lpqF Resolved · high auto-curated
H37Rv Rv3593 · MTBC0 mtbc0_003812 ·
452 aa · 4058029–4059387 (+) ·
RefSeq NP_218110.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqF |
|---|---|
| MTBC0 PGAP re-annotation | serine hydrolase |
| Revised (this work) | Serine hydrolase. Pfam: ORF_12_N (PF18042.8), Beta-lactamase2 (PF13354.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06155
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved lipoprotein LpqF |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| Preferred name | lpqF |
| eggNOG description | Beta-lactamase class A |
| Orthologous group | COG2367 |
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 | 0.398 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 synonymous, 13 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 |
|---|---|---|---|---|
ORF_12_N | PF18042.8 | 1.9e-18 | 51–138 | ORF 12 gene product N-terminal |
Beta-lactamase2 | PF13354.13 | 3.5e-24 | 154–284 | Beta-lactamase enzyme family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mhuD (heme-degrading monooxygenase), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3592 mhuD |
heme-degrading monooxygenase | 984 | 884 ctx | neighborhood:881 textmining:870 |
Rv3591c |
hydrolase | 790 | 791 ctx | neighborhood:791 |
Rv3810 pirG |
cell surface protein | 760 | 761 ctx | cooccurence:757 |
Rv3707c hyp |
hypothetical protein | 753 | 754 ctx | cooccurence:750 |
Rv2743c hyp |
hypothetical protein | 742 | 742 ctx | cooccurence:740 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 737 | 738 ctx | cooccurence:736 |
Rv0817c lmeA hyp |
hypothetical protein | 716 | 717 ctx | cooccurence:716 |
Rv0479c |
membrane protein | 670 | 670 ctx | cooccurence:660 |
Rv0416 thiS |
sulfur carrier protein ThiS | 667 | 667 ctx | cooccurence:666 |
Rv0518 hyp |
hypothetical protein | 621 | 621 ctx | cooccurence:620 |
Rv1275 lprC |
lipoprotein LprC | 606 | 607 ctx | cooccurence:591 |
Rv0320 hyp |
hypothetical protein | 604 | 604 ctx | cooccurence:603 |
Rv1836c hyp |
hypothetical protein | 564 | 564 ctx | cooccurence:535 |
Rv3594 hyp |
hypothetical protein | 578 | 563 ctx | neighborhood:495 |
Rv3244c lpqB |
lipoprotein LpqB | 561 | 562 ctx | cooccurence:548 |
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 LpqF
- MTBC0 PGAP product: serine hydrolase
- Pfam (hmmscan --cut_ga): ORF_12_N PF18042.8 (E=2e-18), Beta-lactamase2 PF13354.13 (E=3e-24)
- (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_218110.1)
- Domains: Pfam-A via hmmscan --cut_ga — ORF_12_N (PF18042.8), Beta-lactamase2 (PF13354.13)
- 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
COG2367 - Curated reference: UniProt O06155 (TrEMBL, unreviewed; Predicted)
- 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 —
66 functional partner(s); context anchor
mhuD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003812|Rv3593|lpqF MGPARLHNRRAGRRMLALSAAAALIVALASGCSSAPTPSANAANHGHRIDTRTPPGLRAQQTMDMLNSDWPIGEIGVGTLAAPGQVDTVKTTMEALWWDRPFALAGVDIGASVAALHLISSYGAQQDIRIHTDDDGWVDRFDVETQAPSIASWRDVDAVLSKTGARYSFQVAKVDNGRCDPVAGTNTGESLPLASIFKLYVLHALAGAVQHNTVSWDDLLTVTAKSKAVGSSGLELPVGARVSVRTAAEKMIATSDNMATDLLIERLGTRAIEEALASAGHHDPASMTPFPTMYELFSVGWGKPDLRDQWKHATQQVRAQILRQTNSTPYQPDPTRAHTPASNYGAEWYGSAEDICRVHAALRADAVGPASPVRQIMSAVPGIQLDRSVWPYIGAKAGGLPGDLTFSWYAVDKTGQPWVVSFQLNWPRDHGPTVTGWMLQVARQVFALIAPQ