gentamicin

naturalproductmech:mibig-b697ac65fb 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	HFLKNINDVFJPQT-UHFFFAOYSA-N
SMILES	CC1(COC(C(C1NC)O)OC2C(CC(C(C2O)OC3C(C(C(C(O3)CO)O)O)N)N)N)O
Stereochemistry	undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers

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: ATCC 15835 NCBITaxon:1877	SOURCE_ASSERTION	mibig:BGC0001603	PMID:25641167, https://www.ncbi.nlm.nih.gov/nuccore/KY971520.1 reference PMID:25641167 evidence type DATABASE_ASSERTION notes MIBiG BGC0001603 entry version 3; citation taken from the entry level reference https://www.ncbi.nlm.nih.gov/nuccore/KY971520.1 evidence type CURATOR_INFERENCE notes Strain context: ATCC 15835. KY971520.1 source feature names ATCC 15835. This qualifies the deposited locus, not exact X2 stereochemistry or experimental product attribution. 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 BGC0001603:1; SHA256 17d841738524b47141cd211d3ba0d0f9a24cfb0a8b7c71952651d0148ba5958d. Curator: codex; date: 2026-10-13.

Occurrences 0

None cited.

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0001603	Micromonospora echinospora NCBITaxon:1877	CLUSTER_UNSTATED	genbank:KY971520.1

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

Explore across X-Mech

AntibioticMech (gentamicin) ↗ MediaIngredientMech (naturalproductmech:mibig-b697ac65fb) ↗ TaxonMech: Micromonospora echinospora (NCBITaxon:1877) ↗ PathwayMech (mibig:BGC0001603) ↗

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
BGC0001603	MIBIG	3

This page is generated from data/natural_products/carbohydrates/gentamicin-2.yaml, which is generated from the committed inventories. Neither is edited by hand.