naphthomycin A

naturalproductmech:mibig-efdb010171 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 InChIKey	AXEGRHYJHHPVDH-UMKVKWLOSA-N
SMILES	C[C@H]1\C=C\C=C/C=C(C)\C(=O)NC2=C(Cl)C(=O)C3=C(C=C(C)C(O)=C3C(=O)\C(C)=C\[C@H](C)[C@@H](O)[C@@H](C)\C=C\[C@@H](O)C\C=C(C)\C(=O)C[C@@H]1O)C2=O
Stereochemistry	fully defined
Cross-references	npatlas:NPA0326

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, 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
Streptomyces sp. CS NCBITaxon:876169	BGC_CHARACTERIZED	mibig:BGC0000106	PMID:21614382

Occurrences 7

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
Streptomyces NCBITaxon:1883	LOTUS	DOI:10.1021/ACS.JNATPROD.6B01059
Streptomyces NCBITaxon:1883	LOTUS	DOI:10.1021/NP300109S
Streptomyces NCBITaxon:1883	LOTUS	DOI:10.1039/C1MB05036B
Streptomyces NCBITaxon:1883	LOTUS	DOI:10.7164/ANTIBIOTICS.28.85
Streptomyces NCBITaxon:1883	LOTUS	DOI:10.7164/ANTIBIOTICS.38.948
Streptomyces NCBITaxon:1883	LOTUS	DOI:10.7164/ANTIBIOTICS.51.845
Streptomyces collinus NCBITaxon:42684	LOTUS	DOI:10.1139/V94-028

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000106	Streptomyces sp. CS NCBITaxon:876169	CLUSTER_DEMONSTRATED	genbank:GQ452266.1

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.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 2 nodes, 1 edge

Native-reference identity only for Nat1 in Streptomyces sp. CS/taxon 876169/GQ452266.1. Placement in this owner is curator-inferred from the shared BGC0000106 context, not proof of a purified reaction, historical assay construct or exact mature-product formation. The MITE listed product and literal SMARTS output agree but leave six alkene configurations unspecified, unlike this exact owner. No source model is repaired or reaction adopted. MITE also describes a separate putative proansamitocin context; no such claim is transferred here. DOI:10.1039/C1MB05036B was inspected only at the publisher abstract level on 2026-10-08; the full-text loader failed and retrieval stopped. No primary experiment is independently adopted.

Subject	Predicate	Object	Notes	Evidence
nat1 CDS (GQ452266.1)	encodes the native protein reference	Nat1 (Streptomyces sp. CS native-reference example)	82335..83678 positive strand; 1344-nt complete CDS including stop, 447 residues. The accession denotes the native reference, not an affinity-tagged or mutated construct. An annotated halogenase name does not establish a reaction.	https://www.ncbi.nlm.nih.gov/nuccore/GQ452266.1 https://www.ncbi.nlm.nih.gov/protein/ADM46362.1 https://rest.uniprot.org/uniprotkb/F8QPG4.json https://rest.uniprot.org/uniprotkb/F8QPG4.json https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000477.json https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000477.json reference https://www.ncbi.nlm.nih.gov/nuccore/GQ452266.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-08 snippet /gene="nat1" notes The 106,181-bp partial cluster deposition names nat1/ADM46362.1 at 82335..83678, codon_start 1 and translation table 11. Source names strain CS/taxon 876169. It is not the whole genome or an independent activity experiment. reference https://www.ncbi.nlm.nih.gov/protein/ADM46362.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-08 notes Versioned GenPept ADM46362.1 names nat1 and codes from GQ452266.1:82335..83678, strain CS. It is a 447-residue author-supplied conceptual translation annotated halogenase. reference https://rest.uniprot.org/uniprotkb/F8QPG4.json evidence type DATABASE_ASSERTION retrieved on 2026-10-08 notes Current unreviewed primary F8QPG4, entry version 33/sequence version 1, names nat1/strain CS/taxon 876169 and directly cross-references GQ452266 with protein ADM46362.1. Homology-based protein existence and automated family annotation are not experimental validation of activity. reference https://rest.uniprot.org/uniprotkb/F8QPG4.json evidence type CURATOR_INFERENCE retrieved on 2026-10-08 notes Complete-CDS-aware translation, deposited translation, independent GenPept and UniProt sequences agree over all 447 residues. Exact gene, accession, strain and taxon agreement supports selecting this native-reference example rather than an arbitrary homolog. This does not identify a historical assay construct. reference https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000477.json evidence type DATABASE_ASSERTION retrieved on 2026-10-08 notes Active MITE0000477 version 1 maps Nat1 to F8QPG4/ADM46362.1/BGC0000106. This supports source mapping only. Source knock-out codes are not independently inspected primary experiments. reference https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000477.json evidence type CURATOR_INFERENCE retrieved on 2026-10-08 notes Under RDKit 2026.03.5 the literal naphthomycin model product and SMARTS output share AXEGRHYJHHPVDH-RRJKCPLYSA-N, not owner AXEGRHYJHHPVDH-UMKVKWLOSA-N. Both leave six alkene configurations unspecified; this is not evidence of isomerization. The source is not silently repaired, and exact-owner reaction adoption is withheld.

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

Causal graph — biosynthesis 2 nodes, 1 edge

Native-reference identity only for Nat2 in Streptomyces sp. CS/taxon 876169/GQ452266.1. Placement in this owner is curator-inferred from the shared deposited cluster and BGC0000106 context; it is not proof of an exact-product reaction. Predicted oxidoreductase and automated MhpA-related annotations are not demonstrated hydroxylation or ring formation. No deletion phenotype, historical assay construct, pathway order or physical complex is asserted. DOI:10.1039/C1MB05036B was inspected only at the publisher abstract level on 2026-10-08; the full-text loader failed and retrieval stopped. No primary experiment is independently adopted.

Subject	Predicate	Object	Notes	Evidence
nat2 CDS (GQ452266.1)	encodes the native protein reference	Nat2 (Streptomyces sp. CS native-reference example)	91304..93061 reverse strand; 1758-nt complete CDS including stop, 585 residues. The accession denotes the native reference, not a tagged or mutated construct. Sequence identity does not experimentally validate activity.	https://www.ncbi.nlm.nih.gov/nuccore/GQ452266.1 https://www.ncbi.nlm.nih.gov/protein/ADM46370.1 https://rest.uniprot.org/uniprotkb/F8QPH2.json https://www.ncbi.nlm.nih.gov/nuccore/GQ452266.1 reference https://www.ncbi.nlm.nih.gov/nuccore/GQ452266.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-08 snippet /gene="nat2" notes The 106,181-bp partial cluster deposition names nat2/ADM46370.1 at complement(91304..93061), codon_start 1 and translation table 11. Source names strain CS/taxon 876169. It is not the whole genome or an independent activity experiment. reference https://www.ncbi.nlm.nih.gov/protein/ADM46370.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-08 notes Versioned GenPept ADM46370.1 names nat2 and codes from complement(GQ452266.1:91304..93061), strain CS. It is a 585-residue author-supplied conceptual translation annotated FAD-dependent oxidoreductase. Its computational MhpA region annotation is not a native-substrate experiment. reference https://rest.uniprot.org/uniprotkb/F8QPH2.json evidence type DATABASE_ASSERTION retrieved on 2026-10-08 notes Current unreviewed primary F8QPH2, entry version 34/sequence version 1, names nat2/strain CS/taxon 876169 and directly cross-references GQ452266 with protein ADM46370.1. Protein existence is Predicted. Automated MhpA-related domain and GO annotations do not demonstrate a reaction on naphthomycin. reference https://www.ncbi.nlm.nih.gov/nuccore/GQ452266.1 evidence type CURATOR_INFERENCE retrieved on 2026-10-08 notes Complete-CDS-aware reverse-strand translation, deposited translation, independent GenPept and UniProt sequences agree over all 585 residues. The exact-gene/taxon UniProt search returned one entry, F8QPH2. Gene, accession, strain and taxon agreement supports this native-reference example, not an arbitrary homolog. Placement in this owner is inferred from its existing GQ452266.1/BGC0000106 cluster context; this does not establish activity or a historical assay construct.

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

Explore across X-Mech

AntibioticMech (naphthomycin A) ↗ MediaIngredientMech (naturalproductmech:mibig-efdb010171) ↗ TaxonMech: Streptomyces sp. CS (NCBITaxon:876169) ↗ PathwayMech (mibig:BGC0000106) ↗

Provenance

Source concept	Source	Version
BGC0000106	MIBIG	5

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