lpqA Family assigned · medium auto-curated
H37Rv Rv3016 · MTBC0 mtbc0_003205 ·
209 aa · 3397067–3397696 (+) ·
RefSeq NP_217532.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqA |
|---|---|
| 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 |
I6Y2A3
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable lipoprotein LpqA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lpqA |
| eggNOG description | PknH-like extracellular domain |
| Orthologous group | 2AG2D |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
PknH_C | PF14032.13 | 7.4e-10 | 42–193 | PknH-like extracellular domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ligA (DNA ligase A), medium confidence from genomic context alone (score 526 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3015c hyp |
hypothetical protein | 782 | 783 ctx | neighborhood:782 |
Rv3014c ligA |
DNA ligase A | 526 | 526 ctx | neighborhood:525 |
Rv0835 lpqQ |
lipoprotein LpqQ | 806 | 47 | textmining:805 |
Rv3576 lppH |
lipoprotein LppH | 656 | 46 | textmining:655 |
Rv1418 lprH |
lipoprotein LprH | 870 | 45 | textmining:870 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 652 | 44 | textmining:651 |
Rv0424c hyp |
hypothetical protein | 432 | 44 | textmining:431 |
Rv3705c hyp |
hypothetical protein | 870 | 42 | textmining:870 |
Rv2781c |
oxidoreductase | 432 | 42 | textmining:432 |
Rv1690 lprJ |
lipoprotein LprJ | 562 | 41 | textmining:562 |
Rv1244 lpqZ |
lipoprotein LpqZ | 541 | 41 | textmining:541 |
Rv0179c lprO |
lipoprotein LprO | 520 | 41 | textmining:520 |
Rv0461 |
transmembrane protein | 431 | 41 | 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 LpqA
- MTBC0 PGAP product: sensor domain-containing protein
- Pfam (hmmscan --cut_ga): PknH_C PF14032.13 (E=7e-10)
- (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_217532.1)
- 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
2AG2D - Curated reference: UniProt I6Y2A3 (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 —
13 functional partner(s); context anchor
ligA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003205|Rv3016|lpqA MVGLTRPLLLCGATLLIAACTRVVGGTASATFGGDRQGMLDVATILLDQSRMQAITGSGDDLTIIPTMDTTYPVDVDDFAQPIPRECRFIYAETAVFGSEIEAFHKTTFQDRPDGSLISEAAAAYRDAGTARRAFDTLAVTVHDCAASPAGWLFVSRWTAGGNSLHIRAGDCGRDYRVLSAALLEVTFCGFPESVSDIVMTNIAANVPG