lprI Family assigned · medium auto-curated
H37Rv Rv1541c · MTBC0 mtbc0_001648 ·
197 aa · 1753587–1754180 (-) ·
RefSeq NP_216057.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LprI |
|---|---|
| MTBC0 PGAP re-annotation | MliC family protein |
| Revised (this work) | MliC family protein. Pfam: LprI (PF07007.18), MliC (PF09864.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WK41
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Lipoprotein LprI |
| Curated function | Strongly binds and inhibits lysozyme, may help bacteria survive in lysozyme-producing host cells. When overexpressed in M.tuberculosis or M.smegmatis increases resistance to hen egg white lysozyme. M.smegmatis overexpressing LprI survive better during intracellular infection of peritoneal and monocyte-derived macrophages, both of which produce lysozyme during infection; M.smegmatis does not encode this protein. Somewhat better survival is seen in human cell lines when M.smegmatis cells express both proteins from this operon, i.e. GlbN (HbN) and LprI. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lprL |
| eggNOG description | Lysozyme inhibitor LprI |
| Orthologous group | COG4461 |
| 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
LprI | PF07007.18 | 6.9e-05 | 35–107 | Lysozyme inhibitor LprI |
MliC | PF09864.16 | 9.2e-15 | 125–190 | Membrane-bound lysozyme-inhibitor of c-type lysozyme |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: frdD (fumarate reductase membrane anchor subunit), medium confidence from genomic context alone (score 668 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1555 frdD |
fumarate reductase membrane anchor subunit | 667 | 668 ctx | cooccurence:666 |
Rv1542c glbN |
hemoglobin GlbN | 697 | 661 ctx | neighborhood:656 |
Rv1554 frdC |
fumarate reductase membrane anchor subunit | 650 | 650 ctx | cooccurence:649 |
Rv0240 vapC24 |
ribonuclease VapC24 | 634 | 635 ctx | cooccurence:632 |
Rv2949c |
chorismate pyruvate-lyase | 632 | 633 ctx | cooccurence:631 |
Rv0613c hyp |
hypothetical protein | 609 | 609 ctx | cooccurence:608 |
Rv0355c PPE8 |
PPE family protein PPE8 | 600 | 600 ctx | cooccurence:598 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 596 | 596 ctx | cooccurence:596 |
Rv1917c PPE34 |
PPE family protein PPE34 | 592 | 592 ctx | cooccurence:591 |
Rv3347c PPE55 |
PPE family protein PPE55 | 574 | 574 ctx | cooccurence:573 |
Rv0304c PPE5 |
PPE family protein PPE5 | 573 | 573 ctx | cooccurence:572 |
Rv3350c PPE56 |
PPE family protein PPE56 | 562 | 562 ctx | cooccurence:562 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 562 | 562 ctx | cooccurence:562 |
Rv2209 |
integral membrane protein | 558 | 559 ctx | cooccurence:557 |
Rv0341 iniB |
isoniazid inducible protein IniB | 555 | 555 ctx | cooccurence:555 |
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 LprI
- MTBC0 PGAP product: MliC family protein
- Pfam (hmmscan --cut_ga): LprI PF07007.18 (E=7e-05), MliC PF09864.16 (E=9e-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_216057.1)
- Domains: Pfam-A via hmmscan --cut_ga — LprI (PF07007.18), MliC (PF09864.16)
- 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
COG4461 - Curated reference: UniProt P9WK41 (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 —
42 functional partner(s); context anchor
frdD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001648|Rv1541c|lprI MRWIGVLVTALVLSACAANPPANTTSPTAGQSLDCTKPATIVQQLVCHDRQLTSLDHRLSTAYQQALAHRRSAALEAAQSSWTMLRDACAQDTDPRTCVQEAYQTRLVQLAIADPATATPPVLTYRCPTQDGPLTAQFYNQFDPKTAVLNWKGDQVIVFVELSGSGARYGRQGIEYWEHQGEVRLDFHGATFVCRTS