borrelidin

naturalproductmech:mibig-af79f8ac64 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	OJCKRNPLOZHAOU-UGKRXNSESA-N
SMILES	[H][C@]1(CCC[C@H]1C(O)=O)[C@]1([H])C\C=C\C=C(C#N)/[C@H](O)[C@@H](C)C[C@H](C)C[C@H](C)C[C@H](C)[C@@H](O)CC(=O)O1
Stereochemistry	fully defined
Cross-references	npatlas:NPA011087

Filing pathway

Polyketides — computed by NPClassifier npclassifier.gnps2.org@2026-09-07, which is why it is pinned rather than recomputed. The gene cluster's asserted class is pks, 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
Streptomyces parvulus NCBITaxon:146923	BGC_CHARACTERIZED	mibig:BGC0000031	PMID:15112998
Streptomyces rochei NCBITaxon:1928	SOURCE_ASSERTION	mibig:BGC0001533	PMID:27451447

Occurrences 9

Somebody found the compound in this organism and cited it. That is not a claim that the organism makes it, and nothing here promotes one to the other.

Taxon	Source	Reference
Streptomyces coelicoflavus NCBITaxon:285562	LOTUS	DOI:10.3389/FMICB.2016.00659
Streptomyces albovinaceus NCBITaxon:66867	LOTUS	DOI:10.1128/AAC.27.2.239
Streptomyces mutabilis NCBITaxon:67332	LOTUS	DOI:10.1515/ZNC-2017-0140
Streptomyces heilongjiangensis NCBITaxon:945052	LOTUS	DOI:10.1099/IJS.0.041483-0
Streptomyces parvulus NCBITaxon:146923	LOTUS	DOI:10.1016/J.CHEMBIOL.2003.12.018
Streptomyces parvulus NCBITaxon:146923	LOTUS	DOI:10.1111/J.1365-2958.2004.04090.X
Streptomyces rochei NCBITaxon:1928	LOTUS	DOI:10.1002/HLCA.19670500303
Streptomyces rochei NCBITaxon:1928	LOTUS	DOI:10.1007/S00253-018-9237-5
Streptomyces rochei NCBITaxon:1928	LOTUS	DOI:10.3389/FMICB.2019.00915

Biosynthetic gene clusters 2

Accession	Host	Locus evidence	Genome
mibig:BGC0000031	Streptomyces parvulus NCBITaxon:146923	CLUSTER_DEMONSTRATED	genbank:AJ580915.1
mibig:BGC0001533	Streptomyces rochei NCBITaxon:1928	CLUSTER_UNSTATED	genbank:KT362046.1

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	Reaction	Substrate → product	Evidence
1	BorI cytochrome P450 UniProtKB:Q70HZ6		ungrounded → ungrounded	https://mite.lisc.univie.ac.at/repository/MITE0000188

Entry 1: Database-proposed BorI aldoxime-to-nitrile function in the borrelidin pathway. MITE's literal aldoxime and nitrile models are not grounded to this exact owner: the nitrile example conflicts at two specified tetrahedral centers and omits additional stereochemistry. The former exact product assignment and step number 5 are withdrawn; reaction-list position is not verified pathway order. No substrate/product CURIE, balanced reaction, isolated BorI assay or corrected source structure is asserted. The prior primary and native-sequence citations are preserved on the graph's broader BorI participation edge, not used to validate the conflicting chemical model. BorJ chemical curation remains on hold.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 4 nodes, 3 edges

Partial Streptomyces parvulus borrelidin graph separating retained BorI pathway participation from MITE's proposed aldoxime-to-nitrile model. The database product conflicts with the owner at specified stereocenters; the model nodes are not an exact chemical route to this borrelidin structure.

Subject	Predicate	Object	Notes	Evidence
C12 aldoxime pre-borrelidin (MITE model)	is_database_proposed_substrate_of	BorI cytochrome P450	MITE-proposed aldoxime substrate only. The model's stereochemistry is unresolved relative to the exact owner; this is not a newly demonstrated isolated-enzyme reaction.	https://mite.lisc.univie.ac.at/repository/MITE0000188 https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000188.json reference https://mite.lisc.univie.ac.at/repository/MITE0000188 evidence type DATABASE_ASSERTION snippet Nitrile-formation via dehydation aldoxime retrieved on 2026-10-01 notes MITE0000188 assigns the proposed aldoxime-to-nitrile dehydration to BorI (UniProtKB:Q70HZ6, CAE45673.1, BGC0000031). This retained database citation and exact snippet describe a source model, not an experimentally established conversion of the exact owner. The 2026-10-08 pinned re-audit below finds two conflicting specified tetrahedral centers as well as missing stereochemistry in its product. Its literal nitrile model is therefore represented separately, with no exact product identifier. reference https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000188.json evidence type CURATOR_INFERENCE retrieved on 2026-10-08 notes RDKit 2026.03.5 re-audit of the pinned MITE0000188 version 3 literal non-intermediate nitrile product gives OJCKRNPLOZHAOU-RQKVFPBWSA-N, not this owner's OJCKRNPLOZHAOU-UGKRXNSESA-N. Full-connectivity mapping is unique, but the chiral match fails: the macrocycle ester-bearing center and the cyclopentane carboxyl-bearing center have opposite specified configurations. In the exact source/owner parsed SMILES, source atom 14 (R) maps to owner atom 8 (S), and source atom 19 (S) maps to owner atom 4 (R), using zero-based atom indices. The source also omits the cyclopentane attachment-center configuration and both alkene configurations. These are not merely unspecified stereochemistry or an exact chemical join. The source structures are neither inverted nor completed, and no biological epimerization is inferred. The graph's MITE product node remains distinct from the exact borrelidin owner; terminal conversion of that owner is not established by this database model. MITE experiment codes are database annotations, not newly inspected primary results.
BorI cytochrome P450	has_database_proposed_product	Nitrile product (MITE model; stereochemistry conflicts)	The literal MITE nitrile-model product is kept distinct from borrelidin. Connectivity alone does not justify the former exact-owner product edge; neither stereochemical completion nor inversion is adopted.	https://mite.lisc.univie.ac.at/repository/MITE0000188 https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000188.json reference https://mite.lisc.univie.ac.at/repository/MITE0000188 evidence type DATABASE_ASSERTION snippet Nitrile-formation via dehydation aldoxime retrieved on 2026-10-01 notes MITE0000188 assigns the proposed aldoxime-to-nitrile dehydration to BorI (UniProtKB:Q70HZ6, CAE45673.1, BGC0000031). This retained database citation and exact snippet describe a source model, not an experimentally established conversion of the exact owner. The 2026-10-08 pinned re-audit below finds two conflicting specified tetrahedral centers as well as missing stereochemistry in its product. Its literal nitrile model is therefore represented separately, with no exact product identifier. reference https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000188.json evidence type CURATOR_INFERENCE retrieved on 2026-10-08 notes RDKit 2026.03.5 re-audit of the pinned MITE0000188 version 3 literal non-intermediate nitrile product gives OJCKRNPLOZHAOU-RQKVFPBWSA-N, not this owner's OJCKRNPLOZHAOU-UGKRXNSESA-N. Full-connectivity mapping is unique, but the chiral match fails: the macrocycle ester-bearing center and the cyclopentane carboxyl-bearing center have opposite specified configurations. In the exact source/owner parsed SMILES, source atom 14 (R) maps to owner atom 8 (S), and source atom 19 (S) maps to owner atom 4 (R), using zero-based atom indices. The source also omits the cyclopentane attachment-center configuration and both alkene configurations. These are not merely unspecified stereochemistry or an exact chemical join. The source structures are neither inverted nor completed, and no biological epimerization is inferred. The graph's MITE product node remains distinct from the exact borrelidin owner; terminal conversion of that owner is not established by this database model. MITE experiment codes are database annotations, not newly inspected primary results.
BorI cytochrome P450	participates_in_biosynthesis_of	borrelidin	Retains the previously curated BorI pathway-participation evidence and native-reference grounding. The primary-paper account concerns genetic/heterologous pathway involvement, including BorI/BorJ co-expression, not a verified BorI-alone conversion of MITE's literal aldoxime model into this exact owner. The four retained EvidenceItems below are unchanged from prior curation. The inaccessible paper was not reread for this correction, and its prior account is neither silently discarded nor newly validated. Protein identity is not evidence for the conflicting chemical join; no new native producer or BGC grade is inferred.	DOI:10.1111/j.1365-2958.2004.04090.x https://www.ncbi.nlm.nih.gov/nuccore/AJ580915.1 https://mibig.secondarymetabolites.org/repository/BGC0000031.5/BGC0000031.gbk https://www.uniprot.org/uniprotkb/Q70HZ6 https://github.com/CultureBotAI/NaturalProductMech/blob/ec47f1839841f4be14e4d798510bfc30eb2906fe/data/natural_products/polyketides/borrelidin.yaml reference DOI:10.1111/j.1365-2958.2004.04090.x evidence type PRIMARY_EXPERIMENT snippet co-expressing borI and borJ in Streptomyces albus J1074 notes Olano et al. showed that borI and borJ insertional mutants no longer produced borrelidin, that a borI-minus mutant accumulated 12-desnitrile-12-methyl-borrelidin, and that heterologous S. albus co-expressing borI and borJ converted 12-desnitrile-12-methyl-borrelidin into borrelidin more efficiently when borK was also expressed. These experiments support BorI participation in the proposed nitrile-forming pathway; MITE assigns the terminal aldoxime dehydration specifically to BorI. reference https://www.ncbi.nlm.nih.gov/nuccore/AJ580915.1 evidence type DATABASE_ASSERTION snippet protein_id="CAE45673.1" retrieved on 2026-10-01 notes GenBank AJ580915.1 is the Streptomyces parvulus Tu4055 borrelidin cluster sequence and maps borI to CAE45673.1. reference https://mibig.secondarymetabolites.org/repository/BGC0000031.5/BGC0000031.gbk evidence type DATABASE_ASSERTION snippet protein_id="CAE45673.1" retrieved on 2026-10-01 notes MIBiG BGC0000031.5 places borI/CAE45673.1 inside the active Streptomyces parvulus borrelidin cluster. reference https://www.uniprot.org/uniprotkb/Q70HZ6 evidence type DATABASE_ASSERTION snippet GN=borI retrieved on 2026-10-01 notes Current unreviewed UniProtKB:Q70HZ6 resolves as Streptomyces parvulus BorI putative cytochrome P450, cross-references EMBL AJ580915 protein CAE45673.1, and is sequence-identical to GenPept CAE45673.1. reference https://github.com/CultureBotAI/NaturalProductMech/blob/ec47f1839841f4be14e4d798510bfc30eb2906fe/data/natural_products/polyketides/borrelidin.yaml evidence type CURATOR_INFERENCE retrieved on 2026-10-08 notes Evidence-preservation boundary: the prior record's one unique primary-paper account and three native-sequence/database citations are retained verbatim here for BorI participation and identity. Duplicate copies on the model-only pathway/edges were consolidated, not deleted as unique evidence. This correction does not treat a failed paper retrieval as evidence against the earlier account.

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

Explore across X-Mech

AntibioticMech (borrelidin) ↗ MediaIngredientMech (naturalproductmech:mibig-af79f8ac64) ↗ TaxonMech: Streptomyces parvulus (NCBITaxon:146923) ↗ TaxonMech: Streptomyces rochei (NCBITaxon:1928) ↗ PathwayMech (mibig:BGC0000031) ↗ PathwayMech (mibig:BGC0001533) ↗

Open questions 1

shared-structure — This structure is reported by more than one MIBiG entry: BGC0000031, BGC0001533. Confirm they describe the same compound rather than an upstream cross-reference error.

Provenance

Source concept	Source	Version
BGC0000031	MIBIG	5
BGC0001533	MIBIG	5

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