gentamicin

naturalproductmech:mibig-ac32edbacd 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	BDTQHFBWYNCGHN-CUYCKOLISA-N
SMILES	CN[C@H]1[C@@H](O)CO[C@H](O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3O[C@H](CN)[C@@H](O)[C@H](O)[C@H]3O)[C@@H]2O)[C@@H]1O
Stereochemistry	fully defined
Cross-references	npatlas:NPA09026

Filing pathway

Carbohydrates — 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 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
Micromonospora echinospora Strain: DSM 43036 NCBITaxon:1877	SOURCE_ASSERTION	mibig:BGC0000696	PMID:15376556, https://www.ncbi.nlm.nih.gov/nuccore/AJ628149.4 reference PMID:15376556 evidence type DATABASE_ASSERTION notes MIBiG BGC0000696 entry version 5; citation taken from the entry level reference https://www.ncbi.nlm.nih.gov/nuccore/AJ628149.4 evidence type CURATOR_INFERENCE notes Strain context: DSM 43036. AJ628149.4 source feature names DSM 43036. This qualifies the deposited locus, not exact gentamicin-congener production. Exact-product assignment remains open in #941. Taxon, chemistry and evidence grades are unchanged. See issue #944. Taxon identity and evidence grade are unchanged; this is not a species-wide experiment. MIBiG source row BGC0000696:1; SHA256 2dfb366df6dedb1474018b61f14f36c7eca4c5f11b1d519686e5be2e097a91ce. Curator: codex; date: 2026-10-13.

Occurrences 2

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
Micromonospora NCBITaxon:1873	LOTUS	DOI:10.1021/JM00340A034
Micromonospora echinospora NCBITaxon:1877	LOTUS	DOI:10.7164/ANTIBIOTICS.57.436

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000696	Micromonospora echinospora NCBITaxon:1877	CLUSTER_UNSTATED	genbank:AJ628149.4

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

Explore across X-Mech

AntibioticMech (gentamicin) ↗ MediaIngredientMech (naturalproductmech:mibig-ac32edbacd) ↗ TaxonMech: Micromonospora echinospora (NCBITaxon:1877) ↗ PathwayMech (mibig:BGC0000696) ↗

Open questions 1

curator-gentamicin-exact-product-assignment — Which exact gentamicin congener and stereochemical resolution do these source claims establish?

Provenance

Source concept	Source	Version
BGC0000696	MIBIG	5

This page is generated from data/natural_products/carbohydrates/gentamicin.yaml, which is generated from the committed inventories. Neither is edited by hand.