lpqQ Family assigned · medium auto-curated
H37Rv Rv0835 · MTBC0 mtbc0_000889 ·
214 aa · 934104–934748 (+) ·
RefSeq NP_215350.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqQ |
|---|---|
| MTBC0 PGAP re-annotation | sensor domain-containing protein |
| Revised (this work) | Sensor domain-containing protein. Pfam: PknH_C (PF14032.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53846
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible lipoprotein LpqQ |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lpqQ |
| eggNOG description | PknH-like extracellular domain |
| Orthologous group | 2B2XV |
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 | 2.625 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 8 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 1.08% of strains (1568) · 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 |
|---|---|---|---|---|
PknH_C | PF14032.13 | 6.3e-21 | 37–212 | PknH-like extracellular domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3198A (glutaredoxin protein), medium confidence from genomic context alone (score 545 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3198A |
glutaredoxin protein | 545 | 545 ctx | neighborhood:544 |
Rv3576 lppH |
lipoprotein LppH | 630 | 65 | textmining:621 |
Rv0556 |
transmembrane protein | 860 | 47 | textmining:860 |
Rv3705c hyp |
hypothetical protein | 810 | 47 | textmining:809 |
Rv3016 lpqA |
lipoprotein LpqA | 806 | 47 | textmining:805 |
Rv0963c hyp |
hypothetical protein | 804 | 47 | textmining:803 |
Rv1022 lpqU |
lipoprotein LpqU | 860 | 46 | textmining:860 |
Rv0403c mmpS1 |
membrane protein MmpS1 | 660 | 46 | textmining:659 |
Rv1418 lprH |
lipoprotein LprH | 870 | 44 | textmining:870 |
Rv0361 |
membrane protein | 860 | 44 | textmining:860 |
Rv0178 |
Mce associated membrane protein | 440 | 44 | textmining:439 |
Rv1754c hyp |
hypothetical protein | 628 | 42 | textmining:628 |
Rv3069 crcB |
fluoride ion transporter CrcB | 860 | 41 | textmining:860 |
Rv3630 |
integral membrane protein | 803 | 41 | textmining:803 |
Rv0200 |
transmembrane protein | 630 | 41 | textmining:630 |
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 LpqQ
- MTBC0 PGAP product: sensor domain-containing protein
- Pfam (hmmscan --cut_ga): PknH_C PF14032.13 (E=6e-21)
- (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_215350.1)
- Domains: Pfam-A via hmmscan --cut_ga — PknH_C (PF14032.13)
- 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
2B2XV - Curated reference: UniProt O53846 (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 —
17 functional partner(s); context anchor
Rv3198A - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000889|Rv0835|lpqQ MCCSTAAKSAVIVCCAAIATTACSFQATSTQPSTAPPTSRVDSLIVSIEDVRRIANYEELAAHFQTDLREPPEADTNVPGPCRVVGSSDRTFGTDWSEFRSAGYHGVTDDLRPGGPVMVETVSQAIALYPDPSTARGVFHRLESSLAECAGLHDPYFDFILDRPDASTVRIGAAGWSHVYRLKSSVFISVGVLGIEPAEPIANVILQTISDRIQ