lomaiviticin A
naturalproductmech:mibig-4b1562dcf5 MINTED SEEDED
What these status tags mean
Curation status describes a workflow state. SEEDED means the record entered through the source-seeding workflow; it does not imply that no later curation occurred. PROPOSED marks an addition awaiting review; REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record. These are workflow decisions, not independently verified human review. Agent-assisted contributions may appear in the record history.
Grounding describes the identifier mapping: EXACT uses an ontology identity asserted by the source; MINTED keeps a local identifier when no defensible ontology identity is available; REVIEW_NEEDED flags an exact structure whose ontology identity needs adjudication. The grounding note retains any unresolved alternatives. These tags do not establish the strength of producer or activity evidence.
Structure
| Standard InChIKey | VGDUHSQTOJRQNB-JGBUZTLDSA-N |
|---|---|
| SMILES | CC[C@@]1(OC2CC(OC)C(O)C(C)O2)[C@H](OC2CC(O)C(C(C)O2)N(C)C)C2=C(C3=C(C2=[N+]=[N-])C(=O)C2=C(O)C=CC(O)=C2C3=O)C(=O)[C@@H]1[C@H]1C(=O)C2=C([C@@H](O[C@H]3CC(O)[C@@H](C(C)O3)N(C)C)[C@@]1(CC)OC1CC(OC)C(O)C(C)O1)C(=[N+]=[N-])C1=C2C(=O)C2=C(O)C=CC(O)=C2C1=O |
| Stereochemistry | undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers |
| Cross-references | npatlas:NPA06818, pubchem:56841540 |
Filing pathway
Polyketides — computed by NPClassifier npclassifier.gnps2.org@2026-09-07, which is why it is pinned rather than recomputed. The gene cluster's asserted class is pks, saccharide, from MIBiG.
Producer organisms 2
A claim that this taxon makes the compound. The basis says what the evidence addressed — a knockout and a database assertion are not the same claim.
| Taxon | Basis | Cluster | Evidence |
|---|---|---|---|
| Salinispora pacifica NCBITaxon:351187 |
BGC_CHARACTERIZED | mibig:BGC0000240 | PMID:23649992 |
| Salinispora tropica CNB-440 NCBITaxon:369723 |
BGC_CHARACTERIZED | mibig:BGC0000241 | PMID:23649992 |
Occurrences 1
Somebody found the compound in this organism and cited it. That is not a claim that the organism makes it, and nothing here promotes one to the other.
| Taxon | Source | Reference |
|---|---|---|
| Salinispora tropica NCBITaxon:168695 |
LOTUS | DOI:10.1002/CBIC.201300147 |
Biosynthetic gene clusters 2
| Accession | Host | Locus evidence | Genome |
|---|---|---|---|
| mibig:BGC0000240 | Salinispora pacifica NCBITaxon:351187 |
CLUSTER_DEMONSTRATED | genbank:KF731828.1 |
| mibig:BGC0000241 | Salinispora tropica CNB-440 NCBITaxon:369723 |
CLUSTER_DEMONSTRATED | genbank:CP000667.1 |
A locus claim and a taxon claim are different questions. Heterologous expression settles the first and leaves the second where the isolation report left it.
Biosynthesis curated
Written by a curator with claim-level evidence on each step; not derived from a source. This is what the rest of the record exists to support.
| Step | Enzyme | Reaction | Substrate → product | Evidence |
|---|---|---|---|---|
| 1 | Lom62 acyltransferase/decarboxylase with Lom63 acyl carrier protein NCBIProtein:AHF72798.1 |
ungrounded → ungrounded | DOI:10.1021/ol403714g |
Step 1: This curates S. pacifica DPJ-0019 Lom62/AHF72798.1 and Lom63/AHF72799.1 as an assayed acyltransferase/decarboxylase plus ACP pair that can generate the proposed propionyl-ACP starter unit for lomaiviticin biosynthesis. The exact DPJ-0019 GenPept accessions did not resolve in UniProtKB exact-accession or KF515737/lom62/lom63 searches on 2026-09-27, so the catalytic enzyme Lom62 is grounded on enzyme_id as NCBIProtein:AHF72798.1 (with Lom63 grounded in the causal graph as NCBIProtein:AHF72799.1; UniParc UPI00035CE3B5 and UPI00037FF3C5 map only to retired/obsolete UniProtKB/TrEMBL entries W0HGI2.1 and W0HKR9.1).
Mechanism & Biosynthesis Overview
Causal graph — biosynthesis 4 nodes, 3 edges
Partial S. pacifica lomaiviticin A biosynthesis graph for the proposed Lom62/Lom63 propionyl-ACP starter-unit branch.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| Lom62 acyltransferase/decarboxylase | catalyzes | propionyl-ACP starter-unit generation | The in vitro assay showed Lom62-dependent propionyl-Lom63 formation from methylmalonyl-CoA; this graph leaves the subsequent propionyl starter-unit transfer to the type II PKS unresolved. | DOI:10.1021/ol403714g |
| Lom63 acyl carrier protein | is the preferred carrier protein for | propionyl-ACP starter-unit generation | Lom63 is represented as the preferred ACP partner because competition and single-ACP assays favored propionyl-Lom63 formation over Lom60. | DOI:10.1021/ol403714g |
| propionyl-ACP starter-unit generation | contributes to | lomaiviticin A | Waldman and Balskus proposed Lom62/Lom63 propionyl-ACP formation as lomaiviticin starter-unit logic based on the lomaiviticin scaffold and cluster context; the edge is therefore narrower than a complete pathway from this starter unit to lomaiviticin A. | DOI:10.1021/ol403714g |
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Explore across X-Mech
Open questions 1
shared-structure — This structure is reported by more than one MIBiG entry: BGC0000240, BGC0000241. Confirm they describe the same compound rather than an upstream cross-reference error.
Provenance
| Source concept | Source | Version |
|---|---|---|
| BGC0000240 | MIBIG | 5 |
| BGC0000241 | MIBIG | 5 |
This page is generated from data/natural_products/polyketides/lomaiviticin-a.yaml, which is generated from the committed inventories. Neither is edited by hand.