lomaiviticin D
naturalproductmech:mibig-ba6ee9b824 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 | WDSXHYIKIDPMFG-JIVPKNBMSA-N |
|---|---|
| SMILES | O=C([C@@]([C@@]([C@@](O[C@H]1C[C@H](OC)[C@@H](O)[C@H](C)O1)(CC)[C@@H]2O[C@@H]3C[C@H](O)[C@@H](N(C)C)[C@H](C)O3)([H])C(C(C4=C5C(C6=C(O)C=CC(O)=C6C4=O)=O)=C2C5=[N+]=[N-])=O)([H])[C@@](O[C@@H]7O[C@@H](C)[C@H](OC)[C@@H](OC)C7)(CC)[C@@H]8O[C@@H]9C[C@H](O)[C@@H](N(C)C)[C@H](C)O9)C%10=C8C=C%11C%10=C(O)C%12=C(O)C=CC(O)=C%12C%11=O |
| Stereochemistry | fully defined |
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 1
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 |
SOURCE_ASSERTION | mibig:BGC0000240 | https://mibig.secondarymetabolites.org/repository/BGC0000240.5/, DOI:10.1016/j.tet.2014.03.009 |
Occurrences 0
None cited.
Biosynthetic gene clusters 1
| Accession | Host | Locus evidence | Genome |
|---|---|---|---|
| mibig:BGC0000240 | Salinispora pacifica NCBITaxon:351187 |
CLUSTER_UNSTATED | genbank:KF731828.1 |
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 | 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 enzyme_id is left unfilled and NCBI Protein records are cited as official sequence evidence. Exact-product identity remains disputed (issue #976). The two deposited D encodings differ by two hydrogens and connectivity. The experiments do not adjudicate which exact D encoding is correct; the 2021 A-C revision is not automatically evidence for revising D.
Mechanism & Biosynthesis Overview
Causal graph — biosynthesis 4 nodes, 3 edges
Partial S. pacifica lomaiviticin D biosynthesis graph for the proposed Lom62/Lom63 propionyl-ACP starter-unit branch. Exact-product identity is unresolved; see the curator identity discussion.
| 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 D | 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 D. Exact-product identity remains disputed (issue #976). The two deposited D encodings differ by two hydrogens and connectivity. The experiments do not adjudicate which exact D encoding is correct; the 2021 A-C revision is not automatically evidence for revising D. | 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 2
curator-lomaiviticin-identity-conflict — Which exact structure is supported for this source product?
curator-lomaiviticin-d-producer-strain — Does the deposited DPJ-0016 locus support the D producer assertion?
Provenance
| Source concept | Source | Version |
|---|---|---|
| BGC0000240 | MIBIG | 5 |
This page is generated from data/natural_products/polyketides/lomaiviticin-d-2.yaml, which is generated from the committed inventories. Neither is edited by hand.