lprL Family assigned · medium auto-curated
H37Rv Rv0593 · MTBC0 - ·
402 aa · 692024–693232 (+) ·
RefSeq NP_215107.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | Mce family lipoprotein LprL |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Mce family lipoprotein LprL. Pfam: MlaD (PF02470.26), Mce4_CUP1 (PF11887.14). |
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 |
I6Y461
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible Mce-family lipoprotein LprL |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | lprL |
| eggNOG description | Virulence factor Mce family protein |
| Orthologous group | COG1463 |
| KEGG orthology |
K02067
|
| KEGG pathways |
map02010
|
| KEGG modules |
M00210, M00669, M00670
|
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) pseudogene candidate
| pN/pS | 1.43 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 8.53% of strains (12382) · 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 |
|---|---|---|---|---|
MlaD | PF02470.26 | 3.0e-14 | 68–139 | MlaD protein |
Mce4_CUP1 | PF11887.14 | 1.2e-09 | 145–313 | Cholesterol uptake porter CUP1 of Mce4, putative |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mce2D (Mce family protein Mce2D), high confidence from genomic context alone (score 988 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0592 mce2D |
Mce family protein Mce2D | 998 | 988 ctx | neighborhood:782 cooccurence:774 coexpression:778 textmining:887 |
Rv0588 yrbE2B hyp |
hypothetical protein | 971 | 969 ctx | neighborhood:781 cooccurence:769 |
Rv0587 yrbE2A hyp |
hypothetical protein | 968 | 968 ctx | neighborhood:781 cooccurence:756 |
Rv0594 mce2F |
Mce family protein Mce2F | 992 | 956 ctx | neighborhood:801 cooccurence:774 textmining:830 |
Rv0589 mce2A |
Mce family protein Mce2A | 990 | 949 ctx | neighborhood:783 cooccurence:774 textmining:822 |
Rv0590 mce2B |
Mce-family protein Mce2B; Rv0590, (MTCY19H5.32c), len: 275 aa. Mce2B; belongs to 24-membered Mycobacterium tuberculosis Mce protein family ( | 965 | 949 ctx | neighborhood:781 cooccurence:772 |
Rv0591 mce2C |
Mce family protein Mce2C | 942 | 899 ctx | neighborhood:785 textmining:446 |
Rv0655 mkl |
ABC transporter ATP-binding protein | 917 | 885 ctx | cooccurence:761 experimental:431 |
Rv0168 yrbE1B |
membrane protein | 880 | 873 ctx | cooccurence:769 |
Rv1965 yrbE3B |
integral membrane protein | 879 | 872 ctx | cooccurence:766 |
Rv3500c yrbE4B |
integral membrane protein | 878 | 870 ctx | cooccurence:770 |
Rv3501c yrbE4A |
integral membrane protein | 873 | 869 ctx | cooccurence:762 |
Rv0167 yrbE1A |
membrane protein | 872 | 868 ctx | cooccurence:759 |
Rv1964 yrbE3A |
integral membrane protein | 880 | 866 ctx | cooccurence:753 |
Rv0170 mce1B |
Mce family protein Mce1B | 807 | 796 ctx | cooccurence:773 |
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): Mce family lipoprotein LprL
- Pfam (hmmscan --cut_ga): MlaD PF02470.26 (E=3e-14), Mce4_CUP1 PF11887.14 (E=1e-09)
- (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_215107.1)
- Domains: Pfam-A via hmmscan --cut_ga — MlaD (PF02470.26), Mce4_CUP1 (PF11887.14)
- 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
COG1463 - Curated reference: UniProt I6Y461 (TrEMBL, unreviewed; Predicted)
- 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 —
47 functional partner(s); context anchor
mce2D - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0593|lprL MRCGVSAGSANGKPNRWTLRCGVSAGHRGSVFLLAVLLAPVVLTSCTWRGIANVPLPVGRGMGPDRMTIYVQMPDTLALNTNSRVRVADVWVGTVRDISLRNWIATLTLELEPTVRLPANATAKIGQTSLLGTQHVELAAPPIPSPQPLKSGDTIGLKNSSAYPTVERTLASVALILTGGGIVNLDVIQTEILNILDGHAGQIREFLERLATFTAELNNQRGDLTRAIDSTNQLLTIIANRNDTLDRVLTDVPPLIEHFADTGQLFADATESLGRFSEVANRALAATRPNLHQTLQSLQRPLRQLERASPYVVGALKLGLTAPFNIDEVPNVIRGDYVNVSATFDVTLSALDNALLSGTGISGMLRALEQAWGRDPDTMIPDVRYTPNPNDAPGGPLVERAE