lpqL Family assigned · medium auto-curated
H37Rv Rv0418 · MTBC0 mtbc0_000439 ·
500 aa · 506861–508363 (+) ·
RefSeq NP_214932.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein aminopeptidase LpqL |
|---|---|
| MTBC0 PGAP re-annotation | M28 family metallopeptidase |
| Revised (this work) | M28 family metallopeptidase. Pfam: PA (PF02225.28), Peptidase_M28 (PF04389.23), Peptidase_M20 (PF01546.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96264
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable lipoprotein aminopeptidase LpqL |
| EC (curated) |
EC 3.4.11.1
|
| Curated function | An aminopeptidase; acts on free N-terminal amino groups with a very strong preference for Leu in the first position. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lpqL |
| eggNOG description | Peptidase, M28 |
| Orthologous group | COG2234 |
| Gene Ontology (7) |
GO:0005575, GO:0005576, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 1.028 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 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 |
|---|---|---|---|---|
PA | PF02225.28 | 7.0e-19 | 140–229 | PA domain |
Peptidase_M28 | PF04389.23 | 2.9e-47 | 252–472 | Peptidase family M28 |
Peptidase_M20 | PF01546.34 | 1.1e-05 | 269–339 | Peptidase family M20/M25/M40 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lpqM (lipoprotein peptidase LpqM), high confidence from genomic context alone (score 782 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0419 lpqM |
lipoprotein peptidase LpqM | 883 | 782 ctx | neighborhood:745 textmining:486 |
Rv1104 |
Rv1104, (MTV017.57), len: 229 aa. Possible para-nitrobenzyl esterase (fragment; possibly first part). Similar to the N-terminal domain of ma | 713 | 698 | database:587 |
Rv1105 |
Rv1105, (MTV017.58), len: 171 aa. Possible para-nitrobenzyl esterase (fragment; possibly second part). Similar to C-terminal domain of many | 711 | 696 | database:587 |
Rv2045c lipT |
carboxylesterase LipT | 711 | 696 | database:587 |
Rv0416 thiS |
sulfur carrier protein ThiS | 622 | 622 ctx | neighborhood:467 |
Rv3372 otsB2 |
trehalose 6-phosphate phosphatase | 611 | 609 | database:584 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 611 | 608 | database:584 |
Rv2124c metH |
methionine synthase | 614 | 584 | database:572 |
Rv3841 bfrB |
bacterioferritin BfrB | 593 | 577 | database:415 |
Rv0342 iniA |
isoniazid inductible protein IniA | 596 | 575 | database:569 |
Rv1488 hyp |
hypothetical protein | 568 | 568 | database:508 |
Rv3147 nuoC |
NADH-quinone oxidoreductase subunit C | 568 | 568 | database:562 |
Rv3090 hyp |
hypothetical protein | 566 | 567 | database:508 |
Rv3418c groES |
chaperonin GroES | 564 | 565 | database:561 |
Rv1305 atpE |
ATP synthase subunit C | 581 | 564 | database:561 |
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 aminopeptidase LpqL
- MTBC0 PGAP product: M28 family metallopeptidase
- Pfam (hmmscan --cut_ga): PA PF02225.28 (E=7e-19), Peptidase_M28 PF04389.23 (E=3e-47), Peptidase_M20 PF01546.34 (E=1e-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_214932.1)
- Domains: Pfam-A via hmmscan --cut_ga — PA (PF02225.28), Peptidase_M28 (PF04389.23), Peptidase_M20 (PF01546.34)
- 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
COG2234 - Curated reference: UniProt P96264 (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 —
123 functional partner(s); context anchor
lpqM - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000439|Rv0418|lpqL MVNKSRMMPAVLAVAVVVAFLTTGCIRWSTQSRPVVNGPAAAEFAVALRNRVSTDAMMAHLSKLQDIANANDGTRAVGTPGYQASVDYVVNTLRNSGFDVQTPEFSARVFKAEKGVVTLGGNTVEARALEYSLGTPPDGVTGPLVAAPADDSPGCSPSDYDRLPVSGAVVLVDRGVCPFAQKEDAAAQRGAVALIIADNIDEQAMGGTLGANTDVKIPVVSVTKSVGFQLRGQSGPTTVKLTASTQSFKARNVIAQTKTGSSANVVMAGAHLDSVPEGPGINDNGSGVAAVLETAVQLGNSPHVSNAVRFAFWGAEEFGLIGSRNYVESLDIDALKGIALYLNFDMLASPNPGYFTYDGDQSLPLDARGQPVVPEGSAGIERTFVAYLKMAGKTAQDTSFDGRSDYDGFTLAGIPSGGLFSGAEVKKSAEQAELWGGTADEPFDPNYHQKTDTLDHIDRTALGINGAGVAYAVGLYAQDLGGPNGVPVMADRTRHLIAKP