Chromobacterium violaceum violacein biosynthetic gene cluster

MIBiG:BGC0000829

Literature-refined cluster scope from C. violaceum JCM 1249 (ATCC 12472), using the experimentally studied AB032799.1 locus. The active MIBiG entry points to AF172851.1; retired BGC0000828 points to AB032799.1 and explicitly merges into BGC0000829. The four AB proteins differ from the AF proteins and are not equated. VioE is independently sequence-resolved in the unannotated AB locus region. This graph records five gene-product contributions and observed violacein output, including subsequent spontaneous chemistry; it does not assign all final chemistry to enzymes or assert elementary reactions. Native MIBiG quality remains questionable.

Pathway type

biosynthetic gene cluster

Organism scope

Chromobacterium violaceum ATCC 12472 NCBITaxon:243365

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Pathway network

7 nodes · 6 asserted directed edges

Arrows show recorded subject → object relationships, not necessarily metabolic flow. Select a node for details or an arrow for evidence. Scroll, zoom or find a node to explore.

Chemical / cofactor
Protein / complex
Pathway
Solid arrow: mechanistic relation
Dashed arrow: membership, location or cofactor relation

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Chromobacterium violaceum ATCC 12472 `NCBITaxon:243365`	taxon
Vio A `NCBIProtein:BAA84782.1`	protein
Vio B `NCBIProtein:BAA84783.1`	protein
Vio C `NCBIProtein:BAA84784.1`	protein
Vio D `NCBIProtein:BAA84785.1`	protein
hypothetical protein `NCBIProtein:AAQ60934.1`	protein
violacein `CHEBI:131914`	small molecule

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
Vio A `NCBIProtein:BAA84782.1`	enables vioA product from the JCM 1249 assay locus contributes within the VioABED enzyme mixture that produced pathway precursor protoviolaceinic acid (compound 8). This supports an enables edge, not isolated elementary catalysis. The differing AF172851.1 protein is not substituted.	JCM 1249 vioABCDE cluster, AB032799.1 literature scope `MIBiG:BGC0000829`	NCBIProtein:BAA84782.1 Source assertion: BAA84782.1 is annotated as Vio A; its CDS is assigned to gene vio A and encoded by AB032799.1:552..1808. Source location `GBSet/GBSeq[GBSeq_accession-version='BAA84782.1']/GBSeq_feature-table/GBFeature[GBFeature_key='Protein' or GBFeature_key='CDS']/GBFeature_quals` MIBiG:BGC0000828 Source assertion: Retired BGC0000828 assigns the violacein cluster to AB032799.1 and explicitly identifies BGC0000829 as its duplicate successor. This is cluster identity lineage, not protein sequence equivalence. Source location `$.status; $.loci[0].accession; $.compounds[0].name; $.retirement_reasons[0]; $.see_also[0]` PMID:17925955 VioABED produced 8
Vio B `NCBIProtein:BAA84783.1`	enables vioB product from the JCM 1249 assay locus contributes within the VioABED enzyme mixture that produced pathway precursor protoviolaceinic acid (compound 8). This supports an enables edge, not isolated elementary catalysis. The differing AF172851.1 protein is not substituted.	JCM 1249 vioABCDE cluster, AB032799.1 literature scope `MIBiG:BGC0000829`	NCBIProtein:BAA84783.1 Source assertion: BAA84783.1 is annotated as Vio B; its CDS is assigned to gene vio B and encoded by AB032799.1:1883..4879. Source location `GBSet/GBSeq[GBSeq_accession-version='BAA84783.1']/GBSeq_feature-table/GBFeature[GBFeature_key='Protein' or GBFeature_key='CDS']/GBFeature_quals` MIBiG:BGC0000828 Source assertion: Retired BGC0000828 assigns the violacein cluster to AB032799.1 and explicitly identifies BGC0000829 as its duplicate successor. This is cluster identity lineage, not protein sequence equivalence. Source location `$.status; $.loci[0].accession; $.compounds[0].name; $.retirement_reasons[0]; $.see_also[0]` PMID:17925955 VioABED produced 8
Vio C `NCBIProtein:BAA84784.1`	enables The AB032799.1 VioC enzyme accepts the assayed pathway precursors protoviolaceinic acid (compound 8) and protodeoxyviolaceinic acid (compound 9). This supports a gene-product contribution; final spontaneous chemistry is not assigned to VioC catalysis.	JCM 1249 vioABCDE cluster, AB032799.1 literature scope `MIBiG:BGC0000829`	NCBIProtein:BAA84784.1 Source assertion: BAA84784.1 is annotated as Vio C; its CDS is assigned to gene vio C and encoded by AB032799.1:4881..6170. Source location `GBSet/GBSeq[GBSeq_accession-version='BAA84784.1']/GBSeq_feature-table/GBFeature[GBFeature_key='Protein' or GBFeature_key='CDS']/GBFeature_quals` MIBiG:BGC0000828 Source assertion: Retired BGC0000828 assigns the violacein cluster to AB032799.1 and explicitly identifies BGC0000829 as its duplicate successor. This is cluster identity lineage, not protein sequence equivalence. Source location `$.status; $.loci[0].accession; $.compounds[0].name; $.retirement_reasons[0]; $.see_also[0]` PMID:17925955 VioC accepts only 8 and 9
Vio D `NCBIProtein:BAA84785.1`	enables vioD product from the JCM 1249 assay locus contributes within the VioABED enzyme mixture that produced pathway precursor protoviolaceinic acid (compound 8). This supports an enables edge, not isolated elementary catalysis. The differing AF172851.1 protein is not substituted.	JCM 1249 vioABCDE cluster, AB032799.1 literature scope `MIBiG:BGC0000829`	NCBIProtein:BAA84785.1 Source assertion: BAA84785.1 is annotated as Vio D; its CDS is assigned to gene vio D and encoded by AB032799.1:6170..7291. Source location `GBSet/GBSeq[GBSeq_accession-version='BAA84785.1']/GBSeq_feature-table/GBFeature[GBFeature_key='Protein' or GBFeature_key='CDS']/GBFeature_quals` MIBiG:BGC0000828 Source assertion: Retired BGC0000828 assigns the violacein cluster to AB032799.1 and explicitly identifies BGC0000829 as its duplicate successor. This is cluster identity lineage, not protein sequence equivalence. Source location `$.status; $.loci[0].accession; $.compounds[0].name; $.retirement_reasons[0]; $.see_also[0]` PMID:17925955 VioABED produced 8
hypothetical protein `NCBIProtein:AAQ60934.1`	enables VioE is resolved by exact 191-aa translation of AB032799.1:7301..7873, followed by TAG, matching deposited AAQ60934.1. The paper amplified vioE from this AB plasmid. The NCBI protein label remains hypothetical protein; no equivalent VioE translation was found in AF172851.1.	JCM 1249 vioABCDE cluster, AB032799.1 literature scope `MIBiG:BGC0000829`	NCBIProtein:AAQ60934.1 Source assertion: AAQ60934.1 is a 191-aa protein of Chromobacterium violaceum ATCC 12472, encoded by CV_3270 at complement(AE016825.1:3558964..3559539); its Region annotation identifies the VioE domain. Source location `GBSet/GBSeq[GBSeq_accession-version='AAQ60934.1']/GBSeq_feature-table/GBFeature[GBFeature_key='source' or GBFeature_key='Region' or GBFeature_key='CDS']/GBFeature_quals` PMID:17925955 VioE is essential MIBiG:BGC0000828 Source assertion: Retired BGC0000828 assigns the violacein cluster to AB032799.1 and explicitly identifies BGC0000829 as its duplicate successor. This is cluster identity lineage, not protein sequence equivalence. Source location `$.status; $.loci[0].accession; $.compounds[0].name; $.retirement_reasons[0]; $.see_also[0]`
JCM 1249 vioABCDE cluster, AB032799.1 literature scope `MIBiG:BGC0000829`	produces The JCM 1249 AB032799.1 cell-free system produces violacein (compound 1): VioABE-derived extract was supplied to VioCD with NADPH. The endpoint includes nonenzymatic oxidative decarboxylation after the last enzyme; this is not a direct VioC-to-violacein catalysis assertion.	violacein `CHEBI:131914`	PMID:17925955 leading to the production of 1 MIBiG:BGC0000829 Source assertion: MIBiG BGC0000829 records violacein as the cluster product. The native entry is active, quality questionable, completeness complete; those source flags are preserved without upgrading experimental certainty. Source location `$.compounds[0].name; $.status; $.quality; $.completeness`

Biosynthetic gene clusters

JCM 1249 vioABCDE cluster, AB032799.1 literature scopeMIBiG:BGC0000829
- Products: violacein
- Classes: other:other
- Loci: AB032799.1
- Genes: 5

References

MIBiG:BGC0000829 MIBiG violacein cluster BGC0000829, entry version 5 (source version: MIBiG 4.0; entry version 5)
MIBiG:BGC0000828 Retired MIBiG violacein cluster BGC0000828: AB032799.1 and explicit duplicate successor BGC0000829 (source version: MIBiG 4.0; retired BGC0000828 entry version 2; exact archive member documented in source manifest)
PMID:17925955 Biosynthesis of violacein: a genuine intermediate, protoviolaceinic acid, produced by VioABDE, and insight into VioC function — Shinoda K et al. Chemical Communications (2007), 4140-4142. doi:10.1039/b705358d.
NCBIProtein:BAA84782.1 GenBank BAA84782.1: Vio A from Chromobacterium violaceum (source version: BAA84782.1; BAA84783.1; BAA84784.1; BAA84785.1; AAQ60934.1 (protein GBSet batch))
NCBIProtein:BAA84783.1 GenBank BAA84783.1: Vio B from Chromobacterium violaceum (source version: BAA84782.1; BAA84783.1; BAA84784.1; BAA84785.1; AAQ60934.1 (protein GBSet batch))
NCBIProtein:BAA84784.1 GenBank BAA84784.1: Vio C from Chromobacterium violaceum (source version: BAA84782.1; BAA84783.1; BAA84784.1; BAA84785.1; AAQ60934.1 (protein GBSet batch))
NCBIProtein:BAA84785.1 GenBank BAA84785.1: Vio D from Chromobacterium violaceum (source version: BAA84782.1; BAA84783.1; BAA84784.1; BAA84785.1; AAQ60934.1 (protein GBSet batch))
NCBIProtein:AAQ60934.1 GenBank AAQ60934.1: hypothetical protein from Chromobacterium violaceum (source version: BAA84782.1; BAA84783.1; BAA84784.1; BAA84785.1; AAQ60934.1 (protein GBSet batch))

Curation history

2026-10-08T02:27:19Z codex
- CREATE — Curate the experimentally studied violacein cluster through explicit MIBiG lineage
  Added five protein enables edges and observed violacein product under active BGC0000829, using retired BGC0000828 duplicate lineage to preserve the experimental AB032799.1 scope. All four differing AF172851.1 proteins are explicitly excluded from sequence equivalence. VioE is independently resolved by full translation match; final spontaneous chemistry is not assigned to an enzyme. Added independent NCBI and OAK authority coverage, a pinned provenance manifest and reproducible comparison. Issue295 supplied direct primary support to every functional edge; all six exact excerpts total24words across repeated instances. Semantic validation, authority extraction and comparison reconstruction passed.
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