piscibactin

naturalproductmech:mibig-81da63fd62 MINTED SEEDED

Grounding review: No 3-star ChEBI entry shares this structure, so the record keeps a content-hashed identifier.

What these status tags mean

Curation status describes a workflow state. SEEDED means the record entered through the source-seeding workflow; it does not imply that no later curation occurred. PROPOSED marks an addition awaiting review; REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record. These are workflow decisions, not independently verified human review. Agent-assisted contributions may appear in the record history.

Grounding describes the identifier mapping: EXACT uses an ontology identity asserted by the source; MINTED keeps a local identifier when no defensible ontology identity is available; REVIEW_NEEDED flags an exact structure whose ontology identity needs adjudication. The grounding note retains any unresolved alternatives. These tags do not establish the strength of producer or activity evidence.

Structure

Standard InChIKey	IHZPBBLBWDEMKS-PDEVRGGCSA-N
SMILES	C[C@@]1(CSC(=N1)C[C@@H]([C@@H]2CS[C@@H](N2)[C@H]3CSC(=N3)C4=CC=CC=C4O)O)C(=O)O
Stereochemistry	fully defined
Cross-references	npatlas:NPA006148

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, pks, from MIBiG.

Producer organisms 2

A claim that this taxon makes the compound. The basis says what the evidence addressed — a knockout and a database assertion are not the same claim.

Taxon	Basis	Cluster	Evidence
Photobacterium damselae subsp. piscicida DI21 NCBITaxon:1200302	BGC_CHARACTERIZED	mibig:BGC0002533	DOI:10.3389/fmicb.2018.01766
Vibrio neptunius NCBITaxon:170651	BGC_CHARACTERIZED	mibig:BGC0002613	DOI:10.1007/s00775-021-01916-1

Occurrences 0

None cited.

Biosynthetic gene clusters 2

Accession	Host	Locus evidence	Genome
mibig:BGC0002533	Photobacterium damselae subsp. piscicida DI21 NCBITaxon:1200302	CLUSTER_DEMONSTRATED	genbank:KP100338.1
mibig:BGC0002613	Vibrio neptunius NCBITaxon:170651	CLUSTER_DEMONSTRATED	genbank:JAFHLB010000021.1

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.

#	Enzyme	Substrate → product	Evidence
1	JYA62_15735 amino acid adenylation domain-containing protein UniProtKB:A0ABS3A8C5	ungrounded → ungrounded	DOI:10.3389/fcimb.2021.750567
2	JYA62_15740 amino acid adenylation domain-containing protein UniProtKB:A0ABS3A787	ungrounded → ungrounded	DOI:10.3389/fcimb.2021.750567
3	JYA62_15745 Gfo/Idh/MocA family oxidoreductase UniProtKB:A0ABS3A5F9	ungrounded → ungrounded	DOI:10.3389/fcimb.2021.750567
4	JYA62_15750 thioesterase UniProtKB:A0ABS3A3Q2	ungrounded → ungrounded	DOI:10.3389/fcimb.2021.750567
5	JYA62_15755 salicylate synthase UniProtKB:A0ABS3A3Q0	ungrounded → ungrounded	DOI:10.3389/fcimb.2021.750567
6	JYA62_15760 AMP-binding protein UniProtKB:A0ABS3A5Z7	ungrounded → ungrounded	DOI:10.3389/fcimb.2021.750567

Entry 1: This proposed pathway entry captures JYA62_15735/MBN3579112.1 as a BGC0002613 member. The exact isolated substrate and product are not resolved, and this entry does not assert JYA62_15735's position in the chemical assembly order.

Entry 2: This proposed pathway entry captures JYA62_15740/MBN3579113.1 as a BGC0002613 member. The exact isolated substrate and product are not resolved, and this entry does not assert JYA62_15740's position in the chemical assembly order.

Entry 3: This proposed pathway entry captures JYA62_15745/MBN3579114.1 as a BGC0002613 member. The exact isolated substrate and product are not resolved, and this entry does not assert JYA62_15745's position in the chemical assembly order.

Entry 4: This proposed pathway entry captures JYA62_15750/MBN3579115.1 as a BGC0002613 member. The exact isolated substrate and product are not resolved, and this entry does not assert JYA62_15750's position in the chemical assembly order.

Entry 5: This proposed pathway entry captures JYA62_15755/MBN3579116.1 as a BGC0002613 member. The exact isolated substrate and product are not resolved, and this entry does not assert JYA62_15755's position in the chemical assembly order.

Entry 6: This proposed pathway entry captures JYA62_15760/MBN3579117.1 as a BGC0002613 member. The exact isolated substrate and product are not resolved, and this entry does not assert JYA62_15760's position in the chemical assembly order.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 8 nodes, 7 edges

Partial Vibrio neptunius BGC0002613 piscibactin biosynthesis graph for six core and tailoring proteins in the JAFHLB010000021.1 locus.

Subject	Predicate	Object	Notes	Evidence
JYA62_15735 amino acid adenylation domain-containing protein	contributes to	Vibrio neptunius piscibactin biosynthesis	This edge follows the BGC0002613 assignment for JYA62_15735/MBN3579112.1 and stops at the piscibactin-biosynthesis process because the isolated substrate-product pair was not assayed.	DOI:10.3389/fcimb.2021.750567 https://mibig.secondarymetabolites.org/repository/BGC0002613.2/index.html https://www.ncbi.nlm.nih.gov/protein/MBN3579112.1 reference DOI:10.3389/fcimb.2021.750567 evidence type PRIMARY_EXPERIMENT snippet Vibrio neptunius Produces Piscibactin and Amphibactin and Both Siderophores Contribute Significantly to Virulence for Clams notes Osorio et al. identified piscibactin synthesis in V. neptunius and used siderophore biosynthetic-gene mutants to connect the BGC0002613 system to the phenotype; this curated graph uses MIBiG/NCBI feature assignments for individual JAFHLB010000021.1 CDS. reference https://mibig.secondarymetabolites.org/repository/BGC0002613.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet biosynthetic (rule-based-clusters) NRP-metallophore: Condensation notes MIBiG BGC0002613.2 lists piscibactin as the product, reports JAFHLB010000021.1 as the locus, and annotates JYA62_15735/MBN3579112.1 as biosynthetic with product amino acid adenylation domain-containing protein. reference https://www.ncbi.nlm.nih.gov/protein/MBN3579112.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet amino acid adenylation domain-containing protein notes NCBI Protein MBN3579112.1 is the 2049 aa JAFHLB010000021.1 JYA62_15735 coding sequence. UniProtKB:A0ABS3A8C5 currently resolves to the same V. neptunius EMBL locus.
JYA62_15740 amino acid adenylation domain-containing protein	contributes to	Vibrio neptunius piscibactin biosynthesis	This edge follows the BGC0002613 assignment for JYA62_15740/MBN3579113.1 and stops at the piscibactin-biosynthesis process because the isolated substrate-product pair was not assayed.	DOI:10.3389/fcimb.2021.750567 https://mibig.secondarymetabolites.org/repository/BGC0002613.2/index.html https://www.ncbi.nlm.nih.gov/protein/MBN3579113.1 reference DOI:10.3389/fcimb.2021.750567 evidence type PRIMARY_EXPERIMENT snippet Vibrio neptunius Produces Piscibactin and Amphibactin and Both Siderophores Contribute Significantly to Virulence for Clams notes Osorio et al. identified piscibactin synthesis in V. neptunius and used siderophore biosynthetic-gene mutants to connect the BGC0002613 system to the phenotype; this curated graph uses MIBiG/NCBI feature assignments for individual JAFHLB010000021.1 CDS. reference https://mibig.secondarymetabolites.org/repository/BGC0002613.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet biosynthetic (rule-based-clusters) NRP-metallophore: AMP-binding notes MIBiG BGC0002613.2 lists piscibactin as the product, reports JAFHLB010000021.1 as the locus, and annotates JYA62_15740/MBN3579113.1 as biosynthetic with product amino acid adenylation domain-containing protein. reference https://www.ncbi.nlm.nih.gov/protein/MBN3579113.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet amino acid adenylation domain-containing protein notes NCBI Protein MBN3579113.1 is the 3992 aa JAFHLB010000021.1 JYA62_15740 coding sequence. UniProtKB:A0ABS3A787 currently resolves to the same V. neptunius EMBL locus.
JYA62_15745 Gfo/Idh/MocA family oxidoreductase	contributes to	Vibrio neptunius piscibactin biosynthesis	This edge follows the BGC0002613 assignment for JYA62_15745/MBN3579114.1 and stops at the piscibactin-biosynthesis process because the isolated substrate-product pair was not assayed.	DOI:10.3389/fcimb.2021.750567 https://mibig.secondarymetabolites.org/repository/BGC0002613.2/index.html https://www.ncbi.nlm.nih.gov/protein/MBN3579114.1 reference DOI:10.3389/fcimb.2021.750567 evidence type PRIMARY_EXPERIMENT snippet Vibrio neptunius Produces Piscibactin and Amphibactin and Both Siderophores Contribute Significantly to Virulence for Clams notes Osorio et al. identified piscibactin synthesis in V. neptunius and used siderophore biosynthetic-gene mutants to connect the BGC0002613 system to the phenotype; this curated graph uses MIBiG/NCBI feature assignments for individual JAFHLB010000021.1 CDS. reference https://mibig.secondarymetabolites.org/repository/BGC0002613.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet biosynthetic-additional (rule-based-clusters) GFO_IDH_MocA notes MIBiG BGC0002613.2 lists piscibactin as the product, reports JAFHLB010000021.1 as the locus, and annotates JYA62_15745/MBN3579114.1 as biosynthetic-additional with product Gfo/Idh/MocA family oxidoreductase. reference https://www.ncbi.nlm.nih.gov/protein/MBN3579114.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet Gfo/Idh/MocA family oxidoreductase notes NCBI Protein MBN3579114.1 is the 361 aa JAFHLB010000021.1 JYA62_15745 coding sequence. UniProtKB:A0ABS3A5F9 currently resolves to the same V. neptunius EMBL locus.
JYA62_15750 thioesterase	contributes to	Vibrio neptunius piscibactin biosynthesis	This edge follows the BGC0002613 assignment for JYA62_15750/MBN3579115.1 and stops at the piscibactin-biosynthesis process because the isolated substrate-product pair was not assayed.	DOI:10.3389/fcimb.2021.750567 https://mibig.secondarymetabolites.org/repository/BGC0002613.2/index.html https://www.ncbi.nlm.nih.gov/protein/MBN3579115.1 reference DOI:10.3389/fcimb.2021.750567 evidence type PRIMARY_EXPERIMENT snippet Vibrio neptunius Produces Piscibactin and Amphibactin and Both Siderophores Contribute Significantly to Virulence for Clams notes Osorio et al. identified piscibactin synthesis in V. neptunius and used siderophore biosynthetic-gene mutants to connect the BGC0002613 system to the phenotype; this curated graph uses MIBiG/NCBI feature assignments for individual JAFHLB010000021.1 CDS. reference https://mibig.secondarymetabolites.org/repository/BGC0002613.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet biosynthetic-additional (rule-based-clusters) Thioesterase notes MIBiG BGC0002613.2 lists piscibactin as the product, reports JAFHLB010000021.1 as the locus, and annotates JYA62_15750/MBN3579115.1 as biosynthetic-additional with product thioesterase. reference https://www.ncbi.nlm.nih.gov/protein/MBN3579115.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet thioesterase notes NCBI Protein MBN3579115.1 is the 278 aa JAFHLB010000021.1 JYA62_15750 coding sequence. UniProtKB:A0ABS3A3Q2 currently resolves to the same V. neptunius EMBL locus.
JYA62_15755 salicylate synthase	contributes to	Vibrio neptunius piscibactin biosynthesis	This edge follows the BGC0002613 assignment for JYA62_15755/MBN3579116.1 and stops at the piscibactin-biosynthesis process because the isolated substrate-product pair was not assayed.	DOI:10.3389/fcimb.2021.750567 https://mibig.secondarymetabolites.org/repository/BGC0002613.2/index.html https://www.ncbi.nlm.nih.gov/protein/MBN3579116.1 reference DOI:10.3389/fcimb.2021.750567 evidence type PRIMARY_EXPERIMENT snippet Vibrio neptunius Produces Piscibactin and Amphibactin and Both Siderophores Contribute Significantly to Virulence for Clams notes Osorio et al. identified piscibactin synthesis in V. neptunius and used siderophore biosynthetic-gene mutants to connect the BGC0002613 system to the phenotype; this curated graph uses MIBiG/NCBI feature assignments for individual JAFHLB010000021.1 CDS. reference https://mibig.secondarymetabolites.org/repository/BGC0002613.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet biosynthetic (rule-based-clusters) NRP-metallophore: SalSyn notes MIBiG BGC0002613.2 lists piscibactin as the product, reports JAFHLB010000021.1 as the locus, and annotates JYA62_15755/MBN3579116.1 as biosynthetic with product salicylate synthase. reference https://www.ncbi.nlm.nih.gov/protein/MBN3579116.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet salicylate synthase notes NCBI Protein MBN3579116.1 is the 465 aa JAFHLB010000021.1 JYA62_15755 coding sequence. UniProtKB:A0ABS3A3Q0 currently resolves to the same V. neptunius EMBL locus.
JYA62_15760 AMP-binding protein	contributes to	Vibrio neptunius piscibactin biosynthesis	This edge follows the BGC0002613 assignment for JYA62_15760/MBN3579117.1 and stops at the piscibactin-biosynthesis process because the isolated substrate-product pair was not assayed.	DOI:10.3389/fcimb.2021.750567 https://mibig.secondarymetabolites.org/repository/BGC0002613.2/index.html https://www.ncbi.nlm.nih.gov/protein/MBN3579117.1 reference DOI:10.3389/fcimb.2021.750567 evidence type PRIMARY_EXPERIMENT snippet Vibrio neptunius Produces Piscibactin and Amphibactin and Both Siderophores Contribute Significantly to Virulence for Clams notes Osorio et al. identified piscibactin synthesis in V. neptunius and used siderophore biosynthetic-gene mutants to connect the BGC0002613 system to the phenotype; this curated graph uses MIBiG/NCBI feature assignments for individual JAFHLB010000021.1 CDS. reference https://mibig.secondarymetabolites.org/repository/BGC0002613.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet biosynthetic-additional (rule-based-clusters) AMP-binding notes MIBiG BGC0002613.2 lists piscibactin as the product, reports JAFHLB010000021.1 as the locus, and annotates JYA62_15760/MBN3579117.1 as biosynthetic-additional with product AMP-binding protein. reference https://www.ncbi.nlm.nih.gov/protein/MBN3579117.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet AMP-binding protein notes NCBI Protein MBN3579117.1 is the 535 aa JAFHLB010000021.1 JYA62_15760 coding sequence. UniProtKB:A0ABS3A5Z7 currently resolves to the same V. neptunius EMBL locus.
Vibrio neptunius piscibactin biosynthesis	produces	piscibactin		DOI:10.3389/fcimb.2021.750567 https://mibig.secondarymetabolites.org/repository/BGC0002613.2/index.html reference DOI:10.3389/fcimb.2021.750567 evidence type PRIMARY_EXPERIMENT snippet Vibrio neptunius Produces Piscibactin and Amphibactin and Both Siderophores Contribute Significantly to Virulence for Clams notes Osorio et al. identified piscibactin synthesis in V. neptunius and used siderophore biosynthetic-gene mutants to connect the BGC0002613 system to the phenotype; this curated graph uses MIBiG/NCBI feature assignments for individual JAFHLB010000021.1 CDS. reference https://mibig.secondarymetabolites.org/repository/BGC0002613.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet piscibactin notes MIBiG BGC0002613.2 lists piscibactin as the V. neptunius product and JAFHLB010000021.1 as the BGC locus.

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

Explore across X-Mech

AntibioticMech (piscibactin) ↗ MediaIngredientMech (naturalproductmech:mibig-81da63fd62) ↗ TaxonMech: Photobacterium damselae subsp. piscicida DI21 (NCBITaxon:1200302) ↗ TaxonMech: Vibrio neptunius (NCBITaxon:170651) ↗ PathwayMech (mibig:BGC0002533) ↗ PathwayMech (mibig:BGC0002613) ↗

Open questions 1

shared-structure — This structure is reported by more than one MIBiG entry: BGC0002533, BGC0002613. Confirm they describe the same compound rather than an upstream cross-reference error.

Provenance

Source concept	Source	Version
BGC0002533	MIBIG	2
BGC0002613	MIBIG	2

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