lpqM Resolved · medium auto-curated
H37Rv Rv0419 · MTBC0 mtbc0_000440 ·
498 aa · 508451–509947 (+) ·
RefSeq NP_214933.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein peptidase LpqM |
|---|---|
| MTBC0 PGAP re-annotation | neutral zinc metallopeptidase |
| Revised (this work) | Neutral zinc metallopeptidase. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96265
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible lipoprotein peptidase LpqM |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lpqM |
| eggNOG description | neutral zinc metallopeptidase |
| Orthologous group | COG2321 |
| KEGG orthology |
K07054
|
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 | 0.786 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.23% of strains (334) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lpqL (lipoprotein aminopeptidase LpqL), high confidence from genomic context alone (score 782 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0418 lpqL |
lipoprotein aminopeptidase LpqL | 883 | 782 ctx | neighborhood:745 textmining:486 |
Rv0882 |
transmembrane protein | 760 | 760 ctx | cooccurence:760 |
Rv3212 hyp |
hypothetical protein | 758 | 759 ctx | cooccurence:750 |
Rv2980 hyp |
hypothetical protein | 735 | 735 ctx | cooccurence:735 |
Rv2091c |
membrane protein | 709 | 709 ctx | cooccurence:706 |
Rv0556 |
transmembrane protein | 704 | 705 ctx | cooccurence:703 |
Rv2049c hyp |
hypothetical protein | 704 | 704 ctx | cooccurence:702 |
Rv2700 cei hyp |
hypothetical protein | 703 | 703 ctx | cooccurence:703 |
Rv1109c hyp |
hypothetical protein | 692 | 693 ctx | cooccurence:691 |
Rv1486c hyp |
hypothetical protein | 692 | 692 ctx | cooccurence:688 |
Rv2695 hyp |
hypothetical protein | 687 | 688 ctx | cooccurence:687 |
Rv1166 lpqW |
monoacyl phosphatidylinositol tetramannoside-binding protein LpqW | 791 | 662 ctx | cooccurence:660 textmining:407 |
Rv3311 hyp |
hypothetical protein | 659 | 659 ctx | cooccurence:657 |
Rv2446c |
integral membrane protein | 652 | 652 ctx | cooccurence:650 |
Rv3415c hyp |
hypothetical protein | 648 | 648 ctx | cooccurence:648 |
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 peptidase LpqM
- MTBC0 PGAP product: neutral zinc metallopeptidase
- (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_214933.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG2321 - Curated reference: UniProt P96265 (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 —
77 functional partner(s); context anchor
lpqL - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000440|Rv0419|lpqM MHGRGRYRPLVRCVRPRRVAASVRTPIACLAAVVVIAGCTTVVDGRALSILNDPFRVGGLPATNGPSGARPDAPAASGTVINTNNGAIDKLSLLSVNDIEDYWMAVYSESLKGTFRPVGKLVSYDSNDPSSPIVCHIDTYQLVNAFFSSRCNLIAWDRGVFMAVAQEYFGDMSVNGVLAHEFGHALQVMANLVTRKDPTIVREQQADCFAGVYLWWVAEGKSTRFTLSTADGLDHVLAGIITTRDPVMEADAENDDEHGSALDRVSAFQLGFINGTPACAAIDEDEVERRRGDLPTTLRVDASGNPETGEVGINEETLSTLMELMGKIFSPKNPPTLSYQPAGCPDAKPSPPAAYCPATNTIVVDLPALARMGKVASAAEHSLPQGDDTSLSIVMSRYALAVQHERGLPMQSPWTALRTACLTGVAHRKMAVPIDLPSGQQLVLTAGDLDEAVSGLLTNRMVASDADGVSVPAGFTRIAAFRAGVGGDMDACYARYPG