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lomaiviticin E

naturalproductmech:mibig-3e651964d5 MINTED SEEDED

Grounding review: No 3-star ChEBI entry shares this structure, so the record keeps a content-hashed identifier.
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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 InChIKeyUUFARPZDPLRTPW-YHYZUSIDSA-N
SMILESCC[C@@]1([C@H](C(=C2C(=CC3=C2C(=C4C(=O)C=CC(=O)C4=C3O)O)[C@H]1O[C@@H]5C[C@@H]([C@H]([C@@H](O5)C)N(C)C)O)O)[C@H]6C(=O)C7=C([C@H]([C@@]6(CC)O[C@H]8C[C@@H]([C@H]([C@@H](O8)C)OC)OC)O[C@@H]9C[C@@H]([C@H]([C@@H](O9)C)N(C)C)O)C(=[N+]=[N-])C1=C7C(=C2C(=O)C=CC(=O)C2=C1O)O)O[C@H]1C[C@@H]([C@H]([C@@H](O1)C)OC)OC
Stereochemistryfully defined
Cross-referencesnpatlas:NPA08789

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.

TaxonBasisClusterEvidence
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.

TaxonSourceReference
Salinispora pacifica
NCBITaxon:351187		 LOTUS DOI:10.1021/JA3074984

Biosynthetic gene clusters 2

AccessionHostLocus evidenceGenome
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.

StepEnzymeReactionSubstrate → productEvidence
1 Strop_2223 beta-ketoacyl synthase
UniProtKB:A4X724		 ungrounded → ungrounded DOI:10.1002/cbic.201300147

Step 1: This curates the S. tropica CNB-440 Strop_2223/ABP54674.1 beta-ketoacyl synthase as a knockout-supported type II PKS enzyme in the ST_pks2/lom scaffold-biosynthesis branch that produces lomaiviticins, including lomaiviticin E. UniProtKB A4X724 resolves to Strop_2223 in the CNB-440 genome; the exact Strop_2223 substrate/product pair and its minimal-PKS partner are left unresolved.

Mechanism & Biosynthesis Overview

PRODUCERS & OCCURRENCE 2 producers (2 causal) 1 cited occurrence BIOSYNTHETIC LOCUS 2 gene clusters 1 curated pathway step NATURAL PRODUCT lomaiviticin E naturalproductmech:mibig-3e651964d5 Polyketides TARGETS & BIOACTIVITY 0 molecular targets 0 bioactivities · 2 graphs

Causal graph — biosynthesis 3 nodes, 2 edges

Partial S. tropica lomaiviticin E biosynthesis graph for the knockout-supported Strop_2223 type II PKS scaffold branch.

SubjectPredicateObjectNotesEvidence
Strop_2223 beta-ketoacyl synthase is required for lomaiviticin type II PKS scaffold biosynthesis Kersten et al. knocked out strop2223 and MIBiG v5 maps that locus to ABP54674.1; the edge stops at scaffold biosynthesis because the exact condensation reaction was not assayed in vitro.
DOI:10.1002/cbic.201300147
https://mibig.secondarymetabolites.org/repository/BGC0000241.5/index.html
https://www.ncbi.nlm.nih.gov/protein/ABP54674.1
https://www.uniprot.org/uniprotkb/A4X724
  • reference
    DOI:10.1002/cbic.201300147
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    lomaiviticins A, D and E
    notes
    Kersten et al. inactivated the S. tropica CNB-440 strop2223 beta-ketosynthase, found that the mutant extract was inactive in the DNA-interference assay, and used LC-MS profiling of wild-type and mutant extracts to identify lomaiviticins, including lomaiviticin E, as ST_pks2/lom products.
  • reference
    https://mibig.secondarymetabolites.org/repository/BGC0000241.5/index.html
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    snippet
    Scaffold biosynthesis
    notes
    MIBiG BGC0000241.5 lists lomaiviticin E among the Salinispora tropica CNB-440 products and annotates Strop_2223/ABP54674.1 as a beta-ketoacyl synthase with scaffold-biosynthesis function and knockout evidence.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/ABP54674.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    snippet
    beta-ketoacyl synthase
    notes
    NCBI Protein ABP54674.1 is the 423 aa Salinispora tropica CNB-440 Strop_2223 product.
  • reference
    https://www.uniprot.org/uniprotkb/A4X724
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    snippet
    Beta-ketoacyl-acyl-carrier-protein synthase I
    notes
    UniProtKB A4X724 resolves to the 423 aa S. tropica CNB-440 Strop_2223 entry and cross-references the CP000667 chromosome.
lomaiviticin type II PKS scaffold biosynthesis contributes to lomaiviticin E LC-MS comparison connected ST_pks2 with the lomaiviticin family and identified lomaiviticin E among the wild-type S. tropica CNB-440 products; this graph does not claim a complete route from the type II PKS scaffold to the fully tailored glycoside.
DOI:10.1002/cbic.201300147
https://mibig.secondarymetabolites.org/repository/BGC0000241.5/index.html
  • reference
    DOI:10.1002/cbic.201300147
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    lomaiviticins A, D and E
    notes
    Kersten et al. inactivated the S. tropica CNB-440 strop2223 beta-ketosynthase, found that the mutant extract was inactive in the DNA-interference assay, and used LC-MS profiling of wild-type and mutant extracts to identify lomaiviticins, including lomaiviticin E, as ST_pks2/lom products.
  • reference
    https://mibig.secondarymetabolites.org/repository/BGC0000241.5/index.html
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    snippet
    Scaffold biosynthesis
    notes
    MIBiG BGC0000241.5 lists lomaiviticin E among the Salinispora tropica CNB-440 products and annotates Strop_2223/ABP54674.1 as a beta-ketoacyl synthase with scaffold-biosynthesis function and knockout evidence.

Every edge carries its own citation; an uncited edge is refused by the corpus tests.

Causal graph — biosynthesis 4 nodes, 3 edges

Partial S. pacifica lomaiviticin E biosynthesis graph for the proposed Lom62/Lom63 propionyl-ACP starter-unit branch.

SubjectPredicateObjectNotesEvidence
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
https://www.ncbi.nlm.nih.gov/protein/AHF72798.1
https://www.uniprot.org/uniparc/UPI00035CE3B5
https://www.ncbi.nlm.nih.gov/protein/AHF72799.1
https://www.uniprot.org/uniparc/UPI00037FF3C5
https://www.ncbi.nlm.nih.gov/nuccore/KF515737.1
  • reference
    DOI:10.1021/ol403714g
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    Robust, Lom62-dependent formation
    notes
    Waldman and Balskus cloned Salinispora pacifica DPJ-0019 lom62, lom60, and lom63, then showed in vitro by HPLC/LC-MS that Lom62 generated the expected propionyl-ACP thioester robustly only with methylmalonyl-CoA and Lom63.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AHF72798.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    snippet
    acyl transferase/decarboxylase
    notes
    NCBI GenPept AHF72798.1 is the 324 aa S. pacifica DPJ-0019 lom62 product on KF515737.1:59562..60536; exact AHF72798.1, AHF72798, lom62, and KF515737 UniProtKB searches did not resolve a S. pacifica accession on 2026-09-27.
  • reference
    https://www.uniprot.org/uniparc/UPI00035CE3B5
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-23
    snippet
    AHF72798.1
    notes
    UniParc UPI00035CE3B5 archives the exact 324 aa S. pacifica DPJ-0019 Lom62 sequence (EMBL KF515737.1:59562..60536, protein AHF72798.1) and records that UniProtKB/TrEMBL entry W0HGI2.1 is inactive/obsolete, confirming no active UniProtKB accession resolves for AHF72798.1.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AHF72799.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    snippet
    phosphopantheine-binding protein
    notes
    NCBI GenPept AHF72799.1 is the 107 aa S. pacifica DPJ-0019 lom63 acyl carrier protein on complement(KF515737.1:60555..60878); exact AHF72799.1, AHF72799, lom63, and KF515737 UniProtKB searches did not resolve a S. pacifica accession on 2026-09-27.
  • reference
    https://www.uniprot.org/uniparc/UPI00037FF3C5
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-23
    snippet
    AHF72799.1
    notes
    UniParc UPI00037FF3C5 archives the exact 107 aa S. pacifica DPJ-0019 Lom63 sequence (EMBL complement(KF515737.1:60555..60878), protein AHF72799.1) and records that UniProtKB/TrEMBL entry W0HKR9.1 is inactive/obsolete, confirming no active UniProtKB accession resolves for AHF72799.1.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/KF515737.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    snippet
    lomaiviticin biosynthetic gene cluster
    notes
    GenBank KF515737.1 is the 72,505 bp S. pacifica DPJ-0019 lomaiviticin biosynthetic gene cluster and carries lom62/AHF72798.1 and lom63/AHF72799.1.
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
https://www.ncbi.nlm.nih.gov/protein/AHF72798.1
https://www.uniprot.org/uniparc/UPI00035CE3B5
https://www.ncbi.nlm.nih.gov/protein/AHF72799.1
https://www.uniprot.org/uniparc/UPI00037FF3C5
https://www.ncbi.nlm.nih.gov/nuccore/KF515737.1
  • reference
    DOI:10.1021/ol403714g
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    Robust, Lom62-dependent formation
    notes
    Waldman and Balskus cloned Salinispora pacifica DPJ-0019 lom62, lom60, and lom63, then showed in vitro by HPLC/LC-MS that Lom62 generated the expected propionyl-ACP thioester robustly only with methylmalonyl-CoA and Lom63.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AHF72798.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    snippet
    acyl transferase/decarboxylase
    notes
    NCBI GenPept AHF72798.1 is the 324 aa S. pacifica DPJ-0019 lom62 product on KF515737.1:59562..60536; exact AHF72798.1, AHF72798, lom62, and KF515737 UniProtKB searches did not resolve a S. pacifica accession on 2026-09-27.
  • reference
    https://www.uniprot.org/uniparc/UPI00035CE3B5
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-23
    snippet
    AHF72798.1
    notes
    UniParc UPI00035CE3B5 archives the exact 324 aa S. pacifica DPJ-0019 Lom62 sequence (EMBL KF515737.1:59562..60536, protein AHF72798.1) and records that UniProtKB/TrEMBL entry W0HGI2.1 is inactive/obsolete, confirming no active UniProtKB accession resolves for AHF72798.1.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AHF72799.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    snippet
    phosphopantheine-binding protein
    notes
    NCBI GenPept AHF72799.1 is the 107 aa S. pacifica DPJ-0019 lom63 acyl carrier protein on complement(KF515737.1:60555..60878); exact AHF72799.1, AHF72799, lom63, and KF515737 UniProtKB searches did not resolve a S. pacifica accession on 2026-09-27.
  • reference
    https://www.uniprot.org/uniparc/UPI00037FF3C5
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-23
    snippet
    AHF72799.1
    notes
    UniParc UPI00037FF3C5 archives the exact 107 aa S. pacifica DPJ-0019 Lom63 sequence (EMBL complement(KF515737.1:60555..60878), protein AHF72799.1) and records that UniProtKB/TrEMBL entry W0HKR9.1 is inactive/obsolete, confirming no active UniProtKB accession resolves for AHF72799.1.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/KF515737.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    snippet
    lomaiviticin biosynthetic gene cluster
    notes
    GenBank KF515737.1 is the 72,505 bp S. pacifica DPJ-0019 lomaiviticin biosynthetic gene cluster and carries lom62/AHF72798.1 and lom63/AHF72799.1.
propionyl-ACP starter-unit generation contributes to lomaiviticin E 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 E.
DOI:10.1021/ol403714g
https://www.ncbi.nlm.nih.gov/protein/AHF72798.1
https://www.uniprot.org/uniparc/UPI00035CE3B5
https://www.ncbi.nlm.nih.gov/protein/AHF72799.1
https://www.uniprot.org/uniparc/UPI00037FF3C5
https://www.ncbi.nlm.nih.gov/nuccore/KF515737.1
  • reference
    DOI:10.1021/ol403714g
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    Robust, Lom62-dependent formation
    notes
    Waldman and Balskus cloned Salinispora pacifica DPJ-0019 lom62, lom60, and lom63, then showed in vitro by HPLC/LC-MS that Lom62 generated the expected propionyl-ACP thioester robustly only with methylmalonyl-CoA and Lom63.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AHF72798.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    snippet
    acyl transferase/decarboxylase
    notes
    NCBI GenPept AHF72798.1 is the 324 aa S. pacifica DPJ-0019 lom62 product on KF515737.1:59562..60536; exact AHF72798.1, AHF72798, lom62, and KF515737 UniProtKB searches did not resolve a S. pacifica accession on 2026-09-27.
  • reference
    https://www.uniprot.org/uniparc/UPI00035CE3B5
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-23
    snippet
    AHF72798.1
    notes
    UniParc UPI00035CE3B5 archives the exact 324 aa S. pacifica DPJ-0019 Lom62 sequence (EMBL KF515737.1:59562..60536, protein AHF72798.1) and records that UniProtKB/TrEMBL entry W0HGI2.1 is inactive/obsolete, confirming no active UniProtKB accession resolves for AHF72798.1.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AHF72799.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    snippet
    phosphopantheine-binding protein
    notes
    NCBI GenPept AHF72799.1 is the 107 aa S. pacifica DPJ-0019 lom63 acyl carrier protein on complement(KF515737.1:60555..60878); exact AHF72799.1, AHF72799, lom63, and KF515737 UniProtKB searches did not resolve a S. pacifica accession on 2026-09-27.
  • reference
    https://www.uniprot.org/uniparc/UPI00037FF3C5
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-23
    snippet
    AHF72799.1
    notes
    UniParc UPI00037FF3C5 archives the exact 107 aa S. pacifica DPJ-0019 Lom63 sequence (EMBL complement(KF515737.1:60555..60878), protein AHF72799.1) and records that UniProtKB/TrEMBL entry W0HKR9.1 is inactive/obsolete, confirming no active UniProtKB accession resolves for AHF72799.1.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/KF515737.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    snippet
    lomaiviticin biosynthetic gene cluster
    notes
    GenBank KF515737.1 is the 72,505 bp S. pacifica DPJ-0019 lomaiviticin biosynthetic gene cluster and carries lom62/AHF72798.1 and lom63/AHF72799.1.

Every edge carries its own citation; an uncited edge is refused by the corpus tests.

Explore across X-Mech

AntibioticMech (lomaiviticin E) ↗ MediaIngredientMech (naturalproductmech:mibig-3e651964d5) ↗ TaxonMech: Salinispora pacifica (NCBITaxon:351187) ↗ TaxonMech: Salinispora tropica CNB-440 (NCBITaxon:369723) ↗ PathwayMech (mibig:BGC0000240) ↗ PathwayMech (mibig:BGC0000241) ↗

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 conceptSourceVersion
BGC0000240MIBIG5
BGC0000241MIBIG5

This page is generated from data/natural_products/polyketides/lomaiviticin-e.yaml, which is generated from the committed inventories. Neither is edited by hand.