NaturalProductMech

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hypeptin

naturalproductmech:mibig-5780b79a20 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 InChIKeyFZKVQDUEWNYBMS-LEGGSXHMSA-N
SMILESCC[C@H](C)[C@H]1C(=O)O[C@@H]([C@H](C(=O)NC(C(=O)N[C@@H](C(=O)N1)[C@H](C(C)C)O)[C@@H](C2=CC=C(C=C2)O)O)NC(=O)[C@H]([C@@H](C(=O)N)O)NC(=O)[C@H](CCCN=C(N)N)NC(=O)[C@@H](CC(C)C)NC(=O)[C@H](C)N)C(=O)N
Stereochemistry undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers
Cross-referencespubchem:121225236, npatlas:NPA020717

Filing pathway

Unclassified — 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
Lysobacter sp. K5869
NCBITaxon:2820808		 SOURCE_ASSERTION mibig:BGC0002126 PMID:33768646

Occurrences 0

None cited.

Biosynthetic gene clusters 1

AccessionHostLocus evidenceGenome
mibig:BGC0002126 Lysobacter sp. K5869
NCBITaxon:2820808 		CLUSTER_DEMONSTRATED genbank:CP072597.1

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.

Mechanism & Biosynthesis Overview

PRODUCERS & OCCURRENCE 1 producer (0 causal) 0 cited occurrences BIOSYNTHETIC LOCUS 1 gene cluster 0 curated pathway steps NATURAL PRODUCT hypeptin naturalproductmech:mibig-5780b79a20 Unclassified TARGETS & BIOACTIVITY 0 molecular targets 0 bioactivities · 1 graph

Causal graph — biosynthesis 6 nodes, 5 edges

Separate database-reported HynC and HynE carrier-bound amino-acid tailoring contexts in the hypeptin BGC. HynA is listed as auxiliary to both; HynB only to HynC. All four nodes denote verified native K5869 protein references, not reconstructed assay constructs. Functional claims remain database assertions. The HynC leucine-description/model carbon-count conflict is unresolved (issue664); no exact chemical reaction, carrier/domain assignment, reaction stereochemistry, pathway order, physical complex, native genetic necessity or direct mature-hypeptin-forming step is asserted.

SubjectPredicateObjectNotesEvidence
HynC, native K5869 reference is_database_assigned_hydroxylase_in HynC-associated carrier-bound hydroxylation context (database role) MITE describes non-heme diiron monooxygenase HynC and PCP-bound tyrosine and leucine hydroxylations. These are source descriptions, not adopted exact chemical transformations. The leucine-labeled example contains a seven-carbon amino-acid moiety rather than six-carbon leucine in both substrate and product; diagnostic thioester cleavage with a leucine control localizes the mismatch to the amino-acid side. This does not establish the actual assay substrate or a correction. Exact HynC chemistry remains unresolved under https://github.com/CultureBotAI/NaturalProductMech/issues/664. No encoded carrier fragment, syn stereochemical outcome, Fe occupancy or corrected model is adopted. The process denotes an intermediate tailoring context, not direct formation of mature hypeptin. The cited 2021 paper was inaccessible; no primary assay, exact construct, substrate order or native deletion/complementation phenotype was independently inspected.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000197.json
https://www.ncbi.nlm.nih.gov/protein/QWP75303.1
https://www.ncbi.nlm.nih.gov/nuccore/CP072597.1
https://dl.secondarymetabolites.org/mibig/mibig_json_4.0.tar.gz
https://rest.uniprot.org/uniparc/UPI001C062D75.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000197.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-06
    snippet
    beta-hydroxylation of PCP-bound tyrosine (syn)
    notes
    MITE0000197 version 3, inspected 2026-10-07, archive member/Git blob verified at the cited commit. The row links HynC to its GenPept reference and BGC0002126. Its in-vitro assay code and DOI:10.1002/anie.202102224 citation remain database metadata, not primary evidence inspected here. All listed reaction examples are flagged as intermediates.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/QWP75303.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Native Lysobacter sp. K5869 reference, taxon 2820808, 531 aa, locus J5226_16935. Complete GenPept sequence equals the native CDS translation. The Hyn name comes from MITE; GenPept and native chromosome have no gene-name qualifier. PGAP/CDD product and domain annotations are computational, not independently inspected function or module assays. Exact-strain/gene and GenPept-xref UniProtKB queries returned no entries on 2026-10-07; bounded absence only, with no homolog selected. This identifier is not a reconstructed historical assay construct.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/CP072597.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    CP072597.1 is the complete circular 5,968,034-bp K5869 chromosome. Reverse-strand CDS 3903191..3904786, table 11/codon 1, translates exactly to QWP75303.1; independent GenPept coded_by coordinates, strand and DNA agree. Native reference identity and neighborhood do not independently prove biochemical function, physical interaction or native genetic necessity.
  • reference
    https://dl.secondarymetabolites.org/mibig/mibig_json_4.0.tar.gz
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-06
    notes
    MIBiG 4.0 archive SHA256 986f1a69fb5eeb84fd7c0175ae921304c22fd5f8ed04c96d8c1c0c95a145837b; BGC0002126 version 3 inspected 2026-10-07. Its hypeptin SMILES exactly matches this owner; strain K5869/taxon 2820808 and CP072597.1 locus 3896012..3931610 agree. This is the compound/locus anchor, not gene-function evidence. Existing SOURCE_ASSERTION producer and CLUSTER_DEMONSTRATED locus grades remain unchanged, as do incomplete owner stereochemistry and SEEDED status.
  • reference
    https://rest.uniprot.org/uniparc/UPI001C062D75.json
    evidence type
    DATABASE_ASSERTION
    notes
    UniParc UPI001C062D75 (531 aa) links active EMBL QWP75303.1 (Lysobacter sp. K5869, taxon 2820808, locus J5226_16935) and inactive UniProtKB/TrEMBL A0A8F1I7A8, with zero active UniProtKB cross-references.
    retrieved on
    2026-10-30
HynE, native K5869 reference is_database_assigned_hydroxylase_in HynE-associated carrier-bound hydroxylation context (database role) MITE describes alpha-ketoglutarate-dependent dioxygenase HynE and PCP-bound asparagine hydroxylation. This is a database-level functional context, not an adopted exact reaction, carrier structure or independently verified anti stereochemical outcome. Its cofactor field is a database annotation, not measured occupancy or a new assay. The process denotes an intermediate tailoring context, not direct formation of mature hypeptin. The cited 2021 paper was inaccessible; no primary assay, exact construct, substrate order or native deletion/complementation phenotype was independently inspected.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000196.json
https://www.ncbi.nlm.nih.gov/protein/QWP75301.1
https://www.ncbi.nlm.nih.gov/nuccore/CP072597.1
https://dl.secondarymetabolites.org/mibig/mibig_json_4.0.tar.gz
https://rest.uniprot.org/uniparc/UPI001C05F185.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000196.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-06
    snippet
    beta-hydroxylation of PCP-bound asparagine (anti)
    notes
    MITE0000196 version 3, inspected 2026-10-07, archive member/Git blob verified at the cited commit. The row links HynE to its GenPept reference and BGC0002126. Its in-vitro assay code and DOI:10.1002/anie.202102224 citation remain database metadata, not primary evidence inspected here. All listed reaction examples are flagged as intermediates.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/QWP75301.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Native Lysobacter sp. K5869 reference, taxon 2820808, 320 aa, locus J5226_16925. Complete GenPept sequence equals the native CDS translation. The Hyn name comes from MITE; GenPept and native chromosome have no gene-name qualifier. PGAP/CDD product and domain annotations are computational, not independently inspected function or module assays. Exact-strain/gene and GenPept-xref UniProtKB queries returned no entries on 2026-10-07; bounded absence only, with no homolog selected. This identifier is not a reconstructed historical assay construct.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/CP072597.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    CP072597.1 is the complete circular 5,968,034-bp K5869 chromosome. Reverse-strand CDS 3900302..3901264, table 11/codon 1, translates exactly to QWP75301.1; independent GenPept coded_by coordinates, strand and DNA agree. Native reference identity and neighborhood do not independently prove biochemical function, physical interaction or native genetic necessity.
  • reference
    https://dl.secondarymetabolites.org/mibig/mibig_json_4.0.tar.gz
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-06
    notes
    MIBiG 4.0 archive SHA256 986f1a69fb5eeb84fd7c0175ae921304c22fd5f8ed04c96d8c1c0c95a145837b; BGC0002126 version 3 inspected 2026-10-07. Its hypeptin SMILES exactly matches this owner; strain K5869/taxon 2820808 and CP072597.1 locus 3896012..3931610 agree. This is the compound/locus anchor, not gene-function evidence. Existing SOURCE_ASSERTION producer and CLUSTER_DEMONSTRATED locus grades remain unchanged, as do incomplete owner stereochemistry and SEEDED status.
  • reference
    https://rest.uniprot.org/uniparc/UPI001C05F185.json
    evidence type
    DATABASE_ASSERTION
    notes
    UniParc UPI001C05F185 (320 aa) links active EMBL QWP75301.1 (Lysobacter sp. K5869, taxon 2820808, locus J5226_16925) and inactive UniProtKB/TrEMBL A0A8F1L6H1, with zero active UniProtKB cross-references.
    retrieved on
    2026-10-30
HynA, native K5869 reference is_database_listed_auxiliary_synthetase_in HynC-associated carrier-bound hydroxylation context (database role) MITE lists HynA as an auxiliary nonribosomal peptide synthetase in the HynC entry. This records that database role only. It does not establish a physical complex, direct binding, a necessary partner under specific assay conditions, an exact PCP/module assignment, chain-transfer direction, pathway order, historical construct identity or native genetic necessity. No auxiliary role of HynB in the HynE context is asserted.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000197.json
https://www.ncbi.nlm.nih.gov/protein/QWP75305.1
https://www.ncbi.nlm.nih.gov/nuccore/CP072597.1
https://rest.uniprot.org/uniparc/UPI001C0620D5.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000197.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-06
    snippet
    nonribosomal peptide synthetase
    notes
    MITE0000197 version 3 auxiliaryEnzymes entry names HynA and GenPept QWP75305.1. Stable source snapshot inspected 2026-10-07. The protein name/accession link is explicit; auxiliary-list membership does not supply an independently inspected physical or catalytic interaction experiment.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/QWP75305.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Native Lysobacter sp. K5869 reference, taxon 2820808, 6491 aa, locus J5226_16945. Complete GenPept sequence equals the native CDS translation. The Hyn name comes from MITE; GenPept and native chromosome have no gene-name qualifier. PGAP/CDD product and domain annotations are computational, not independently inspected function or module assays. Exact-strain/gene and GenPept-xref UniProtKB queries returned no entries on 2026-10-07; bounded absence only, with no homolog selected. This identifier is not a reconstructed historical assay construct.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/CP072597.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    CP072597.1 is the complete circular 5,968,034-bp K5869 chromosome. Reverse-strand CDS 3912135..3931610, table 11/codon 1, translates exactly to QWP75305.1; independent GenPept coded_by coordinates, strand and DNA agree. Native reference identity and neighborhood do not independently prove biochemical function, physical interaction or native genetic necessity.
  • reference
    https://rest.uniprot.org/uniparc/UPI001C0620D5.json
    evidence type
    DATABASE_ASSERTION
    notes
    UniParc UPI001C0620D5 (6491 aa) links active EMBL QWP75305.1 (Lysobacter sp. K5869, taxon 2820808, locus J5226_16945) and inactive UniProtKB/TrEMBL A0A8F1I6R9, with zero active UniProtKB cross-references.
    retrieved on
    2026-10-30
HynB, native K5869 reference is_database_listed_auxiliary_synthetase_in HynC-associated carrier-bound hydroxylation context (database role) MITE lists HynB as an auxiliary nonribosomal peptide synthetase in the HynC entry. This records that database role only. It does not establish a physical complex, direct binding, a necessary partner under specific assay conditions, an exact PCP/module assignment, chain-transfer direction, pathway order, historical construct identity or native genetic necessity. No auxiliary role of HynB in the HynE context is asserted.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000197.json
https://www.ncbi.nlm.nih.gov/protein/QWP75304.1
https://www.ncbi.nlm.nih.gov/nuccore/CP072597.1
https://rest.uniprot.org/uniparc/UPI001C0636B4.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000197.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-06
    snippet
    nonribosomal peptide synthetase
    notes
    MITE0000197 version 3 auxiliaryEnzymes entry names HynB and GenPept QWP75304.1. Stable source snapshot inspected 2026-10-07. The protein name/accession link is explicit; auxiliary-list membership does not supply an independently inspected physical or catalytic interaction experiment.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/QWP75304.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Native Lysobacter sp. K5869 reference, taxon 2820808, 2447 aa, locus J5226_16940. Complete GenPept sequence equals the native CDS translation. The Hyn name comes from MITE; GenPept and native chromosome have no gene-name qualifier. PGAP/CDD product and domain annotations are computational, not independently inspected function or module assays. Exact-strain/gene and GenPept-xref UniProtKB queries returned no entries on 2026-10-07; bounded absence only, with no homolog selected. This identifier is not a reconstructed historical assay construct.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/CP072597.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    CP072597.1 is the complete circular 5,968,034-bp K5869 chromosome. Reverse-strand CDS 3904795..3912138, table 11/codon 1, translates exactly to QWP75304.1; independent GenPept coded_by coordinates, strand and DNA agree. Native reference identity and neighborhood do not independently prove biochemical function, physical interaction or native genetic necessity.
  • reference
    https://rest.uniprot.org/uniparc/UPI001C0636B4.json
    evidence type
    DATABASE_ASSERTION
    notes
    UniParc UPI001C0636B4 (2447 aa) links active EMBL QWP75304.1 (Lysobacter sp. K5869, taxon 2820808, locus J5226_16940) and inactive UniProtKB/TrEMBL A0A8F1L663, with zero active UniProtKB cross-references.
    retrieved on
    2026-10-30
HynA, native K5869 reference is_database_listed_auxiliary_synthetase_in HynE-associated carrier-bound hydroxylation context (database role) MITE lists HynA as an auxiliary nonribosomal peptide synthetase in the HynE entry. This records that database role only. It does not establish a physical complex, direct binding, a necessary partner under specific assay conditions, an exact PCP/module assignment, chain-transfer direction, pathway order, historical construct identity or native genetic necessity. No auxiliary role of HynB in the HynE context is asserted.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000196.json
https://www.ncbi.nlm.nih.gov/protein/QWP75305.1
https://www.ncbi.nlm.nih.gov/nuccore/CP072597.1
https://rest.uniprot.org/uniparc/UPI001C0620D5.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000196.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-06
    snippet
    nonribosomal peptide synthetase
    notes
    MITE0000196 version 3 auxiliaryEnzymes entry names HynA and GenPept QWP75305.1. Stable source snapshot inspected 2026-10-07. The protein name/accession link is explicit; auxiliary-list membership does not supply an independently inspected physical or catalytic interaction experiment.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/QWP75305.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Native Lysobacter sp. K5869 reference, taxon 2820808, 6491 aa, locus J5226_16945. Complete GenPept sequence equals the native CDS translation. The Hyn name comes from MITE; GenPept and native chromosome have no gene-name qualifier. PGAP/CDD product and domain annotations are computational, not independently inspected function or module assays. Exact-strain/gene and GenPept-xref UniProtKB queries returned no entries on 2026-10-07; bounded absence only, with no homolog selected. This identifier is not a reconstructed historical assay construct.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/CP072597.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    CP072597.1 is the complete circular 5,968,034-bp K5869 chromosome. Reverse-strand CDS 3912135..3931610, table 11/codon 1, translates exactly to QWP75305.1; independent GenPept coded_by coordinates, strand and DNA agree. Native reference identity and neighborhood do not independently prove biochemical function, physical interaction or native genetic necessity.
  • reference
    https://rest.uniprot.org/uniparc/UPI001C0620D5.json
    evidence type
    DATABASE_ASSERTION
    notes
    UniParc UPI001C0620D5 (6491 aa) links active EMBL QWP75305.1 (Lysobacter sp. K5869, taxon 2820808, locus J5226_16945) and inactive UniProtKB/TrEMBL A0A8F1I6R9, with zero active UniProtKB cross-references.
    retrieved on
    2026-10-30

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

Explore across X-Mech

AntibioticMech (hypeptin) ↗ MediaIngredientMech (naturalproductmech:mibig-5780b79a20) ↗ TaxonMech: Lysobacter sp. K5869 (NCBITaxon:2820808) ↗ PathwayMech (mibig:BGC0002126) ↗

Provenance

Source conceptSourceVersion
BGC0002126MIBIG3

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