lpqK Family assigned · medium auto-curated
H37Rv Rv0399c · MTBC0 mtbc0_000419 ·
409 aa · 480691–481920 (-) ·
RefSeq NP_214913.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqK |
|---|---|
| MTBC0 PGAP re-annotation | serine hydrolase domain-containing protein |
| Revised (this work) | Serine hydrolase domain-containing protein. Pfam: Beta-lactamase (PF00144.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95207
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible conserved lipoprotein LpqK |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| Preferred name | lpqK |
| eggNOG description | beta-lactamase |
| Orthologous group | COG1680 |
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 | 1.381 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 12 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.45% of strains (659) · 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 |
|---|---|---|---|---|
Beta-lactamase | PF00144.30 | 7.0e-55 | 42–388 | Beta-lactamase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE7 (acyl-CoA dehydrogenase FadE7), high confidence from genomic context alone (score 887 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0400c fadE7 |
acyl-CoA dehydrogenase FadE7 | 887 | 887 ctx | neighborhood:882 |
Rv0398c hyp |
hypothetical protein | 882 | 882 ctx | neighborhood:881 |
Rv0907 hyp |
hypothetical protein | 738 | 739 ctx | cooccurence:736 |
Rv0401 |
transmembrane protein | 649 | 649 ctx | neighborhood:649 |
Rv3372 otsB2 |
trehalose 6-phosphate phosphatase | 546 | 547 ctx | neighborhood:544 |
Rv2305 hyp |
hypothetical protein | 509 | 510 ctx | cooccurence:495 |
Rv1367c hyp |
hypothetical protein | 503 | 503 ctx | cooccurence:496 |
Rv1215c hyp |
hypothetical protein | 425 | 425 ctx | cooccurence:406 |
Rv0237 lpqI |
lipoprotein LpqI | 708 | 207 | textmining:647 |
Rv1368 lprF |
lipoprotein LprF | 411 | 167 | |
Rv3627c dacB hyp |
hypothetical protein | 423 | 56 | textmining:414 |
Rv2403c lppR |
lipoprotein LppR | 658 | 53 | textmining:654 |
Rv1166 lpqW |
monoacyl phosphatidylinositol tetramannoside-binding protein LpqW | 459 | 52 | textmining:454 |
Rv0483 lprQ |
lipoprotein LprQ | 420 | 52 | textmining:414 |
Rv1857 modA |
molybdate ABC transporter substrate-binding lipoprotein ModA | 519 | 51 | textmining:514 |
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 LpqK
- MTBC0 PGAP product: serine hydrolase domain-containing protein
- Pfam (hmmscan --cut_ga): Beta-lactamase PF00144.30 (E=7e-55)
- (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_214913.1)
- Domains: Pfam-A via hmmscan --cut_ga — Beta-lactamase (PF00144.30)
- 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
COG1680 - Curated reference: UniProt P95207 (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 —
23 functional partner(s); context anchor
fadE7 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000419|Rv0399c|lpqK MPVLRRLGCSVLALGLLAGCAPPRTGPASSPTNNGAKADAVIRIVRDFMTQAHLKAVLVRVTVAGKEVVTRAVGDSMTGVPATTAMHFRNGAVAISYVATLLLKLVDEKKLRLDDKLSRWLPDFPHADRVTLGQLAQMTSGYPDYVLGNEAFDAELYANPFRQWTTQELLDQISSRPLLYDPGTNWNYAHTNYLLLGLALEKAAGQDMPTLLQRKVLSPLGLTATANSDTPAIPEPALHAFTSERRAALKIPAGVPFYEESTFWNPSWTITHGAIQTTTIYDMEATAVGIGSGRLLSADSYKKMVSTELRGKTRAQPGCPTCFEQNDGYSYGLGIVISGHWLLQNPMFAGYAAVEAYLPSQRVAVAVAVTYAPEAFDDQGNYRNQADILFRKIGAEVAPNDAPPMPPGR