | 544 | 93 | textmining:518 |
Rv1270c lprA |
lipoprotein LprA | 955 | 87 | textmining:954 |
Rv0934 pstS1 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 867 | 87 | textmining:861 |
Rv1310 atpD |
ATP synthase subunit beta | 429 | 71 | textmining:411 |
Rv1368 lprF |
lipoprotein LprF | 753 | 70 | textmining:745 |
Rv0475 hbhA |
heparin binding hemagglutinin HbhA | 549 | 67 | textmining:537 |
Rv1860 apa hyp |
hypothetical protein | 681 | 64 | textmining:674 |
Rv3006 lppZ |
lipoprotein LppZ | 582 | 64 | textmining:573 |
Rv0583c lpqN |
lipoprotein LpqN | 687 | 55 | textmining:683 |
Rv0431 |
tuberculin-like peptide | 518 | 55 | textmining:511 |
Rv1488 hyp |
hypothetical protein | 517 | 55 | textmining:510 |
Rv3491 hyp |
hypothetical protein | 439 | 55 | textmining:431 |
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 LpqH
- MTBC0 PGAP product: lipoprotein LpqH
- Pfam (hmmscan --cut_ga): Myco_19_kDa PF05481.18 (E=5e-36)
- (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_218280.1)
- Domains: Pfam-A via hmmscan --cut_ga — Myco_19_kDa (PF05481.18)
- 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
28UBJ - Curated reference: UniProt P9WK61 (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 —
30 functional partner(s); context anchor
Rv3762c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003987|Rv3763|lpqH MKRGLTVAVAGAAILVAGLSGCSSNKSTTGSGETTTAAGTTASPGAASGPKVVIDGKDQNVTGSVVCTTAAGNVNIAIGGAATGIAAVLTDGNPPEVKSVGLGNVNGVTLGYTSGTGQGNASATKDGSHYKITGTATGVDMANPMSPVNKSFEIEVTCS