lprE Family assigned · medium auto-curated
H37Rv Rv1252c · MTBC0 mtbc0_001341 ·
202 aa · 1407740–1408348 (-) ·
RefSeq NP_215768.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LprE |
|---|---|
| MTBC0 PGAP re-annotation | LppP/LprE family lipoprotein |
| Revised (this work) | LppP/LprE family lipoprotein. Pfam: Lipoprotein_21 (PF14041.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WK49
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative lipoprotein LprE |
UniProt still lists this protein as Putative lipoprotein LprE; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lprE |
| eggNOG description | LppP/LprE lipoprotein |
| Orthologous group | 2AS1M |
| 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 | 0.236 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 2 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 |
|---|---|---|---|---|
Lipoprotein_21 | PF14041.12 | 3.5e-15 | 113–190 | LppP/LprE lipoprotein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: deaD (ATP-dependent RNA helicase DeaD), high confidence from genomic context alone (score 785 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2697c dut |
deoxyuridine 5'-triphosphate nucleotidohydrolase | 964 | 963 | experimental:837 database:782 |
Rv2529 hyp |
hypothetical protein | 946 | 945 | experimental:864 database:607 |
Rv1251c hyp |
hypothetical protein | 905 | 902 ctx | neighborhood:682 coexpression:703 |
Rv1629 polA |
DNA polymerase I | 878 | 861 | database:844 |
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 797 | 785 ctx | neighborhood:675 |
Rv3807c |
decaprenylphosphoryl-5-phosphoribose phosphatase | 763 | 755 | experimental:405 database:599 |
Rv0308 |
integral membrane protein | 762 | 754 | experimental:405 database:599 |
Rv0719 rplF |
50S ribosomal protein L6 | 739 | 735 | database:584 |
Rv1329c dinG |
ATP-dependent helicase DinG | 711 | 712 | database:543 |
Rv0641 rplA |
50S ribosomal protein L1 | 705 | 697 | database:542 |
Rv2116 lppK |
lipoprotein LppK | 592 | 592 | database:587 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 590 | 590 | database:587 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 592 | 589 | |
Rv0435c |
ATPase | 587 | 587 | database:542 |
Rv3884c eccA2 |
ESX-2 secretion system protein EccA | 585 | 585 | database:542 |
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 LprE
- MTBC0 PGAP product: LppP/LprE family lipoprotein
- Pfam (hmmscan --cut_ga): Lipoprotein_21 PF14041.12 (E=4e-15)
- (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_215768.1)
- Domains: Pfam-A via hmmscan --cut_ga — Lipoprotein_21 (PF14041.12)
- 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
2AS1M - Curated reference: UniProt P9WK49 (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 —
137 functional partner(s); context anchor
deaD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001341|Rv1252c|lprE MPGVWSPPCPTTPRVGVVAALVAATLTGCGSGDSTVAKTPEATPSLSTAHPAPPSSEPSPPSATAAPPSNHSAAPVDPCAVNLASPTIAKVVSELPRDPRSEQPWNPEPLAGNYNECAQLSAVVIKANTNAGNPTTRAVMFHLGKYIPQGVPDTYGFTGIDTSQCTGDTVALTYASGIGLNNVVKFRWNGGGVELIGNTTGG