lpqI Resolved · high auto-curated
H37Rv Rv0237 · MTBC0 - ·
388 aa · 287186–288352 (+) ·
RefSeq YP_177702.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqI |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Lipoprotein LpqI. Pfam: Glyco_hydro_3 (PF00933.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
L7N6B0
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Beta-hexosaminidase LpqI |
| EC (curated) |
EC 3.2.1.52
|
| Curated function | Plays a role in peptidoglycan recycling by cleaving the terminal beta-1,4-linked N-acetylglucosamine (GlcNAc) from peptidoglycan fragments. Acts as a regulator for GlcNAc-MurNAc levels by cleaving disaccharides and allowing the breakdown of MurNAc. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | lpqI |
| eggNOG description | hydrolase, family 3 |
| Orthologous group | COG1472 |
| EC number |
EC 3.2.1.52
|
| KEGG orthology |
K01207
|
| KEGG pathways |
map00520, map00531, map01100, map01501
|
| KEGG modules |
M00628
|
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 | 1.038 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 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 |
|---|---|---|---|---|
Glyco_hydro_3 | PF00933.28 | 5.4e-88 | 62–378 | Glycosyl hydrolase family 3 N terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0238 (transcriptional regulator), high confidence from genomic context alone (score 746 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0236A hyp |
hypothetical protein | 781 | 781 ctx | neighborhood:778 |
Rv0238 |
transcriptional regulator | 746 | 746 ctx | neighborhood:743 |
Rv0236c aftD |
alpha-(1->3)-arabinofuranosyltransferase | 583 | 561 ctx | neighborhood:555 |
Rv0838 lpqR |
lipoprotein LpqR | 454 | 454 ctx | fusion:452 |
Rv0239 vapB24 |
antitoxin VapB24 | 444 | 444 ctx | neighborhood:440 |
Rv0240 vapC24 |
ribonuclease VapC24 | 443 | 444 ctx | neighborhood:440 |
Rv3332 nagA |
N-acetylglucosamine-6-phosphate deacetylase NagA | 897 | 424 | textmining:830 |
Rv0235c |
transmembrane protein | 415 | 415 ctx | neighborhood:415 |
Rv3242c hyp |
hypothetical protein | 404 | 404 | coexpression:400 |
Rv0418 lpqL |
lipoprotein aminopeptidase LpqL | 634 | 217 | textmining:552 |
Rv0399c lpqK |
lipoprotein LpqK | 708 | 207 | textmining:647 |
Rv2525c hyp |
hypothetical protein | 491 | 197 | |
Rv3044 fecB |
FeIII-dicitrate-binding periplasmic lipoprotein | 539 | 181 | textmining:461 |
Rv3244c lpqB |
lipoprotein LpqB | 591 | 79 | textmining:575 |
Rv1166 lpqW |
monoacyl phosphatidylinositol tetramannoside-binding protein LpqW | 465 | 74 | textmining:446 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): lipoprotein LpqI
- Pfam (hmmscan --cut_ga): Glyco_hydro_3 PF00933.28 (E=5e-88)
- (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 YP_177702.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glyco_hydro_3 (PF00933.28)
- 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
COG1472 - Curated reference: UniProt L7N6B0 (SwissProt, reviewed; 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 —
27 functional partner(s); context anchor
Rv0238 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0237|lpqI MAFPRTLAILAAAAALVVACSHGGTPTGSSTTSGASPATPVAVPVPRSCAEPAGIPALLSPRDKLAQLLVVGVRDAADAQAVVTNYHVGGILIGSDTDLTIFDGALAEIVAGGGPLPLAVSVDEEGGRVSRLRSLIGGTGPSARELAQTRTVQQVRDLARDRGRQMRKLGITIDFAPVVDVTDAPDDTVIGDRSFGSDPATVTAYAGAYAQGLRDAGVLPVLKHFPGHGRGSGDSHNGGVTTPPLDDLVGDDLVPYRTLVTQAPVGVMVGHLQVPGLTGSEPASLSKAAVNLLRTGTGYGAPPFDGPVFSDDLSGMAAISDRFGVSEAVLRTLQAGADIALWVTTKEVPAVLDRLEQALRAGELPMSAVDRSVVRVATMKGPNPGCGR