lpqN Family assigned · medium auto-curated
H37Rv Rv0583c · MTBC0 mtbc0_000613 ·
228 aa · 681940–682626 (-) ·
RefSeq NP_215097.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqN |
|---|---|
| MTBC0 PGAP re-annotation | LpqN/LpqT family lipoprotein |
| Revised (this work) | LpqN/LpqT family lipoprotein. 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.
Curated reference (UniProt)
| UniProt |
O53780
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Lipoprotein LpqN |
| Curated function | Involved in cell envelope biogenesis. May act as a membrane fusion protein, connecting MmpL transporters with periplasmic proteins, and play a role in cell envelope lipid changes during biofilm maturation..; FUNCTION: Is also a virulence factor required for intracellular survival. Associates with CBL, a host ubiquitin ligase, and probably blocks the normal functions of CBL and disturbs CBL-mediated antibacterial activity. Interaction counteracts antibacterial defense but causes a reciprocal enhancement of antiviral defense. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lpqN |
| eggNOG description | Probable lipoprotein LpqN |
| Orthologous group | 2FK6M |
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 | 1.353 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 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 |
|---|---|---|---|---|
Lpp-LpqN | PF10738.16 | 2.1e-59 | 57–227 | Probable lipoprotein LpqN |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0584 (glycosidase), high confidence from genomic context alone (score 772 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0584 |
glycosidase | 771 | 772 ctx | neighborhood:771 |
Rv1270c lprA |
lipoprotein LprA | 755 | 83 | textmining:745 |
Rv0418 lpqL |
lipoprotein aminopeptidase LpqL | 724 | 75 | textmining:715 |
Rv2299c htpG |
chaperone protein HtpG | 566 | 70 | textmining:553 |
Rv3763 lpqH |
lipoprotein LpqH | 687 | 55 | textmining:683 |
Rv1368 lprF |
lipoprotein LprF | 819 | 52 | textmining:818 |
Rv1876 bfrA |
bacterioferritin BfrA | 433 | 51 | textmining:427 |
Rv0350 dnaK |
chaperone protein DnaK | 417 | 51 | textmining:411 |
Rv3006 lppZ |
lipoprotein LppZ | 836 | 50 | textmining:835 |
Rv1411c lprG |
lipoprotein LprG | 722 | 50 | textmining:720 |
Rv2945c lppX |
lipoprotein LppX | 794 | 47 | textmining:793 |
Rv2873 mpt83 |
cell surface lipoprotein | 484 | 47 | textmining:481 |
Rv3418c groES |
chaperonin GroES | 452 | 47 | textmining:449 |
Rv0033 acpA |
acyl carrier protein AcpA | 429 | 47 | textmining:425 |
Rv1816 |
HTH-type transcriptional regulator | 641 | 46 | textmining:640 |
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 LpqN
- MTBC0 PGAP product: LpqN/LpqT family lipoprotein
- Pfam (hmmscan --cut_ga): Lpp-LpqN PF10738.16 (E=2e-59)
- (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_215097.1)
- 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
2FK6M - Curated reference: UniProt O53780 (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 —
18 functional partner(s); context anchor
Rv0584 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000613|Rv0583c|lpqN MKHFTAAVATVALSLALAGCSFNIKTDSAPTTSPTTTSPTTSTTTTSATTSAQAAGPNYTIADYIRDNHIQETPVHHGDPGSPTIDLPVPDDWRLLPESSRAPYGGIVYTQPADPNDPPTIVAILSKLTGDIDPAKVLQFAPGELKNLPGFQGSGDGSAATLGGFSAWQLGGSYSKNGKLRTVAQKTVVIPSQGAVFVLQLNADALDDETMTLMDAANVIDEQTTITP