flaviolin

naturalproductmech:mibig-cfe2b5c0a9 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	XNPCAGMCQDGQKK-UHFFFAOYSA-N
SMILES	C1=C(C=C2C(=C1O)C(=CC(=O)C2=O)O)O
Stereochemistry	fully defined
Cross-references	pubchem:160478, npatlas:NPA032742

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 3

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
Saccharopolyspora erythraea NCBITaxon:1836	BGC_CHARACTERIZED	mibig:BGC0000285	PMID:12028378
Saccharopolyspora erythraea NRRL 2338 NCBITaxon:405948	SOURCE_ASSERTION	mibig:BGC0000902	PMID:22187221
Streptomyces coelicolor A3(2) NCBITaxon:100226	SOURCE_ASSERTION	mibig:BGC0002127	PMID:12905073

Occurrences 12

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 albidoflavus NCBITaxon:1886	LOTUS	DOI:10.1007/S10295-003-0075-8
Streptomyces albidoflavus NCBITaxon:1886	LOTUS	DOI:10.1007/S10295-013-1383-2
Streptomyces albidoflavus NCBITaxon:1886	LOTUS	DOI:10.1186/S12934-015-0335-0
Streptomyces coelicolor NCBITaxon:1902	LOTUS	DOI:10.1007/S10295-003-0075-8
Streptomyces coelicolor NCBITaxon:1902	LOTUS	DOI:10.1007/S10295-013-1383-2
Streptomyces coelicolor NCBITaxon:1902	LOTUS	DOI:10.1186/S12934-015-0335-0
Verticillium dahliae NCBITaxon:27337	LOTUS	DOI:10.1007/BF00567298
Verticillium dahliae NCBITaxon:27337	LOTUS	DOI:10.1007/BF00567299
Leptosphaeria maculans NCBITaxon:5022	LOTUS	DOI:10.1016/0031-9422(88)80752-0
Streptomyces venezuelae NCBITaxon:54571	LOTUS	DOI:10.1007/S10529-009-0152-9
Aspergillus fumigatus NCBITaxon:746128	LOTUS	DOI:10.1080/13693780802307720
Saccharopolyspora erythraea NCBITaxon:1836	LOTUS	DOI:10.1046/J.1365-2958.2002.02975.X

Biosynthetic gene clusters 3

Accession	Host	Locus evidence	Genome
mibig:BGC0000285	Saccharopolyspora erythraea NCBITaxon:1836	CLUSTER_DEMONSTRATED	genbank:AY078067.1
mibig:BGC0000902	Saccharopolyspora erythraea NRRL 2338 NCBITaxon:405948	CLUSTER_UNSTATED	genbank:AM420293.1
mibig:BGC0002127	Streptomyces coelicolor A3(2) NCBITaxon:100226	CLUSTER_DEMONSTRATED	genbank:AL645882.2

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.

#	Enzyme	Reaction	Substrate → product	Evidence
1	RppA UniProtKB:Q8KQM3		ungrounded → CHEBI:18365	DOI:10.1046/j.1365-2958.2002.02975.x
2	SCO1206 UniProtKB:Q9FCA7	RHEA:41524	CHEBI:57384 → CHEBI:18365	DOI:10.1007/s10295-003-0075-8

Entry 1: This curates the Saccharopolyspora erythraea BGC0000285/AY078067.1 RppA type III PKS as the knockout-supported scaffold enzyme in the red-brown pigment locus. The record does not assert direct biochemical characterization of purified S. erythraea RppA or a single-enzyme reaction from RppA to exact flaviolin.

Entry 2: This curates Streptomyces coelicolor A3(2) SCO1206 as the biochemically characterized type III PKS that condenses malonyl-CoA to 1,3,6,8-tetrahydroxynaphthalene upstream of spontaneous oxidation to flaviolin.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 6 nodes, 6 edges

Partial Saccharopolyspora erythraea RppA and Streptomyces coelicolor SCO1206 type III PKS graph for formation of 1,3,6,8-tetrahydroxynaphthalene upstream of flaviolin.

Subject	Predicate	Object	Notes	Evidence
malonyl-CoA(5-)	is condensed by	RppA	The S. erythraea RppA edge is proposed from the cloned rppA sequence, knockout of the pigment locus, and homology to biochemically characterized bacterial THN synthases.	DOI:10.1046/j.1365-2958.2002.02975.x https://mibig.secondarymetabolites.org/repository/BGC0000285.5/index.html https://www.uniprot.org/uniprotkb/Q8KQM3 https://www.ncbi.nlm.nih.gov/protein/AAL78053.1 reference DOI:10.1046/j.1365-2958.2002.02975.x evidence type PRIMARY_EXPERIMENT snippet disrupt the red-brown pigment-producing (rpp) locus in S. erythraea, generating a mutant that displayed an albino phenotype notes Cortes et al. used rpp-locus disruption and vector recapture in Saccharopolyspora erythraea to connect the cloned chalcone-synthase-like rppA locus to diffusible red-brown flaviolin-derived pigment biosynthesis; the RppA-to-THN product assignment is proposed from type III PKS homology rather than an assay of purified S. erythraea RppA. reference https://mibig.secondarymetabolites.org/repository/BGC0000285.5/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes MIBiG BGC0000285.5 names flaviolin among products of the Saccharopolyspora erythraea AY078067.1 red-brown-pigment locus and annotates AAL78053.1/rppA as a knockout-supported Type III PKS scaffold-biosynthesis gene. reference https://www.uniprot.org/uniprotkb/Q8KQM3 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes Unreviewed UniProtKB:Q8KQM3 is the 367 aa Saccharopolyspora erythraea RppA/rppA protein and cross-references EMBL AY078067 protein AAL78053.1. reference https://www.ncbi.nlm.nih.gov/protein/AAL78053.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes NCBI GenPept AAL78053.1 is the AY078067.1 rppA CDS from the Saccharopolyspora erythraea red-brown-pigment locus and is sequence-identical to UniProtKB:Q8KQM3.
RppA	catalyzes proposed formation of	1,3,6,8-tetrahydroxynaphthalene	The edge stops at the proposed THN synthase product rather than assigning RppA to exact flaviolin, flaviolin rhamnoside, or 3,3'-diflaviolin formation.	DOI:10.1046/j.1365-2958.2002.02975.x https://mibig.secondarymetabolites.org/repository/BGC0000285.5/index.html https://www.uniprot.org/uniprotkb/Q8KQM3 https://www.ncbi.nlm.nih.gov/protein/AAL78053.1 reference DOI:10.1046/j.1365-2958.2002.02975.x evidence type PRIMARY_EXPERIMENT snippet disrupt the red-brown pigment-producing (rpp) locus in S. erythraea, generating a mutant that displayed an albino phenotype notes Cortes et al. used rpp-locus disruption and vector recapture in Saccharopolyspora erythraea to connect the cloned chalcone-synthase-like rppA locus to diffusible red-brown flaviolin-derived pigment biosynthesis; the RppA-to-THN product assignment is proposed from type III PKS homology rather than an assay of purified S. erythraea RppA. reference https://mibig.secondarymetabolites.org/repository/BGC0000285.5/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes MIBiG BGC0000285.5 names flaviolin among products of the Saccharopolyspora erythraea AY078067.1 red-brown-pigment locus and annotates AAL78053.1/rppA as a knockout-supported Type III PKS scaffold-biosynthesis gene. reference https://www.uniprot.org/uniprotkb/Q8KQM3 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes Unreviewed UniProtKB:Q8KQM3 is the 367 aa Saccharopolyspora erythraea RppA/rppA protein and cross-references EMBL AY078067 protein AAL78053.1. reference https://www.ncbi.nlm.nih.gov/protein/AAL78053.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes NCBI GenPept AAL78053.1 is the AY078067.1 rppA CDS from the Saccharopolyspora erythraea red-brown-pigment locus and is sequence-identical to UniProtKB:Q8KQM3.
malonyl-CoA(5-)	is condensed by	SCO1206 THNS	RHEA:41524 selects malonyl-CoA as the sole CoA-linked substrate for the SCO1206 THN synthase reaction.	DOI:10.1007/s10295-003-0075-8 https://www.uniprot.org/uniprotkb/Q9FCA7 https://www.ncbi.nlm.nih.gov/protein/CAC01488.1 reference DOI:10.1007/s10295-003-0075-8 evidence type PRIMARY_EXPERIMENT snippet Expression and characterization of the type III polyketide synthase 1,3,6,8-tetrahydroxynaphthalene synthase from Streptomyces coelicolor A3(2) notes Izumikawa et al. expressed and characterized Streptomyces coelicolor A3(2) SCO1206 as the type III PKS that catalyzes malonyl-CoA condensation to 1,3,6,8-tetrahydroxynaphthalene. reference https://www.uniprot.org/uniprotkb/Q9FCA7 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes Reviewed UniProtKB:Q9FCA7 is the 374 aa Streptomyces coelicolor A3(2) SCO1206 1,3,6,8-tetrahydroxynaphthalene synthase and annotates EC:2.3.1.233/RHEA:41524 with PMID:12905073. reference https://www.ncbi.nlm.nih.gov/protein/CAC01488.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes NCBI GenPept CAC01488.1 is the Streptomyces coelicolor A3(2) SCO1206/2SCG58.06 putative polyketide synthase CDS and cross-references GOA:Q9FCA7.
SCO1206 THNS	catalyzes formation of	1,3,6,8-tetrahydroxynaphthalene	SCO1206 is curated at the exact reaction characterized in the Streptomyces coelicolor type III PKS study and annotated in UniProt with RHEA:41524.	DOI:10.1007/s10295-003-0075-8 https://www.uniprot.org/uniprotkb/Q9FCA7 https://www.ncbi.nlm.nih.gov/protein/CAC01488.1 reference DOI:10.1007/s10295-003-0075-8 evidence type PRIMARY_EXPERIMENT snippet Expression and characterization of the type III polyketide synthase 1,3,6,8-tetrahydroxynaphthalene synthase from Streptomyces coelicolor A3(2) notes Izumikawa et al. expressed and characterized Streptomyces coelicolor A3(2) SCO1206 as the type III PKS that catalyzes malonyl-CoA condensation to 1,3,6,8-tetrahydroxynaphthalene. reference https://www.uniprot.org/uniprotkb/Q9FCA7 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes Reviewed UniProtKB:Q9FCA7 is the 374 aa Streptomyces coelicolor A3(2) SCO1206 1,3,6,8-tetrahydroxynaphthalene synthase and annotates EC:2.3.1.233/RHEA:41524 with PMID:12905073. reference https://www.ncbi.nlm.nih.gov/protein/CAC01488.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes NCBI GenPept CAC01488.1 is the Streptomyces coelicolor A3(2) SCO1206/2SCG58.06 putative polyketide synthase CDS and cross-references GOA:Q9FCA7.
1,3,6,8-tetrahydroxynaphthalene	spontaneously oxidizes through	THN oxidation	The non-enzymatic process captures THN oxidation without assigning an exact downstream tailoring enzyme in either cluster.	DOI:10.1046/j.1365-2958.2002.02975.x reference DOI:10.1046/j.1365-2958.2002.02975.x evidence type PRIMARY_EXPERIMENT snippet Flaviolin is a spontaneous oxidation product of 1,3,6,8-tetrahydroxynaphthalene notes Cortes et al. place flaviolin downstream of the THN synthase product; the BGC0000285 cluster also encodes RppB and ORF3 oxidases, but those tailoring enzymes are not assigned here to the exact flaviolin branch.
THN oxidation	forms	flaviolin	The exact flaviolin product is supported by the spontaneous-oxidation statement and by the BGC0000285 and BGC0002127 MIBiG product assertions.	DOI:10.1046/j.1365-2958.2002.02975.x https://mibig.secondarymetabolites.org/repository/BGC0000285.5/index.html https://mibig.secondarymetabolites.org/repository/BGC0002127.3/index.html reference DOI:10.1046/j.1365-2958.2002.02975.x evidence type PRIMARY_EXPERIMENT snippet Flaviolin is a spontaneous oxidation product of 1,3,6,8-tetrahydroxynaphthalene notes Cortes et al. place flaviolin downstream of the THN synthase product; the BGC0000285 cluster also encodes RppB and ORF3 oxidases, but those tailoring enzymes are not assigned here to the exact flaviolin branch. reference https://mibig.secondarymetabolites.org/repository/BGC0000285.5/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes MIBiG BGC0000285.5 names flaviolin among products of the Saccharopolyspora erythraea AY078067.1 red-brown-pigment locus and annotates AAL78053.1/rppA as a knockout-supported Type III PKS scaffold-biosynthesis gene. reference https://mibig.secondarymetabolites.org/repository/BGC0002127.3/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes MIBiG BGC0002127.3 names flaviolin and 1,3,6,8-tetrahydroxynaphthalene as products of the Streptomyces coelicolor A3(2) AL645882.2 flaviolin locus.

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

Bioactivities 8

Entries preserve source qualifiers, targets and evidence. Repeated assay names or values are not independent replications; inspect source detail for differences.

Assay	Result	Target enzyme	Source detail
OTUD3 deubiquitinase inhibition: Primary qHTS	ACTIVE	Not recorded	pubchem.aid:1645858 assay OTUD3 deubiquitinase inhibition: Primary qHTS evidence reference pubchem.aid:1645858 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1645858, deposited by 24642; assay type Other. Target accession NP_056022 was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE
UCHL1 deubiquitinase inhibition: Primary qHTS	ACTIVE	UniProtKB:P09936	pubchem.aid:1645859 assay UCHL1 deubiquitinase inhibition: Primary qHTS evidence reference pubchem.aid:1645859 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1645859, deposited by 24642; assay type Other. call ACTIVE target enzyme UniProtKB:P09936
USP10 deubiquitinase inhibition: Primary qHTS	ACTIVE	UniProtKB:Q14694	pubchem.aid:1645856 assay USP10 deubiquitinase inhibition: Primary qHTS evidence reference pubchem.aid:1645856 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1645856, deposited by 24642; assay type Other. call ACTIVE target enzyme UniProtKB:Q14694
USP17 deubiquitinase inhibition: Primary qHTS	ACTIVE	UniProtKB:A8MUK1	pubchem.aid:1645855 assay USP17 deubiquitinase inhibition: Primary qHTS evidence reference pubchem.aid:1645855 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1645855, deposited by 24642; assay type Other. call ACTIVE target enzyme UniProtKB:A8MUK1
USP28 deubiquitinase inhibition: Primary qHTS	ACTIVE	UniProtKB:Q96RU2	pubchem.aid:1645857 assay USP28 deubiquitinase inhibition: Primary qHTS evidence reference pubchem.aid:1645857 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1645857, deposited by 24642; assay type Other. call ACTIVE target enzyme UniProtKB:Q96RU2
USP30 deubiquitinase inhibition: Primary qHTS	ACTIVE	UniProtKB:Q70CQ3	pubchem.aid:1645860 assay USP30 deubiquitinase inhibition: Primary qHTS evidence reference pubchem.aid:1645860 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1645860, deposited by 24642; assay type Other. call ACTIVE target enzyme UniProtKB:Q70CQ3
USP7 deubiquitinase inhibition: Primary qHTS	ACTIVE	Not recorded	pubchem.aid:1645854 assay USP7 deubiquitinase inhibition: Primary qHTS evidence reference pubchem.aid:1645854 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1645854, deposited by 24642; assay type Other. Target accession NP_003461 was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE
USP8 deubiquitinase inhibition: Primary qHTS	ACTIVE	UniProtKB:P40818	pubchem.aid:1645853 assay USP8 deubiquitinase inhibition: Primary qHTS evidence reference pubchem.aid:1645853 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1645853, deposited by 24642; assay type Other. call ACTIVE target enzyme UniProtKB:P40818

Explore across X-Mech

AntibioticMech (flaviolin) ↗ MediaIngredientMech (naturalproductmech:mibig-cfe2b5c0a9) ↗ TaxonMech: Saccharopolyspora erythraea (NCBITaxon:1836) ↗ TaxonMech: Saccharopolyspora erythraea NRRL 2338 (NCBITaxon:405948) ↗ TaxonMech: Streptomyces coelicolor A3(2) (NCBITaxon:100226) ↗ PathwayMech (mibig:BGC0000285) ↗ PathwayMech (mibig:BGC0000902) ↗ PathwayMech (mibig:BGC0002127) ↗

Open questions 1

shared-structure — This structure is reported by more than one MIBiG entry: BGC0000285, BGC0000902, BGC0002127. Confirm they describe the same compound rather than an upstream cross-reference error.

Provenance

Source concept	Source	Version
BGC0000285	MIBIG	5
BGC0000902	MIBIG	4
BGC0002127	MIBIG	3

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