ppm1 Resolved · high auto-curated
H37Rv Rv2051c · MTBC0 mtbc0_002184 ·
874 aa · 2336744–2339368 (-) ·
RefSeq NP_216567.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | polyprenol-monophosphomannose synthase |
|---|---|
| MTBC0 PGAP re-annotation | apolipoprotein N-acyltransferase |
| Revised (this work) | Apolipoprotein N-acyltransferase. Pfam: LNT_N (PF20154.5), CN_hydrolase (PF00795.28), Glycos_transf_2 (PF00535.33). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53493
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Bifunctional apolipoprotein N-acyltransferase/polyprenol monophosphomannose synthase [Includes: Apolipoprotein N-acyltransferase |
| EC (curated) |
EC 2.3.1.269, EC 2.4.1.-, EC 2.4.1.83
|
| Curated function | Catalyzes the phospholipid dependent N-acylation of the N-terminal cysteine of apolipoprotein, the last step in lipoprotein maturation..; FUNCTION: Transfers mannose from GDP-mannose to lipid acceptors (works best on C20-C95 lipid monophosphate substrates in which the lipid can be modified, tested with the C-terminal domain expressed in M.smegmatis) to form polyprenol monophosphomannose (PPM). PMM is an alkai-stable sugar donor which adds mannose-phosphate residues to triacylated-phosphatidyl-myo-inositol mannosides (PIM2), eventually leading to generation of the cell wall glycolipid lipoglyca. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | lnt |
| eggNOG description | Transfers the fatty acyl group on membrane lipoproteins |
| Orthologous group | COG0463 |
| KEGG orthology |
K03820
|
| CAZy family |
GT2
|
| Gene Ontology (62) |
GO:0000030, GO:0003674, GO:0003824, GO:0004582, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006629 +50 more
|
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 | 0.287 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 8 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 |
|---|---|---|---|---|
LNT_N | PF20154.5 | 6.6e-32 | 31–182 | Apolipoprotein N-acyltransferase N-terminal domain |
CN_hydrolase | PF00795.28 | 4.8e-15 | 243–487 | Carbon-nitrogen hydrolase |
Glycos_transf_2 | PF00535.33 | 4.9e-32 | 614–780 | Glycosyl transferase family 2 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fxsA (transmembrane protein FxsA), high confidence from genomic context alone (score 870 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2052c hyp |
hypothetical protein | 897 | 898 ctx | neighborhood:510 coexpression:800 |
Rv2053c fxsA |
transmembrane protein FxsA | 869 | 870 ctx | neighborhood:534 coexpression:732 |
Rv0983 pepD |
serine protease PepD | 769 | 759 | coexpression:730 |
Rv0204c |
transmembrane protein | 500 | 475 ctx | cooccurence:408 |
Rv0112 gca |
GDP-mannose 4,6-dehydratase | 491 | 475 | |
Rv0236c aftD |
alpha-(1->3)-arabinofuranosyltransferase | 513 | 448 | |
Rv3784 |
dTDP-glucose 4,6-dehydratase | 503 | 434 | |
Rv0256c PPE2 |
PPE family protein PPE2 | 419 | 420 | |
Rv3907c pcnA |
poly(A) polymerase PcnA | 422 | 409 | |
Rv0225 hyp |
hypothetical protein | 432 | 404 | |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 484 | 349 | |
Rv2173 idsA2 |
geranylgeranyl pyrophosphate synthetase IdsA | 406 | 340 | |
Rv3265c wbbL1 |
N-acetylglucosaminyl-diphospho-decaprenol L-rhamnosyltransferase | 434 | 329 | |
Rv2048c pks12 |
polyketide synthase | 513 | 303 | |
Rv3781 rfbE |
O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE | 450 | 303 |
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: polyprenol-monophosphomannose synthase
- MTBC0 PGAP product: apolipoprotein N-acyltransferase
- Pfam (hmmscan --cut_ga): LNT_N PF20154.5 (E=7e-32), CN_hydrolase PF00795.28 (E=5e-15), Glycos_transf_2 PF00535.33 (E=5e-32)
- (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_216567.1)
- Domains: Pfam-A via hmmscan --cut_ga — LNT_N (PF20154.5), CN_hydrolase (PF00795.28), Glycos_transf_2 (PF00535.33)
- 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
COG0463 - Curated reference: UniProt O53493 (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 —
41 functional partner(s); context anchor
fxsA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002184|Rv2051c|ppm1 MKLGAWVAAQLPTTRTAVRTRLTRLVVSIVAGLLLYASFPPRNCWWAAVVALALLAWVLTHRATTPVGGLGYGLLFGLVFYVSLLPWIGELVGPGPWLALATTCALFPGIFGLFAVVVRLLPGWPIWFAVGWAAQEWLKSILPFGGFPWGSVAFGQAEGPLLPLVQLGGVALLSTGVALVGCGLTAIALEIEKWWRTGGQGDAPPAVVLPAACICLVLFAAIVVWPQVRHAGSGSGGEPTVTVAVVQGNVPRLGLDFNAQRRAVLDNHVEETLRLAADVHAGLAQQPQFVIWPENSSDIDPFVNPDAGQRISAAAEAIGAPILIGTLMDVPGRPRENPEWTNTAIVWNPGTGPADRHDKAIVQPFGEYLPMPWLFRHLSGYADRAGHFVPGNGTGVVRIAGVPVGVATCWEVIFDRAPRKSILGGAQLLTVPSNNATFNKTMSEQQLAFAKVRAVEHDRYVVVAGTTGISAVIAPDGGELIRTDFFQPAYLDSQVRLKTRLTPATRWGPILQWILVGAAAAVVLVAMRQNGWFPRPRRSEPKGENDDSDAPPGRSEASGPPALSESDDELIQPEQGGRHSSGFGRHRATSRSYMTTGQPAPPAPGNRPSQRVLVIIPTFNERENLPVIHRRLTQACPAVHVLVVDDSSPDGTGQLADELAQADPGRTHVMHRTAKNGLGAAYLAGFAWGLSREYSVLVEMDADGSHAPEQLQRLLDAVDAGADLAIGSRYVAGGTVRNWPWRRLVLSKTANTYSRLALGIGIHDITAGYRAYRREALEAIDLDGVDSKGYCFQIDLTWRTVSNGFVVTEVPITFTERELGVSKMSGSNIREALVKVARWGIEGRLSRSDHARARPDIARPGAGGSRVSRADVTE