lprQ Resolved · high auto-curated
H37Rv Rv0483 · MTBC0 mtbc0_000508 ·
451 aa · 575075–576430 (+) ·
RefSeq NP_214997.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LprQ |
|---|---|
| MTBC0 PGAP re-annotation | L%2CD-transpeptidase LdtMt5 |
| Revised (this work) | L%2CD-transpeptidase LdtMt5. Pfam: Big_10 (PF17964.8), YkuD (PF03734.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKV3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | L,D-transpeptidase 5 |
| EC (curated) |
EC 2.3.2.-
|
| Curated function | Generates 3->3 cross-links in peptidoglycan, catalyzing the cleavage of the mDap(3)-D-Ala(4) bond of a tetrapeptide donor stem and the formation of a bond between the carbonyl of mDap(3) of the donor stem and the side chain of mDap(3) of the acceptor stem. Is specific for donor substrates containing a stem tetrapeptide since it cannot use pentapeptide stems. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lprQ |
| eggNOG description | ErfK YbiS YcfS YnhG family protein |
| Orthologous group | COG1376 |
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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 | 0.193 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 4 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 |
|---|---|---|---|---|
Big_10 | PF17964.8 | 5.7e-53 | 76–241 | Bacterial Ig domain |
YkuD | PF03734.20 | 3.7e-17 | 263–383 | L,D-transpeptidase catalytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: murB (UDP-N-acetylenolpyruvoylglucosamine reductase), high confidence from genomic context alone (score 801 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0481c hyp |
hypothetical protein | 809 | 809 ctx | neighborhood:734 |
Rv0482 murB |
UDP-N-acetylenolpyruvoylglucosamine reductase | 824 | 801 ctx | neighborhood:800 |
Rv0480c |
amidohydrolase | 667 | 667 ctx | neighborhood:661 |
Rv1332 |
transcriptional regulator | 621 | 607 ctx | cooccurence:601 |
Rv3015c hyp |
hypothetical protein | 590 | 575 ctx | cooccurence:575 |
Rv0990c hyp |
hypothetical protein | 541 | 541 ctx | cooccurence:540 |
Rv0479c |
membrane protein | 490 | 491 ctx | neighborhood:483 |
Rv3657c |
membrane protein | 467 | 467 ctx | cooccurence:467 |
Rv0996 |
transmembrane protein | 451 | 452 ctx | cooccurence:449 |
Rv3660c ssd hyp |
hypothetical protein | 445 | 445 ctx | cooccurence:445 |
Rv0868c moaD2 |
cyclic pyranopterin monophosphate synthase | 495 | 437 ctx | cooccurence:433 |
Rv3231c hyp |
hypothetical protein | 428 | 428 ctx | cooccurence:426 |
Rv3311 hyp |
hypothetical protein | 419 | 419 ctx | cooccurence:413 |
Rv3118 sseC1 hyp |
hypothetical protein | 410 | 411 ctx | cooccurence:402 |
Rv0814c sseC2 hyp |
hypothetical protein | 410 | 411 ctx | cooccurence:402 |
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 LprQ
- MTBC0 PGAP product: L%2CD-transpeptidase LdtMt5
- Pfam (hmmscan --cut_ga): Big_10 PF17964.8 (E=6e-53), YkuD PF03734.20 (E=4e-17)
- (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_214997.1)
- Domains: Pfam-A via hmmscan --cut_ga — Big_10 (PF17964.8), YkuD (PF03734.20)
- 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
COG1376 - Curated reference: UniProt P9WKV3 (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 —
36 functional partner(s); context anchor
murB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000508|Rv0483|lprQ MVIRVLFRPVSLIPVNNSSTPQSQGPISRRLALTALGFGVLAPNVLVACAGKVTKLAEKRPPPAPRLTFRPADSAADVVPIAPISVEVGDGWFQRVALTNSAGKVVAGAYSRDRTIYTITEPLGYDTTYTWSGSAVGHDGKAVPVAGKFTTVAPVKTINAGFQLADGQTVGIAAPVIIQFDSPISDKAAVERALTVTTDPPVEGGWAWLPDEAQGARVHWRPREYYPAGTTVDVDAKLYGLPFGDGAYGAQDMSLHFQIGRRQVVKAEVSSHRIQVVTDAGVIMDFPCSYGEADLARNVTRNGIHVVTEKYSDFYMSNPAAGYSHIHERWAVRISNNGEFIHANPMSAGAQGNSNVTNGCINLSTENAEQYYRSAVYGDPVEVTGSSIQLSYADGDIWDWAVDWDTWVSMSALPPPAAKPAATQIPVTAPVTPSDAPTPSGTPTTTNGPGG