NaturalProductMech

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coelimycin P1

naturalproductmech:mibig-5c75ae209a 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 InChIKeyRHGMVWUZXGSXCT-HXNNLKDLSA-N
SMILESC/C=C/C(=O)/C/1=C/C(=C\2/C=CCCN2)/SC[CH](C(=O)O1)NC(=O)C
Stereochemistry undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers

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 pks, from MIBiG.

Producer organisms 1

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

TaxonBasisClusterEvidence
Streptomyces coelicolor A3(2)
NCBITaxon:100226		 BGC_CHARACTERIZED mibig:BGC0000038 DOI:10.1039/c2sc20410j

Occurrences 2

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

TaxonSourceReference
Streptomyces albidoflavus
NCBITaxon:1886		 LOTUS DOI:10.1007/S00203-006-0176-7
Streptomyces coelicolor
NCBITaxon:1902		 LOTUS DOI:10.1007/S00203-006-0176-7

Biosynthetic gene clusters 1

AccessionHostLocus evidenceGenome
mibig:BGC0000038 Streptomyces coelicolor A3(2)
NCBITaxon:100226 		CLUSTER_DEMONSTRATED genbank:AL645882.2

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 (1 causal) 2 cited occurrences BIOSYNTHETIC LOCUS 1 gene cluster 0 curated pathway steps NATURAL PRODUCT coelimycin P1 naturalproductmech:mibig-5c75ae209a Unclassified TARGETS & BIOACTIVITY 0 molecular targets 0 bioactivities · 5 graphs

Causal graph — biosynthesis 2 nodes, 1 edge

Native-reference identity for Streptomyces coelicolor A3(2), taxon 100226/BGC0000038. UniProt names ATCC BAA-471/A3(2)/M145. Matching references do not establish measured expression, a verified assay construct, mature-chain processing, enzyme activity, native assembly or cofactor occupancy. Coelimycin P1 is not equated with P2.

SubjectPredicateObjectNotesEvidence
SCO6272 CDS (AL645882.2) encodes the native protein reference SCO6272 (A3(2) native-reference example) Forward-strand 6899170..6900822; 1653-nt complete CDS including stop, 550 residues.
https://www.ncbi.nlm.nih.gov/nuccore/AL645882.2
https://www.ncbi.nlm.nih.gov/protein/CAC22143.1
https://www.uniprot.org/uniprotkb/Q9EX55/entry
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000337.json
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AL645882.2
    evidence type
    DATABASE_ASSERTION
    notes
    GenBank names SCO6272 (alias SC2C4.02) and assigns CAC22143.1, codon_start 1, translation table 11. The inspected sequence is the 6890528..6948414 window, not a new whole-chromosome audit.
    retrieved on
    2026-10-08
    snippet
    /gene="SCO6272"
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAC22143.1
    evidence type
    DATABASE_ASSERTION
    notes
    GenPept identifies A3(2)/taxon 100226. Its coded_by uses AL939127.1; the AL645882.2 CDS independently names the same protein accession.
    retrieved on
    2026-10-08
  • reference
    https://www.uniprot.org/uniprotkb/Q9EX55/entry
    evidence type
    CURATOR_INFERENCE
    notes
    Unreviewed entry version 122, sequence version 1. CDS-aware translation, deposited translation, GenPept and UniProt agree over all 550 residues. No specific FUNCTION or CATALYTIC ACTIVITY comment. Computational family, cofactor and localization annotations are not direct enzyme evidence. Predicted signal residues 1..32 and cleavage are not experimentally established.
    retrieved on
    2026-10-08
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000337.json
    evidence type
    DATABASE_ASSERTION
    notes
    Active MITE0000337 version 1 maps SCO6272 to Q9EX55/CAC22143.1/BGC0000038. Native sequence identity does not independently validate the reaction annotation.
    retrieved on
    2026-10-08

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

Causal graph — biosynthesis 4 nodes, 3 edges

Partial proposed monooxygenation graph from MITE0000337 version 1. MITE labels its evidence Inference from genomic data and chemical structure and cites DOI:10.1039/C2SC20410J. Only the paper abstract was inspected; official full-text access returned 403 and retrieval stopped. The distinct DOI:10.1039/C6SC02803A also remains abstract-level after a separate 403. Neither supplies an inspected individual enzyme assay here. These are separate inferred models, not an ordered or complete route to the owner. Chemical and process nodes stay ungrounded; no exact owner-product identity, experimental substrate specificity or P1/P2 equivalence is asserted.

SubjectPredicateObjectNotesEvidence
SCO6272 (A3(2) native-reference example) is inferred by the database to catalyze proposed monooxygenation (inferred model) Genomic/chemical inference, not a directly inspected enzyme experiment.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000337.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000337.json
    evidence type
    DATABASE_ASSERTION
    notes
    Active MITE0000337 version 1 maps SCO6272 to Q9EX55/CAC22143.1/BGC0000038. Native sequence identity does not independently validate the reaction annotation. No rates, cofactor specificity, assembly or verified native-substrate assay are adopted.
    retrieved on
    2026-10-08
    snippet
    Catalyse an monooxygenation reaction from compound 4 to compound 5
SCO6272 substrate (MITE model) is the modeled substrate of proposed monooxygenation (inferred model) Source model only; no independently verified assay substrate or reaction order.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000337.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000337.json
    evidence type
    DATABASE_ASSERTION
    notes
    RDKit 2026.03.5 substrate key SMVMDJWFLAJVIY-XRNPITFCSA-N. Different connectivity from the owner; no ChEBI/Rhea identifier chosen.
    retrieved on
    2026-10-08
proposed monooxygenation (inferred model) is modeled to yield SCO6272 product (MITE model) Inferred intermediate model, not exact coelimycin P1.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000337.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000337.json
    evidence type
    DATABASE_ASSERTION
    notes
    RDKit 2026.03.5 product key HEDIIZOUHIVCIU-UNXYVOJBSA-N. MITE marks it as an intermediate; different owner connectivity. The product retains two unspecified tetrahedral centers and three unspecified double bonds. Missing configurations are not filled from the substrate.
    retrieved on
    2026-10-08

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

Causal graph — biosynthesis 2 nodes, 1 edge

Native-reference identity for Streptomyces coelicolor A3(2), taxon 100226/BGC0000038. UniProt names ATCC BAA-471/A3(2)/M145. Matching references do not establish measured expression, a verified assay construct, mature-chain processing, enzyme activity, native assembly or cofactor occupancy. Coelimycin P1 is not equated with P2.

SubjectPredicateObjectNotesEvidence
SCO6279 CDS (AL645882.2) encodes the native protein reference SCO6279 (A3(2) native-reference example) Forward-strand 6936149..6937705; 1557-nt complete CDS including stop, 518 residues.
https://www.ncbi.nlm.nih.gov/nuccore/AL645882.2
https://www.ncbi.nlm.nih.gov/protein/CAC37880.1
https://www.uniprot.org/uniprotkb/Q93S10/entry
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000338.json
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AL645882.2
    evidence type
    DATABASE_ASSERTION
    notes
    GenBank names SCO6279 (alias SC1G7.05) and assigns CAC37880.1, codon_start 1, translation table 11. The inspected sequence is the 6890528..6948414 window, not a new whole-chromosome audit.
    retrieved on
    2026-10-08
    snippet
    /gene="SCO6279"
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAC37880.1
    evidence type
    DATABASE_ASSERTION
    notes
    GenPept identifies A3(2)/taxon 100226. Its coded_by uses AL939127.1; the AL645882.2 CDS independently names the same protein accession.
    retrieved on
    2026-10-08
  • reference
    https://www.uniprot.org/uniprotkb/Q93S10/entry
    evidence type
    CURATOR_INFERENCE
    notes
    Unreviewed entry version 123, sequence version 1. CDS-aware translation, deposited translation, GenPept and UniProt agree over all 518 residues. No specific FUNCTION or CATALYTIC ACTIVITY comment. Computational family, cofactor and localization annotations are not direct enzyme evidence. The deposited diaminobutyrate-pyruvate aminotransferase name and inferred GO functions are not verified native-substrate specificity.
    retrieved on
    2026-10-08
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000338.json
    evidence type
    DATABASE_ASSERTION
    notes
    Active MITE0000338 version 1 maps SCO6279 to Q93S10/CAC37880.1/BGC0000038. Native sequence identity does not independently validate the reaction annotation.
    retrieved on
    2026-10-08

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

Causal graph — biosynthesis 4 nodes, 3 edges

Partial proposed amination graph from MITE0000338 version 1. MITE labels its evidence Inference from genomic data and chemical structure and cites DOI:10.1039/C2SC20410J. Only the paper abstract was inspected; official full-text access returned 403 and retrieval stopped. The distinct DOI:10.1039/C6SC02803A also remains abstract-level after a separate 403. Neither supplies an inspected individual enzyme assay here. These are separate inferred models, not an ordered or complete route to the owner. Chemical and process nodes stay ungrounded; no exact owner-product identity, experimental substrate specificity or P1/P2 equivalence is asserted.

SubjectPredicateObjectNotesEvidence
SCO6279 (A3(2) native-reference example) is inferred by the database to catalyze proposed amination (inferred model) Genomic/chemical inference, not a directly inspected enzyme experiment.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000338.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000338.json
    evidence type
    DATABASE_ASSERTION
    notes
    Active MITE0000338 version 1 maps SCO6279 to Q93S10/CAC37880.1/BGC0000038. Native sequence identity does not independently validate the reaction annotation. No rates, cofactor specificity, assembly or verified native-substrate assay are adopted.
    retrieved on
    2026-10-08
    snippet
    Putatively responsible for amination reaction from compound 3 to compound 4
SCO6279 substrate (MITE model) is the modeled substrate of proposed amination (inferred model) Source model only; no independently verified assay substrate or reaction order.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000338.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000338.json
    evidence type
    DATABASE_ASSERTION
    notes
    RDKit 2026.03.5 substrate key VOQWPAWOYDDQGN-XRNPITFCSA-N. Different connectivity from the owner; no ChEBI/Rhea identifier chosen.
    retrieved on
    2026-10-08
proposed amination (inferred model) is modeled to yield SCO6279 product (MITE model) Inferred intermediate model, not exact coelimycin P1.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000338.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000338.json
    evidence type
    DATABASE_ASSERTION
    notes
    RDKit 2026.03.5 product key SMVMDJWFLAJVIY-GFCCVEGCSA-N. MITE marks it as an intermediate; different owner connectivity. The product retains four unspecified double bonds. It shares connectivity but not the exact key with the separate SCO6272 model substrate; no automatic inter-graph connection is made. Missing configurations are not filled from the substrate.
    retrieved on
    2026-10-08

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

Causal graph — biosynthesis 2 nodes, 1 edge

Native-reference identity for Streptomyces coelicolor A3(2), taxon 100226/BGC0000038. UniProt names ATCC BAA-471/A3(2)/M145. Matching references do not establish measured expression, a verified assay construct, mature-chain processing, enzyme activity, native assembly or cofactor occupancy. Coelimycin P1 is not equated with P2.

SubjectPredicateObjectNotesEvidence
SCO6281 CDS (AL645882.2) encodes the native protein reference SCO6281 (A3(2) native-reference example) Forward-strand 6939907..6941544; 1638-nt complete CDS including stop, 545 residues.
https://www.ncbi.nlm.nih.gov/nuccore/AL645882.2
https://www.ncbi.nlm.nih.gov/protein/CAC37882.1
https://www.uniprot.org/uniprotkb/Q93S08/entry
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000339.json
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AL645882.2
    evidence type
    DATABASE_ASSERTION
    notes
    GenBank names SCO6281 (alias SC1G7.07) and assigns CAC37882.1, codon_start 1, translation table 11. The inspected sequence is the 6890528..6948414 window, not a new whole-chromosome audit.
    retrieved on
    2026-10-08
    snippet
    /gene="SCO6281"
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAC37882.1
    evidence type
    DATABASE_ASSERTION
    notes
    GenPept identifies A3(2)/taxon 100226. Its coded_by uses AL939127.1; the AL645882.2 CDS independently names the same protein accession.
    retrieved on
    2026-10-08
  • reference
    https://www.uniprot.org/uniprotkb/Q93S08/entry
    evidence type
    CURATOR_INFERENCE
    notes
    Unreviewed entry version 118, sequence version 1. CDS-aware translation, deposited translation, GenPept and UniProt agree over all 545 residues. No specific FUNCTION or CATALYTIC ACTIVITY comment. Computational family, cofactor and localization annotations are not direct enzyme evidence. Predicted signal residues 1..35 and cleavage are not experimentally established. MITE0000339 reaction assignment is withheld under https://github.com/CultureBotAI/NaturalProductMech/issues/695: its Monooxygenation label needs reconciliation with modeled C12H19NO3 to C12H17NO3, retaining three oxygens. No catalytic reaction edge is added.
    retrieved on
    2026-10-08
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000339.json
    evidence type
    DATABASE_ASSERTION
    notes
    Active MITE0000339 version 1 maps SCO6281 to Q93S08/CAC37882.1/BGC0000038. Native sequence identity does not independently validate the reaction annotation.
    retrieved on
    2026-10-08

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

Explore across X-Mech

AntibioticMech (coelimycin P1) ↗ MediaIngredientMech (naturalproductmech:mibig-5c75ae209a) ↗ TaxonMech: Streptomyces coelicolor A3(2) (NCBITaxon:100226) ↗ PathwayMech (mibig:BGC0000038) ↗

Provenance

Source conceptSourceVersion
BGC0000038MIBIG5

This page is generated from data/natural_products/unclassified/coelimycin-p1.yaml, which is generated from the committed inventories. Neither is edited by hand.