lpqR Family assigned · medium auto-curated
H37Rv Rv0838 · MTBC0 mtbc0_000893 ·
256 aa · 937871–938641 (+) ·
RefSeq NP_215353.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqR |
|---|---|
| MTBC0 PGAP re-annotation | M15 family metallopeptidase |
| Revised (this work) | M15 family metallopeptidase. Pfam: Peptidase_M15 (PF01427.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53850
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | D-alanyl-D-alanine dipeptidase |
| EC (curated) |
EC 3.4.13.22
|
| Curated function | Catalyzes hydrolysis of the D-alanyl-D-alanine dipeptide. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | lpqR |
| eggNOG description | Catalyzes hydrolysis of the D-alanyl-D-alanine dipeptide |
| Orthologous group | COG2173 |
| EC number |
EC 3.4.13.22
|
| KEGG orthology |
K08641
|
| KEGG pathways |
map01502, map02020
|
| KEGG modules |
M00651
|
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 | 0.89 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.17% of strains (250) · 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 |
|---|---|---|---|---|
Peptidase_M15 | PF01427.23 | 5.3e-85 | 63–255 | D-ala-D-ala dipeptidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lpqI (lipoprotein LpqI), medium confidence from genomic context alone (score 454 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0839 hyp |
hypothetical protein | 781 | 781 ctx | neighborhood:780 |
Rv0237 lpqI |
lipoprotein LpqI | 454 | 454 ctx | fusion:452 |
Rv0315 |
beta-1,3-glucanase | 665 | 316 | textmining:531 |
Rv2981c ddlA |
D-alanine--D-alanine ligase | 520 | 182 | textmining:438 |
Rv1493 mutB |
methylmalonyl-CoA mutase large subunit | 453 | 77 | textmining:432 |
Rv0175 |
Mce associated membrane protein | 550 | 46 | textmining:548 |
Rv1252c lprE |
lipoprotein LprE | 401 | 46 | |
Rv3491 hyp |
hypothetical protein | 805 | 44 | textmining:805 |
Rv0852 fadD16 hyp |
hypothetical protein | 680 | 42 | textmining:680 |
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 LpqR
- MTBC0 PGAP product: M15 family metallopeptidase
- Pfam (hmmscan --cut_ga): Peptidase_M15 PF01427.23 (E=5e-85)
- (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_215353.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_M15 (PF01427.23)
- 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
COG2173 - Curated reference: UniProt O53850 (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 —
9 functional partner(s); context anchor
lpqI - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000893|Rv0838|lpqR MRLIGRLRLLMVGLVVICGACACDRVSAGRWSESPSATSWPVRPVNTTTPSGPVPPVSEAARAAGLVDVRGVVPDAAIDLRYATANNFTGTQLYPPGARCLVHESMAEGLAAAAAVLRPHGQVLVFWDCYRPHDVQVRMFDVVPNPAWVARPGKYAHSHEAGRSVDVTFASAQRQCPSVRRSGELCLADMGTDFDDFSSRATAFATQGVSAEAQANRAHLRAAMQAGGLTVYSGEWWHFDGPGAGVDRPILEVPVD