lprF Resolved · high auto-curated
H37Rv Rv1368 · MTBC0 mtbc0_001471 ·
261 aa · 1551722–1552507 (+) ·
RefSeq NP_215884.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LprF |
|---|---|
| MTBC0 PGAP re-annotation | lipoprotein LprF |
| Revised (this work) | Lipoprotein LprF. Pfam: LppX_LprAFG (PF07161.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WK47
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative diacylated glycolipid transporter LprF |
| Curated function | Might be involved in transporting short diacylated glycolipids to the cell outer membrane (By similarity). Overexpression induces expression of sensor protein kdpD gene at low K(+) concentrations (0 and 250 uM, tested in M.smegatis). |
UniProt still lists this protein as Putative diacylated glycolipid transporter LprF; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lprF |
| eggNOG description | LppX_LprAFG lipoprotein |
| Orthologous group | 2DQVM |
| KEGG orthology |
K14954, K14955
|
| KEGG pathways |
map05152
|
| Gene Ontology (9) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, 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 | 2.112 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
LppX_LprAFG | PF07161.20 | 1.0e-68 | 57–256 | LppX_LprAFG lipoprotein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1371 (membrane protein), high confidence from genomic context alone (score 819 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1371 |
membrane protein | 819 | 819 ctx | cooccurence:752 |
Rv2608 PPE42 |
PPE family protein PPE42 | 717 | 717 ctx | cooccurence:711 |
Rv2695 hyp |
hypothetical protein | 568 | 569 ctx | cooccurence:566 |
Rv2939 papA5 |
phthiocerol/phthiodiolone dimycocerosyl transferase | 568 | 568 ctx | cooccurence:562 |
Rv1546 hyp |
hypothetical protein | 541 | 542 ctx | cooccurence:536 |
Rv3415c hyp |
hypothetical protein | 539 | 539 ctx | cooccurence:539 |
Rv0128 |
transmembrane protein | 522 | 522 ctx | cooccurence:519 |
Rv0755c PPE12 |
PPE family protein PPE12 | 517 | 517 ctx | cooccurence:514 |
Rv3217c |
integral membrane protein | 482 | 483 ctx | cooccurence:478 |
Rv0355c PPE8 |
PPE family protein PPE8 | 481 | 480 ctx | cooccurence:477 |
Rv3732 hyp |
hypothetical protein | 478 | 479 ctx | cooccurence:471 |
Rv1917c PPE34 |
PPE family protein PPE34 | 473 | 453 ctx | cooccurence:445 |
Rv1410c |
aminoglycosides/tetracycline-transport integral membrane protein | 482 | 450 ctx | cooccurence:411 |
Rv3343c PPE54 |
PPE family protein PPE54 | 469 | 449 ctx | cooccurence:441 |
Rv1365c rsfA |
anti-sigma-F factor antagonist RsfA | 446 | 446 ctx | cooccurence:438 |
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 LprF
- MTBC0 PGAP product: lipoprotein LprF
- Pfam (hmmscan --cut_ga): LppX_LprAFG PF07161.20 (E=1e-68)
- (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_215884.1)
- Domains: Pfam-A via hmmscan --cut_ga — LppX_LprAFG (PF07161.20)
- 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
2DQVM - Curated reference: UniProt P9WK47 (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 —
51 functional partner(s); context anchor
Rv1371 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001471|Rv1368|lprF MNGLISQACGSHRPRRPSSLGAVAILIAATLFATVVAGCGKKPTTASSPSPGSPSPEAQQILQDSSKATKGLHSVHVVVTVNNLSTLPFESVDADVTNQPQGNGQAVGNAKVRMKPNTPVVATEFLVTNKTMYTKRGGDYVSVGPAEKIYDPGIILDKDRGLGAVVGQVQNPTIQGRDAIDGLATVKVSGTIDAAVIDPIVPQLGKGGGRLPITLWIVDTNASTPAPAANLVRMVIDKDQGNVDITLSNWGAPVTIPNPAG