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indigoidine

CHEBI:79296 EXACT SEEDED

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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.

A member of the class of pyridone that is a dimeric blue pigment biosynthesised from L-glutamine.

Structure

Standard InChIKeyALDIVIWLBSDGGN-ONEGZZNKSA-N
SMILESC\1=C(C(=O)NC(=O)/C1=C/2\C=C(C(=O)NC2=O)N)N
Stereochemistryfully defined
Cross-referencespubchem:5492261

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 nrps, 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.

TaxonBasisClusterEvidence
Streptomyces chromofuscus
NCBITaxon:42881		 SOURCE_ASSERTION mibig:BGC0000375 PMID:23053349

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.

TaxonSourceReference
Streptomyces lavendulae
NCBITaxon:1914		 CHEBI PMID:17237222
Streptomyces chromofuscus
NCBITaxon:42881		 LOTUS DOI:10.1007/S10295-012-1207-9

Biosynthetic gene clusters 1

AccessionHostLocus evidenceGenome
mibig:BGC0000375 Streptomyces chromofuscus
NCBITaxon:42881 		CLUSTER_UNSTATED genbank:JX499187.1

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.

StepEnzymeReactionSubstrate → productEvidence
1 Sc-IndC indigoidine synthase
UniProtKB:K4MP98		 RHEA:81499 CHEBI:58210 + CHEBI:58359 + CHEBI:30616 + CHEBI:15379 → CHEBI:79296 + CHEBI:57618 + CHEBI:456215 + CHEBI:33019 + CHEBI:15377 DOI:10.1007/s10295-012-1207-9

Step 1: Streptomyces chromofuscus ATCC 49982 Sc-IndC is the exact indigoidine synthase encoded by the MIBiG BGC0000375 indC CDS. The Sc-IndB coexpression effect is represented separately in the Sc-IndC causal graph; it is not assigned this Rhea-grounded synthase reaction or an additional ordered pathway step.

Mechanism & Biosynthesis Overview

PRODUCERS & OCCURRENCE 1 producer (0 causal) 2 cited occurrences BIOSYNTHETIC LOCUS 1 gene cluster 1 curated pathway step NATURAL PRODUCT indigoidine CHEBI:79296 Alkaloids TARGETS & BIOACTIVITY 0 molecular targets 0 bioactivities · 5 graphs

Causal graph — biosynthesis 5 nodes, 4 edges

Streptomyces chromofuscus ATCC 49982 Sc-IndC converts L-glutamine to the blue pigment indigoidine. Sc-IndB is represented as the native reference for a conditional yield-enhancing coexpression effect with Sc-IndC in E. coli BAP1, not as an assigned catalytic step. Additional GlnA coexpression is represented as host engineering; the reported BL21(DE3) protein sequence remains unresolved.

SubjectPredicateObjectNotesEvidence
L-glutamine is converted to indigoidine by Sc-IndC Sc-IndC catalyzes the RHEA:81499 overall conversion from two L-glutamine molecules to indigoidine.
DOI:10.1007/s10295-012-1207-9
https://mibig.secondarymetabolites.org/repository/BGC0000375.5/BGC0000375.gbk
https://www.uniprot.org/uniprotkb/K4MP98
https://www.rhea-db.org/rhea/81499
  • reference
    DOI:10.1007/s10295-012-1207-9
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    Sc-IndC was functionally characterized as an indigoidine synthase through heterologous expression
    notes
    Yu et al. located the silent Streptomyces chromofuscus ATCC 49982 cluster and showed that Sc-IndC produces indigoidine in heterologous Streptomyces coelicolor CH999 and Escherichia coli BAP1 hosts.
  • reference
    https://mibig.secondarymetabolites.org/repository/BGC0000375.5/BGC0000375.gbk
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    MIBiG BGC0000375.5 places indC at 1630..5763 in the Streptomyces chromofuscus ATCC 49982 JX499187.1 cluster, with protein_id AFV27434.1 and product indigoidine synthase.
  • reference
    https://www.uniprot.org/uniprotkb/K4MP98
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    UniProtKB:K4MP98 is the unreviewed Streptomyces chromofuscus indC gene product and cross-references EMBL JX499187 protein AFV27434.1.
  • reference
    https://www.rhea-db.org/rhea/81499
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    RHEA:81499 is the overall indigoidine synthase reaction consuming FMN, L-glutamine, ATP and O2 to form indigoidine, FMNH2, AMP, diphosphate and H2O; RHEA:81500 is its left-to-right direction.
Sc-IndC forms indigoidine Heterologous expression of Sc-IndC established it as the indigoidine synthase in the Streptomyces chromofuscus ATCC 49982 BGC0000375 cluster.
DOI:10.1007/s10295-012-1207-9
https://mibig.secondarymetabolites.org/repository/BGC0000375.5/BGC0000375.gbk
https://www.uniprot.org/uniprotkb/K4MP98
https://www.rhea-db.org/rhea/81499
  • reference
    DOI:10.1007/s10295-012-1207-9
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    Sc-IndC was functionally characterized as an indigoidine synthase through heterologous expression
    notes
    Yu et al. located the silent Streptomyces chromofuscus ATCC 49982 cluster and showed that Sc-IndC produces indigoidine in heterologous Streptomyces coelicolor CH999 and Escherichia coli BAP1 hosts.
  • reference
    https://mibig.secondarymetabolites.org/repository/BGC0000375.5/BGC0000375.gbk
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    MIBiG BGC0000375.5 places indC at 1630..5763 in the Streptomyces chromofuscus ATCC 49982 JX499187.1 cluster, with protein_id AFV27434.1 and product indigoidine synthase.
  • reference
    https://www.uniprot.org/uniprotkb/K4MP98
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    UniProtKB:K4MP98 is the unreviewed Streptomyces chromofuscus indC gene product and cross-references EMBL JX499187 protein AFV27434.1.
  • reference
    https://www.rhea-db.org/rhea/81499
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    RHEA:81499 is the overall indigoidine synthase reaction consuming FMN, L-glutamine, ATP and O2 to form indigoidine, FMNH2, AMP, diphosphate and H2O; RHEA:81500 is its left-to-right direction.
Sc-IndB (S. chromofuscus native reference) increases yield of when coexpressed with Sc-IndC indigoidine Conditional coexpression effect reported in E. coli BAP1, represented by the exact native Sc-IndB reference. This is not an isolated Sc-IndB catalytic reaction, a demonstrated physical complex, or native essentiality.
DOI:10.1007/s10295-012-1207-9
https://www.uniprot.org/uniprotkb/K4MZR0/entry
https://www.ncbi.nlm.nih.gov/protein/AFV27436.1
https://www.ncbi.nlm.nih.gov/nuccore/JX499187.1
https://mibig.secondarymetabolites.org/repository/BGC0000375.5/index.html
  • reference
    DOI:10.1007/s10295-012-1207-9
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-11
    notes
    The primary abstract reports increased indigoidine yield when Sc-IndB and Sc-IndC were coexpressed in E. coli BAP1. No quantitative value is curated here. Full text, methods, figures, tags and exact experimental constructs remain uninspected after the failed DOI access attempt.
    snippet
    The yield of indigoidine was dramatically increased
  • reference
    https://www.uniprot.org/uniprotkb/K4MZR0/entry
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Unreviewed entry 34, sequence 1, release 2026_03: indB, S. chromofuscus, 614 residues, EMBL JX499187/AFV27436.1; the reference comment names ATCC 49982. The automated PtkA/tyrosine-kinase name and RHEA:10596 annotation carry ECO:0000256 support, not a measured Sc-IndB kinase reaction. They are not adopted.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AFV27436.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Native indB/Sc-indB record: S. chromofuscus ATCC 49982, taxon 42881, 614 residues, coded_by JX499187.1:6835..8679. Its putative-phosphatase product label and HAD/Questin-oxidase-like domain annotations do not establish a measured catalytic function and are not reconciled into a reaction claim.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/JX499187.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-11
    notes
    The complete 1845-nt forward indB CDS, ATG start and TGA stop, independently translates under code 11 to all 614 residues of the deposited translation, AFV27436.1 and K4MZR0. Native-reference identity does not verify expression tags, engineered constructs or historical stock equivalence.
  • reference
    https://mibig.secondarymetabolites.org/repository/BGC0000375.5/index.html
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    BGC0000375.5 links JX499187.1 and indB/AFV27436.1 to indigoidine, C10H8N4O4, the existing CHEBI:79296 owner. Compound correspondence is database-grounded; primary chemical-analysis data were not re-inspected. Entry quality is questionable and completeness unknown; no producer or cluster grade is upgraded.
GlnA (BL21(DE3), sequence unresolved) increases yield of when coexpressed with Sc-IndC indigoidine Reported additional GlnA expression in E. coli BAP1 carrying Sc-IndC, with or without Sc-IndB. This is a host-engineering yield effect, not native cluster membership, an isolated catalytic reaction or direct glutamine-flux measurement. The exact expressed sequence is unresolved; no protein accession is assigned.
DOI:10.1007/s10295-015-1642-5
https://www.ncbi.nlm.nih.gov/protein/ACT45548.1
https://www.ncbi.nlm.nih.gov/protein/CAQ34221.1
https://www.ncbi.nlm.nih.gov/nuccore/CP001509.3
https://www.ncbi.nlm.nih.gov/nuccore/AM946981.2
https://www.uniprot.org/uniprotkb/C6EF31/entry
  • reference
    DOI:10.1007/s10295-015-1642-5
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-11
    notes
    Inspected methods/results identify BL21(DE3) as the glnA donor and pFC6/pFC7 coexpression in BAP1. The reported insert length is 1284 bp. Figure pixels, supplements and remaining text were not inspected after a failed continuation read; no quantitative titer or exact construct-sequence claim is curated.
    snippet
    overexpression of GlnA in E. coli BAP1 can greatly increase the production of indigoidine.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/ACT45548.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Native BL21(DE3) glnA/ECD_03755 reference: 469 residues, coded_by complement(CP001509.3:3963323..3964732). This is a reference record, not an identification of the protein actually expressed in the paper.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAQ34221.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Independent BL21(DE3) glnA/B21_03704 reference: 469 residues, coded_by complement(AM946981.2:3963317..3964726). Its historical UniProt C6EF31 cross-reference is not evidence of current UniProt availability or construct equality.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/CP001509.3
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-11
    notes
    Complete 1410-nt reverse CDS, ATG start/TAA stop, code 11: independent translation matches all 469 residues of ACT45548.1 and CAQ34221.1. The reported primer template segments match both native endpoints. This does not reconcile the paper's 1284-bp length or prove an experimental stock/insert.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AM946981.2
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-11
    notes
    The independently deposited complete 1410-nt reverse CDS has identical coding DNA and translation. Agreement between native references does not establish the actual pFC6/pFC7 sequence; the 126-bp length discrepancy remains open.
  • reference
    https://www.uniprot.org/uniprotkb/C6EF31/entry
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    UniProt release 2026_03 returns C6EF31 as Inactive/DELETED, reason Not part of a reference proteome. It is not used as an active protein identifier. No alternative UniProt exemplar is selected from name similarity.

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

Causal graph — biosynthesis 3 nodes, 2 edges

S. lavendulae ATCC11924 BpsA indigoidine biosynthesis, represented by its exact native reference. Catalytic activity requires the phosphopantetheinylated enzyme. This is an independent organism-specific mechanism, not a downstream step of the existing Sc-IndC pathway.

SubjectPredicateObjectNotesEvidence
L-glutamine zwitterion is_substrate_for BpsA (S. lavendulae native reference) Substrate use by the phosphopantetheinylated enzyme; no activity claim for apo-BpsA.
DOI:10.1074/jbc.M611319200
https://www.uniprot.org/uniprotkb/Q1MWN4/entry
https://www.ncbi.nlm.nih.gov/protein/BAE93896.1
https://www.ncbi.nlm.nih.gov/nuccore/AB240063.1
https://www.rhea-db.org/rhea/81499
  • reference
    DOI:10.1074/jbc.M611319200
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-11
    notes
    Primary abstract reports purified recombinant BPSA from S. lavendulae ATCC11924 using L-Gln. Activity required phosphopantetheinylation by a Streptomyces PPTase. Full text, methods, figures, tags and complete experimental constructs were not inspected.
    snippet
    recombinant enzyme prefers L-Gln as a substrate.
  • reference
    https://www.uniprot.org/uniprotkb/Q1MWN4/entry
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Reviewed entry 88, sequence 1, release 2026_03: bpsA, Streptomyces lavendulae, 1282 residues; FUNCTION and RHEA:81499 annotations cite PMID:17237222. This is the exact native reference, not the S. chromofuscus Sc-IndC protein.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/BAE93896.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Blue-pigment synthetase bpsA; coded_by AB240063.1:686..4534, code 11. NCBI uses subspecies taxon 58340; UniProt uses species taxon 1914. Native records have no strain qualifier; ATCC11924 is attributed by the primary abstract and UniProt reference comment, not inferred from a native strain field.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AB240063.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-11
    notes
    The complete 3849-nt forward CDS, ATG start and TGA stop, independently translates to all 1282 residues in the deposited translation, BAE93896.1 and Q1MWN4. Native-reference equality does not verify historical expression tags, mutants or stocks.
  • reference
    https://www.rhea-db.org/rhea/81499
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Overall reaction connects L-glutamine to CHEBI:79296, key ALDIVIWLBSDGGN-ONEGZZNKSA-N; RHEA:81500 is its forward direction. CHEBI:58359 is Rhea's zwitterionic substrate representation, not a measured assay microspecies. This graph does not assign every intermediate step to BpsA.
BpsA (S. lavendulae native reference) catalyzes_overall_formation_of indigoidine Overall pigment formation in the reported activated-enzyme context. No direct assignment of spontaneous dimerization, reaction intermediates, native essentiality or membership in BGC0000375/BGC0002295 is made.
DOI:10.1074/jbc.M611319200
https://www.uniprot.org/uniprotkb/Q1MWN4/entry
https://www.rhea-db.org/rhea/81499
https://www.ebi.ac.uk/chebi/CHEBI:79296
  • reference
    DOI:10.1074/jbc.M611319200
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-11
    notes
    Primary abstract reports indigoidine formation by phosphopantetheinylated purified BPSA and pigment production in heterologous hosts. This is not a native knockout or producer-grade upgrade.
  • reference
    https://www.uniprot.org/uniprotkb/Q1MWN4/entry
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Reviewed entry 88, sequence 1, release 2026_03: bpsA, Streptomyces lavendulae, 1282 residues; FUNCTION and RHEA:81499 annotations cite PMID:17237222. This is the exact native reference, not the S. chromofuscus Sc-IndC protein.
  • reference
    https://www.rhea-db.org/rhea/81499
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Overall reaction connects L-glutamine to CHEBI:79296, key ALDIVIWLBSDGGN-ONEGZZNKSA-N; RHEA:81500 is its forward direction. CHEBI:58359 is Rhea's zwitterionic substrate representation, not a measured assay microspecies. This graph does not assign every intermediate step to BpsA.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:79296
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Current ChEBI structure matches this owner: C10H8N4O4, charge 0, ALDIVIWLBSDGGN-ONEGZZNKSA-N. Compound correspondence is database-grounded; the original structure-analysis data were not re-inspected. The differently structured BGC0002295 record also named indigoidine is not treated as equivalent.

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

Causal graph — biosynthesis 5 nodes, 5 edges

PPTase deletion/rescue in engineered J1074 carrying a heterologous BpsA indigoidine reporter. AGI92022.1 denotes the native PPTase reference, not a verified engineered allele. The reporter sequence is unresolved; this graph does not extend the canonical BpsA or native IndC mechanism.

SubjectPredicateObjectNotesEvidence
XNR_5716 PPTase (J1074 native reference) has its encoding locus targeted by PPTase deletion in J1074 BpsA reporter Reference-to-intervention correspondence, not a direct catalytic edge.
DOI:10.1093/femsle/fnx155
https://www.ncbi.nlm.nih.gov/protein/AGI92022.1
https://www.ncbi.nlm.nih.gov/nuccore/CP004370.1
  • reference
    DOI:10.1093/femsle/fnx155
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-11
    notes
    Methods identify xnr_5716 as the J1074 Sfp-type PPTase locus deleted using CRISPR/Cas9.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AGI92022.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Native XNR_5716 reference, J1074, 226 residues; complement(CP004370.1:6439414..6440094). Current NCBI taxon 1886 is S. albidoflavus; the paper uses S. albus. Actual engineered alleles were not sequenced here.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/CP004370.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-11
    notes
    Complete 681-nt reverse CDS (ATG/TAG, code 11) translates to all 226 residues of AGI92022.1. Both reported CRISPR guide template segments match uniquely inside this locus; screening primers flank it. Reference/guide correspondence is not verification of an experimental stock or rescue insert. A bounded UniProt query for XNR_5716 or EMBL AGI92022 returned no entries; no UniProt exemplar is assigned.
PPTase deletion in J1074 BpsA reporter abolishes detectable reporter production of indigoidine Restricted to the tested engineered reporter context; not universal essentiality or native IndC dependence.
DOI:10.1093/femsle/fnx155
https://www.ebi.ac.uk/chebi/CHEBI:79296
https://mibig.secondarymetabolites.org/repository/BGC0000375.5/index.html
DOI:10.1093/femsle/fnx155
  • reference
    DOI:10.1093/femsle/fnx155
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-11
    notes
    Results and Figure 1C report loss of blue pigment following deletion. The full main text and relevant figure were inspected; supplemental PCR data were not inspected.
    snippet
    no longer produces indigoidine.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:79296
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    CHEBI:79296 denotes indigoidine: ALDIVIWLBSDGGN-ONEGZZNKSA-N, C10H8N4O4, charge 0.
  • reference
    https://mibig.secondarymetabolites.org/repository/BGC0000375.5/index.html
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-11
    notes
    Pinned BGC0000375.5 row and owner SMILES/InChI independently parse with RDKit 2026.03.5 to the same Standard InChIKey ALDIVIWLBSDGGN-ONEGZZNKSA-N, formula C10H8N4O4 and charge 0. The different BGC0002295 owner is excluded. This is a curator comparison, not new primary analytical confirmation.
  • reference
    DOI:10.1093/femsle/fnx155
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-11
    notes
    The inspected Figure 1 indigoidine schematic is consistent with this owner structure. This visual interpretation is not new analytical confirmation.
XNR_5716 PPTase (J1074 native reference) is native reference for protein supplied in PPTase reintroduction in deletion reporter Reference-to-intervention correspondence; complete rescue-construct sequence remains unverified.
DOI:10.1093/femsle/fnx155
https://www.ncbi.nlm.nih.gov/protein/AGI92022.1
  • reference
    DOI:10.1093/femsle/fnx155
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-11
    notes
    Results describe reintroduction of the deleted PPTase in trans at phiC31 under ermE* control.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AGI92022.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Native XNR_5716 reference, J1074, 226 residues; complement(CP004370.1:6439414..6440094). Current NCBI taxon 1886 is S. albidoflavus; the paper uses S. albus. Actual engineered alleles were not sequenced here.
PPTase reintroduction in deletion reporter restores reporter production of indigoidine Genetic complementation readout, not purified phosphopantetheinyl-transfer activity, a physical complex, or membership in BGC0000375/BGC0002295.
DOI:10.1093/femsle/fnx155
  • reference
    DOI:10.1093/femsle/fnx155
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-11
    notes
    Native-PPTase rescue is described in Results text. Figure 1C bottom instead illustrates eDNA-clone complementation; it is not an image of this native-PPTase rescue.
    snippet
    Production of indigoidine was restored
XNR_5716 PPTase (J1074 native reference) has a sequence-identical UniProtKB example XNR_5716 PPTase (S. wadayamensis DC60_07595 UniProtKB example) UniProtKB:A0ABR4SFP3 (Streptomyces wadayamensis DC60_07595) shares 100% amino-acid sequence identity (UPI0001AEDEA9) with Streptomyces albus J1074 XNR_5716 PPTase (AGI92022.1).
https://www.uniprot.org/uniprotkb/A0ABR4SFP3
https://www.uniprot.org/uniparc/UPI0001AEDEA9
https://www.ncbi.nlm.nih.gov/protein/AGI92022.1
  • reference
    https://www.uniprot.org/uniprotkb/A0ABR4SFP3
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-17
    notes
    Active Streptomyces wadayamensis UniProtKB entry (A0ABR4SFP3, DC60_07595) for the UPI0001AEDEA9 4'-phosphopantetheinyl transferase sequence.
  • reference
    https://www.uniprot.org/uniparc/UPI0001AEDEA9
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-17
    notes
    UniParc UPI0001AEDEA9 links CP004370.1 AGI92022.1 (XNR_5716) and active UniProtKB:A0ABR4SFP3 under a single 100%-identical sequence.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AGI92022.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-17
    notes
    CP004370.1 GenPept AGI92022.1 is the Streptomyces albus J1074 XNR_5716 PPTase translation.

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

Causal graph — biosynthesis 4 nodes, 3 edges

FRI-5 LbpA heterologous-expression evidence in S. avermitilis SUKA22. The protein node is the exact native reference, not a verified engineered construct. This independent graph does not extend the Sc-IndC, ATCC11924 BpsA or J1074 reporter mechanisms.

SubjectPredicateObjectNotesEvidence
LbpA (S. lavendulae FRI-5 native reference) is native reference for protein encoded in Heterologous lbpA expression in SUKA22 Reference-to-expression correspondence; not an isolated catalytic reaction or proof of construct identity.
DOI:10.1016/j.jbiosc.2017.04.020
https://www.ncbi.nlm.nih.gov/protein/BAW81991.1
https://www.uniprot.org/uniprotkb/A0A1Q2SRM5/entry
https://www.ncbi.nlm.nih.gov/nuccore/LC209815.1
  • reference
    DOI:10.1016/j.jbiosc.2017.04.020
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-11
    notes
    The inspected primary abstract identifies FRI-5 lbpA and heterologous expression in S. avermitilis SUKA22. Main text, methods, figures and supplements remain uninspected.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/BAW81991.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Native lbpA reference from S. lavendulae FRI-5, taxon 1914: 1282 residues, coded_by complement(LC209815.1:7353..11201). The deposit cites PMID:28533156.
  • reference
    https://www.uniprot.org/uniprotkb/A0A1Q2SRM5/entry
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Unreviewed entry 36, sequence 1: lbpA, S. lavendulae, 1282 residues; EMBL LC209815/BAW81991.1 and a FRI-5 reference comment. Automated cofactor, residue and enzyme-family annotations are not adopted as experiments.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/LC209815.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-11
    notes
    Complete 3849-nt reverse CDS, ATG start/TGA stop, code 11: independent translation matches all 1282 residues of the deposited translation, BAW81991.1 and A0A1Q2SRM5. This grounds the native reference, not the uninspected experimental insert or tags. The equal-length ATCC11924 BpsA reference BAE93896.1 differs at 22 positions; Q1MWN4 is not substituted for FRI-5 LbpA.
Heterologous lbpA expression in SUKA22 enables reported production of indigoidine Host-level expression result, not purified-enzyme catalysis, native essentiality, a physical complex or membership in BGC0000375/BGC0002295.
DOI:10.1016/j.jbiosc.2017.04.020
https://www.ebi.ac.uk/chebi/CHEBI:79296
  • reference
    DOI:10.1016/j.jbiosc.2017.04.020
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-11
    notes
    The primary abstract reports pigment production after heterologous lbpA expression. No titer, control comparison or analytical method is curated from the uninspected full text.
    snippet
    led to indigoidine production
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:79296
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    CHEBI:79296 denotes indigoidine, C10H8N4O4, charge 0, ALDIVIWLBSDGGN-ONEGZZNKSA-N. Compound correspondence is name/database-grounded; primary chemical-analysis data for the FRI-5 experiment were not inspected. The differently structured BGC0002295 owner is not treated as equivalent.
L-glutamine feeding of SUKA22 expressing lbpA enhances reported production of indigoidine Conditional feeding effect in the lbpA-expressing heterologous host; not direct substrate specificity, isotope incorporation or measured precursor flux.
DOI:10.1016/j.jbiosc.2017.04.020
  • reference
    DOI:10.1016/j.jbiosc.2017.04.020
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-11
    notes
    The primary abstract reports enhanced production with L-glutamine feeding. No concentration, fold change, assay timing or mechanistic intermediate is assigned.
    snippet
    enhanced dramatically by feeding of the indigoidine precursor l-glutamine.

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

Causal graph — biosynthesis 5 nodes, 4 edges

CCM3239 bpsA deletion and upstream-promoter interventions. Historical and current native protein references differ at residue 385 and are separate nodes, not verified experimental alleles. The readouts support genetic involvement, not isolated catalysis or a mechanism shared with the other indigoidine graphs.

SubjectPredicateObjectNotesEvidence
BpsA (CCM3239 historical reference, Ala385) is historical reference for the gene product targeted by Reported bpsA deletion in CCM3239 Reference-to-locus correspondence, not proof of the tested parental allele.
DOI:10.1007/s12223-010-0018-5
https://www.ncbi.nlm.nih.gov/protein/ACK77757.1
https://www.ncbi.nlm.nih.gov/nuccore/FJ479754.1
https://www.ncbi.nlm.nih.gov/nuccore/FJ479754.1
https://rest.uniprot.org/uniparc/UPI0001895A6C.json
  • reference
    DOI:10.1007/s12223-010-0018-5
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-11
    notes
    The public abstract identifies bpsA and its deletion in the strain then named S. aureofaciens CCM3239. Full methods, deletion boundaries and figures are uninspected.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/ACK77757.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Historical 1283-residue reference: sa8, coded_by FJ479754.1:14654..18505; replaced by ACK77757.2. It is not assigned the current UniProt accession.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/FJ479754.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    CCM3239 historical deposit, taxon 1894, cites PMID:20490753 and was replaced by KJ396772.1 in 2014. Native reference identity does not verify an experimental stock.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/FJ479754.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-11
    notes
    Complete 3852-nt forward CDS, ATG/TAG, code 11, translates exactly to all 1283 residues of ACK77757.1. Comparison with the current KJ396772.2 bpsA CDS finds changes at coding positions 15, 1152 and 1153; only the last changes a residue, Ala385 (GCC) to Thr385 (ACC). This is reference-version comparison, not an experimentally demonstrated mutation or a UniProt equivalence.
  • reference
    https://rest.uniprot.org/uniparc/UPI0001895A6C.json
    evidence type
    DATABASE_ASSERTION
    notes
    UniParc UPI0001895A6C (1283 aa) archives historical EMBL ACK77757.1 (Ala385 version 1) and links inactive UniProtKB/TrEMBL B8Y4G4 (Kitasatospora aureofaciens, taxon 1894, gene sa8), distinct from revised ACK77757.2 (Thr385, UPI0001DE5E11).
    retrieved on
    2026-10-30
Reported bpsA deletion in CCM3239 abolishes reported blue-pigment production of indigoidine Abstract-level deletion phenotype in the tested strain. No rescue, isolated catalytic step, universal essentiality or BGC membership is asserted.
DOI:10.1007/s12223-010-0018-5
https://www.ebi.ac.uk/chebi/CHEBI:79296
  • reference
    DOI:10.1007/s12223-010-0018-5
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-11
    notes
    The abstract reports loss of extracellular blue pigment after deletion and attributes the pigment to indigoidine by its properties. Primary chemical analyses and assay conditions are uninspected.
    snippet
    failed to produce the blue pigment.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:79296
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Indigoidine: C10H8N4O4, charge 0, ALDIVIWLBSDGGN-ONEGZZNKSA-N. Compound correspondence for both interventions is name/database-grounded, not new structural verification. The differently structured BGC0002295 owner is excluded.
BpsA (CCM3239 current reference, Thr385) has its encoding locus preceded by AprR-kasOp* insertion upstream of CCM3239 bpsA Reference-to-intervention correspondence only; the complete engineered bpsA allele and residue 385 genotype are unresolved.
DOI:10.1007/s00253-026-13908-9
https://www.uniprot.org/uniprotkb/A0A2K8PVS5/entry
https://www.ncbi.nlm.nih.gov/nuccore/KJ396772.2
https://www.ncbi.nlm.nih.gov/nuccore/CP024986.1
DOI:10.1007/s00253-026-13908-9
  • reference
    DOI:10.1007/s00253-026-13908-9
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-11
    notes
    Methods, Figure 1, Table S2, Table S3 and Figure S1 identify upstream cassette insertion using pCosSA19 and BpsAkasDir/Rev, with four mutants and Southern controls. The study names KJ396772/CP024986 as pSA3239 references.
  • reference
    https://www.uniprot.org/uniprotkb/A0A2K8PVS5/entry
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    Unreviewed entry 32, sequence 1: 1283 residues; CCM3239, taxon 58340, tycC5/SLAV_40115, CP024986/ATZ29785.1. The automated Tyrocidine synthase 3 name is not adopted as the measured function.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/KJ396772.2
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-11
    notes
    bpsA/ACK77757.2 at 93052..96903 on plasmid pSA3239 in S. lavendulae subsp. lavendulae CCM3239. Historical S. aureofaciens naming is retained as source context, not another producer assignment.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/CP024986.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-11
    notes
    Complete reverse CDS at 144174..148025 is identical to the KJ396772.1/.2 3852-nt bpsA CDS. All code-11 translations equal ACK77757.2, ATZ29785.1 and A0A2K8PVS5. This establishes the current native reference, not the engineered stock or identity with historical ACK77757.1.
  • reference
    DOI:10.1007/s00253-026-13908-9
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-11
    notes
    Both reported cassette primers have unique 40-nt native homology prefixes at the bpsA upstream/start region in all three current deposits. Prefix agreement and Southern blots do not sequence the complete mutant allele. Generic chromosomal wording does not override the pSA3239 locus mapping.
AprR-kasOp* insertion upstream of CCM3239 bpsA increases the reported pigment readout for indigoidine Intervention-level result; neighboring transcriptional effects remain possible. Not proof that BpsA alone accounts for the increase.
DOI:10.1007/s00253-026-13908-9
  • reference
    DOI:10.1007/s00253-026-13908-9
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-11
    notes
    Results and Figure 1 compare mutants with WT after 22 h in Bennet medium. The DMSO-extract measurement is OD613 per mg wet cells, not a mass concentration or a purified-enzyme rate. No numerical fold change is curated.
    snippet
    dramatic overproduction of indigoidine compared to the wild-type (WT) strain.

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

Explore across X-Mech

AntibioticMech (indigoidine) ↗ MediaIngredientMech (CHEBI:79296) ↗ TaxonMech: Streptomyces chromofuscus (NCBITaxon:42881) ↗ PathwayMech (mibig:BGC0000375) ↗

Open questions 3

curator-indigoidine-glna-construct-identity — Which complete GlnA protein sequence was expressed in pFC6/pFC7, and how should the reported 1284-bp fragment be reconciled with the 1410-bp BL21(DE3) references?

curator-indigoidine-bpsa-reporter-construct — What is the complete sequence of the BpsA reporter used in the J1074 PPTase experiment?

curator-indigoidine-ccm3239-bpsa-alleles — Which complete bpsA alleles occur in the parental stocks and engineered strains used for the 2010 deletion and 2026 upstream-promoter experiments?

Provenance

Source conceptSourceVersion
BGC0000375MIBIG5
CHEBI:79296CHEBI3-star

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