gladiofungin B

naturalproductmech:mibig-67868173e8 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	OOTQTRXEOBAJEW-UCTNKHALSA-N
SMILES	CC1=C(C(=O)CCCCCC/C=C/C=C/[C@H](C)C(=O)C[C@H](O)CC2CC(=O)NC(=O)C2)C(=O)OC1O
Stereochemistry	undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers
Cross-references	npatlas:NPA031555

Filing pathway

Alkaloids — 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
Burkholderia gladioli NCBITaxon:28095	BGC_CHARACTERIZED	mibig:BGC0002083	DOI:10.1002/anie.202005711

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.

Taxon	Source	Reference
Burkholderia gladioli NCBITaxon:28095	LOTUS	DOI:10.1002/ANIE.202005711

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0002083	Burkholderia gladioli NCBITaxon:28095	CLUSTER_DEMONSTRATED	genbank:WITE01000004.1

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	LvStA_05069 AfsA-like offloading domain NCBIProtein:KAF1058474.1		ungrounded → ungrounded	DOI:10.1002/anie.202005711

Step 1: This curates the terminal AfsA-like offloading domain of the Burkholderia gladioli Lv-StA LvStA_05069/KAF1058474.1 trans-AT PKS as a required contributor to noncanonical chain release and butenolide formation in BGC0002083 gladiofungin B biosynthesis. The exact KAF1058474.1 GenPept accession did not resolve in UniProtKB accession search on 2026-09-27, so enzyme_id is grounded to the native GenPept accession NCBIProtein:KAF1058474.1 (UniParc UPI00139C1DD8 maps only to retired/obsolete UniProtKB/TrEMBL entry A0A833UU34.1).

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 3 nodes, 2 edges

Partial Burkholderia gladioli Lv-StA gladiofungin B biosynthesis graph for the terminal AfsA-like LvStA_05069 offloading-domain contribution to butenolide-containing chain release.

Subject	Predicate	Object	Notes	Evidence
LvStA_05069 AfsA-like offloading domain	is required for	butenolide-forming polyketide chain release	CRISPR/Cas deletion inside the AfsA-like terminal domain abolished gladiofungin A/B production without detectable polar effects on the downstream glaF and glaG genes. This edge is scoped to the terminal domain and does not assert a free substrate or the full PKS assembly order.	DOI:10.1002/anie.202005711 mibig:BGC0002083 https://www.ncbi.nlm.nih.gov/protein/KAF1058474.1 https://www.uniprot.org/uniparc/UPI00139C1DD8 https://www.ncbi.nlm.nih.gov/nuccore/WITE01000004.1 reference DOI:10.1002/anie.202005711 evidence type PRIMARY_EXPERIMENT snippet the AfsA domain plays a key role notes Florez et al. used a CRISPR/Cas marker-less deletion to remove part of the AfsA-like terminal offloading domain in the Burkholderia gladioli HKI0739/Lv-StA gla trans-AT PKS assembly line and showed that the mutant no longer produced gladiofungin A or B. reference mibig:BGC0002083 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes MIBiG BGC0002083 version 3 maps module 10 of the Burkholderia gladioli Lv-StA gladiofungin trans-AT PKS assembly line to LvStA_05069 and annotates its terminal modification domain as A-factor synthase A. reference https://www.ncbi.nlm.nih.gov/protein/KAF1058474.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet Polyketide synthase PksN notes NCBI GenPept KAF1058474.1 is the 10,181 aa LvStA_05069 CDS on complement(WITE01000004.1:1156002..1186547) from Burkholderia gladioli Lv-StA. The exact KAF1058474.1 GenPept accession did not resolve in UniProtKB accession search on 2026-09-27. reference https://www.uniprot.org/uniparc/UPI00139C1DD8 evidence type DATABASE_ASSERTION retrieved on 2026-10-23 snippet KAF1058474.1 notes UniParc UPI00139C1DD8 archives the exact 10,181 aa Burkholderia gladioli Lv-StA LvStA_05069 sequence (EMBL complement(WITE01000004.1:1156002..1186547), protein KAF1058474.1) and records that UniProtKB/TrEMBL entry A0A833UU34.1 is inactive/obsolete, confirming no active UniProtKB accession resolves for KAF1058474.1. reference https://www.ncbi.nlm.nih.gov/nuccore/WITE01000004.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet Burkholderia gladioli strain Lv-StA LvStA_4 notes GenBank WITE01000004.1 contains the BGC0002083 region used by MIBiG; within that contig, LvStA_05069 encodes protein KAF1058474.1.
butenolide-forming polyketide chain release	contributes to	gladiofungin B	The terminal AfsA-like domain is curated as a required domain for the butenolide-bearing chain-release phase of gladiofungin B biosynthesis; earlier glutarimide and polyketide-chain assembly steps remain unexpanded.	DOI:10.1002/anie.202005711 mibig:BGC0002083 https://www.ncbi.nlm.nih.gov/protein/KAF1058474.1 https://www.uniprot.org/uniparc/UPI00139C1DD8 https://www.ncbi.nlm.nih.gov/nuccore/WITE01000004.1 reference DOI:10.1002/anie.202005711 evidence type PRIMARY_EXPERIMENT snippet the AfsA domain plays a key role notes Florez et al. used a CRISPR/Cas marker-less deletion to remove part of the AfsA-like terminal offloading domain in the Burkholderia gladioli HKI0739/Lv-StA gla trans-AT PKS assembly line and showed that the mutant no longer produced gladiofungin A or B. reference mibig:BGC0002083 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes MIBiG BGC0002083 version 3 maps module 10 of the Burkholderia gladioli Lv-StA gladiofungin trans-AT PKS assembly line to LvStA_05069 and annotates its terminal modification domain as A-factor synthase A. reference https://www.ncbi.nlm.nih.gov/protein/KAF1058474.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet Polyketide synthase PksN notes NCBI GenPept KAF1058474.1 is the 10,181 aa LvStA_05069 CDS on complement(WITE01000004.1:1156002..1186547) from Burkholderia gladioli Lv-StA. The exact KAF1058474.1 GenPept accession did not resolve in UniProtKB accession search on 2026-09-27. reference https://www.uniprot.org/uniparc/UPI00139C1DD8 evidence type DATABASE_ASSERTION retrieved on 2026-10-23 snippet KAF1058474.1 notes UniParc UPI00139C1DD8 archives the exact 10,181 aa Burkholderia gladioli Lv-StA LvStA_05069 sequence (EMBL complement(WITE01000004.1:1156002..1186547), protein KAF1058474.1) and records that UniProtKB/TrEMBL entry A0A833UU34.1 is inactive/obsolete, confirming no active UniProtKB accession resolves for KAF1058474.1. reference https://www.ncbi.nlm.nih.gov/nuccore/WITE01000004.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet Burkholderia gladioli strain Lv-StA LvStA_4 notes GenBank WITE01000004.1 contains the BGC0002083 region used by MIBiG; within that contig, LvStA_05069 encodes protein KAF1058474.1.

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

Explore across X-Mech

AntibioticMech (gladiofungin B) ↗ MediaIngredientMech (naturalproductmech:mibig-67868173e8) ↗ TaxonMech: Burkholderia gladioli (NCBITaxon:28095) ↗ PathwayMech (mibig:BGC0002083) ↗

Provenance

Source concept	Source	Version
BGC0002083	MIBIG	3

This page is generated from data/natural_products/alkaloids/gladiofungin-b.yaml, which is generated from the committed inventories. Neither is edited by hand.