lpqU Resolved · high auto-curated
H37Rv Rv1022 · MTBC0 mtbc0_001098 ·
243 aa · 1151073–1151804 (+) ·
RefSeq NP_215538.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqU |
|---|---|
| MTBC0 PGAP re-annotation | lytic murein transglycosylase |
| Revised (this work) | Lytic murein transglycosylase. Pfam: SLT_2 (PF13406.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96378
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved lipoprotein LpqU |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | lpqU |
| eggNOG description | Transglycosylase SLT domain |
| Orthologous group | COG2951 |
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 | 1.059 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
SLT_2 | PF13406.12 | 2.8e-05 | 160–201 | Transglycosylase SLT domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1024 (membrane protein), high confidence from genomic context alone (score 776 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1024 |
membrane protein | 775 | 776 ctx | neighborhood:774 |
Rv1026 ppx2 hyp |
hypothetical protein | 764 | 765 ctx | neighborhood:762 |
Rv1025 hyp |
hypothetical protein | 763 | 763 ctx | neighborhood:762 |
Rv1021 mazG |
nucleoside triphosphate pyrophosphohydrolase | 662 | 662 ctx | neighborhood:657 |
Rv1020 mfd |
transcription-repair coupling factor | 669 | 656 ctx | neighborhood:654 |
Rv1023 eno |
enolase | 625 | 625 ctx | neighborhood:620 |
Rv1019 |
transcriptional regulator | 459 | 459 ctx | neighborhood:459 |
Rv2698 |
transmembrane protein | 426 | 426 ctx | cooccurence:426 |
Rv2518c ldtB |
L,D-transpeptidase LdtB | 419 | 419 ctx | cooccurence:418 |
Rv0813c hyp |
hypothetical protein | 403 | 404 ctx | cooccurence:402 |
Rv2163c pbpB |
penicillin-binding membrane protein PbpB | 409 | 377 | |
Rv0556 |
transmembrane protein | 893 | 218 | textmining:870 |
Rv0418 lpqL |
lipoprotein aminopeptidase LpqL | 716 | 207 | textmining:657 |
Rv3069 crcB |
fluoride ion transporter CrcB | 886 | 165 | textmining:870 |
Rv3630 |
integral membrane protein | 863 | 61 | textmining:861 |
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 LpqU
- MTBC0 PGAP product: lytic murein transglycosylase
- Pfam (hmmscan --cut_ga): SLT_2 PF13406.12 (E=3e-05)
- (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_215538.1)
- Domains: Pfam-A via hmmscan --cut_ga — SLT_2 (PF13406.12)
- 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
COG2951 - Curated reference: UniProt P96378 (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 —
22 functional partner(s); context anchor
Rv1024 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001098|Rv1022|lpqU MSPRRWLRAVAVIGATAMLLASSCTWQLSLFIPDGVPPPPGDPVPPVDTHAGGRPADQLREWAEKRAAALGIPVIALEAYAYAARVAEVENPKCHLAWTTLAGIGRVESHHGTYRGATIAPNGDVSPPIRGVRLDGTGGTLRIVDRDGGGLDGDAAVERAMGPMQFISETWRLYGVAARNDGIANVDNIDDAALSAAGYLCWRGKDLATPRGWITALRAYNNSVIYARAVRDWATAYAAGHPL