NaturalProductMech

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vibriobactin

CHEBI:9973 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 catecholate siderophore produced exclusively by Vibrio cholerae. It contains three molecules of 2,3-dihydroxybenzoate linked either directly or through L-threonine residues to the polyamine norspermidine.

Structure

Standard InChIKeyLLMKLMMXMOTPRU-YOAXHERRSA-N
SMILESC[C@@H]1OC(C2=C(O)C(O)=CC=C2)=N[C@H]1C(=O)NCCCN(CCCNC(=O)C1=C(O)C(O)=CC=C1)C(=O)[C@H]1N=C(C2=C(O)C(O)=CC=C2)O[C@@H]1C
Stereochemistryfully defined
Cross-referencesnpatlas:NPA033096

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
Vibrio cholerae
Strain: Lou15 (El Tor)
NCBITaxon:666		 SOURCE_ASSERTION mibig:BGC0002494
PMID:10601218, DOI:10.1128/JB.181.24.7588-7596.1999, https://www.ebi.ac.uk/ena/browser/view/U52150.2
  • reference
    PMID:10601218
    evidence type
    DATABASE_ASSERTION
    notes
    MIBiG BGC0002494 entry version 3; citation taken from the entry level
  • reference
    DOI:10.1128/JB.181.24.7588-7596.1999
    evidence type
    CURATOR_INFERENCE
    notes
    Curated exclusion of source locus methods from this taxon/locus claim: Heterologous expression. Wyckoff et al. test ViuPDGC-dependent siderophore utilization, not heterologous biosynthesis. Exclude that method from biosynthetic locus grading without denying native production or VibD/VibH participation. Curator: codex; date: 2026-10-13.
  • reference
    https://www.ebi.ac.uk/ena/browser/view/U52150.2
    evidence type
    CURATOR_INFERENCE
    notes
    Strain context: Lou15 (El Tor). The U52150.2 source feature identifies Lou15 (El Tor), consistent with the transport study's strain table; this qualification does not identify N16961 or O395 as the source of this locus. Taxon identity and evidence grade are unchanged; this is not a species-wide experiment. MIBiG source row BGC0002494:1; SHA256 94ff03aee66f2d1c214158e27380175dcacbfce8564b6b881b056f4c2c513ea2. Curator: codex; date: 2026-10-13.

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.

TaxonSourceReference
Vibrio cholerae
NCBITaxon:666		 LOTUS DOI:10.1128/JB.181.24.7588-7596.1999

Biosynthetic gene clusters 1

AccessionHostLocus evidenceGenome
mibig:BGC0002494 Vibrio cholerae
NCBITaxon:666 		CLUSTER_UNSTATED genbank:U52150.2

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.

Mechanism & Biosynthesis Overview

PRODUCERS & OCCURRENCE 1 producer (0 causal) 1 cited occurrence BIOSYNTHETIC LOCUS 1 gene cluster 0 curated pathway steps NATURAL PRODUCT vibriobactin CHEBI:9973 Alkaloids TARGETS & BIOACTIVITY 0 molecular targets 0 bioactivities · 1 graph

Causal graph — biosynthesis 12 nodes, 11 edges

Eleven selected canonical references across N16961, Lou15 and O395, not a reconstructed single-strain pathway. Canonical reference proteins, not independently inspected assay constructs. These edges describe database-associated or explicitly putative biosynthetic participation, not a direct reaction, ordered pathway, substrate specificity, stoichiometry or physical complex. GROUNDED denotes identifier identity, not experimental validation. Strain references are not interchangeable. This owner is free vibriobactin, CHEBI:9973, Standard InChIKey LLMKLMMXMOTPRU-YOAXHERRSA-N. Owner and local ChEBI cache agree within each representation (SMILES versus SMILES; InChI versus InChI) under RDKit 2026.03.5: C35H39N5O11, net charge zero, no iron. Standard InChI reconstruction changes amide/imidic-acid tautomer encoding; equal keys do not establish microstate identity. The separate BGC0000945-derived record has key SNUNDXZQRUCXRW-KDUQSJINSA-N and incomplete stereo; it is not merged or treated as an exact product equivalent. This supports named-compound correspondence, not an exact assay-product microstate, ferric complex or Rhea reaction. Ontology values were checked in the local cache on 2026-10-10, not freshly downloaded. Primary methods, figures, supplements and constructs were not independently inspected. The PMID:11112537 abstract is not full-methods evidence; its publisher returned 403. PMID:11112538 returned no usable article content and PMID:11160122 presented a browser challenge. No biochemical assay or genetic-result claim is imported from these access-limited sources.

SubjectPredicateObjectNotesEvidence
vibA (N16961 reference) is_database_supported_biosynthetic_participant_for vibriobactin Canonical reference proteins, not independently inspected assay constructs. These edges describe database-associated or explicitly putative biosynthetic participation, not a direct reaction, ordered pathway, substrate specificity, stoichiometry or physical complex. GROUNDED denotes identifier identity, not experimental validation. Strain references are not interchangeable. UniProt protein existence is inferred from homology; its Met-1 versus Met-4 initiation caution remains unresolved. Primary methods, figures, supplements and constructs were not independently inspected. The PMID:11112537 abstract is not full-methods evidence; its publisher returned 403. PMID:11112538 returned no usable article content and PMID:11160122 presented a browser challenge. No biochemical assay or genetic-result claim is imported from these access-limited sources.
https://www.uniprot.org/uniprotkb/Q56632
https://www.ebi.ac.uk/ena/browser/view/AE003852.1
https://www.ebi.ac.uk/chebi/CHEBI:9973
  • reference
    https://www.uniprot.org/uniprotkb/Q56632
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    UniProtKB reviewed (Swiss-Prot), entry 148, sequence 1, 262 residues; protein existence 3: Inferred from homology. UniProt taxon 243277. The selected canonical reference matches deposited AAF93939.1 from N16961. UniProt protein existence is inferred from homology; its Met-1 versus Met-4 initiation caution remains unresolved. Its PATHWAY comment explicitly names vibriobactin biosynthesis, adopted as a database assertion only.
    snippet
    Siderophore biosynthesis; vibriobactin biosynthesis
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AE003852.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete native CDS [830175:830964](+) (zero-based, end-exclusive), 789 nucleotides, ATG start, TGA stop, codon_start 1, bacterial code 11. Biopython strand-aware cds=True translation equals deposited AAF93939.1 and all 262 canonical Q56632 residues. Source strain N16961 is explicit; CDS bounds are exact and no translational exceptions are annotated. Alternative start codons are translated as initiating methionine under code 11. This establishes reference-sequence correspondence, not biological initiation, processing, tags, mutations, exact assay stock or strain equivalence.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:9973
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    This owner is free vibriobactin, CHEBI:9973, Standard InChIKey LLMKLMMXMOTPRU-YOAXHERRSA-N. Owner and local ChEBI cache agree within each representation (SMILES versus SMILES; InChI versus InChI) under RDKit 2026.03.5: C35H39N5O11, net charge zero, no iron. Standard InChI reconstruction changes amide/imidic-acid tautomer encoding; equal keys do not establish microstate identity. The separate BGC0000945-derived record has key SNUNDXZQRUCXRW-KDUQSJINSA-N and incomplete stereo; it is not merged or treated as an exact product equivalent. This supports named-compound correspondence, not an exact assay-product microstate, ferric complex or Rhea reaction. Ontology values were checked in the local cache on 2026-10-10, not freshly downloaded.
vibB (N16961 reference) is_database_supported_biosynthetic_participant_for vibriobactin Canonical reference proteins, not independently inspected assay constructs. These edges describe database-associated or explicitly putative biosynthetic participation, not a direct reaction, ordered pathway, substrate specificity, stoichiometry or physical complex. GROUNDED denotes identifier identity, not experimental validation. Strain references are not interchangeable. UniProt protein-level existence does not identify an inspected assay stock. Its phosphopantetheine cofactor annotation is by similarity; no loading-site or activation reaction is adopted. Primary methods, figures, supplements and constructs were not independently inspected. The PMID:11112537 abstract is not full-methods evidence; its publisher returned 403. PMID:11112538 returned no usable article content and PMID:11160122 presented a browser challenge. No biochemical assay or genetic-result claim is imported from these access-limited sources.
https://www.uniprot.org/uniprotkb/P0C6D3
https://www.ebi.ac.uk/ena/browser/view/AE003852.1
https://www.ebi.ac.uk/chebi/CHEBI:9973
  • reference
    https://www.uniprot.org/uniprotkb/P0C6D3
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    UniProtKB reviewed (Swiss-Prot), entry 89, sequence 1, 293 residues; protein existence 1: Evidence at protein level. UniProt taxon 243277. The selected canonical reference matches deposited AAF93936.1 from N16961. UniProt protein-level existence does not identify an inspected assay stock. Its phosphopantetheine cofactor annotation is by similarity; no loading-site or activation reaction is adopted. Its PATHWAY comment explicitly names vibriobactin biosynthesis, adopted as a database assertion only.
    snippet
    Siderophore biosynthesis; vibriobactin biosynthesis
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AE003852.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete native CDS [826196:827078](+) (zero-based, end-exclusive), 882 nucleotides, ATG start, TGA stop, codon_start 1, bacterial code 11. Biopython strand-aware cds=True translation equals deposited AAF93936.1 and all 293 canonical P0C6D3 residues. Source strain N16961 is explicit; CDS bounds are exact and no translational exceptions are annotated. Alternative start codons are translated as initiating methionine under code 11. This establishes reference-sequence correspondence, not biological initiation, processing, tags, mutations, exact assay stock or strain equivalence.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:9973
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    This owner is free vibriobactin, CHEBI:9973, Standard InChIKey LLMKLMMXMOTPRU-YOAXHERRSA-N. Owner and local ChEBI cache agree within each representation (SMILES versus SMILES; InChI versus InChI) under RDKit 2026.03.5: C35H39N5O11, net charge zero, no iron. Standard InChI reconstruction changes amide/imidic-acid tautomer encoding; equal keys do not establish microstate identity. The separate BGC0000945-derived record has key SNUNDXZQRUCXRW-KDUQSJINSA-N and incomplete stereo; it is not merged or treated as an exact product equivalent. This supports named-compound correspondence, not an exact assay-product microstate, ferric complex or Rhea reaction. Ontology values were checked in the local cache on 2026-10-10, not freshly downloaded.
vibC (N16961 reference) is_database_supported_biosynthetic_participant_for vibriobactin Canonical reference proteins, not independently inspected assay constructs. These edges describe database-associated or explicitly putative biosynthetic participation, not a direct reaction, ordered pathway, substrate specificity, stoichiometry or physical complex. GROUNDED denotes identifier identity, not experimental validation. Strain references are not interchangeable. UniProt protein existence is inferred from homology; its Met-1 versus Met-3 initiation caution remains unresolved. Primary methods, figures, supplements and constructs were not independently inspected. The PMID:11112537 abstract is not full-methods evidence; its publisher returned 403. PMID:11112538 returned no usable article content and PMID:11160122 presented a browser challenge. No biochemical assay or genetic-result claim is imported from these access-limited sources.
https://www.uniprot.org/uniprotkb/O07898
https://www.ebi.ac.uk/ena/browser/view/AE003852.1
https://www.ebi.ac.uk/chebi/CHEBI:9973
  • reference
    https://www.uniprot.org/uniprotkb/O07898
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    UniProtKB reviewed (Swiss-Prot), entry 127, sequence 1, 395 residues; protein existence 3: Inferred from homology. UniProt taxon 243277. The selected canonical reference matches deposited AAF93938.1 from N16961. UniProt protein existence is inferred from homology; its Met-1 versus Met-3 initiation caution remains unresolved. Its PATHWAY comment explicitly names vibriobactin biosynthesis, adopted as a database assertion only.
    snippet
    Siderophore biosynthesis; vibriobactin biosynthesis
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AE003852.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete native CDS [828820:830008](-) (zero-based, end-exclusive), 1188 nucleotides, ATG start, TAA stop, codon_start 1, bacterial code 11. Biopython strand-aware cds=True translation equals deposited AAF93938.1 and all 395 canonical O07898 residues. Source strain N16961 is explicit; CDS bounds are exact and no translational exceptions are annotated. Alternative start codons are translated as initiating methionine under code 11. This establishes reference-sequence correspondence, not biological initiation, processing, tags, mutations, exact assay stock or strain equivalence.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:9973
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    This owner is free vibriobactin, CHEBI:9973, Standard InChIKey LLMKLMMXMOTPRU-YOAXHERRSA-N. Owner and local ChEBI cache agree within each representation (SMILES versus SMILES; InChI versus InChI) under RDKit 2026.03.5: C35H39N5O11, net charge zero, no iron. Standard InChI reconstruction changes amide/imidic-acid tautomer encoding; equal keys do not establish microstate identity. The separate BGC0000945-derived record has key SNUNDXZQRUCXRW-KDUQSJINSA-N and incomplete stereo; it is not merged or treated as an exact product equivalent. This supports named-compound correspondence, not an exact assay-product microstate, ferric complex or Rhea reaction. Ontology values were checked in the local cache on 2026-10-10, not freshly downloaded.
vibE (N16961 reference) is_database_supported_biosynthetic_participant_for vibriobactin Canonical reference proteins, not independently inspected assay constructs. These edges describe database-associated or explicitly putative biosynthetic participation, not a direct reaction, ordered pathway, substrate specificity, stoichiometry or physical complex. GROUNDED denotes identifier identity, not experimental validation. Strain references are not interchangeable. UniProt FUNCTION and catalytic assignments are transferred by similarity from P10378. The PATHWAY assertion is used only for named-compound participation, not an exact carrier-loading reaction or membrane topology. Primary methods, figures, supplements and constructs were not independently inspected. The PMID:11112537 abstract is not full-methods evidence; its publisher returned 403. PMID:11112538 returned no usable article content and PMID:11160122 presented a browser challenge. No biochemical assay or genetic-result claim is imported from these access-limited sources.
https://www.uniprot.org/uniprotkb/O07899
https://www.ebi.ac.uk/ena/browser/view/AE003852.1
https://www.ebi.ac.uk/chebi/CHEBI:9973
  • reference
    https://www.uniprot.org/uniprotkb/O07899
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    UniProtKB reviewed (Swiss-Prot), entry 134, sequence 1, 543 residues; protein existence 3: Inferred from homology. UniProt taxon 243277. The selected canonical reference matches deposited AAF93937.1 from N16961. UniProt FUNCTION and catalytic assignments are transferred by similarity from P10378. The PATHWAY assertion is used only for named-compound participation, not an exact carrier-loading reaction or membrane topology. Its PATHWAY comment explicitly names vibriobactin biosynthesis, adopted as a database assertion only.
    snippet
    Siderophore biosynthesis; vibriobactin biosynthesis
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AE003852.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete native CDS [827178:828810](-) (zero-based, end-exclusive), 1632 nucleotides, ATG start, TGA stop, codon_start 1, bacterial code 11. Biopython strand-aware cds=True translation equals deposited AAF93937.1 and all 543 canonical O07899 residues. Source strain N16961 is explicit; CDS bounds are exact and no translational exceptions are annotated. Alternative start codons are translated as initiating methionine under code 11. This establishes reference-sequence correspondence, not biological initiation, processing, tags, mutations, exact assay stock or strain equivalence.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:9973
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    This owner is free vibriobactin, CHEBI:9973, Standard InChIKey LLMKLMMXMOTPRU-YOAXHERRSA-N. Owner and local ChEBI cache agree within each representation (SMILES versus SMILES; InChI versus InChI) under RDKit 2026.03.5: C35H39N5O11, net charge zero, no iron. Standard InChI reconstruction changes amide/imidic-acid tautomer encoding; equal keys do not establish microstate identity. The separate BGC0000945-derived record has key SNUNDXZQRUCXRW-KDUQSJINSA-N and incomplete stereo; it is not merged or treated as an exact product equivalent. This supports named-compound correspondence, not an exact assay-product microstate, ferric complex or Rhea reaction. Ontology values were checked in the local cache on 2026-10-10, not freshly downloaded.
VC_0775 (putative VibH, N16961 reference) is_putative_biosynthetic_participant_for vibriobactin Canonical reference proteins, not independently inspected assay constructs. These edges describe database-associated or explicitly putative biosynthetic participation, not a direct reaction, ordered pathway, substrate specificity, stoichiometry or physical complex. GROUNDED denotes identifier identity, not experimental validation. Strain references are not interchangeable. The native assignment is explicitly putative by sequence similarity. GTG is the annotated start codon. PDB:1L5A and its mapped 3..438 range are uninspected structural leads, not verified assay constructs. Primary methods, figures, supplements and constructs were not independently inspected. The PMID:11112537 abstract is not full-methods evidence; its publisher returned 403. PMID:11112538 returned no usable article content and PMID:11160122 presented a browser challenge. No biochemical assay or genetic-result claim is imported from these access-limited sources.
https://www.uniprot.org/uniprotkb/Q9KTV9
https://www.ebi.ac.uk/ena/browser/view/AE003852.1
https://www.ebi.ac.uk/ena/browser/view/AE003852.1
https://www.ebi.ac.uk/chebi/CHEBI:9973
  • reference
    https://www.uniprot.org/uniprotkb/Q9KTV9
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    UniProtKB unreviewed (TrEMBL), entry 116, sequence 1, 438 residues; protein existence 1: Evidence at protein level. UniProt taxon 243277. The selected canonical reference matches deposited AAF93940.1 from N16961. The native assignment is explicitly putative by sequence similarity. GTG is the annotated start codon. PDB:1L5A and its mapped 3..438 range are uninspected structural leads, not verified assay constructs.
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AE003852.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Native deposit AE003852.1, source strain N16961, CDS AAF93940.1; the quoted product/note is the named-compound association. Its note explicitly says identified by sequence similarity; putative. This is a prediction, not demonstrated function. The native assignment is explicitly putative by sequence similarity. GTG is the annotated start codon. PDB:1L5A and its mapped 3..438 range are uninspected structural leads, not verified assay constructs.
    snippet
    vibriobactin synthesis protein, putative
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AE003852.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete native CDS [830975:832292](-) (zero-based, end-exclusive), 1317 nucleotides, GTG start, TGA stop, codon_start 1, bacterial code 11. Biopython strand-aware cds=True translation equals deposited AAF93940.1 and all 438 canonical Q9KTV9 residues. Source strain N16961 is explicit; CDS bounds are exact and no translational exceptions are annotated. Alternative start codons are translated as initiating methionine under code 11. This establishes reference-sequence correspondence, not biological initiation, processing, tags, mutations, exact assay stock or strain equivalence.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:9973
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    This owner is free vibriobactin, CHEBI:9973, Standard InChIKey LLMKLMMXMOTPRU-YOAXHERRSA-N. Owner and local ChEBI cache agree within each representation (SMILES versus SMILES; InChI versus InChI) under RDKit 2026.03.5: C35H39N5O11, net charge zero, no iron. Standard InChI reconstruction changes amide/imidic-acid tautomer encoding; equal keys do not establish microstate identity. The separate BGC0000945-derived record has key SNUNDXZQRUCXRW-KDUQSJINSA-N and incomplete stereo; it is not merged or treated as an exact product equivalent. This supports named-compound correspondence, not an exact assay-product microstate, ferric complex or Rhea reaction. Ontology values were checked in the local cache on 2026-10-10, not freshly downloaded.
VC_0780 (putative VibD, N16961 reference) is_putative_biosynthetic_participant_for vibriobactin Canonical reference proteins, not independently inspected assay constructs. These edges describe database-associated or explicitly putative biosynthetic participation, not a direct reaction, ordered pathway, substrate specificity, stoichiometry or physical complex. GROUNDED denotes identifier identity, not experimental validation. Strain references are not interchangeable. The native assignment is explicitly putative by sequence similarity, with a TTG start. UniProt automated ARBA name/FUNCTION/PATHWAY/SUBUNIT annotations concern enterobactin and EntB/EntF; those are not transferred to vibriobactin or adopted as complex evidence. Lou15 Q9RCF2 remains a separate functional hold. Primary methods, figures, supplements and constructs were not independently inspected. The PMID:11112537 abstract is not full-methods evidence; its publisher returned 403. PMID:11112538 returned no usable article content and PMID:11160122 presented a browser challenge. No biochemical assay or genetic-result claim is imported from these access-limited sources.
https://www.uniprot.org/uniprotkb/Q9KTV7
https://www.ebi.ac.uk/ena/browser/view/AE003852.1
https://www.ebi.ac.uk/ena/browser/view/AE003852.1
https://www.ebi.ac.uk/chebi/CHEBI:9973
  • reference
    https://www.uniprot.org/uniprotkb/Q9KTV7
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    UniProtKB unreviewed (TrEMBL), entry 117, sequence 1, 261 residues; protein existence 3: Inferred from homology. UniProt taxon 243277. The selected canonical reference matches deposited AAF93945.1 from N16961. The native assignment is explicitly putative by sequence similarity, with a TTG start. UniProt automated ARBA name/FUNCTION/PATHWAY/SUBUNIT annotations concern enterobactin and EntB/EntF; those are not transferred to vibriobactin or adopted as complex evidence. Lou15 Q9RCF2 remains a separate functional hold.
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AE003852.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Native deposit AE003852.1, source strain N16961, CDS AAF93945.1; the quoted product/note is the named-compound association. Its note explicitly says identified by sequence similarity; putative. This is a prediction, not demonstrated function. The native assignment is explicitly putative by sequence similarity, with a TTG start. UniProt automated ARBA name/FUNCTION/PATHWAY/SUBUNIT annotations concern enterobactin and EntB/EntF; those are not transferred to vibriobactin or adopted as complex evidence. Lou15 Q9RCF2 remains a separate functional hold.
    snippet
    vibriobactin synthase component D
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AE003852.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete native CDS [836437:837223](+) (zero-based, end-exclusive), 786 nucleotides, TTG start, TGA stop, codon_start 1, bacterial code 11. Biopython strand-aware cds=True translation equals deposited AAF93945.1 and all 261 canonical Q9KTV7 residues. Source strain N16961 is explicit; CDS bounds are exact and no translational exceptions are annotated. Alternative start codons are translated as initiating methionine under code 11. This establishes reference-sequence correspondence, not biological initiation, processing, tags, mutations, exact assay stock or strain equivalence.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:9973
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    This owner is free vibriobactin, CHEBI:9973, Standard InChIKey LLMKLMMXMOTPRU-YOAXHERRSA-N. Owner and local ChEBI cache agree within each representation (SMILES versus SMILES; InChI versus InChI) under RDKit 2026.03.5: C35H39N5O11, net charge zero, no iron. Standard InChI reconstruction changes amide/imidic-acid tautomer encoding; equal keys do not establish microstate identity. The separate BGC0000945-derived record has key SNUNDXZQRUCXRW-KDUQSJINSA-N and incomplete stereo; it is not merged or treated as an exact product equivalent. This supports named-compound correspondence, not an exact assay-product microstate, ferric complex or Rhea reaction. Ontology values were checked in the local cache on 2026-10-10, not freshly downloaded.
vibH (Lou15 (El Tor) reference) is_database_supported_biosynthetic_participant_for vibriobactin Canonical reference proteins, not independently inspected assay constructs. These edges describe database-associated or explicitly putative biosynthetic participation, not a direct reaction, ordered pathway, substrate specificity, stoichiometry or physical complex. GROUNDED denotes identifier identity, not experimental validation. Strain references are not interchangeable. UniProt is unreviewed and has no FUNCTION comment in the inspected entry. The U52150.2 native note explicitly associates VibH with vibriobactin biosynthesis. Lou15, O395 and N16961 references are not equated as alleles or constructs. Primary methods, figures, supplements and constructs were not independently inspected. The PMID:11112537 abstract is not full-methods evidence; its publisher returned 403. PMID:11112538 returned no usable article content and PMID:11160122 presented a browser challenge. No biochemical assay or genetic-result claim is imported from these access-limited sources.
https://www.uniprot.org/uniprotkb/Q9RCF7
https://www.ebi.ac.uk/ena/browser/view/U52150.2
https://www.ebi.ac.uk/ena/browser/view/U52150.2
https://www.ebi.ac.uk/chebi/CHEBI:9973
  • reference
    https://www.uniprot.org/uniprotkb/Q9RCF7
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    UniProtKB unreviewed (TrEMBL), entry 56, sequence 1, 436 residues; protein existence 4: Predicted. UniProt taxon 666. The selected canonical reference matches deposited AAD48879.1 from Lou15 (El Tor). UniProt is unreviewed and has no FUNCTION comment in the inspected entry. The U52150.2 native note explicitly associates VibH with vibriobactin biosynthesis. Lou15, O395 and N16961 references are not equated as alleles or constructs.
  • reference
    https://www.ebi.ac.uk/ena/browser/view/U52150.2
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Native deposit U52150.2, source strain Lou15 (El Tor), CDS AAD48879.1; the quoted product/note is the named-compound association. It is a database annotation, not an independently reviewed experiment. UniProt is unreviewed and has no FUNCTION comment in the inspected entry. The U52150.2 native note explicitly associates VibH with vibriobactin biosynthesis. Lou15, O395 and N16961 references are not equated as alleles or constructs.
    snippet
    required for vibriobactin biosynthesis
  • reference
    https://www.ebi.ac.uk/ena/browser/view/U52150.2
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete native CDS [5052:6363](-) (zero-based, end-exclusive), 1311 nucleotides, ATG start, TGA stop, codon_start 1, bacterial code 11. Biopython strand-aware cds=True translation equals deposited AAD48879.1 and all 436 canonical Q9RCF7 residues. Source strain Lou15 (El Tor) is explicit; CDS bounds are exact and no translational exceptions are annotated. Alternative start codons are translated as initiating methionine under code 11. This establishes reference-sequence correspondence, not biological initiation, processing, tags, mutations, exact assay stock or strain equivalence.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:9973
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    This owner is free vibriobactin, CHEBI:9973, Standard InChIKey LLMKLMMXMOTPRU-YOAXHERRSA-N. Owner and local ChEBI cache agree within each representation (SMILES versus SMILES; InChI versus InChI) under RDKit 2026.03.5: C35H39N5O11, net charge zero, no iron. Standard InChI reconstruction changes amide/imidic-acid tautomer encoding; equal keys do not establish microstate identity. The separate BGC0000945-derived record has key SNUNDXZQRUCXRW-KDUQSJINSA-N and incomplete stereo; it is not merged or treated as an exact product equivalent. This supports named-compound correspondence, not an exact assay-product microstate, ferric complex or Rhea reaction. Ontology values were checked in the local cache on 2026-10-10, not freshly downloaded.
vibB (O395 reference) is_database_supported_biosynthetic_participant_for vibriobactin Canonical reference proteins, not independently inspected assay constructs. These edges describe database-associated or explicitly putative biosynthetic participation, not a direct reaction, ordered pathway, substrate specificity, stoichiometry or physical complex. GROUNDED denotes identifier identity, not experimental validation. Strain references are not interchangeable. UniProt FUNCTION and cofactor annotations are by similarity. Native AF287252.1 explicitly names a vibriobactin synthetase subunit. Neither sequence identity to another strain reference nor a shared paper citation proves assay-stock equivalence. Primary methods, figures, supplements and constructs were not independently inspected. The PMID:11112537 abstract is not full-methods evidence; its publisher returned 403. PMID:11112538 returned no usable article content and PMID:11160122 presented a browser challenge. No biochemical assay or genetic-result claim is imported from these access-limited sources.
https://www.uniprot.org/uniprotkb/A5F3F4
https://www.ebi.ac.uk/ena/browser/view/AF287252.1
https://www.ebi.ac.uk/ena/browser/view/AF287252.1
https://www.ebi.ac.uk/chebi/CHEBI:9973
  • reference
    https://www.uniprot.org/uniprotkb/A5F3F4
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    UniProtKB reviewed (Swiss-Prot), entry 88, sequence 1, 293 residues; protein existence 3: Inferred from homology. UniProt taxon 345073. The selected canonical reference matches deposited AAG00563.1 from O395. UniProt FUNCTION and cofactor annotations are by similarity. Native AF287252.1 explicitly names a vibriobactin synthetase subunit. Neither sequence identity to another strain reference nor a shared paper citation proves assay-stock equivalence.
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AF287252.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Native deposit AF287252.1, source strain O395, CDS AAG00563.1; the quoted product/note is the named-compound association. It is a database annotation, not an independently reviewed experiment. UniProt FUNCTION and cofactor annotations are by similarity. Native AF287252.1 explicitly names a vibriobactin synthetase subunit. Neither sequence identity to another strain reference nor a shared paper citation proves assay-stock equivalence.
    snippet
    vibriobactin synthetase subunit VibB
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AF287252.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete native CDS [0:882](+) (zero-based, end-exclusive), 882 nucleotides, ATG start, TGA stop, codon_start 1, bacterial code 11. Biopython strand-aware cds=True translation equals deposited AAG00563.1 and all 293 canonical A5F3F4 residues. Source strain O395 is explicit; CDS bounds are exact and no translational exceptions are annotated. Alternative start codons are translated as initiating methionine under code 11. This establishes reference-sequence correspondence, not biological initiation, processing, tags, mutations, exact assay stock or strain equivalence.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:9973
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    This owner is free vibriobactin, CHEBI:9973, Standard InChIKey LLMKLMMXMOTPRU-YOAXHERRSA-N. Owner and local ChEBI cache agree within each representation (SMILES versus SMILES; InChI versus InChI) under RDKit 2026.03.5: C35H39N5O11, net charge zero, no iron. Standard InChI reconstruction changes amide/imidic-acid tautomer encoding; equal keys do not establish microstate identity. The separate BGC0000945-derived record has key SNUNDXZQRUCXRW-KDUQSJINSA-N and incomplete stereo; it is not merged or treated as an exact product equivalent. This supports named-compound correspondence, not an exact assay-product microstate, ferric complex or Rhea reaction. Ontology values were checked in the local cache on 2026-10-10, not freshly downloaded.
vibE (O395 reference) is_database_supported_biosynthetic_participant_for vibriobactin Canonical reference proteins, not independently inspected assay constructs. These edges describe database-associated or explicitly putative biosynthetic participation, not a direct reaction, ordered pathway, substrate specificity, stoichiometry or physical complex. GROUNDED denotes identifier identity, not experimental validation. Strain references are not interchangeable. UniProt is unreviewed; its automated PATHWAY comment says only siderophore biosynthesis. Exact named-compound association comes from the native AF287253.1 subunit annotation, not from a generic pathway transfer. Primary methods, figures, supplements and constructs were not independently inspected. The PMID:11112537 abstract is not full-methods evidence; its publisher returned 403. PMID:11112538 returned no usable article content and PMID:11160122 presented a browser challenge. No biochemical assay or genetic-result claim is imported from these access-limited sources.
https://www.uniprot.org/uniprotkb/Q9FDB2
https://www.ebi.ac.uk/ena/browser/view/AF287253.1
https://www.ebi.ac.uk/ena/browser/view/AF287253.1
https://www.ebi.ac.uk/chebi/CHEBI:9973
  • reference
    https://www.uniprot.org/uniprotkb/Q9FDB2
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    UniProtKB unreviewed (TrEMBL), entry 79, sequence 1, 543 residues; protein existence 3: Inferred from homology. UniProt taxon 666. The selected canonical reference matches deposited AAG00564.1 from O395. UniProt is unreviewed; its automated PATHWAY comment says only siderophore biosynthesis. Exact named-compound association comes from the native AF287253.1 subunit annotation, not from a generic pathway transfer.
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AF287253.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Native deposit AF287253.1, source strain O395, CDS AAG00564.1; the quoted product/note is the named-compound association. It is a database annotation, not an independently reviewed experiment. UniProt is unreviewed; its automated PATHWAY comment says only siderophore biosynthesis. Exact named-compound association comes from the native AF287253.1 subunit annotation, not from a generic pathway transfer.
    snippet
    vibriobactin synthetase subunit VibE
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AF287253.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete native CDS [0:1632](+) (zero-based, end-exclusive), 1632 nucleotides, ATG start, TGA stop, codon_start 1, bacterial code 11. Biopython strand-aware cds=True translation equals deposited AAG00564.1 and all 543 canonical Q9FDB2 residues. Source strain O395 is explicit; CDS bounds are exact and no translational exceptions are annotated. Alternative start codons are translated as initiating methionine under code 11. This establishes reference-sequence correspondence, not biological initiation, processing, tags, mutations, exact assay stock or strain equivalence.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:9973
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    This owner is free vibriobactin, CHEBI:9973, Standard InChIKey LLMKLMMXMOTPRU-YOAXHERRSA-N. Owner and local ChEBI cache agree within each representation (SMILES versus SMILES; InChI versus InChI) under RDKit 2026.03.5: C35H39N5O11, net charge zero, no iron. Standard InChI reconstruction changes amide/imidic-acid tautomer encoding; equal keys do not establish microstate identity. The separate BGC0000945-derived record has key SNUNDXZQRUCXRW-KDUQSJINSA-N and incomplete stereo; it is not merged or treated as an exact product equivalent. This supports named-compound correspondence, not an exact assay-product microstate, ferric complex or Rhea reaction. Ontology values were checked in the local cache on 2026-10-10, not freshly downloaded.
vibH (O395 reference) is_database_supported_biosynthetic_participant_for vibriobactin Canonical reference proteins, not independently inspected assay constructs. These edges describe database-associated or explicitly putative biosynthetic participation, not a direct reaction, ordered pathway, substrate specificity, stoichiometry or physical complex. GROUNDED denotes identifier identity, not experimental validation. Strain references are not interchangeable. UniProt is unreviewed and has no FUNCTION comment in the inspected entry. The selected reference is tied to the O395 deposit, not every strain or synonym merged into the UniProt entry; no N16961 or Lou15 construct equivalence is asserted. Primary methods, figures, supplements and constructs were not independently inspected. The PMID:11112537 abstract is not full-methods evidence; its publisher returned 403. PMID:11112538 returned no usable article content and PMID:11160122 presented a browser challenge. No biochemical assay or genetic-result claim is imported from these access-limited sources.
https://www.uniprot.org/uniprotkb/Q9FDB1
https://www.ebi.ac.uk/ena/browser/view/AF287254.1
https://www.ebi.ac.uk/ena/browser/view/AF287254.1
https://www.ebi.ac.uk/chebi/CHEBI:9973
  • reference
    https://www.uniprot.org/uniprotkb/Q9FDB1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    UniProtKB unreviewed (TrEMBL), entry 91, sequence 1, 436 residues; protein existence 4: Predicted. UniProt taxon 666. The selected canonical reference matches deposited AAG00565.1 from O395. UniProt is unreviewed and has no FUNCTION comment in the inspected entry. The selected reference is tied to the O395 deposit, not every strain or synonym merged into the UniProt entry; no N16961 or Lou15 construct equivalence is asserted.
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AF287254.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Native deposit AF287254.1, source strain O395, CDS AAG00565.1; the quoted product/note is the named-compound association. It is a database annotation, not an independently reviewed experiment. UniProt is unreviewed and has no FUNCTION comment in the inspected entry. The selected reference is tied to the O395 deposit, not every strain or synonym merged into the UniProt entry; no N16961 or Lou15 construct equivalence is asserted.
    snippet
    vibriobactin synthetase subunit VibH
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AF287254.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete native CDS [0:1311](+) (zero-based, end-exclusive), 1311 nucleotides, ATG start, TGA stop, codon_start 1, bacterial code 11. Biopython strand-aware cds=True translation equals deposited AAG00565.1 and all 436 canonical Q9FDB1 residues. Source strain O395 is explicit; CDS bounds are exact and no translational exceptions are annotated. Alternative start codons are translated as initiating methionine under code 11. This establishes reference-sequence correspondence, not biological initiation, processing, tags, mutations, exact assay stock or strain equivalence.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:9973
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    This owner is free vibriobactin, CHEBI:9973, Standard InChIKey LLMKLMMXMOTPRU-YOAXHERRSA-N. Owner and local ChEBI cache agree within each representation (SMILES versus SMILES; InChI versus InChI) under RDKit 2026.03.5: C35H39N5O11, net charge zero, no iron. Standard InChI reconstruction changes amide/imidic-acid tautomer encoding; equal keys do not establish microstate identity. The separate BGC0000945-derived record has key SNUNDXZQRUCXRW-KDUQSJINSA-N and incomplete stereo; it is not merged or treated as an exact product equivalent. This supports named-compound correspondence, not an exact assay-product microstate, ferric complex or Rhea reaction. Ontology values were checked in the local cache on 2026-10-10, not freshly downloaded.
vibF (O395 reference) is_database_supported_biosynthetic_participant_for vibriobactin Canonical reference proteins, not independently inspected assay constructs. These edges describe database-associated or explicitly putative biosynthetic participation, not a direct reaction, ordered pathway, substrate specificity, stoichiometry or physical complex. GROUNDED denotes identifier identity, not experimental validation. Strain references are not interchangeable. UniProt is unreviewed with predicted protein existence; its automated PATHWAY comment is generic. The complete O395 AF287255.1 reference is selected. Partial Q9RR50 and N16961 frameshift locus VC_2209 are not adopted as equivalent complete proteins. Primary methods, figures, supplements and constructs were not independently inspected. The PMID:11112537 abstract is not full-methods evidence; its publisher returned 403. PMID:11112538 returned no usable article content and PMID:11160122 presented a browser challenge. No biochemical assay or genetic-result claim is imported from these access-limited sources.
https://www.uniprot.org/uniprotkb/Q9FDB0
https://www.ebi.ac.uk/ena/browser/view/AF287255.1
https://www.ebi.ac.uk/ena/browser/view/AF287255.1
https://www.ebi.ac.uk/chebi/CHEBI:9973
  • reference
    https://www.uniprot.org/uniprotkb/Q9FDB0
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    UniProtKB unreviewed (TrEMBL), entry 139, sequence 1, 2413 residues; protein existence 4: Predicted. UniProt taxon 666. The selected canonical reference matches deposited AAG00566.1 from O395. UniProt is unreviewed with predicted protein existence; its automated PATHWAY comment is generic. The complete O395 AF287255.1 reference is selected. Partial Q9RR50 and N16961 frameshift locus VC_2209 are not adopted as equivalent complete proteins.
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AF287255.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Native deposit AF287255.1, source strain O395, CDS AAG00566.1; the quoted product/note is the named-compound association. It is a database annotation, not an independently reviewed experiment. UniProt is unreviewed with predicted protein existence; its automated PATHWAY comment is generic. The complete O395 AF287255.1 reference is selected. Partial Q9RR50 and N16961 frameshift locus VC_2209 are not adopted as equivalent complete proteins.
    snippet
    vibriobactin synthetase subunit VibF
  • reference
    https://www.ebi.ac.uk/ena/browser/view/AF287255.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete native CDS [0:7242](+) (zero-based, end-exclusive), 7242 nucleotides, ATG start, TAG stop, codon_start 1, bacterial code 11. Biopython strand-aware cds=True translation equals deposited AAG00566.1 and all 2413 canonical Q9FDB0 residues. Source strain O395 is explicit; CDS bounds are exact and no translational exceptions are annotated. Alternative start codons are translated as initiating methionine under code 11. This establishes reference-sequence correspondence, not biological initiation, processing, tags, mutations, exact assay stock or strain equivalence.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:9973
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    This owner is free vibriobactin, CHEBI:9973, Standard InChIKey LLMKLMMXMOTPRU-YOAXHERRSA-N. Owner and local ChEBI cache agree within each representation (SMILES versus SMILES; InChI versus InChI) under RDKit 2026.03.5: C35H39N5O11, net charge zero, no iron. Standard InChI reconstruction changes amide/imidic-acid tautomer encoding; equal keys do not establish microstate identity. The separate BGC0000945-derived record has key SNUNDXZQRUCXRW-KDUQSJINSA-N and incomplete stereo; it is not merged or treated as an exact product equivalent. This supports named-compound correspondence, not an exact assay-product microstate, ferric complex or Rhea reaction. Ontology values were checked in the local cache on 2026-10-10, not freshly downloaded.

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

Explore across X-Mech

AntibioticMech (vibriobactin) ↗ MediaIngredientMech (CHEBI:9973) ↗ TaxonMech: Vibrio cholerae (NCBITaxon:666) ↗ PathwayMech (mibig:BGC0002494) ↗

Provenance

Source conceptSourceVersion
BGC0002494MIBIG3
CHEBI:9973CHEBI3-star

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