NaturalProductMech

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β-carotene

CHEBI:17579 EXACT SEEDED antiviralenzyme inhibitor

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 cyclic carotene obtained by dimerisation of all-trans-retinol. A strongly-coloured red-orange pigment abundant in plants and fruit and the most active and important provitamin A carotenoid.

Structure

Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N
SMILESCC1=C(C(CCC1)(C)C)/C=C/C(=C/C=C/C(=C/C=C/C=C(/C=C/C=C(/C=C/C2=C(CCCC2(C)C)C)\C)\C)/C)/C
Stereochemistryfully defined
Cross-referencespubchem:5280489

Filing pathway

Terpenoids — 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 terpene, from MIBiG.

Producer organisms 0

None. The compound has a characterized gene cluster whose host NCBI does not name, which for an uncultured symbiont is the honest state — see the discussion below.

Occurrences 25

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
Mus musculus
NCBITaxon:10090		 CHEBI PMID:19425150
Epicoccum nigrum
NCBITaxon:105696		 LOTUS DOI:10.1042/BJ1060097
Lonicera japonica
NCBITaxon:105884		 LOTUS DOI:10.1042/BJ0510458
Eleutherococcus sessiliflorus
NCBITaxon:105886		 LOTUS DOI:10.1007/BF00576204
Hibiscus syriacus
NCBITaxon:106335		 LOTUS DOI:10.1021/JF60182A030
Rhodomicrobium vannielii
NCBITaxon:1069		 LOTUS DOI:10.3891/ACTA.CHEM.SCAND.18-0643
Ascidia zara
NCBITaxon:107392		 LOTUS DOI:10.1016/0305-0491(85)90174-9
Cladonia gracilis
NCBITaxon:111668		 LOTUS DOI:10.1016/0305-1978(85)90064-X
Cladonia rangiferina
NCBITaxon:111670		 LOTUS DOI:10.1016/0305-1978(85)90064-X
Artemia monica
NCBITaxon:112778		 LOTUS DOI:10.2331/FISHSCI.65.173
Equisetum palustre
NCBITaxon:113538		 LOTUS DOI:10.1016/0305-1978(85)90030-4
Cetrariella delisei
NCBITaxon:115238		 LOTUS DOI:10.1016/0305-1978(87)90002-0
Spirulina
NCBITaxon:1154		 LOTUS DOI:10.1080/01635588809513979
Spirulina
NCBITaxon:1154		 LOTUS DOI:10.1080/01635589309514236
Planktothrix agardhii
NCBITaxon:1160		 LOTUS DOI:10.1016/S0031-9422(00)81568-X
Planktothrix agardhii
NCBITaxon:1160		 LOTUS DOI:10.1016/S0031-9422(00)85703-9
Ianthella flabelliformis
NCBITaxon:1162769		 LOTUS DOI:10.1016/0305-1978(89)90042-2
Medicago saxatilis
NCBITaxon:119392		 LOTUS DOI:10.1016/0305-1978(75)90058-7
Psidium guajava
NCBITaxon:120290		 LOTUS DOI:10.1021/JF980405R
Lilium tenuifolium
NCBITaxon:1218746		 LOTUS DOI:10.1016/S0031-9422(98)00661-X
Murraya euchrestifolia
NCBITaxon:1224773		 LOTUS DOI:10.1016/0031-9422(91)85313-O
Azadirachta indica
NCBITaxon:124943		 LOTUS DOI:10.1016/S0031-9422(00)97156-5
Azadirachta indica
NCBITaxon:124943		 LOTUS DOI:10.1016/S0031-9422(00)97305-9
Navicula delognei
NCBITaxon:1259760		 LOTUS DOI:10.1021/NP50035A010
Euglena sanguinea
NCBITaxon:130315		 LOTUS DOI:10.1016/0305-1978(93)90088-9

Biosynthetic gene clusters 1

AccessionHostLocus evidenceGenome
mibig:BGC0000646 not named CLUSTER_DEMONSTRATED genbank:FJ151553.1

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.

#EnzymeReactionSubstrate → productEvidence
1 CrtY (Pantoea ananas reference)
UniProtKB:P21687		 RHEA:32239 CHEBI:27740 → CHEBI:17579 https://www.uniprot.org/uniprotkb/P21687
2 CrtY (Halobacterium salinarum R1 reference)
UniProtKB:B0R753		 RHEA:32239 CHEBI:27740 → CHEBI:17579 https://www.uniprot.org/uniprotkb/B0R753
3 CrtY (Paracoccus sp. N81106 reference)
UniProtKB:P54974		 RHEA:32239 CHEBI:27740 → CHEBI:17579 https://www.uniprot.org/uniprotkb/P54974
4 CrtY (H. salinarum NRC-1 canonical reference)
UniProtKB:Q9HNE5		 RHEA:32239 CHEBI:27740 → CHEBI:17579 https://www.uniprot.org/uniprotkb/Q9HNE5
5 CrtY (Eho 10 database reference)
UniProtKB:Q01331		 RHEA:32239 CHEBI:27740 → CHEBI:17579 https://www.uniprot.org/uniprotkb/Q01331
6 CarRA (P. blakesleeanus canonical reference)
UniProtKB:Q9P854		 RHEA:32239 CHEBI:27740 → CHEBI:17579 https://www.uniprot.org/uniprotkb/Q9P854
7 CrtL (Synechococcus PCC 7942 reference)
UniProtKB:Q55276		 RHEA:32239 CHEBI:27740 → CHEBI:17579 https://www.uniprot.org/uniprotkb/Q55276
8 CarRP (M. lusitanicus CBS277.49 reference)
UniProtKB:Q9UUQ6		 RHEA:32239 CHEBI:27740 → CHEBI:17579 https://www.uniprot.org/uniprotkb/Q9UUQ6
9 CarRA (B. trispora canonical P143 reference)
UniProtKB:Q67GH9		 RHEA:32239 CHEBI:27740 → CHEBI:17579 https://www.uniprot.org/uniprotkb/Q67GH9

Entry 1: Unnumbered alternative reference example; no common pathway order or physical assembly is invented. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternatives are not a multi-organism pathway or physical assembly. No native-producer, occurrence or BGC grade upgrade. The earlier lycopene step is not adopted; its cached chemical representations require separate review.

Entry 2: Unnumbered alternative reference example; no common pathway order or physical assembly is invented. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternatives are not a multi-organism pathway or physical assembly. No native-producer, occurrence or BGC grade upgrade. The earlier lycopene step is not adopted; its cached chemical representations require separate review.

Entry 3: Unnumbered alternative reference example; no common pathway order or physical assembly is invented. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternatives are not a multi-organism pathway or physical assembly. No native-producer, occurrence or BGC grade upgrade. The earlier lycopene step is not adopted; its cached chemical representations require separate review.

Entry 4: Unnumbered alternative reference example; no common pathway order. Proposed marks qualified reference applicability, not a newly demonstrated assay. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.

Entry 5: Unnumbered alternative reference example; no common pathway order. Proposed marks qualified reference applicability, not a newly demonstrated assay. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.

Entry 6: Unnumbered alternative reference example; no common pathway order. Proposed marks qualified reference applicability, not a newly demonstrated assay. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.

Entry 7: Unnumbered alternative reference example; no common pathway order. Proposed marks qualified reference applicability, not a newly demonstrated assay. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.

Entry 8: Unnumbered alternative reference example; no common pathway order. Proposed marks qualified reference applicability, not a newly demonstrated assay. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.

Entry 9: Unnumbered alternative reference example; no common pathway order. Proposed marks qualified reference applicability, not a newly demonstrated assay. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.

Mechanism & Biosynthesis Overview

PRODUCERS & OCCURRENCE 0 producers (0 causal) 25 cited occurrences BIOSYNTHETIC LOCUS 1 gene cluster 9 curated pathway steps NATURAL PRODUCT β-carotene CHEBI:17579 Terpenoids TARGETS & BIOACTIVITY 0 molecular targets 25 bioactivities · 31 graphs

Causal graph — biosynthesis 4 nodes, 3 edges

Qualified Pantoea ananas reference CrtY terminal-cyclization annotation. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternatives are not a multi-organism pathway or physical assembly. No native-producer, occurrence or BGC grade upgrade. The earlier lycopene step is not adopted; its cached chemical representations require separate review.

SubjectPredicateObjectNotesEvidence
CrtY (Pantoea ananas reference) is_database_proposed_catalyst_of Database-proposed terminal carotene cyclization Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternatives are not a multi-organism pathway or physical assembly. No native-producer, occurrence or BGC grade upgrade. The earlier lycopene step is not adopted; its cached chemical representations require separate review. Native BAA14126.1 and D90087.2 name Pantoea ananatis/taxon553 with no strain qualifier; UniProt names Pantoea ananas/taxon553. UniProt bibliographic aliases ATCC19321/DSM30080/NCPPB800/NRRL B-14773/20D3 are not an independently verified historical assay stock.
https://www.uniprot.org/uniprotkb/P21687
https://www.ncbi.nlm.nih.gov/protein/BAA14126.1
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/P21687
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry83/sequence1, 382aa, protein existence1. The terminal reaction has ECO0000269/PMID20178989 in UniProt; the earlier lycopene step has ECO0000305. RHEA32239 names gamma-carotene and all-trans-beta-carotene (CHEBI27740/CHEBI17579). The cited primary paper was not independently accessible; this remains DATABASE_ASSERTION, not an inspected assay or experimentally verified construct. Rhea identifiers were inspected through UniProt, not a fresh Rhea retrieval. No cofactor, mutant, flux or quantitative stereoselectivity claim is added.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/BAA14126.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Complete crtY reference CDS D90087.2:2422..3570, 1149nt including stop, codon_start1/table11, independently translates to native BAA14126.1 and canonical UniProtP21687, all382aa. Native BAA14126.1 and D90087.2 name Pantoea ananatis/taxon553 with no strain qualifier; UniProt names Pantoea ananas/taxon553. UniProt bibliographic aliases ATCC19321/DSM30080/NCPPB800/NRRL B-14773/20D3 are not an independently verified historical assay stock. Reference equality is not historical assay-stock/construct identity or functional proof. Clipped neighboring CDS annotations in the bounded slice were not adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Database-proposed terminal carotene cyclization Principal carotenoid substrate of the annotated terminal step only; not generic RHEA55620 or the overall two-end lycopene reaction.
https://www.uniprot.org/uniprotkb/P21687
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/P21687
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry83/sequence1, 382aa, protein existence1. The terminal reaction has ECO0000269/PMID20178989 in UniProt; the earlier lycopene step has ECO0000305. RHEA32239 names gamma-carotene and all-trans-beta-carotene (CHEBI27740/CHEBI17579). The cited primary paper was not independently accessible; this remains DATABASE_ASSERTION, not an inspected assay or experimentally verified construct. Rhea identifiers were inspected through UniProt, not a fresh Rhea retrieval. No cofactor, mutant, flux or quantitative stereoselectivity claim is added.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Database-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner, not an assertion of the last metabolite in each source organism. No native-production or measured stereoselectivity upgrade.
https://www.uniprot.org/uniprotkb/P21687
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/P21687
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry83/sequence1, 382aa, protein existence1. The terminal reaction has ECO0000269/PMID20178989 in UniProt; the earlier lycopene step has ECO0000305. RHEA32239 names gamma-carotene and all-trans-beta-carotene (CHEBI27740/CHEBI17579). The cited primary paper was not independently accessible; this remains DATABASE_ASSERTION, not an inspected assay or experimentally verified construct. Rhea identifiers were inspected through UniProt, not a fresh Rhea retrieval. No cofactor, mutant, flux or quantitative stereoselectivity claim is added.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

Qualified Halobacterium salinarum R1 reference CrtY terminal-cyclization annotation. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternatives are not a multi-organism pathway or physical assembly. No native-producer, occurrence or BGC grade upgrade. The earlier lycopene step is not adopted; its cached chemical representations require separate review.

SubjectPredicateObjectNotesEvidence
CrtY (Halobacterium salinarum R1 reference) is_database_proposed_catalyst_of Database-proposed terminal carotene cyclization Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternatives are not a multi-organism pathway or physical assembly. No native-producer, occurrence or BGC grade upgrade. The earlier lycopene step is not adopted; its cached chemical representations require separate review. Native CAP14572.1 and AM774415.1 name Halobacterium salinarum R1, strain DSM671=R1, taxon478009 and BioSample SAMEA3138275. This is the R1/OE_3983R reference, not an assay-stock or NRC-1/Q9HNE5 substitution. Predicted transmembrane helices do not establish an assembly.
https://www.uniprot.org/uniprotkb/B0R753
https://www.ncbi.nlm.nih.gov/protein/CAP14572.1
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/B0R753
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry73/sequence1, 237aa, protein existence1. UniProt attaches ECO0000269/PMID12003928 to the terminal reaction. RHEA32239 names gamma-carotene and all-trans-beta-carotene (CHEBI27740/CHEBI17579). The cited primary paper was not independently accessible; this remains DATABASE_ASSERTION, not an inspected assay or experimentally verified construct. Rhea identifiers were inspected through UniProt, not a fresh Rhea retrieval. No cofactor, mutant, flux or quantitative stereoselectivity claim is added.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAP14572.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Complete crtY reference CDS complement(AM774415.1:1560531..1561244), 714nt including stop, codon_start1/table11, independently translates to native CAP14572.1 and canonical UniProtB0R753, all237aa. GTG initiates as methionine under table11. Native CAP14572.1 and AM774415.1 name Halobacterium salinarum R1, strain DSM671=R1, taxon478009 and BioSample SAMEA3138275. This is the R1/OE_3983R reference, not an assay-stock or NRC-1/Q9HNE5 substitution. Predicted transmembrane helices do not establish an assembly. Reference equality is not historical assay-stock/construct identity or functional proof. Clipped neighboring CDS annotations in the bounded slice were not adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Database-proposed terminal carotene cyclization Principal carotenoid substrate of the annotated terminal step only; not generic RHEA55620 or the overall two-end lycopene reaction.
https://www.uniprot.org/uniprotkb/B0R753
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/B0R753
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry73/sequence1, 237aa, protein existence1. UniProt attaches ECO0000269/PMID12003928 to the terminal reaction. RHEA32239 names gamma-carotene and all-trans-beta-carotene (CHEBI27740/CHEBI17579). The cited primary paper was not independently accessible; this remains DATABASE_ASSERTION, not an inspected assay or experimentally verified construct. Rhea identifiers were inspected through UniProt, not a fresh Rhea retrieval. No cofactor, mutant, flux or quantitative stereoselectivity claim is added.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Database-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner, not an assertion of the last metabolite in each source organism. No native-production or measured stereoselectivity upgrade.
https://www.uniprot.org/uniprotkb/B0R753
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/B0R753
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry73/sequence1, 237aa, protein existence1. UniProt attaches ECO0000269/PMID12003928 to the terminal reaction. RHEA32239 names gamma-carotene and all-trans-beta-carotene (CHEBI27740/CHEBI17579). The cited primary paper was not independently accessible; this remains DATABASE_ASSERTION, not an inspected assay or experimentally verified construct. Rhea identifiers were inspected through UniProt, not a fresh Rhea retrieval. No cofactor, mutant, flux or quantitative stereoselectivity claim is added.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

Qualified Paracoccus sp. N81106 reference CrtY terminal-cyclization annotation. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternatives are not a multi-organism pathway or physical assembly. No native-producer, occurrence or BGC grade upgrade. The earlier lycopene step is not adopted; its cached chemical representations require separate review.

SubjectPredicateObjectNotesEvidence
CrtY (Paracoccus sp. N81106 reference) is_database_proposed_catalyst_of Database-proposed terminal carotene cyclization Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternatives are not a multi-organism pathway or physical assembly. No native-producer, occurrence or BGC grade upgrade. The earlier lycopene step is not adopted; its cached chemical representations require separate review. Both native deposits name Paracoccus sp. N81106/taxon81397 and give MBIC01143 as a distribution alias, with former name Agrobacterium aurantiacum. Their complete CrtY CDSs are nucleotide-identical. The old pAK32 cloning-vector note does not establish an inspected assay construct.
https://www.uniprot.org/uniprotkb/P54974
https://www.ncbi.nlm.nih.gov/protein/BAA09593.1
https://www.ncbi.nlm.nih.gov/protein/BAE47467.1
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/P54974
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry61/sequence1, 386aa, protein existence1. The exact terminal reaction is ECO0000250 by similarity to P21687; literature codes on the broader FUNCTION do not promote this step to a direct assay. RHEA32239 names gamma-carotene and all-trans-beta-carotene (CHEBI27740/CHEBI17579). The cited primary paper was not independently accessible; this remains DATABASE_ASSERTION, not an inspected assay or experimentally verified construct. Rhea identifiers were inspected through UniProt, not a fresh Rhea retrieval. No cofactor, mutant, flux or quantitative stereoselectivity claim is added.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/BAA09593.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Complete crtY reference CDS D58420.2:1349..2509, 1161nt including stop, codon_start1/table11, independently translates to native BAA09593.1 and canonical UniProtP54974, all386aa. GTG initiates as methionine under table11. Both native deposits name Paracoccus sp. N81106/taxon81397 and give MBIC01143 as a distribution alias, with former name Agrobacterium aurantiacum. Their complete CrtY CDSs are nucleotide-identical. The old pAK32 cloning-vector note does not establish an inspected assay construct. Reference equality is not historical assay-stock/construct identity or functional proof. Clipped neighboring CDS annotations in the bounded slice were not adopted.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/BAE47467.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Complete crtY reference CDS AB206672.1:2954..4114, 1161nt including stop, codon_start1/table11, independently translates to native BAE47467.1 and canonical UniProtP54974, all386aa. GTG initiates as methionine under table11. Both native deposits name Paracoccus sp. N81106/taxon81397 and give MBIC01143 as a distribution alias, with former name Agrobacterium aurantiacum. Their complete CrtY CDSs are nucleotide-identical. The old pAK32 cloning-vector note does not establish an inspected assay construct. Reference equality is not historical assay-stock/construct identity or functional proof. Clipped neighboring CDS annotations in the bounded slice were not adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Database-proposed terminal carotene cyclization Principal carotenoid substrate of the annotated terminal step only; not generic RHEA55620 or the overall two-end lycopene reaction.
https://www.uniprot.org/uniprotkb/P54974
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/P54974
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry61/sequence1, 386aa, protein existence1. The exact terminal reaction is ECO0000250 by similarity to P21687; literature codes on the broader FUNCTION do not promote this step to a direct assay. RHEA32239 names gamma-carotene and all-trans-beta-carotene (CHEBI27740/CHEBI17579). The cited primary paper was not independently accessible; this remains DATABASE_ASSERTION, not an inspected assay or experimentally verified construct. Rhea identifiers were inspected through UniProt, not a fresh Rhea retrieval. No cofactor, mutant, flux or quantitative stereoselectivity claim is added.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Database-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner, not an assertion of the last metabolite in each source organism. No native-production or measured stereoselectivity upgrade.
https://www.uniprot.org/uniprotkb/P54974
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/P54974
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry61/sequence1, 386aa, protein existence1. The exact terminal reaction is ECO0000250 by similarity to P21687; literature codes on the broader FUNCTION do not promote this step to a direct assay. RHEA32239 names gamma-carotene and all-trans-beta-carotene (CHEBI27740/CHEBI17579). The cited primary paper was not independently accessible; this remains DATABASE_ASSERTION, not an inspected assay or experimentally verified construct. Rhea identifiers were inspected through UniProt, not a fresh Rhea retrieval. No cofactor, mutant, flux or quantitative stereoselectivity claim is added.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

CrtY (H. salinarum NRC-1 canonical reference): qualified terminal-cyclization annotation. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.

SubjectPredicateObjectNotesEvidence
CrtY (H. salinarum NRC-1 canonical reference) is_database_proposed_catalyst_of Database-proposed terminal carotene cyclization Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.
https://www.uniprot.org/uniprotkb/Q9HNE5
https://www.ncbi.nlm.nih.gov/nuccore/NC_002607.1
https://www.ncbi.nlm.nih.gov/protein/AAG20275.1
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q9HNE5
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry88/sequence2, 237aa. Protein existence3, inferred from homology. Exact terminal reaction ECO:0000250 from B0R753; identical canonical sequence does not transfer R1 strain, assay or evidence grade. UniProt cautions that AAG20275.1 has a truncated N-terminus. RHEA:32239 cross-references CHEBI:27740 and CHEBI:17579. The primary papers were not independently inspected; this remains DATABASE_ASSERTION, not an independently verified assay, construct or stereoselectivity measurement. Rhea was read through UniProt, not independently retrieved.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/NC_002607.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Complete complement(NC_002607.1:1571291..1572004), crtY/VNG_RS08285 with old locus VNG_2137G, is 714nt including stop. GTG initiation under table11 produces canonical Q9HNE5 and WP_012289440.1, all237aa. DNA source is NRC-1; ATCC700922, tax64091, BioSampleSAMN02604216. The WP protein record alone is species tax2242 without strain. PGAP6.10/GCF_000006805.1-RS_2026_04_06 Protein Homology annotation is automated, not experimental initiation or historical assay-stock proof.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AAG20275.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Original ggt/VNG_2137G complement(AE004437.1:1571291..1571779) is 489nt, ATG/table11, yielding162aa identical to canonical residues76..237; its coding DNA equals canonical coding nucleotides226..714 including stop. Preserve UniProt ALT_INIT/truncated-N-terminus caution; this is not a verified162aa assay construct or evidence that the canonical reference is experimentally full-length. The old IEA phytoene-synthase label and clipped Blh neighbor are not adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Database-proposed terminal carotene cyclization Principal carotenoid substrate of the exact annotated terminal reaction, not generic RHEA:55620 or the overall two-end lycopene reaction.
https://www.uniprot.org/uniprotkb/Q9HNE5
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q9HNE5
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry88/sequence2, 237aa. Protein existence3, inferred from homology. Exact terminal reaction ECO:0000250 from B0R753; identical canonical sequence does not transfer R1 strain, assay or evidence grade. UniProt cautions that AAG20275.1 has a truncated N-terminus. RHEA:32239 cross-references CHEBI:27740 and CHEBI:17579. The primary papers were not independently inspected; this remains DATABASE_ASSERTION, not an independently verified assay, construct or stereoselectivity measurement. Rhea was read through UniProt, not independently retrieved.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Database-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner, not the final metabolite in every source organism or an independently measured stereoselective product.
https://www.uniprot.org/uniprotkb/Q9HNE5
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q9HNE5
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry88/sequence2, 237aa. Protein existence3, inferred from homology. Exact terminal reaction ECO:0000250 from B0R753; identical canonical sequence does not transfer R1 strain, assay or evidence grade. UniProt cautions that AAG20275.1 has a truncated N-terminus. RHEA:32239 cross-references CHEBI:27740 and CHEBI:17579. The primary papers were not independently inspected; this remains DATABASE_ASSERTION, not an independently verified assay, construct or stereoselectivity measurement. Rhea was read through UniProt, not independently retrieved.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

CrtY (Eho 10 database reference): qualified terminal-cyclization annotation. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.

SubjectPredicateObjectNotesEvidence
CrtY (Eho 10 database reference) is_database_proposed_catalyst_of Database-proposed terminal carotene cyclization Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.
https://www.uniprot.org/uniprotkb/Q01331
https://www.ncbi.nlm.nih.gov/protein/AAA64980.1
https://www.atcc.org/products/39368
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q01331
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry76/sequence1, 386aa. Protein existence1. Exact terminal reaction ECO:0000250 from P21687. Broader FUNCTION evidence ECO:0000269/PMID:8422926 and ECO:0000305/PMID:7808389 does not upgrade this exact step. RHEA:32239 cross-references CHEBI:27740 and CHEBI:17579. The primary papers were not independently inspected; this remains DATABASE_ASSERTION, not an independently verified assay, construct or stereoselectivity measurement. Rhea was read through UniProt, not independently retrieved.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AAA64980.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Complete M87280.1:6799..7959 CDS,1161nt including stop, GTG/table11, translates to native AAA64980.1 and canonical Q01331, all386aa. Both native source records name Pantoea agglomerans/tax549 and lack strain or culture-collection qualifiers. UniProt instead names Pseudescherichia vulneris/tax566 with bibliographic Eho10/ATCC39368. Keep source scopes distinct; alignment is not assay-stock equality. No clipped CrtX/CrtI, binding site or cofactor claim is adopted.
  • reference
    https://www.atcc.org/products/39368
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    The inspected public ATCC39368 catalogue names Eho 10 as Pseudescherichia vulneris, deposited as Erwinia herbicola, and explicitly cross-references M87280 with its Pantoea agglomerans description. This supports a qualified identity-history mapping, not tax549=tax566 synonymy, independently verified historical assay stock, lot-specific genome or construct identity. The cited2017 taxonomy paper was not independently inspected.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Database-proposed terminal carotene cyclization Principal carotenoid substrate of the exact annotated terminal reaction, not generic RHEA:55620 or the overall two-end lycopene reaction.
https://www.uniprot.org/uniprotkb/Q01331
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q01331
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry76/sequence1, 386aa. Protein existence1. Exact terminal reaction ECO:0000250 from P21687. Broader FUNCTION evidence ECO:0000269/PMID:8422926 and ECO:0000305/PMID:7808389 does not upgrade this exact step. RHEA:32239 cross-references CHEBI:27740 and CHEBI:17579. The primary papers were not independently inspected; this remains DATABASE_ASSERTION, not an independently verified assay, construct or stereoselectivity measurement. Rhea was read through UniProt, not independently retrieved.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Database-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner, not the final metabolite in every source organism or an independently measured stereoselective product.
https://www.uniprot.org/uniprotkb/Q01331
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q01331
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry76/sequence1, 386aa. Protein existence1. Exact terminal reaction ECO:0000250 from P21687. Broader FUNCTION evidence ECO:0000269/PMID:8422926 and ECO:0000305/PMID:7808389 does not upgrade this exact step. RHEA:32239 cross-references CHEBI:27740 and CHEBI:17579. The primary papers were not independently inspected; this remains DATABASE_ASSERTION, not an independently verified assay, construct or stereoselectivity measurement. Rhea was read through UniProt, not independently retrieved.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

CarRA (P. blakesleeanus canonical reference): qualified terminal-cyclization annotation. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.

SubjectPredicateObjectNotesEvidence
CarRA (P. blakesleeanus canonical reference) is_database_proposed_catalyst_of Database-proposed terminal carotene cyclization Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.
https://www.uniprot.org/uniprotkb/Q9P854
https://www.ncbi.nlm.nih.gov/protein/CAB93661.1
https://www.ncbi.nlm.nih.gov/protein/CAB86388.1
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q9P854
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry85/sequence1, 602aa. Protein existence1. Exact terminal reaction ECO:0000269/PMID:11172012 in UniProt. Bifunctional cyclase/phytoene-synthase architecture is not a physical assembly; the separate phytoene reaction is not adopted. Preserve canonical A436 versus alternate CAB86388.1 G436 and secondary accession Q9P877. RHEA:32239 cross-references CHEBI:27740 and CHEBI:17579. The primary papers were not independently inspected; this remains DATABASE_ASSERTION, not an independently verified assay, construct or stereoselectivity measurement. Rhea was read through UniProt, not independently retrieved.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAB93661.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Complete join(AJ278287.1:275..673,939..2348) gives1809nt including stop with a265nt intron, ATG and standard code1 (no explicit transl_table). Translation matches CAB93661.1 and canonical Q9P854, all602aa. Native source is Phycomyces blakesleeanus/tax4837, strainNRRL1555; UniProt uses named-strain tax763407 and lists NRRL1555. This is reference identity, not independent historical-stock, transcript, proteolytic-processing or assay-construct proof.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAB86388.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Alternative complete join(AJ276965.1:470..868,1134..2543),1809nt,265nt intron, ATG/code1, translates to CAB86388.1. Relative to canonical coding DNA, positions 1307 C->G and1629 C->T yield the sole protein change A436->G436, matching the UniProt conflict and secondary Q9P877. Native source is tax4837/NRRL1555. Fuzzy gene/mRNA bounds in the bounded interval do not make the complete CDS partial. Do not adjudicate biological variant versus sequencing error or transfer mutant phenotypes. XP_018294563.1/XM_018438264.1 were not inspected.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Database-proposed terminal carotene cyclization Principal carotenoid substrate of the exact annotated terminal reaction, not generic RHEA:55620 or the overall two-end lycopene reaction.
https://www.uniprot.org/uniprotkb/Q9P854
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q9P854
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry85/sequence1, 602aa. Protein existence1. Exact terminal reaction ECO:0000269/PMID:11172012 in UniProt. Bifunctional cyclase/phytoene-synthase architecture is not a physical assembly; the separate phytoene reaction is not adopted. Preserve canonical A436 versus alternate CAB86388.1 G436 and secondary accession Q9P877. RHEA:32239 cross-references CHEBI:27740 and CHEBI:17579. The primary papers were not independently inspected; this remains DATABASE_ASSERTION, not an independently verified assay, construct or stereoselectivity measurement. Rhea was read through UniProt, not independently retrieved.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Database-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner, not the final metabolite in every source organism or an independently measured stereoselective product.
https://www.uniprot.org/uniprotkb/Q9P854
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q9P854
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry85/sequence1, 602aa. Protein existence1. Exact terminal reaction ECO:0000269/PMID:11172012 in UniProt. Bifunctional cyclase/phytoene-synthase architecture is not a physical assembly; the separate phytoene reaction is not adopted. Preserve canonical A436 versus alternate CAB86388.1 G436 and secondary accession Q9P877. RHEA:32239 cross-references CHEBI:27740 and CHEBI:17579. The primary papers were not independently inspected; this remains DATABASE_ASSERTION, not an independently verified assay, construct or stereoselectivity measurement. Rhea was read through UniProt, not independently retrieved.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

CrtL (Synechococcus PCC 7942 reference): qualified terminal-cyclization annotation. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.

SubjectPredicateObjectNotesEvidence
CrtL (Synechococcus PCC 7942 reference) is_database_proposed_catalyst_of Database-proposed terminal carotene cyclization Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.
https://www.uniprot.org/uniprotkb/Q55276
https://www.ncbi.nlm.nih.gov/protein/CAA52677.1
https://www.ncbi.nlm.nih.gov/protein/ABB58092.1
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q55276
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry129/sequence1, 411aa. Protein existence1. Exact terminal reaction ECO:0000269/PMID:7919981 and PMID:8344419 in UniProt. No independent cofactor, herbicide, neurosporene, secretion or mature-chain claim. RHEA:32239 cross-references CHEBI:27740 and CHEBI:17579. The primary papers were not independently inspected; this remains DATABASE_ASSERTION, not an independently verified assay, construct or stereoselectivity measurement. Rhea was read through UniProt, not independently retrieved.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAA52677.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Historical lcy CDS X74599.1:121..1356 is1236nt including stop; GTG/table11 translation matches CAA52677.1 and canonical Q55276, all411aa. Native source is Synechococcus PCC7942/tax1140. This is sequence-reference correspondence, not independently inspected assay-construct or historical-stock identity.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/ABB58092.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Later complement(CP000100.1:2138585..2139820), locusSynpcc7942_2062 without a gene qualifier, is nucleotide-identical to the historical1236nt CDS. GTG/table11 translation matches ABB58092.1 and canonical411aa. Native PCC7942/tax1140 is consistent; BioSampleSAMN02598254 belongs only to the later genome. Native SignalP prediction1..18 is not proof of secretion or a mature chain. Predicted NAD binding and similarity FAD annotation are not independently adopted. WP_011378296.1/NC_007604.1 were not inspected.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Database-proposed terminal carotene cyclization Principal carotenoid substrate of the exact annotated terminal reaction, not generic RHEA:55620 or the overall two-end lycopene reaction.
https://www.uniprot.org/uniprotkb/Q55276
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q55276
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry129/sequence1, 411aa. Protein existence1. Exact terminal reaction ECO:0000269/PMID:7919981 and PMID:8344419 in UniProt. No independent cofactor, herbicide, neurosporene, secretion or mature-chain claim. RHEA:32239 cross-references CHEBI:27740 and CHEBI:17579. The primary papers were not independently inspected; this remains DATABASE_ASSERTION, not an independently verified assay, construct or stereoselectivity measurement. Rhea was read through UniProt, not independently retrieved.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Database-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner, not the final metabolite in every source organism or an independently measured stereoselective product.
https://www.uniprot.org/uniprotkb/Q55276
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q55276
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry129/sequence1, 411aa. Protein existence1. Exact terminal reaction ECO:0000269/PMID:7919981 and PMID:8344419 in UniProt. No independent cofactor, herbicide, neurosporene, secretion or mature-chain claim. RHEA:32239 cross-references CHEBI:27740 and CHEBI:17579. The primary papers were not independently inspected; this remains DATABASE_ASSERTION, not an independently verified assay, construct or stereoselectivity measurement. Rhea was read through UniProt, not independently retrieved.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

CarRP (M. lusitanicus CBS277.49 reference): qualified terminal-cyclization annotation. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.

SubjectPredicateObjectNotesEvidence
CarRP (M. lusitanicus CBS277.49 reference) is_database_proposed_catalyst_of Database-proposed terminal carotene cyclization Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.
https://www.uniprot.org/uniprotkb/Q9UUQ6
https://www.ncbi.nlm.nih.gov/protein/CAB60272.1
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q9UUQ6
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry96/sequence1, 614aa, protein existence1. Exact terminal reaction RHEA:32239 has ECO:0000269/PMID:10951210 in UniProt, with CHEBI:27740 and CHEBI:17579. Native CBS277.49 reference, not the UniProt-listed MS21/MS35/MS36 mutant proteins. The primary paper was not independently inspected; retain DATABASE_ASSERTION, not an independently verified assay, construct, historical stock or stereoselectivity measurement. Rhea was inspected through UniProt, not independently retrieved. Bifunctional cyclase/phytoene-synthase architecture is not physical assembly; the separate phytoene reaction is not adopted.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAB60272.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Complete carRP join(AJ250827.1:114..515,577..2019),1845nt including stop with61nt intron, ATG/codon_start1 and standard code1 (no explicit transl_table), independently translates to CAB60272.1 and canonical Q9UUQ6, all614aa. Native source is Mucor lusitanicus/tax29924, strainCBS277.49; UniProt uses Mucor circinelloides f. lusitanicus/tax29924 and CARRP. This establishes reference correspondence, not an inspected transcript or assay-stock/construct. UniProt bibliographic ATCC1216b/BCRC32522/NRRL3631 aliases are not independently verified. E78K/MS21,T86I/MS35,D409G/MS36 and their phenotype annotations are not canonical source evidence and are not adopted. Predicted transmembrane segments do not prove assembly or processing. Related AJ238028 was not inspected; no cofactor or induction claim.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Database-proposed terminal carotene cyclization Principal carotenoid substrate of the exact terminal reaction; not generic RHEA:55620 or the overall two-end lycopene reaction.
https://www.uniprot.org/uniprotkb/Q9UUQ6
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q9UUQ6
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry96/sequence1, 614aa, protein existence1. Exact terminal reaction RHEA:32239 has ECO:0000269/PMID:10951210 in UniProt, with CHEBI:27740 and CHEBI:17579. Native CBS277.49 reference, not the UniProt-listed MS21/MS35/MS36 mutant proteins. The primary paper was not independently inspected; retain DATABASE_ASSERTION, not an independently verified assay, construct, historical stock or stereoselectivity measurement. Rhea was inspected through UniProt, not independently retrieved. Bifunctional cyclase/phytoene-synthase architecture is not physical assembly; the separate phytoene reaction is not adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Database-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner, not necessarily the final native metabolite or an independently measured stereoselective product.
https://www.uniprot.org/uniprotkb/Q9UUQ6
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q9UUQ6
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry96/sequence1, 614aa, protein existence1. Exact terminal reaction RHEA:32239 has ECO:0000269/PMID:10951210 in UniProt, with CHEBI:27740 and CHEBI:17579. Native CBS277.49 reference, not the UniProt-listed MS21/MS35/MS36 mutant proteins. The primary paper was not independently inspected; retain DATABASE_ASSERTION, not an independently verified assay, construct, historical stock or stereoselectivity measurement. Rhea was inspected through UniProt, not independently retrieved. Bifunctional cyclase/phytoene-synthase architecture is not physical assembly; the separate phytoene reaction is not adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

CarRA (B. trispora canonical P143 reference): qualified terminal-cyclization annotation. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.

SubjectPredicateObjectNotesEvidence
CarRA (B. trispora canonical P143 reference) is_database_proposed_catalyst_of Database-proposed terminal carotene cyclization Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternative examples are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.
https://www.uniprot.org/uniprotkb/Q67GH9
https://www.ncbi.nlm.nih.gov/protein/AAO46895.1
https://www.ncbi.nlm.nih.gov/protein/AAX20904.1
https://www.ncbi.nlm.nih.gov/protein/AAO46893.1
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q67GH9
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry73/sequence1, 608aa, protein existence1. Exact terminal reaction RHEA:32239 has ECO:0000269/PMID:15345447 in UniProt, with CHEBI:27740 and CHEBI:17579. Canonical P143 reference matches NRRL2457/F921 and ATCC14272 deposits, not L25 S143. The primary paper was not independently inspected; retain DATABASE_ASSERTION, not an independently verified assay, construct, historical stock or stereoselectivity measurement. Rhea was inspected through UniProt, not independently retrieved. Bifunctional cyclase/phytoene-synthase architecture is not physical assembly; the separate phytoene reaction is not adopted.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AAO46895.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Complete carRA join(AY176663.1:2807..3211,3282..4703),1827nt including stop with70nt intron, ATG/codon_start1 and standard code1 (no explicit transl_table), independently translates to AAO46895.1 and canonical Q67GH9, all608aa with P143. Native Blakeslea trispora/tax4850, strainNRRL2457; F921. Native low-producing description is not an independently inspected quantitative phenotype or historical assay-stock/construct identity.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AAX20904.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Complete carRA join(AY884174.1:3048..3452,3523..4944),1827nt,ATG/codon_start1/code1, translates to AAX20904.1 and canonical608aa/P143. Native tax4850,strainATCC14272, with ATCC:14272 cross-reference. Its entire1897nt bounded genomic interval is identical to the NRRL2457 reference interval, not proof of strain, assay stock or construct equivalence. Fuzzy gene/mRNA bounds do not make either complete CDS partial.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AAO46893.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    L25 carRA join(AY176662.1:5690..6094,6165..7586),1827nt,ATG/codon_start1/code1, independently translates to AAO46893.1,608aa. Relative to canonical-reference coding DNA, 427C->T and498C->T yield the sole protein difference P143->S143, matching the UniProt F-744/L25 variant annotation; secondary Q67GI1 is not a second canonical example. Do not transfer L25 assays or overproduction causality to P143, infer engineered origin, or treat the source industrial-strain note as a measured phenotype. PatentP200200202 was not inspected. No induction, cofactor, processing or assembly claim.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Database-proposed terminal carotene cyclization Principal carotenoid substrate of the exact terminal reaction; not generic RHEA:55620 or the overall two-end lycopene reaction.
https://www.uniprot.org/uniprotkb/Q67GH9
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q67GH9
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry73/sequence1, 608aa, protein existence1. Exact terminal reaction RHEA:32239 has ECO:0000269/PMID:15345447 in UniProt, with CHEBI:27740 and CHEBI:17579. Canonical P143 reference matches NRRL2457/F921 and ATCC14272 deposits, not L25 S143. The primary paper was not independently inspected; retain DATABASE_ASSERTION, not an independently verified assay, construct, historical stock or stereoselectivity measurement. Rhea was inspected through UniProt, not independently retrieved. Bifunctional cyclase/phytoene-synthase architecture is not physical assembly; the separate phytoene reaction is not adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Database-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner, not necessarily the final native metabolite or an independently measured stereoselective product.
https://www.uniprot.org/uniprotkb/Q67GH9
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q67GH9
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry73/sequence1, 608aa, protein existence1. Exact terminal reaction RHEA:32239 has ECO:0000269/PMID:15345447 in UniProt, with CHEBI:27740 and CHEBI:17579. Canonical P143 reference matches NRRL2457/F921 and ATCC14272 deposits, not L25 S143. The primary paper was not independently inspected; retain DATABASE_ASSERTION, not an independently verified assay, construct, historical stock or stereoselectivity measurement. Rhea was inspected through UniProt, not independently retrieved. Bifunctional cyclase/phytoene-synthase architecture is not physical assembly; the separate phytoene reaction is not adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

CrtYB (P. rhodozyma canonical E307 reference): Canonical ATCC24230 E307 is a deliberately selected database reference, not the CBS6938 K307 sequence associated with the 1999 functional reference. Neither the historical assay construct nor activity of the 645aa isoform2 is established here. REVIEW_NEEDED concerns assay-to-reference applicability, not whether Q7Z859 resolves. See curator-q7z859-assay-reference. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.

SubjectPredicateObjectNotesEvidence
CrtYB (P. rhodozyma canonical E307 reference) is_database_proposed_catalyst_of Database-proposed terminal carotene cyclization Canonical ATCC24230 E307 is a deliberately selected database reference, not the CBS6938 K307 sequence associated with the 1999 functional reference. Neither the historical assay construct nor activity of the 645aa isoform2 is established here. REVIEW_NEEDED concerns assay-to-reference applicability, not whether Q7Z859 resolves. See curator-q7z859-assay-reference. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.
https://www.uniprot.org/uniprotkb/Q7Z859
https://www.ncbi.nlm.nih.gov/protein/AAO47570.1
https://www.ncbi.nlm.nih.gov/protein/AAY33923.1
https://www.ncbi.nlm.nih.gov/protein/CAB51949.1
https://www.ncbi.nlm.nih.gov/protein/AAO73816.1
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q7Z859
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry85/sequence1, 673aa, protein existence1. Exact RHEA:32239 reaction with CHEBI:27740 and CHEBI:17579 has ECO:0000269/PMID:10589832 in UniProt. Canonical ATCC24230 E307 is a deliberately selected database reference, not the CBS6938 K307 sequence associated with the 1999 functional reference. Neither the historical assay construct nor activity of the 645aa isoform2 is established here. REVIEW_NEEDED concerns assay-to-reference applicability, not whether Q7Z859 resolves. See curator-q7z859-assay-reference. Primary papers were not independently inspected; retain DATABASE_ASSERTION, not an independently verified assay, historical stock, construct or stereoselectivity measurement. Rhea was inspected through UniProt, not independently retrieved. No additional phytoene, cofactor, induction, mutant-phenotype or physical-assembly claim is adopted.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AAO47570.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    ATCC24230 crtYB mRNA AY177204.1:67..2088, complete2022nt CDS including stop, ATG/codon_start1/standardcode1, translates to AAO47570.1 and canonical673aa/E307. Native tax264483 and ATCC:24230 cross-reference. This is reference correspondence, not historical assay-stock or construct identity.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AAY33923.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    ATCC24230 crtYB join(DQ016503.1:1591..1616,1728..1934,2015..2527,2610..2852,2944..3976) gives2022nt, ATG/code1, and canonical673aa/E307. Coding66C>T and1359C>T relative to AY177204.1 are synonymous. Native tax264483/ATCC:24230. No transcript or biological-initiation proof.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAB51949.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    CBS6938 pbs join(AJ133646.1:1109..1134,1246..1452,1533..2045,2128..2370,2461..3493), 2022nt ATG/code1, translates to673aa CAB51949.1. Relative to canonical mRNA, coding919G>A yields sole protein difference E307K, matching the UniProt variant. Native tax264483; do not transfer the CBS6938 functional-reference claim to canonical ATCC24230.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AAO73816.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    ATCC24230 AY174117.1:72..2009 is a complete1938nt mRNA CDS without a gene qualifier, TTG/codon_start1/code1. Its translation matches645aa AAO73816.1 and UniProt isoform2 VSP_041283: canonical residues1..46 replaced by18aa MSPYLFFVLHTTHVCICV. Coding55..1938 equals canonical139..2022. Table1 initiation translation is not experimental non-AUG initiation or isoform2 activity proof. Native tax264483/ATCC:24230.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Database-proposed terminal carotene cyclization Principal substrate of the exact terminal reaction, not the overall two-end lycopene reaction.
https://www.uniprot.org/uniprotkb/Q7Z859
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q7Z859
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry85/sequence1, 673aa, protein existence1. Exact RHEA:32239 reaction with CHEBI:27740 and CHEBI:17579 has ECO:0000269/PMID:10589832 in UniProt. Canonical ATCC24230 E307 is a deliberately selected database reference, not the CBS6938 K307 sequence associated with the 1999 functional reference. Neither the historical assay construct nor activity of the 645aa isoform2 is established here. REVIEW_NEEDED concerns assay-to-reference applicability, not whether Q7Z859 resolves. See curator-q7z859-assay-reference. Primary papers were not independently inspected; retain DATABASE_ASSERTION, not an independently verified assay, historical stock, construct or stereoselectivity measurement. Rhea was inspected through UniProt, not independently retrieved. No additional phytoene, cofactor, induction, mutant-phenotype or physical-assembly claim is adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Database-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner, not necessarily the major or final native metabolite or an independently measured stereoselective product.
https://www.uniprot.org/uniprotkb/Q7Z859
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q7Z859
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry85/sequence1, 673aa, protein existence1. Exact RHEA:32239 reaction with CHEBI:27740 and CHEBI:17579 has ECO:0000269/PMID:10589832 in UniProt. Canonical ATCC24230 E307 is a deliberately selected database reference, not the CBS6938 K307 sequence associated with the 1999 functional reference. Neither the historical assay construct nor activity of the 645aa isoform2 is established here. REVIEW_NEEDED concerns assay-to-reference applicability, not whether Q7Z859 resolves. See curator-q7z859-assay-reference. Primary papers were not independently inspected; retain DATABASE_ASSERTION, not an independently verified assay, historical stock, construct or stereoselectivity measurement. Rhea was inspected through UniProt, not independently retrieved. No additional phytoene, cofactor, induction, mutant-phenotype or physical-assembly claim is adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

AL-2 (N. crassa canonical 602aa reference): Canonical 602aa is a deliberately selected database reference, not the historical partial 601aa model. UniProt reports preferential single-end cyclization: this terminal reaction does not establish beta-carotene as the major native product. REVIEW_NEEDED concerns assay-to-model applicability, not whether P37295 resolves. See curator-p37295-assay-reference. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.

SubjectPredicateObjectNotesEvidence
AL-2 (N. crassa canonical 602aa reference) is_database_proposed_catalyst_of Database-proposed terminal carotene cyclization Canonical 602aa is a deliberately selected database reference, not the historical partial 601aa model. UniProt reports preferential single-end cyclization: this terminal reaction does not establish beta-carotene as the major native product. REVIEW_NEEDED concerns assay-to-model applicability, not whether P37295 resolves. See curator-p37295-assay-reference. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.
https://www.uniprot.org/uniprotkb/P37295
https://www.ncbi.nlm.nih.gov/protein/EAA36489.3
https://www.ncbi.nlm.nih.gov/protein/CAE76609.1
https://www.ncbi.nlm.nih.gov/protein/AAA19428.1
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/P37295
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry138/sequence1, 602aa, protein existence1. Exact RHEA:32239 reaction with CHEBI:27740 and CHEBI:17579 has ECO:0000269/PMID:11862485 and PMID:16928467 in UniProt. Canonical 602aa is a deliberately selected database reference, not the historical partial 601aa model. UniProt reports preferential single-end cyclization: this terminal reaction does not establish beta-carotene as the major native product. REVIEW_NEEDED concerns assay-to-model applicability, not whether P37295 resolves. See curator-p37295-assay-reference. Primary papers were not independently inspected; retain DATABASE_ASSERTION, not an independently verified assay, historical stock, construct or stereoselectivity measurement. Rhea was inspected through UniProt, not independently retrieved. No additional phytoene, cofactor, induction, mutant-phenotype or physical-assembly claim is adopted.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/EAA36489.3
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    OR74A al-2/NCU00585 complement(join(CM002236.1:7921219..7922080,7922138..7923064,7923136..7923155)), 1809nt ATG/codon_start1/standardcode1 including stop, translates to canonical602aa. Native tax367110, BioProjectPRJNA13841/BioSampleSAMN02953583. Entry stock aliases are not independently verified catalogue or assay-stock equality.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAE76609.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    B22I21.230 complement(join(BX842641.1:69740..70601,70659..71585,71657..71676)), 1809nt ATG/code1, translates to canonical602aa. Source tax5141 has no strain qualifier; OR74A appears in record comments. Its1937nt interval equals the later OR74A interval.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AAA19428.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Partial al-2 join(L27652.1:<1362..1379,1453..2379,2437..3298) annotates1807nt before codon_start2 offset. Standard-code translation yields601aa, CTTMLF replacing canonical MYDYAFV with the remaining595aa identical. All three1937nt genomic intervals are identical after orientation. First coding exon18 versus20nt, first intron73 versus71nt and codon offset distinguish the models, not demonstrated strain variation or biological splicing. Native tax5141 lacks a strain qualifier; no correct-transcript or assay-model proof. XP_965725.3/XM_960632.3 were not inspected.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Database-proposed terminal carotene cyclization Principal substrate of the exact terminal reaction, not the overall two-end lycopene reaction.
https://www.uniprot.org/uniprotkb/P37295
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/P37295
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry138/sequence1, 602aa, protein existence1. Exact RHEA:32239 reaction with CHEBI:27740 and CHEBI:17579 has ECO:0000269/PMID:11862485 and PMID:16928467 in UniProt. Canonical 602aa is a deliberately selected database reference, not the historical partial 601aa model. UniProt reports preferential single-end cyclization: this terminal reaction does not establish beta-carotene as the major native product. REVIEW_NEEDED concerns assay-to-model applicability, not whether P37295 resolves. See curator-p37295-assay-reference. Primary papers were not independently inspected; retain DATABASE_ASSERTION, not an independently verified assay, historical stock, construct or stereoselectivity measurement. Rhea was inspected through UniProt, not independently retrieved. No additional phytoene, cofactor, induction, mutant-phenotype or physical-assembly claim is adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Database-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner, not necessarily the major or final native metabolite or an independently measured stereoselective product.
https://www.uniprot.org/uniprotkb/P37295
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/P37295
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry138/sequence1, 602aa, protein existence1. Exact RHEA:32239 reaction with CHEBI:27740 and CHEBI:17579 has ECO:0000269/PMID:11862485 and PMID:16928467 in UniProt. Canonical 602aa is a deliberately selected database reference, not the historical partial 601aa model. UniProt reports preferential single-end cyclization: this terminal reaction does not establish beta-carotene as the major native product. REVIEW_NEEDED concerns assay-to-model applicability, not whether P37295 resolves. See curator-p37295-assay-reference. Primary papers were not independently inspected; retain DATABASE_ASSERTION, not an independently verified assay, historical stock, construct or stereoselectivity measurement. Rhea was inspected through UniProt, not independently retrieved. No additional phytoene, cofactor, induction, mutant-phenotype or physical-assembly claim is adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

LCY1 (C. annuum canonical 498aa reference): Canonical 498aa is a deliberately selected database precursor reference. The Lamuyo deposit has T146A/N152K sequence conflicts, and the 2010 functional construct was not inspected. Predicted transit residues1..79 and chain80..498 do not prove processing or a mature assay construct. REVIEW_NEEDED concerns assay-to-reference applicability, not whether Q43415 resolves. See curator-q43415-assay-reference. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.

SubjectPredicateObjectNotesEvidence
LCY1 (C. annuum canonical 498aa reference) is_database_proposed_catalyst_of Database-proposed terminal carotene cyclization Canonical 498aa is a deliberately selected database precursor reference. The Lamuyo deposit has T146A/N152K sequence conflicts, and the 2010 functional construct was not inspected. Predicted transit residues1..79 and chain80..498 do not prove processing or a mature assay construct. REVIEW_NEEDED concerns assay-to-reference applicability, not whether Q43415 resolves. See curator-q43415-assay-reference. Separate organism-specific database example of terminal gamma-carotene cyclization, not the uncultured-organism BGC0000646/FJ151553.1 enzyme. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene step remains excluded because its cached chemical representations require separate review.
https://www.uniprot.org/uniprotkb/Q43415
https://www.ncbi.nlm.nih.gov/protein/ADH04271.1
https://www.ncbi.nlm.nih.gov/protein/CAA60119.1
https://www.ncbi.nlm.nih.gov/protein/PHT80580.1
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q43415
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry118/sequence2, 498aa, protein existence1. Exact RHEA:32239 reaction with CHEBI:27740 and CHEBI:17579 has ECO:0000269/PMID:20460582 in UniProt. Canonical 498aa is a deliberately selected database precursor reference. The Lamuyo deposit has T146A/N152K sequence conflicts, and the 2010 functional construct was not inspected. Predicted transit residues1..79 and chain80..498 do not prove processing or a mature assay construct. REVIEW_NEEDED concerns assay-to-reference applicability, not whether Q43415 resolves. See curator-q43415-assay-reference. Primary papers were not independently inspected; retain DATABASE_ASSERTION, not an independently verified assay, historical stock, construct or stereoselectivity measurement. Rhea was inspected through UniProt, not independently retrieved. No additional phytoene, cofactor, induction, mutant-phenotype or physical-assembly claim is adopted.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/ADH04271.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Valencia Lcyb GU085266.1:1..1497, single-exon1497nt ATG/codon_start1/standardcode1 including stop, translates to canonical498aa. Oriole, Orange Grande, NuMex Sunset, Fogo, Dove and Canary deposits ADH04272.1..ADH04277.1/GU085267.1..GU085272.1 have identical coding sequences and translations. Native tax4072, not independent cultivar assay-stock or functional-construct equality.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAA60119.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Lamuyo crtL mRNA X86221.1:266..1762,1497nt ATG/codon_start1/code1, translates to its own498aa deposit. Relative to Valencia coding DNA,436A>G and456T>A yield T146A/N152K, matching UniProt sequence conflicts. Do not relabel these as demonstrated natural variants or equate the1995 Lamuyo functional reference with canonical Q43415.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/PHT80580.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    CM334 locusT459_13595 AYRZ02000005.1:656813..658309,1497nt ATG/codon_start1/code1, translates to canonical498aa;807T>G is synonymous relative to Valencia. Native tax4072, BioProjectPRJNA223222/BioSampleSAMN02981571. This does not establish the2010 functional assay construct, precursor cleavage, plastid localization or mutant phenotypes. RefSeq and Zunla-1 references were not inspected.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Database-proposed terminal carotene cyclization Principal substrate of the exact terminal reaction, not the overall two-end lycopene reaction.
https://www.uniprot.org/uniprotkb/Q43415
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q43415
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry118/sequence2, 498aa, protein existence1. Exact RHEA:32239 reaction with CHEBI:27740 and CHEBI:17579 has ECO:0000269/PMID:20460582 in UniProt. Canonical 498aa is a deliberately selected database precursor reference. The Lamuyo deposit has T146A/N152K sequence conflicts, and the 2010 functional construct was not inspected. Predicted transit residues1..79 and chain80..498 do not prove processing or a mature assay construct. REVIEW_NEEDED concerns assay-to-reference applicability, not whether Q43415 resolves. See curator-q43415-assay-reference. Primary papers were not independently inspected; retain DATABASE_ASSERTION, not an independently verified assay, historical stock, construct or stereoselectivity measurement. Rhea was inspected through UniProt, not independently retrieved. No additional phytoene, cofactor, induction, mutant-phenotype or physical-assembly claim is adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Database-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner, not necessarily the major or final native metabolite or an independently measured stereoselective product.
https://www.uniprot.org/uniprotkb/Q43415
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q43415
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry118/sequence2, 498aa, protein existence1. Exact RHEA:32239 reaction with CHEBI:27740 and CHEBI:17579 has ECO:0000269/PMID:20460582 in UniProt. Canonical 498aa is a deliberately selected database precursor reference. The Lamuyo deposit has T146A/N152K sequence conflicts, and the 2010 functional construct was not inspected. Predicted transit residues1..79 and chain80..498 do not prove processing or a mature assay construct. REVIEW_NEEDED concerns assay-to-reference applicability, not whether Q43415 resolves. See curator-q43415-assay-reference. Primary papers were not independently inspected; retain DATABASE_ASSERTION, not an independently verified assay, historical stock, construct or stereoselectivity measurement. Rhea was inspected through UniProt, not independently retrieved. No additional phytoene, cofactor, induction, mutant-phenotype or physical-assembly claim is adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

UMAG_06287 (M. maydis reference; similarity assignment): Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Seven transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.

SubjectPredicateObjectNotesEvidence
UMAG_06287 (M. maydis reference; similarity assignment) is_database_similarity_proposed_catalyst_of Similarity-proposed terminal carotene cyclization Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Seven transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.
https://www.uniprot.org/uniprotkb/Q4P0S6
https://www.ncbi.nlm.nih.gov/protein/KIS70197.1
https://www.ncbi.nlm.nih.gov/nuccore/CM003143.1?from=638652&to=640724
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q4P0S6
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry96/sequence1, 690aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Seven transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/KIS70197.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Native UMAG_06287 complement(CM003143.1:638652..640724) is a complete single-exon 2073nt CDS including stop, ATG/codon_start1/standardcode1. Independent translation equals KIS70197.1 and canonical 690aa Q4P0S6. Native tax5270, BioProjectPRJNA1446/BioSampleSAMN02900459. Native strain521 and culture_collection FGSC:9021 identify the deposited reference, not independent culture-catalogue, assay-stock or DSM14603/UM521 alias equivalence. TGA stop; the complete CDS is distinct from the fuzzy bounded gene/mRNA ends. Native product is hypothetical protein and the method is conceptual translation. RefSeq XP_011388293.1/XM_011389991.1 was not inspected. Reference correspondence is CURATOR_INFERENCE, not native expression, exact assay construct or function proof; native CDD sites are not adopted.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/CM003143.1?from=638652&to=640724
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected bounded native coding interval; Native UMAG_06287 complement(CM003143.1:638652..640724) is a complete single-exon 2073nt CDS including stop, ATG/codon_start1/standardcode1. Independent translation equals KIS70197.1 and canonical 690aa Q4P0S6. Native tax5270, BioProjectPRJNA1446/BioSampleSAMN02900459. Native strain521 and culture_collection FGSC:9021 identify the deposited reference, not independent culture-catalogue, assay-stock or DSM14603/UM521 alias equivalence. TGA stop; the complete CDS is distinct from the fuzzy bounded gene/mRNA ends. Native product is hypothetical protein and the method is conceptual translation. RefSeq XP_011388293.1/XM_011389991.1 was not inspected. Reference correspondence is CURATOR_INFERENCE, not native expression, exact assay construct or function proof; native CDD sites are not adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Similarity-proposed terminal carotene cyclization Substrate of this similarity-assigned terminal reaction, not an independently assayed substrate or the earlier lycopene reaction.
https://www.uniprot.org/uniprotkb/Q4P0S6
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q4P0S6
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry96/sequence1, 690aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Seven transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Similarity-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner in the similarity-based annotation, not proof of a measured product, native production or major-product distribution.
https://www.uniprot.org/uniprotkb/Q4P0S6
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q4P0S6
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry96/sequence1, 690aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Seven transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

sr13176 (S. reilianum reference; similarity assignment): Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Seven transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.

SubjectPredicateObjectNotesEvidence
sr13176 (S. reilianum reference; similarity assignment) is_database_similarity_proposed_catalyst_of Similarity-proposed terminal carotene cyclization Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Seven transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.
https://www.uniprot.org/uniprotkb/E6ZZ11
https://www.ncbi.nlm.nih.gov/protein/CBQ72468.1
https://www.ncbi.nlm.nih.gov/nuccore/FQ311463.1?from=544860&to=546917
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/E6ZZ11
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry53/sequence1, 685aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Seven transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CBQ72468.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Native sr13176 complement(FQ311463.1:544860..546917) is a complete single-exon 2058nt CDS including stop, ATG/codon_start1/standardcode1. Independent translation equals CBQ72468.1 and canonical 685aa E6ZZ11. Native tax999809, BioProjectPRJNA64587/BioSampleSAMEA3138400. SRZ2 occurs in the organism name and named-strain taxon, but no separate strain or culture_collection qualifier is present. TAG stop; gene/CDS/exon locations agree. Native product is related to Phytoene synthase, not an independent cyclase experiment. Automated geranylgeranyl-diphosphate-synthase GO annotation is not adopted. Reference correspondence is CURATOR_INFERENCE, not native expression, exact assay construct or function proof; native CDD sites are not adopted.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/FQ311463.1?from=544860&to=546917
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected bounded native coding interval; Native sr13176 complement(FQ311463.1:544860..546917) is a complete single-exon 2058nt CDS including stop, ATG/codon_start1/standardcode1. Independent translation equals CBQ72468.1 and canonical 685aa E6ZZ11. Native tax999809, BioProjectPRJNA64587/BioSampleSAMEA3138400. SRZ2 occurs in the organism name and named-strain taxon, but no separate strain or culture_collection qualifier is present. TAG stop; gene/CDS/exon locations agree. Native product is related to Phytoene synthase, not an independent cyclase experiment. Automated geranylgeranyl-diphosphate-synthase GO annotation is not adopted. Reference correspondence is CURATOR_INFERENCE, not native expression, exact assay construct or function proof; native CDD sites are not adopted.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Similarity-proposed terminal carotene cyclization Substrate of this similarity-assigned terminal reaction, not an independently assayed substrate or the earlier lycopene reaction.
https://www.uniprot.org/uniprotkb/E6ZZ11
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/E6ZZ11
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry53/sequence1, 685aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Seven transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Similarity-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner in the similarity-based annotation, not proof of a measured product, native production or major-product distribution.
https://www.uniprot.org/uniprotkb/E6ZZ11
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/E6ZZ11
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry53/sequence1, 685aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Seven transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

Pa_1_15240 (P. anserina reference; similarity assignment): Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.

SubjectPredicateObjectNotesEvidence
Pa_1_15240 (P. anserina reference; similarity assignment) is_database_similarity_proposed_catalyst_of Similarity-proposed terminal carotene cyclization Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.
https://www.uniprot.org/uniprotkb/B2ATB0
https://www.ncbi.nlm.nih.gov/protein/CAP67633.1
https://www.ncbi.nlm.nih.gov/nuccore/CU633899.1?from=349996&to=351901
https://www.ncbi.nlm.nih.gov/protein/CDP23892.1
https://www.ncbi.nlm.nih.gov/nuccore/FO904936.1?from=5388605&to=5390510
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/B2ATB0
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry77/sequence1, 593aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAP67633.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Exact native protein CAP67633.1; CU633899.1 CDS exon coordinates in genomic order: 349996..350827, 350882..351808, 351879..351901. Pa_1_15240/PODANS_1_15240, native tax515849, BioProjectPRJNA12954; no BioSample. Both complete three-exon minus-strand1782nt ATG/code1 CDSs translate exactly to593aa native proteins and canonicalUniProt. Bounded1906nt intervals and coding sequences are identical; introns70/54nt in transcription order. Exact terminal function is ECO0000250 from P37295;protein existence3. Native annotation/PaAl2 product label and predictedCDS note are not an assay,transcript or stock proof. Native source S mat+ preserved; CU has explicitstrain,FO has no separate strain qualifier or locus_tag. No independent ATCCMYA4624/DSM980/FGSC10383 catalogue mapping. No Neurospora model/assay/preferential phenotype transfer,production,phytoene,cofactor,processing or assembly claim. Automated GO squalene-synthase/geranylgeranyl-diphosphate-synthase and CDDsite annotations not adopted. Genome DOI10.1186/gb-2008-9-5-r77 was tool-inaccessible; no alternate copy or primary claim. DOI10.1534/genetics.113.159988 and RefSeqXP_001906962.1/XM_001906927.1 remain uninspected.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/CU633899.1?from=349996&to=351901
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected bounded native coding interval. Exact native protein CAP67633.1; CU633899.1 CDS exon coordinates in genomic order: 349996..350827, 350882..351808, 351879..351901. Pa_1_15240/PODANS_1_15240, native tax515849, BioProjectPRJNA12954; no BioSample. Both complete three-exon minus-strand1782nt ATG/code1 CDSs translate exactly to593aa native proteins and canonicalUniProt. Bounded1906nt intervals and coding sequences are identical; introns70/54nt in transcription order. Exact terminal function is ECO0000250 from P37295;protein existence3. Native annotation/PaAl2 product label and predictedCDS note are not an assay,transcript or stock proof. Native source S mat+ preserved; CU has explicitstrain,FO has no separate strain qualifier or locus_tag. No independent ATCCMYA4624/DSM980/FGSC10383 catalogue mapping. No Neurospora model/assay/preferential phenotype transfer,production,phytoene,cofactor,processing or assembly claim. Automated GO squalene-synthase/geranylgeranyl-diphosphate-synthase and CDDsite annotations not adopted. Genome DOI10.1186/gb-2008-9-5-r77 was tool-inaccessible; no alternate copy or primary claim. DOI10.1534/genetics.113.159988 and RefSeqXP_001906962.1/XM_001906927.1 remain uninspected.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CDP23892.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Exact native protein CDP23892.1; FO904936.1 CDS exon coordinates in genomic order: 5388605..5389436, 5389491..5390417, 5390488..5390510. Pa_1_15240/PODANS_1_15240, native tax515849, BioProjectPRJNA12954; no BioSample. Both complete three-exon minus-strand1782nt ATG/code1 CDSs translate exactly to593aa native proteins and canonicalUniProt. Bounded1906nt intervals and coding sequences are identical; introns70/54nt in transcription order. Exact terminal function is ECO0000250 from P37295;protein existence3. Native annotation/PaAl2 product label and predictedCDS note are not an assay,transcript or stock proof. Native source S mat+ preserved; CU has explicitstrain,FO has no separate strain qualifier or locus_tag. No independent ATCCMYA4624/DSM980/FGSC10383 catalogue mapping. No Neurospora model/assay/preferential phenotype transfer,production,phytoene,cofactor,processing or assembly claim. Automated GO squalene-synthase/geranylgeranyl-diphosphate-synthase and CDDsite annotations not adopted. Genome DOI10.1186/gb-2008-9-5-r77 was tool-inaccessible; no alternate copy or primary claim. DOI10.1534/genetics.113.159988 and RefSeqXP_001906962.1/XM_001906927.1 remain uninspected.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/FO904936.1?from=5388605&to=5390510
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected bounded native coding interval. Exact native protein CDP23892.1; FO904936.1 CDS exon coordinates in genomic order: 5388605..5389436, 5389491..5390417, 5390488..5390510. Pa_1_15240/PODANS_1_15240, native tax515849, BioProjectPRJNA12954; no BioSample. Both complete three-exon minus-strand1782nt ATG/code1 CDSs translate exactly to593aa native proteins and canonicalUniProt. Bounded1906nt intervals and coding sequences are identical; introns70/54nt in transcription order. Exact terminal function is ECO0000250 from P37295;protein existence3. Native annotation/PaAl2 product label and predictedCDS note are not an assay,transcript or stock proof. Native source S mat+ preserved; CU has explicitstrain,FO has no separate strain qualifier or locus_tag. No independent ATCCMYA4624/DSM980/FGSC10383 catalogue mapping. No Neurospora model/assay/preferential phenotype transfer,production,phytoene,cofactor,processing or assembly claim. Automated GO squalene-synthase/geranylgeranyl-diphosphate-synthase and CDDsite annotations not adopted. Genome DOI10.1186/gb-2008-9-5-r77 was tool-inaccessible; no alternate copy or primary claim. DOI10.1534/genetics.113.159988 and RefSeqXP_001906962.1/XM_001906927.1 remain uninspected.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Similarity-proposed terminal carotene cyclization Substrate of this similarity-assigned terminal reaction, not an independently assayed substrate or the earlier lycopene reaction.
https://www.uniprot.org/uniprotkb/B2ATB0
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/B2ATB0
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry77/sequence1, 593aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Similarity-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner in the similarity-based annotation, not proof of a measured product, native production or major-product distribution.
https://www.uniprot.org/uniprotkb/B2ATB0
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/B2ATB0
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry77/sequence1, 593aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

PTRG_07366 (P. tritici-repentis reference; similarity assignment): Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.

SubjectPredicateObjectNotesEvidence
PTRG_07366 (P. tritici-repentis reference; similarity assignment) is_database_similarity_proposed_catalyst_of Similarity-proposed terminal carotene cyclization Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.
https://www.uniprot.org/uniprotkb/B2WAQ3
https://www.ncbi.nlm.nih.gov/protein/EDU50285.1
https://www.ncbi.nlm.nih.gov/nuccore/DS231621.1?from=1486336&to=1488255
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/B2WAQ3
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry70/sequence1, 583aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/EDU50285.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Exact native protein EDU50285.1; DS231621.1 CDS exon coordinates in genomic order: 1486336..1486358, 1486415..1486514, 1486576..1486943, 1486995..1488255. Native PTRG_07366, tax426418; strain=Pt-1C-BFP; bioproject=PRJNA18815; biosample=SAMN02953676; Complete four-exon plus-strand1752nt ATG/code1 CDS includingTAAstop independently translates to583aa native and canonicalUniProt. Bounded1920nt interval has56/61/51nt introns. Fuzzy bounded gene/mRNA ends do not make the CDS partial. Exact terminal function is ECO0000250 from P37295;protein existence3. Native phytoene-synthase product and conceptual translation are not a cyclase assay or native expression proof. Reference strain correspondence is not experimental stock/construct equality. No Neurospora model/assay/preferential phenotype transfer,production,phytoene,cofactor,processing or assembly claim. SevenTM segments predicted;automated GO squalene-synthase/geranylgeranyl-diphosphate-synthase and CDDsite annotations not adopted. RefSeqXP_001937698.1/XM_001937663.2 not inspected. Genome DOI10.1534/g3.112.004044/PMID23316438 unattempted/uninspected. Prior primary-access holds retained,not retried.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/DS231621.1?from=1486336&to=1488255
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected bounded native coding interval. Exact native protein EDU50285.1; DS231621.1 CDS exon coordinates in genomic order: 1486336..1486358, 1486415..1486514, 1486576..1486943, 1486995..1488255. Native PTRG_07366, tax426418; strain=Pt-1C-BFP; bioproject=PRJNA18815; biosample=SAMN02953676; Complete four-exon plus-strand1752nt ATG/code1 CDS includingTAAstop independently translates to583aa native and canonicalUniProt. Bounded1920nt interval has56/61/51nt introns. Fuzzy bounded gene/mRNA ends do not make the CDS partial. Exact terminal function is ECO0000250 from P37295;protein existence3. Native phytoene-synthase product and conceptual translation are not a cyclase assay or native expression proof. Reference strain correspondence is not experimental stock/construct equality. No Neurospora model/assay/preferential phenotype transfer,production,phytoene,cofactor,processing or assembly claim. SevenTM segments predicted;automated GO squalene-synthase/geranylgeranyl-diphosphate-synthase and CDDsite annotations not adopted. RefSeqXP_001937698.1/XM_001937663.2 not inspected. Genome DOI10.1534/g3.112.004044/PMID23316438 unattempted/uninspected. Prior primary-access holds retained,not retried.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Similarity-proposed terminal carotene cyclization Substrate of this similarity-assigned terminal reaction, not an independently assayed substrate or the earlier lycopene reaction.
https://www.uniprot.org/uniprotkb/B2WAQ3
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/B2WAQ3
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry70/sequence1, 583aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Similarity-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner in the similarity-based annotation, not proof of a measured product, native production or major-product distribution.
https://www.uniprot.org/uniprotkb/B2WAQ3
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/B2WAQ3
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry70/sequence1, 583aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

AO090020000159 (A. oryzae reference; similarity assignment): Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.

SubjectPredicateObjectNotesEvidence
AO090020000159 (A. oryzae reference; similarity assignment) is_database_similarity_proposed_catalyst_of Similarity-proposed terminal carotene cyclization Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.
https://www.uniprot.org/uniprotkb/Q2U4X9
https://www.ncbi.nlm.nih.gov/protein/BAE63386.1
https://www.ncbi.nlm.nih.gov/nuccore/AP007167.1?from=408098&to=410119
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q2U4X9
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry89/sequence1, 587aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/BAE63386.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Exact native protein BAE63386.1; AP007167.1 CDS exon coordinates in genomic order: 408098..408926, 408988..409278, 409331..409504, 409553..409899, 409949..410048, 410097..410119. Native AO090020000159, tax510516; strain=RIB 40; bioproject=PRJNA20809; biosample=SAMD00067075; old_locus=AO070327000109; Actual native complete six-exon minus-strand1764nt ATG/code1 CDS includingTAGstop independently translates to587aa native and canonicalUniProt. Bounded2022nt interval has48/49/48/52/61nt introns in transcription order. Gene usesorder while CDSusesjoin over the same parts;this is not experimental splicing proof. Exact terminal function is ECO0000250 from P37295;protein existence3. Native unnamed/predicted annotation is not a cyclase assay or native expression proof. Native coded_by AP007167.1 is independently verified;UniProt EMBLxref BA000054 chromosome coordinates/contig correspondence uninspected,not assumed equal or declared erroneous. RIB40 reference correspondence is not ATCC42149 catalogue/experimental-stock equality. No Neurospora model/assay/preferential phenotype transfer,production,phytoene,cofactor,processing or assembly claim. SevenTM segments predicted;automated GO geranylgeranyl-diphosphate-synthase/CDDsite annotations not adopted. RefSeqXP_001824519.1/XM_001824467.1 and BA000054 mapping not inspected. Genome DOI10.1038/nature04300/PMID16372010 not inspected in this audit;prior access dispositions retained,not retried.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AP007167.1?from=408098&to=410119
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected bounded native coding interval. Exact native protein BAE63386.1; AP007167.1 CDS exon coordinates in genomic order: 408098..408926, 408988..409278, 409331..409504, 409553..409899, 409949..410048, 410097..410119. Native AO090020000159, tax510516; strain=RIB 40; bioproject=PRJNA20809; biosample=SAMD00067075; old_locus=AO070327000109; Actual native complete six-exon minus-strand1764nt ATG/code1 CDS includingTAGstop independently translates to587aa native and canonicalUniProt. Bounded2022nt interval has48/49/48/52/61nt introns in transcription order. Gene usesorder while CDSusesjoin over the same parts;this is not experimental splicing proof. Exact terminal function is ECO0000250 from P37295;protein existence3. Native unnamed/predicted annotation is not a cyclase assay or native expression proof. Native coded_by AP007167.1 is independently verified;UniProt EMBLxref BA000054 chromosome coordinates/contig correspondence uninspected,not assumed equal or declared erroneous. RIB40 reference correspondence is not ATCC42149 catalogue/experimental-stock equality. No Neurospora model/assay/preferential phenotype transfer,production,phytoene,cofactor,processing or assembly claim. SevenTM segments predicted;automated GO geranylgeranyl-diphosphate-synthase/CDDsite annotations not adopted. RefSeqXP_001824519.1/XM_001824467.1 and BA000054 mapping not inspected. Genome DOI10.1038/nature04300/PMID16372010 not inspected in this audit;prior access dispositions retained,not retried.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Similarity-proposed terminal carotene cyclization Substrate of this similarity-assigned terminal reaction, not an independently assayed substrate or the earlier lycopene reaction.
https://www.uniprot.org/uniprotkb/Q2U4X9
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q2U4X9
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry89/sequence1, 587aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Similarity-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner in the similarity-based annotation, not proof of a measured product, native production or major-product distribution.
https://www.uniprot.org/uniprotkb/Q2U4X9
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q2U4X9
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry89/sequence1, 587aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

Lema_P114090.1 (L. maculans reference; similarity assignment): Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.

SubjectPredicateObjectNotesEvidence
Lema_P114090.1 (L. maculans reference; similarity assignment) is_database_similarity_proposed_catalyst_of Similarity-proposed terminal carotene cyclization Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.
https://www.uniprot.org/uniprotkb/E4ZUB5
https://www.ncbi.nlm.nih.gov/protein/CBX94994.1
https://www.ncbi.nlm.nih.gov/nuccore/FP929126.1?from=485243&to=487140
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/E4ZUB5
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry63/sequence1, 581aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CBX94994.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Exact native protein CBX94994.1; FP929126.1 CDS exon coordinates in genomic order: 485243..486497, 486546..486913, 486959..487058, 487118..487140. Native LEMA_P114090.1, tax985895; isolate=v23.1.3; bioproject=PRJNA63129; uniprot_locus=Lema_P114090.1; Complete four-exon minus-strand1746nt ATG/code1 CDS includingTGAstop independently translates to581aa native and canonicalUniProt. Bounded1898nt interval;introns59/45/48nt in transcription order. No transcript or functional assay is implied. Same tax985895 and exact native accession/sequence link differently named UniProtLeptosphaeria and NCBIPlenodomus references. JN3 appears in native organism;isolatev23.1.3 explicit,no separate strain/culture/BioSample qualifier. No independent race,stock or catalogue equivalence. Function remains ECO0000250 from P37295,protein existence3. SevenTM segments predicted;automated GO squalene/GGPP-synthase and CDDsites not adopted. No Neurospora phenotype,earlier lycopene chemistry,phytoene,cofactor,production,BGC,taxonomy,origin or physical-assembly upgrade. Genome DOI10.1038/ncomms1189/PMID21326234 unattempted/uninspected. No primary functional study inspected;all prior access holds retained.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/FP929126.1?from=485243&to=487140
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected bounded native coding interval. Exact native protein CBX94994.1; FP929126.1 CDS exon coordinates in genomic order: 485243..486497, 486546..486913, 486959..487058, 487118..487140. Native LEMA_P114090.1, tax985895; isolate=v23.1.3; bioproject=PRJNA63129; uniprot_locus=Lema_P114090.1; Complete four-exon minus-strand1746nt ATG/code1 CDS includingTGAstop independently translates to581aa native and canonicalUniProt. Bounded1898nt interval;introns59/45/48nt in transcription order. No transcript or functional assay is implied. Same tax985895 and exact native accession/sequence link differently named UniProtLeptosphaeria and NCBIPlenodomus references. JN3 appears in native organism;isolatev23.1.3 explicit,no separate strain/culture/BioSample qualifier. No independent race,stock or catalogue equivalence. Function remains ECO0000250 from P37295,protein existence3. SevenTM segments predicted;automated GO squalene/GGPP-synthase and CDDsites not adopted. No Neurospora phenotype,earlier lycopene chemistry,phytoene,cofactor,production,BGC,taxonomy,origin or physical-assembly upgrade. Genome DOI10.1038/ncomms1189/PMID21326234 unattempted/uninspected. No primary functional study inspected;all prior access holds retained.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Similarity-proposed terminal carotene cyclization Substrate of this similarity-assigned terminal reaction, not an independently assayed substrate or the earlier lycopene reaction.
https://www.uniprot.org/uniprotkb/E4ZUB5
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/E4ZUB5
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry63/sequence1, 581aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Similarity-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner in the similarity-based annotation, not proof of a measured product, native production or major-product distribution.
https://www.uniprot.org/uniprotkb/E4ZUB5
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/E4ZUB5
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry63/sequence1, 581aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

TRV_03236 (T. verrucosum reference; similarity assignment): Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.

SubjectPredicateObjectNotesEvidence
TRV_03236 (T. verrucosum reference; similarity assignment) is_database_similarity_proposed_catalyst_of Similarity-proposed terminal carotene cyclization Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.
https://www.uniprot.org/uniprotkb/D4D802
https://www.ncbi.nlm.nih.gov/protein/EFE42031.1
https://www.ncbi.nlm.nih.gov/nuccore/ACYE01000166.1?from=33254&to=35345
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/D4D802
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry62/sequence1, 595aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/EFE42031.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Exact native protein EFE42031.1; ACYE01000166.1 CDS exon coordinates in genomic order: 33254..33276, 33333..33432, 33501..33886, 33944..34117, 34180..34473, 34535..35345. Native TRV_03236, tax663202; strain=HKI 0517; bioproject=PRJNA39693; biosample=SAMN02953766; Complete six-exon plus-strand1788nt ATG/code1 CDS includingTGAstop independently translates to595aa native and canonicalUniProt. Bounded2092nt interval;introns56/68/57/62/61nt. Fuzzy bounded gene/mRNA ends do not make this CDS partial. Function ECO0000250 from P37295,protein existence3;native hypothetical-protein/conceptual-translation annotation is not an assay. Native genome metadata says3x/454,not transcript or model validation. Exact deposited strain reference is not independently verified assay stock. No Neurospora assay/phenotype,earlier lycopene chemistry,phytoene,cofactor,production,BGC,taxonomy,origin or assembly upgrade. PredictedTM,automated squalene/GGPP-synthase GO and CDDsites not adopted. RefSeqXP_003022649.1/XM_003022603.1 and genome DOI10.1186/gb-2011-12-1-r7/PMID21247460 remain unattempted/uninspected. Native unpublished reference not silently equated to UniProt publication. Prior primary-access holds retained.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/ACYE01000166.1?from=33254&to=35345
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected bounded native coding interval. Exact native protein EFE42031.1; ACYE01000166.1 CDS exon coordinates in genomic order: 33254..33276, 33333..33432, 33501..33886, 33944..34117, 34180..34473, 34535..35345. Native TRV_03236, tax663202; strain=HKI 0517; bioproject=PRJNA39693; biosample=SAMN02953766; Complete six-exon plus-strand1788nt ATG/code1 CDS includingTGAstop independently translates to595aa native and canonicalUniProt. Bounded2092nt interval;introns56/68/57/62/61nt. Fuzzy bounded gene/mRNA ends do not make this CDS partial. Function ECO0000250 from P37295,protein existence3;native hypothetical-protein/conceptual-translation annotation is not an assay. Native genome metadata says3x/454,not transcript or model validation. Exact deposited strain reference is not independently verified assay stock. No Neurospora assay/phenotype,earlier lycopene chemistry,phytoene,cofactor,production,BGC,taxonomy,origin or assembly upgrade. PredictedTM,automated squalene/GGPP-synthase GO and CDDsites not adopted. RefSeqXP_003022649.1/XM_003022603.1 and genome DOI10.1186/gb-2011-12-1-r7/PMID21247460 remain unattempted/uninspected. Native unpublished reference not silently equated to UniProt publication. Prior primary-access holds retained.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Similarity-proposed terminal carotene cyclization Substrate of this similarity-assigned terminal reaction, not an independently assayed substrate or the earlier lycopene reaction.
https://www.uniprot.org/uniprotkb/D4D802
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/D4D802
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry62/sequence1, 595aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Similarity-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner in the similarity-based annotation, not proof of a measured product, native production or major-product distribution.
https://www.uniprot.org/uniprotkb/D4D802
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/D4D802
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry62/sequence1, 595aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

SMAC_01277 (S. macrospora reference; similarity assignment): Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.

SubjectPredicateObjectNotesEvidence
SMAC_01277 (S. macrospora reference; similarity assignment) is_database_similarity_proposed_catalyst_of Similarity-proposed terminal carotene cyclization Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.
https://www.uniprot.org/uniprotkb/D1Z4K7
https://www.ncbi.nlm.nih.gov/protein/CCC07710.1
https://www.ncbi.nlm.nih.gov/nuccore/CABT02000004.1?from=272699&to=274636
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/D1Z4K7
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry74/sequence1, 602aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CCC07710.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Exact native protein CCC07710.1; CABT02000004.1 CDS exon coordinates in genomic order: 272699..272718, 272790..273716, 273775..274636. Native SMAC_01277, tax771870; strain=k-hell; BioSampleSAMEA3138314; BioProjectPRJNA39253; plus strand; 1809nt coding, 1938nt bounded interval, 602aa; stopTAG; introns[71, 58]nt in transcription order. Complete ATG/code1 CDS including stop independently translates to exact native/canonical reference. Fuzzy bounded gene/mRNA ends do not make this CDS partial. Native k-hell/mycelium and putative al2 do not independently establish ATCCMYA333/DSM997/K(L3346) catalogue or assay-stock equivalence. SecondaryF7VQC8 is a UniProt alias,not a second tested protein. Exact terminal assignment remains ECO0000250 from P37295,protein existence3. Native CDS/reference correspondence is a curator inference,not a functional assay,transcript validation or native expression. No Neurospora model/assay/preferential phenotype,earlier lycopene chemistry,phytoene,cofactor,production,BGC,taxonomy,origin or physical-assembly upgrade. PredictedTM,automatedGO and CDDsites are not measurements. Genome papers are not functional proof;all earlier access holds persist. Genome DOI10.1371/journal.pgen.1000891/PMID20386741 and RefSeqXP_003352443.1/XM_003352395.2 not inspected by this audit.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/CABT02000004.1?from=272699&to=274636
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Inspected bounded native coding interval. Exact native protein CCC07710.1; CABT02000004.1 CDS exon coordinates in genomic order: 272699..272718, 272790..273716, 273775..274636. Native SMAC_01277, tax771870; strain=k-hell; BioSampleSAMEA3138314; BioProjectPRJNA39253; plus strand; 1809nt coding, 1938nt bounded interval, 602aa; stopTAG; introns[71, 58]nt in transcription order. Complete ATG/code1 CDS including stop independently translates to exact native/canonical reference. Fuzzy bounded gene/mRNA ends do not make this CDS partial. Native k-hell/mycelium and putative al2 do not independently establish ATCCMYA333/DSM997/K(L3346) catalogue or assay-stock equivalence. SecondaryF7VQC8 is a UniProt alias,not a second tested protein. Exact terminal assignment remains ECO0000250 from P37295,protein existence3. Native CDS/reference correspondence is a curator inference,not a functional assay,transcript validation or native expression. No Neurospora model/assay/preferential phenotype,earlier lycopene chemistry,phytoene,cofactor,production,BGC,taxonomy,origin or physical-assembly upgrade. PredictedTM,automatedGO and CDDsites are not measurements. Genome papers are not functional proof;all earlier access holds persist. Genome DOI10.1371/journal.pgen.1000891/PMID20386741 and RefSeqXP_003352443.1/XM_003352395.2 not inspected by this audit.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Similarity-proposed terminal carotene cyclization Substrate of this similarity-assigned terminal reaction, not an independently assayed substrate or the earlier lycopene reaction.
https://www.uniprot.org/uniprotkb/D1Z4K7
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/D1Z4K7
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry74/sequence1, 602aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Similarity-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner in the similarity-based annotation, not proof of a measured product, native production or major-product distribution.
https://www.uniprot.org/uniprotkb/D1Z4K7
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/D1Z4K7
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry74/sequence1, 602aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

GLRG_02475 (C. graminicola reference; similarity assignment): Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.

SubjectPredicateObjectNotesEvidence
GLRG_02475 (C. graminicola reference; similarity assignment) is_database_similarity_proposed_catalyst_of Similarity-proposed terminal carotene cyclization Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.
https://www.uniprot.org/uniprotkb/E3Q717
https://www.ncbi.nlm.nih.gov/protein/EFQ26655.1
https://www.ncbi.nlm.nih.gov/nuccore/GG697335.1?from=342902&to=344772
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/E3Q717
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry56/sequence1, 587aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/EFQ26655.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Exact native protein EFQ26655.1; GG697335.1 CDS exon coordinates in genomic order: 342902..342924, 342979..343902, 343956..344772. Native GLRG_02475, tax645133; strain=M1.001; BioSampleSAMN02953757; BioProjectPRJNA37879; plus strand; 1764nt coding, 1871nt bounded interval, 587aa; stopTAG; introns[54, 53]nt in transcription order. Complete ATG/code1 CDS including stop independently translates to exact native/canonical reference. Fuzzy bounded gene/mRNA ends do not make this CDS partial. Native culture-from-epitype qualifier is retained;M2/FGSC10212 catalogue and assay-stock equivalence was not independently established. Conceptual translation and genome coverage metadata do not prove cyclase activity or transcript validation. Exact terminal assignment remains ECO0000250 from P37295,protein existence3. Native CDS/reference correspondence is a curator inference,not a functional assay,transcript validation or native expression. No Neurospora model/assay/preferential phenotype,earlier lycopene chemistry,phytoene,cofactor,production,BGC,taxonomy,origin or physical-assembly upgrade. PredictedTM,automatedGO and CDDsites are not measurements. Genome papers are not functional proof;all earlier access holds persist. Genome DOI10.1038/ng.2372/PMID22885923 and RefSeqXP_008090675.1/XM_008092484.1 not inspected by this audit.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/GG697335.1?from=342902&to=344772
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Inspected bounded native coding interval. Exact native protein EFQ26655.1; GG697335.1 CDS exon coordinates in genomic order: 342902..342924, 342979..343902, 343956..344772. Native GLRG_02475, tax645133; strain=M1.001; BioSampleSAMN02953757; BioProjectPRJNA37879; plus strand; 1764nt coding, 1871nt bounded interval, 587aa; stopTAG; introns[54, 53]nt in transcription order. Complete ATG/code1 CDS including stop independently translates to exact native/canonical reference. Fuzzy bounded gene/mRNA ends do not make this CDS partial. Native culture-from-epitype qualifier is retained;M2/FGSC10212 catalogue and assay-stock equivalence was not independently established. Conceptual translation and genome coverage metadata do not prove cyclase activity or transcript validation. Exact terminal assignment remains ECO0000250 from P37295,protein existence3. Native CDS/reference correspondence is a curator inference,not a functional assay,transcript validation or native expression. No Neurospora model/assay/preferential phenotype,earlier lycopene chemistry,phytoene,cofactor,production,BGC,taxonomy,origin or physical-assembly upgrade. PredictedTM,automatedGO and CDDsites are not measurements. Genome papers are not functional proof;all earlier access holds persist. Genome DOI10.1038/ng.2372/PMID22885923 and RefSeqXP_008090675.1/XM_008092484.1 not inspected by this audit.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Similarity-proposed terminal carotene cyclization Substrate of this similarity-assigned terminal reaction, not an independently assayed substrate or the earlier lycopene reaction.
https://www.uniprot.org/uniprotkb/E3Q717
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/E3Q717
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry56/sequence1, 587aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Similarity-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner in the similarity-based annotation, not proof of a measured product, native production or major-product distribution.
https://www.uniprot.org/uniprotkb/E3Q717
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/E3Q717
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry56/sequence1, 587aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

MGYG_02096 (A. gypseum reference; similarity assignment): Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.

SubjectPredicateObjectNotesEvidence
MGYG_02096 (A. gypseum reference; similarity assignment) is_database_similarity_proposed_catalyst_of Similarity-proposed terminal carotene cyclization Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.
https://www.uniprot.org/uniprotkb/E4UPP6
https://www.ncbi.nlm.nih.gov/protein/EFQ99083.1
https://www.ncbi.nlm.nih.gov/nuccore/DS989823.1?from=275220&to=277295
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/E4UPP6
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry64/sequence1, 594aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/EFQ99083.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Exact native protein EFQ99083.1; DS989823.1 CDS exon coordinates in genomic order: 275220..276030, 276093..276383, 276436..276609, 276668..277053, 277119..277218, 277273..277295. Native MGYG_02096, tax535722; strain=CBS 118893; BioSampleSAMN02953728; BioProjectPRJNA20599; minus strand; 1785nt coding, 2076nt bounded interval, 594aa; stopTGA; introns[54, 65, 58, 52, 62]nt in transcription order. Complete ATG/code1 CDS including stop independently translates to exact native/canonical reference. Fuzzy bounded gene/mRNA ends do not make this CDS partial. UniProtArthroderma/nativeNannizzia reference naming retained;same tax535722 and exact protein/native-sequence mapping. No independently verified ATCCMYA4604 catalogue or assay-stock equivalence. Native phytoene/conceptual-translation annotation is not a cyclase assay. Exact terminal assignment remains ECO0000250 from P37295,protein existence3. Native CDS/reference correspondence is a curator inference,not a functional assay,transcript validation or native expression. No Neurospora model/assay/preferential phenotype,earlier lycopene chemistry,phytoene,cofactor,production,BGC,taxonomy,origin or physical-assembly upgrade. PredictedTM,automatedGO and CDDsites are not measurements. Genome papers are not functional proof;all earlier access holds persist. Genome DOI10.1128/mbio.00259-12/PMID22951933 and RefSeqXP_003174566.1/XM_003174518.1 not inspected by this audit.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/DS989823.1?from=275220&to=277295
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Inspected bounded native coding interval. Exact native protein EFQ99083.1; DS989823.1 CDS exon coordinates in genomic order: 275220..276030, 276093..276383, 276436..276609, 276668..277053, 277119..277218, 277273..277295. Native MGYG_02096, tax535722; strain=CBS 118893; BioSampleSAMN02953728; BioProjectPRJNA20599; minus strand; 1785nt coding, 2076nt bounded interval, 594aa; stopTGA; introns[54, 65, 58, 52, 62]nt in transcription order. Complete ATG/code1 CDS including stop independently translates to exact native/canonical reference. Fuzzy bounded gene/mRNA ends do not make this CDS partial. UniProtArthroderma/nativeNannizzia reference naming retained;same tax535722 and exact protein/native-sequence mapping. No independently verified ATCCMYA4604 catalogue or assay-stock equivalence. Native phytoene/conceptual-translation annotation is not a cyclase assay. Exact terminal assignment remains ECO0000250 from P37295,protein existence3. Native CDS/reference correspondence is a curator inference,not a functional assay,transcript validation or native expression. No Neurospora model/assay/preferential phenotype,earlier lycopene chemistry,phytoene,cofactor,production,BGC,taxonomy,origin or physical-assembly upgrade. PredictedTM,automatedGO and CDDsites are not measurements. Genome papers are not functional proof;all earlier access holds persist. Genome DOI10.1128/mbio.00259-12/PMID22951933 and RefSeqXP_003174566.1/XM_003174518.1 not inspected by this audit.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Similarity-proposed terminal carotene cyclization Substrate of this similarity-assigned terminal reaction, not an independently assayed substrate or the earlier lycopene reaction.
https://www.uniprot.org/uniprotkb/E4UPP6
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/E4UPP6
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry64/sequence1, 594aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Similarity-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner in the similarity-based annotation, not proof of a measured product, native production or major-product distribution.
https://www.uniprot.org/uniprotkb/E4UPP6
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/E4UPP6
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry64/sequence1, 594aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

SNOG_00339 (P. nodorum reference; similarity assignment): Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.

SubjectPredicateObjectNotesEvidence
SNOG_00339 (P. nodorum reference; similarity assignment) is_database_similarity_proposed_catalyst_of Similarity-proposed terminal carotene cyclization Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.
https://www.uniprot.org/uniprotkb/Q0V6M5
https://www.ncbi.nlm.nih.gov/protein/EAT91834.1
https://www.ncbi.nlm.nih.gov/nuccore/CH445325.1?from=794133&to=796063
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q0V6M5
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry80/sequence1, 585aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/EAT91834.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Exact native protein EAT91834.1; CH445325.1 CDS exon coordinates in genomic order: 794133..795399, 795449..795816, 795874..795973, 796041..796063. Native SNOG_00339, tax321614; strain=SN15; BioSampleSAMN02953619; BioProjectPRJNA13754; minus strand; 1758nt coding, 1931nt bounded interval, 585aa; stopTAG; introns[67, 57, 49]nt in transcription order. Complete ATG/code1 CDS including stop independently translates to exact native/canonical reference. Fuzzy bounded gene/mRNA ends do not make this CDS partial. UniProtPhaeosphaeria/nativeParastagonospora naming retained;same tax321614. Unveil1.0 ab-initio/gene-prediction-v2 and project-level EST annotation remarks do not prove a transcript or assay for this CDS. ATCCMYA4574/FGSC10173 stock aliases unverified. Existing phomacin BGC0002205 uses this chromosome at714900..745000,not the inspected794133..796063 interval;no BGC assignment follows. Exact terminal assignment remains ECO0000250 from P37295,protein existence3. Native CDS/reference correspondence is a curator inference,not a functional assay,transcript validation or native expression. No Neurospora model/assay/preferential phenotype,earlier lycopene chemistry,phytoene,cofactor,production,BGC,taxonomy,origin or physical-assembly upgrade. PredictedTM,automatedGO and CDDsites are not measurements. Genome papers are not functional proof;all earlier access holds persist. Genome DOI10.1105/tpc.107.052829/PMID18024570 and RefSeqXP_001791029.1/XM_001790977.1 not inspected by this audit.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/CH445325.1?from=794133&to=796063
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Inspected bounded native coding interval. Exact native protein EAT91834.1; CH445325.1 CDS exon coordinates in genomic order: 794133..795399, 795449..795816, 795874..795973, 796041..796063. Native SNOG_00339, tax321614; strain=SN15; BioSampleSAMN02953619; BioProjectPRJNA13754; minus strand; 1758nt coding, 1931nt bounded interval, 585aa; stopTAG; introns[67, 57, 49]nt in transcription order. Complete ATG/code1 CDS including stop independently translates to exact native/canonical reference. Fuzzy bounded gene/mRNA ends do not make this CDS partial. UniProtPhaeosphaeria/nativeParastagonospora naming retained;same tax321614. Unveil1.0 ab-initio/gene-prediction-v2 and project-level EST annotation remarks do not prove a transcript or assay for this CDS. ATCCMYA4574/FGSC10173 stock aliases unverified. Existing phomacin BGC0002205 uses this chromosome at714900..745000,not the inspected794133..796063 interval;no BGC assignment follows. Exact terminal assignment remains ECO0000250 from P37295,protein existence3. Native CDS/reference correspondence is a curator inference,not a functional assay,transcript validation or native expression. No Neurospora model/assay/preferential phenotype,earlier lycopene chemistry,phytoene,cofactor,production,BGC,taxonomy,origin or physical-assembly upgrade. PredictedTM,automatedGO and CDDsites are not measurements. Genome papers are not functional proof;all earlier access holds persist. Genome DOI10.1105/tpc.107.052829/PMID18024570 and RefSeqXP_001791029.1/XM_001790977.1 not inspected by this audit.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Similarity-proposed terminal carotene cyclization Substrate of this similarity-assigned terminal reaction, not an independently assayed substrate or the earlier lycopene reaction.
https://www.uniprot.org/uniprotkb/Q0V6M5
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q0V6M5
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry80/sequence1, 585aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Similarity-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner in the similarity-based annotation, not proof of a measured product, native production or major-product distribution.
https://www.uniprot.org/uniprotkb/Q0V6M5
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/Q0V6M5
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry80/sequence1, 585aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

An07g00800 (A. niger reference; similarity assignment): Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.

SubjectPredicateObjectNotesEvidence
An07g00800 (A. niger reference; similarity assignment) is_database_similarity_proposed_catalyst_of Similarity-proposed terminal carotene cyclization Deliberately selected organism-specific reference example of a database similarity assignment for terminal gamma-carotene cyclization, not an assayed enzyme or the uncultured-organism BGC0000646/FJ151553.1 enzyme. GROUNDED identifies the exact reference sequence, not experimental validation of its function. These alternatives are not a shared pathway or physical assembly. No native-production, occurrence, producer, BGC, taxonomy or origin upgrade. The earlier lycopene reaction remains excluded pending chemical-representation review. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted.
https://www.uniprot.org/uniprotkb/A2QM49
https://www.ncbi.nlm.nih.gov/protein/CAK39303.1
https://www.ncbi.nlm.nih.gov/nuccore/AM270119.1?from=141476&to=143644
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/A2QM49
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry85/sequence1, 582aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
    snippet
    gamma-carotene = all-trans-beta-carotene
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAK39303.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Exact native protein CAK39303.1; AM270119.1 CDS exon coordinates in genomic order: 141476..141670, 141730..142082, 142134..142304, 142356..142640, 142688..143130, 143307..143501, 143538..143644. Native An07g00800, tax5061; strain=CBS 513.88; BioSampleSAMEA3283178; no BioProject; plus strand; 1749nt coding, 2169nt bounded interval, 582aa; stopTGA; introns[59, 51, 51, 47, 176, 36]nt in transcription order. Complete ATG/code1 CDS including stop independently translates to exact native/canonical reference. Fuzzy bounded gene/mRNA ends do not make this CDS partial. Native species tax5061 and UniProt named-strain425011 are not asserted equal. Exact accession,sequence,locus and native CBS513.88 qualifier identify the selected reference;ATCCMYA4892/FGSCA1513 catalogue and assay-stock aliases unverified. Native note explicitly invokes similarity to Neurosporaal2/PMID8163509;its photoinduced RNA remark is not adopted as an A.niger observation. Six predictedTM segments and fuzzy CDDregion are not experimental localization,partial-CDS or activity proof. Exact terminal assignment remains ECO0000250 from P37295,protein existence3. Native CDS/reference correspondence is a curator inference,not a functional assay,transcript validation or native expression. No Neurospora model/assay/preferential phenotype,earlier lycopene chemistry,phytoene,cofactor,production,BGC,taxonomy,origin or physical-assembly upgrade. PredictedTM,automatedGO and CDDsites are not measurements. Genome papers are not functional proof;all earlier access holds persist. Genome DOI10.1038/nbt1282/PMID17259976 not inspected by this audit;no primary interpretation of PMID8163509 was made.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AM270119.1?from=141476&to=143644
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Inspected bounded native coding interval. Exact native protein CAK39303.1; AM270119.1 CDS exon coordinates in genomic order: 141476..141670, 141730..142082, 142134..142304, 142356..142640, 142688..143130, 143307..143501, 143538..143644. Native An07g00800, tax5061; strain=CBS 513.88; BioSampleSAMEA3283178; no BioProject; plus strand; 1749nt coding, 2169nt bounded interval, 582aa; stopTGA; introns[59, 51, 51, 47, 176, 36]nt in transcription order. Complete ATG/code1 CDS including stop independently translates to exact native/canonical reference. Fuzzy bounded gene/mRNA ends do not make this CDS partial. Native species tax5061 and UniProt named-strain425011 are not asserted equal. Exact accession,sequence,locus and native CBS513.88 qualifier identify the selected reference;ATCCMYA4892/FGSCA1513 catalogue and assay-stock aliases unverified. Native note explicitly invokes similarity to Neurosporaal2/PMID8163509;its photoinduced RNA remark is not adopted as an A.niger observation. Six predictedTM segments and fuzzy CDDregion are not experimental localization,partial-CDS or activity proof. Exact terminal assignment remains ECO0000250 from P37295,protein existence3. Native CDS/reference correspondence is a curator inference,not a functional assay,transcript validation or native expression. No Neurospora model/assay/preferential phenotype,earlier lycopene chemistry,phytoene,cofactor,production,BGC,taxonomy,origin or physical-assembly upgrade. PredictedTM,automatedGO and CDDsites are not measurements. Genome papers are not functional proof;all earlier access holds persist. Genome DOI10.1038/nbt1282/PMID17259976 not inspected by this audit;no primary interpretation of PMID8163509 was made.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
gamma-carotene is_database_proposed_substrate_of Similarity-proposed terminal carotene cyclization Substrate of this similarity-assigned terminal reaction, not an independently assayed substrate or the earlier lycopene reaction.
https://www.uniprot.org/uniprotkb/A2QM49
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/A2QM49
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry85/sequence1, 582aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
Similarity-proposed terminal carotene cyclization has_database_proposed_product beta-carotene Exact beta-carotene owner in the similarity-based annotation, not proof of a measured product, native production or major-product distribution.
https://www.uniprot.org/uniprotkb/A2QM49
https://www.ebi.ac.uk/chebi/CHEBI:27740
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    https://www.uniprot.org/uniprotkb/A2QM49
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-09
    notes
    Reviewed UniProt entry85/sequence1, 582aa; exact RHEA:32239 annotation names CHEBI:27740 and CHEBI:17579. ECO:0000250 from UniProtKB:P37295 is inference by similarity, not ECO:0000269 or an assay of this protein. Do not transfer the Neurospora historical model, assay construct, preferential single-end phenotype or major-product distribution. Protein existence3 is inferred from homology. Transmembrane segments are predicted, not localization or processing proof. No phytoene reaction, cofactor, mutant phenotype, measured stereoselectivity or physical-assembly claim is adopted. Functional evidence remains DATABASE_ASSERTION. Rhea was inspected through UniProt, not independently retrieved. Genome papers and primary functional papers were not independently inspected; the native sequence deposits are not functional experiments.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:27740
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 gamma-carotene: neutral C40H56, Standard InChIKeyHRQKOYFGHJYEFS-BXOLYSJBSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 3 nodes, 2 edges

LCY1 (Arabidopsis thaliana canonical reference): Deliberately selected canonical protein reference for a database-proposed biosynthetic process, not an independently inspected assay construct. GROUNDED denotes reference identity, not experimental function. These organism-specific alternatives are not a shared pathway or physical assembly and are not BGC0000646/FJ151553.1 assignments. No producer, occurrence, BGC, taxonomy or origin upgrade. No exact substrate, intermediate, reaction order, cofactor or measured stereoselectivity is adopted; the earlier lycopene chemical-representation hold remains.

SubjectPredicateObjectNotesEvidence
LCY1 (Arabidopsis thaliana canonical reference) is_database_proposed_participant_in beta-carotene biosynthetic process Deliberately selected canonical protein reference for a database-proposed biosynthetic process, not an independently inspected assay construct. GROUNDED denotes reference identity, not experimental function. These organism-specific alternatives are not a shared pathway or physical assembly and are not BGC0000646/FJ151553.1 assignments. No producer, occurrence, BGC, taxonomy or origin upgrade. No exact substrate, intermediate, reaction order, cofactor or measured stereoselectivity is adopted; the earlier lycopene chemical-representation hold remains.
https://www.uniprot.org/uniprotkb/Q38933
http://purl.obolibrary.org/obo/GO_1901812
https://www.ncbi.nlm.nih.gov/protein/AAB53337.1
https://www.ncbi.nlm.nih.gov/nuccore/U50739.1?from=174&to=1679
  • reference
    https://www.uniprot.org/uniprotkb/Q38933
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Reviewed UniProt entry182/sequence1, 501aa, 1: Evidence at protein level. PATHWAY has ECO:0000305. FUNCTION also names beta-carotene formation; no independent assay claim is made. Generic reaction carries ECO:0000269/PMID:8837512 in UniProt. Only generic RHEA:55620 (CHEBI:139114 to CHEBI:139120) is annotated, not RHEA:32239. The graph represents process participation, not an exact terminal reaction or substrate; the separate beta-zeacarotene PATHWAY annotation is not adopted for this owner. GO:1901812 is a curator mapping of PATHWAY wording, not a retrieved GO gene-product annotation. Functional evidence remains DATABASE_ASSERTION; primary assays were not independently inspected. Native Columbia ecotype, lambda PRL2 cDNA library/CD4-7 qualifier, LCY1/LCYB/LYC/SZL1, At3g10230/F14P13.17. The selected 501aa canonical reference matches this original deposit and six other inspected deposits with identical 1506nt CDSs. Historical Wassilewskija AAA81880.1/L40176.1 has H31P/V243I, not canonical sequence equality. The 369aa AEE74875.1 reference matches canonical residues133..501; its complete nested CDS does not establish experimental splicing, initiation or activity. Historical transit1..80/mature81..501 differs from current UniProt transit1..48/chain49..501. The latter and Val49 acetylation carry ECO:0007744/PMID:22223895 large-scale proteomic annotation, not a verified assay construct. No G451E phenotype, salt-response or localization claim is adopted. RefSeq NP_001078131.1 and NP_187634.1 remain uninspected. DOI10.1105/tpc.8.9.1613 was tool-inaccessible; not retried. The CP002686.1 reference interval3164340..3165845 does not overlap BGC0002398/2401; a shared chromosome is not BGC membership.
    snippet
    Carotenoid biosynthesis; beta-carotene biosynthesis
  • reference
    http://purl.obolibrary.org/obo/GO_1901812
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Curator maps the explicit UniProt beta-carotene biosynthesis PATHWAY wording to GO:1901812, not to an exact reaction. This is not a GO gene-product annotation. Existing local OAK GO cache version2026-07-26 inspected2026-10-10; term label and definition denote beta-carotene biosynthesis. AmiGO timed out; no fresh ontology download is claimed.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AAB53337.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete plus-strand mRNA CDS U50739.1:174..1679, 1506nt including stop, ATG/codon_start1/standard code1, independently translates to AAB53337.1 and canonical UniProtKB:Q38933, all 501aa. Native taxon3702. TAA stop. Native Columbia ecotype, lambda PRL2 cDNA library/CD4-7 qualifier, LCY1/LCYB/LYC/SZL1, At3g10230/F14P13.17. The selected 501aa canonical reference matches this original deposit and six other inspected deposits with identical 1506nt CDSs. Historical Wassilewskija AAA81880.1/L40176.1 has H31P/V243I, not canonical sequence equality. The 369aa AEE74875.1 reference matches canonical residues133..501; its complete nested CDS does not establish experimental splicing, initiation or activity. Historical transit1..80/mature81..501 differs from current UniProt transit1..48/chain49..501. The latter and Val49 acetylation carry ECO:0007744/PMID:22223895 large-scale proteomic annotation, not a verified assay construct. No G451E phenotype, salt-response or localization claim is adopted. RefSeq NP_001078131.1 and NP_187634.1 remain uninspected. DOI10.1105/tpc.8.9.1613 was tool-inaccessible; not retried. The CP002686.1 reference interval3164340..3165845 does not overlap BGC0002398/2401; a shared chromosome is not BGC membership. Exact reference/CDS correspondence is CURATOR_INFERENCE, not assay-stock identity, experimental processing, genomic exon structure, native production or functional proof.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/U50739.1?from=174&to=1679
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete plus-strand mRNA CDS U50739.1:174..1679, 1506nt including stop, ATG/codon_start1/standard code1, independently translates to AAB53337.1 and canonical UniProtKB:Q38933, all 501aa. Native taxon3702. TAA stop. Native Columbia ecotype, lambda PRL2 cDNA library/CD4-7 qualifier, LCY1/LCYB/LYC/SZL1, At3g10230/F14P13.17. The selected 501aa canonical reference matches this original deposit and six other inspected deposits with identical 1506nt CDSs. Historical Wassilewskija AAA81880.1/L40176.1 has H31P/V243I, not canonical sequence equality. The 369aa AEE74875.1 reference matches canonical residues133..501; its complete nested CDS does not establish experimental splicing, initiation or activity. Historical transit1..80/mature81..501 differs from current UniProt transit1..48/chain49..501. The latter and Val49 acetylation carry ECO:0007744/PMID:22223895 large-scale proteomic annotation, not a verified assay construct. No G451E phenotype, salt-response or localization claim is adopted. RefSeq NP_001078131.1 and NP_187634.1 remain uninspected. DOI10.1105/tpc.8.9.1613 was tool-inaccessible; not retried. The CP002686.1 reference interval3164340..3165845 does not overlap BGC0002398/2401; a shared chromosome is not BGC membership. Exact reference/CDS correspondence is CURATOR_INFERENCE, not assay-stock identity, experimental processing, genomic exon structure, native production or functional proof.
beta-carotene biosynthetic process has_ontology_defined_primary_output beta-carotene Process-class output definition only; not an enzyme-specific reaction experiment.
http://purl.obolibrary.org/obo/GO_1901812
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    http://purl.obolibrary.org/obo/GO_1901812
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Existing local OAK GO cache version2026-07-26 inspected2026-10-10: GO:1901812 has the RO:0004008 has primary output restriction to CHEBI:17579. This is an ontology-level process definition, not an enzyme-specific terminal reaction, assayed product, measured stereoselectivity or proof of native production. AmiGO timed out on the attempted open; no retry or fresh ontology download.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 3 nodes, 2 edges

LCY-B (Narcissus pseudonarcissus reference): Deliberately selected canonical protein reference for a database-proposed biosynthetic process, not an independently inspected assay construct. GROUNDED denotes reference identity, not experimental function. These organism-specific alternatives are not a shared pathway or physical assembly and are not BGC0000646/FJ151553.1 assignments. No producer, occurrence, BGC, taxonomy or origin upgrade. No exact substrate, intermediate, reaction order, cofactor or measured stereoselectivity is adopted; the earlier lycopene chemical-representation hold remains.

SubjectPredicateObjectNotesEvidence
LCY-B (Narcissus pseudonarcissus reference) is_database_proposed_participant_in beta-carotene biosynthetic process Deliberately selected canonical protein reference for a database-proposed biosynthetic process, not an independently inspected assay construct. GROUNDED denotes reference identity, not experimental function. These organism-specific alternatives are not a shared pathway or physical assembly and are not BGC0000646/FJ151553.1 assignments. No producer, occurrence, BGC, taxonomy or origin upgrade. No exact substrate, intermediate, reaction order, cofactor or measured stereoselectivity is adopted; the earlier lycopene chemical-representation hold remains.
https://www.uniprot.org/uniprotkb/Q40424
http://purl.obolibrary.org/obo/GO_1901812
https://www.ncbi.nlm.nih.gov/protein/CAA67331.1
https://www.ncbi.nlm.nih.gov/nuccore/X98796.1?from=153&to=1664
  • reference
    https://www.uniprot.org/uniprotkb/Q40424
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Reviewed UniProt entry97/sequence1, 503aa, 2: Evidence at transcript level. PATHWAY has no explicit evidence tag. FUNCTION also names beta-carotene formation; no independent assay claim is made. Generic reaction has no explicit evidence tag. Only generic RHEA:55620 (CHEBI:139114 to CHEBI:139120) is annotated, not RHEA:32239. The graph represents process participation, not an exact terminal reaction or substrate; the separate beta-zeacarotene PATHWAY annotation is not adopted for this owner. GO:1901812 is a curator mapping of PATHWAY wording, not a retrieved GO gene-product annotation. Functional evidence remains DATABASE_ASSERTION; primary assays were not independently inspected. Native gene lyc, lambda ZAP library, no cultivar qualifier. Native beta-carotene formation annotation is a database assertion, not an inspected experiment. UniProt PMID:9288918 is linked to localization, not automatically the generic reaction. DOI10.1111/j.1432-1033.1997.00942.x was tool-inaccessible; not retried. Transit1..85 is ECO:0000255 prediction; chain86..503 and predicted NAD binding are not assay constructs.
    snippet
    Carotenoid biosynthesis; beta-carotene biosynthesis
  • reference
    http://purl.obolibrary.org/obo/GO_1901812
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Curator maps the explicit UniProt beta-carotene biosynthesis PATHWAY wording to GO:1901812, not to an exact reaction. This is not a GO gene-product annotation. Existing local OAK GO cache version2026-07-26 inspected2026-10-10; term label and definition denote beta-carotene biosynthesis. AmiGO timed out; no fresh ontology download is claimed.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAA67331.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete plus-strand mRNA CDS X98796.1:153..1664, 1512nt including stop, ATG/codon_start1/standard code1, independently translates to CAA67331.1 and canonical UniProtKB:Q40424, all 503aa. Native taxon39639. TGA stop. Native gene lyc, lambda ZAP library, no cultivar qualifier. Native beta-carotene formation annotation is a database assertion, not an inspected experiment. UniProt PMID:9288918 is linked to localization, not automatically the generic reaction. DOI10.1111/j.1432-1033.1997.00942.x was tool-inaccessible; not retried. Transit1..85 is ECO:0000255 prediction; chain86..503 and predicted NAD binding are not assay constructs. Exact reference/CDS correspondence is CURATOR_INFERENCE, not assay-stock identity, experimental processing, genomic exon structure, native production or functional proof.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/X98796.1?from=153&to=1664
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete plus-strand mRNA CDS X98796.1:153..1664, 1512nt including stop, ATG/codon_start1/standard code1, independently translates to CAA67331.1 and canonical UniProtKB:Q40424, all 503aa. Native taxon39639. TGA stop. Native gene lyc, lambda ZAP library, no cultivar qualifier. Native beta-carotene formation annotation is a database assertion, not an inspected experiment. UniProt PMID:9288918 is linked to localization, not automatically the generic reaction. DOI10.1111/j.1432-1033.1997.00942.x was tool-inaccessible; not retried. Transit1..85 is ECO:0000255 prediction; chain86..503 and predicted NAD binding are not assay constructs. Exact reference/CDS correspondence is CURATOR_INFERENCE, not assay-stock identity, experimental processing, genomic exon structure, native production or functional proof.
beta-carotene biosynthetic process has_ontology_defined_primary_output beta-carotene Process-class output definition only; not an enzyme-specific reaction experiment.
http://purl.obolibrary.org/obo/GO_1901812
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    http://purl.obolibrary.org/obo/GO_1901812
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Existing local OAK GO cache version2026-07-26 inspected2026-10-10: GO:1901812 has the RO:0004008 has primary output restriction to CHEBI:17579. This is an ontology-level process definition, not an enzyme-specific terminal reaction, assayed product, measured stereoselectivity or proof of native production. AmiGO timed out on the attempted open; no retry or fresh ontology download.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 3 nodes, 2 edges

LCY1 (Solanum lycopersicum reference): Deliberately selected canonical protein reference for a database-proposed biosynthetic process, not an independently inspected assay construct. GROUNDED denotes reference identity, not experimental function. These organism-specific alternatives are not a shared pathway or physical assembly and are not BGC0000646/FJ151553.1 assignments. No producer, occurrence, BGC, taxonomy or origin upgrade. No exact substrate, intermediate, reaction order, cofactor or measured stereoselectivity is adopted; the earlier lycopene chemical-representation hold remains.

SubjectPredicateObjectNotesEvidence
LCY1 (Solanum lycopersicum reference) is_database_proposed_participant_in beta-carotene biosynthetic process Deliberately selected canonical protein reference for a database-proposed biosynthetic process, not an independently inspected assay construct. GROUNDED denotes reference identity, not experimental function. These organism-specific alternatives are not a shared pathway or physical assembly and are not BGC0000646/FJ151553.1 assignments. No producer, occurrence, BGC, taxonomy or origin upgrade. No exact substrate, intermediate, reaction order, cofactor or measured stereoselectivity is adopted; the earlier lycopene chemical-representation hold remains.
https://www.uniprot.org/uniprotkb/Q43503
http://purl.obolibrary.org/obo/GO_1901812
https://www.ncbi.nlm.nih.gov/protein/CAA60170.1
https://www.ncbi.nlm.nih.gov/nuccore/X86452.1?from=112&to=1614
  • reference
    https://www.uniprot.org/uniprotkb/Q43503
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Reviewed UniProt entry142/sequence1, 500aa, 1: Evidence at protein level. PATHWAY has no explicit evidence tag. FUNCTION also names beta-carotene formation; no independent assay claim is made. Generic reaction carries ECO:0000269/PMID:8624411 in UniProt. Only generic RHEA:55620 (CHEBI:139114 to CHEBI:139120) is annotated, not RHEA:32239. The graph represents process participation, not an exact terminal reaction or substrate; the separate beta-zeacarotene PATHWAY annotation is not adopted for this owner. GO:1901812 is a curator mapping of PATHWAY wording, not a retrieved GO gene-product annotation. Functional evidence remains DATABASE_ASSERTION; primary assays were not independently inspected. Native CrtL-1, cultivar VF36, leaf; UniProt LCY1/CRTL-1 and Solyc04g040190.1. Do not substitute the distinct tomato K4C9E2/NSY/B paralog, whose functional conflict remains held. DOI10.1007/bf00019013 and DOI10.1105/tpc.8.9.1613 access holds remain; neither primary assay was independently inspected. Transit1..81 is ECO:0000255 prediction; chain82..500 is not a verified assay construct. RefSeq NP_001234226.1 and NP_001303688.1 remain uninspected; no genomic-exon claim.
    snippet
    Carotenoid biosynthesis; beta-carotene biosynthesis
  • reference
    http://purl.obolibrary.org/obo/GO_1901812
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Curator maps the explicit UniProt beta-carotene biosynthesis PATHWAY wording to GO:1901812, not to an exact reaction. This is not a GO gene-product annotation. Existing local OAK GO cache version2026-07-26 inspected2026-10-10; term label and definition denote beta-carotene biosynthesis. AmiGO timed out; no fresh ontology download is claimed.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAA60170.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete plus-strand mRNA CDS X86452.1:112..1614, 1503nt including stop, ATG/codon_start1/standard code1, independently translates to CAA60170.1 and canonical UniProtKB:Q43503, all 500aa. Native taxon4081. TGA stop. Native CrtL-1, cultivar VF36, leaf; UniProt LCY1/CRTL-1 and Solyc04g040190.1. Do not substitute the distinct tomato K4C9E2/NSY/B paralog, whose functional conflict remains held. DOI10.1007/bf00019013 and DOI10.1105/tpc.8.9.1613 access holds remain; neither primary assay was independently inspected. Transit1..81 is ECO:0000255 prediction; chain82..500 is not a verified assay construct. RefSeq NP_001234226.1 and NP_001303688.1 remain uninspected; no genomic-exon claim. Exact reference/CDS correspondence is CURATOR_INFERENCE, not assay-stock identity, experimental processing, genomic exon structure, native production or functional proof.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/X86452.1?from=112&to=1614
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete plus-strand mRNA CDS X86452.1:112..1614, 1503nt including stop, ATG/codon_start1/standard code1, independently translates to CAA60170.1 and canonical UniProtKB:Q43503, all 500aa. Native taxon4081. TGA stop. Native CrtL-1, cultivar VF36, leaf; UniProt LCY1/CRTL-1 and Solyc04g040190.1. Do not substitute the distinct tomato K4C9E2/NSY/B paralog, whose functional conflict remains held. DOI10.1007/bf00019013 and DOI10.1105/tpc.8.9.1613 access holds remain; neither primary assay was independently inspected. Transit1..81 is ECO:0000255 prediction; chain82..500 is not a verified assay construct. RefSeq NP_001234226.1 and NP_001303688.1 remain uninspected; no genomic-exon claim. Exact reference/CDS correspondence is CURATOR_INFERENCE, not assay-stock identity, experimental processing, genomic exon structure, native production or functional proof.
beta-carotene biosynthetic process has_ontology_defined_primary_output beta-carotene Process-class output definition only; not an enzyme-specific reaction experiment.
http://purl.obolibrary.org/obo/GO_1901812
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    http://purl.obolibrary.org/obo/GO_1901812
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Existing local OAK GO cache version2026-07-26 inspected2026-10-10: GO:1901812 has the RO:0004008 has primary output restriction to CHEBI:17579. This is an ontology-level process definition, not an enzyme-specific terminal reaction, assayed product, measured stereoselectivity or proof of native production. AmiGO timed out on the attempted open; no retry or fresh ontology download.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 3 nodes, 2 edges

LCY-B (Oncidium hybrid reference; similarity assignment): Deliberately selected canonical protein reference for a database-proposed biosynthetic process, not an independently inspected assay construct. GROUNDED denotes reference identity, not experimental function. These organism-specific alternatives are not a shared pathway or physical assembly and are not BGC0000646/FJ151553.1 assignments. No producer, occurrence, BGC, taxonomy or origin upgrade. No exact substrate, intermediate, reaction order, cofactor or measured stereoselectivity is adopted; the earlier lycopene chemical-representation hold remains.

SubjectPredicateObjectNotesEvidence
LCY-B (Oncidium hybrid reference; similarity assignment) is_database_similarity_proposed_participant_in beta-carotene biosynthetic process Deliberately selected canonical protein reference for a database-proposed biosynthetic process, not an independently inspected assay construct. GROUNDED denotes reference identity, not experimental function. These organism-specific alternatives are not a shared pathway or physical assembly and are not BGC0000646/FJ151553.1 assignments. No producer, occurrence, BGC, taxonomy or origin upgrade. No exact substrate, intermediate, reaction order, cofactor or measured stereoselectivity is adopted; the earlier lycopene chemical-representation hold remains.
https://www.uniprot.org/uniprotkb/D9IL23
http://purl.obolibrary.org/obo/GO_1901812
https://www.ncbi.nlm.nih.gov/protein/ADJ67814.1
https://www.ncbi.nlm.nih.gov/nuccore/HM146076.1?from=50&to=1468
  • reference
    https://www.uniprot.org/uniprotkb/D9IL23
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Reviewed UniProt entry38/sequence1, 472aa, 2: Evidence at transcript level. PATHWAY has no explicit evidence tag. FUNCTION has ECO:0000250 with no donor named; participation remains similarity-proposed. Generic reaction has no explicit evidence tag. Only generic RHEA:55620 (CHEBI:139114 to CHEBI:139120) is annotated, not RHEA:32239. The graph represents process participation, not an exact terminal reaction or substrate; the separate beta-zeacarotene PATHWAY annotation is not adopted for this owner. GO:1901812 is a curator mapping of PATHWAY wording, not a retrieved GO gene-product annotation. Functional evidence remains DATABASE_ASSERTION; primary assays were not independently inspected. Native gene Lcy-b; Oncidium Gower Ramsey is in the mRNA definition, with no separate cultivar qualifier. Conceptual translation and floral expression are not an enzyme assay. DOI10.1007/s00425-010-1222-x access hold remains; no primary claim. Transit1..25 is ECO:0000255 prediction; chain26..472 and predicted NAD binding62..90 are not experimentally verified processing or constructs.
    snippet
    Carotenoid biosynthesis; beta-carotene biosynthesis
  • reference
    http://purl.obolibrary.org/obo/GO_1901812
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Curator maps the explicit UniProt beta-carotene biosynthesis PATHWAY wording to GO:1901812, not to an exact reaction. This is not a GO gene-product annotation. Existing local OAK GO cache version2026-07-26 inspected2026-10-10; term label and definition denote beta-carotene biosynthesis. AmiGO timed out; no fresh ontology download is claimed.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/ADJ67814.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete plus-strand mRNA CDS HM146076.1:50..1468, 1419nt including stop, ATG/codon_start1/standard code1, independently translates to ADJ67814.1 and canonical UniProtKB:D9IL23, all 472aa. Native taxon141207. TGA stop. Native gene Lcy-b; Oncidium Gower Ramsey is in the mRNA definition, with no separate cultivar qualifier. Conceptual translation and floral expression are not an enzyme assay. DOI10.1007/s00425-010-1222-x access hold remains; no primary claim. Transit1..25 is ECO:0000255 prediction; chain26..472 and predicted NAD binding62..90 are not experimentally verified processing or constructs. Exact reference/CDS correspondence is CURATOR_INFERENCE, not assay-stock identity, experimental processing, genomic exon structure, native production or functional proof.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/HM146076.1?from=50&to=1468
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete plus-strand mRNA CDS HM146076.1:50..1468, 1419nt including stop, ATG/codon_start1/standard code1, independently translates to ADJ67814.1 and canonical UniProtKB:D9IL23, all 472aa. Native taxon141207. TGA stop. Native gene Lcy-b; Oncidium Gower Ramsey is in the mRNA definition, with no separate cultivar qualifier. Conceptual translation and floral expression are not an enzyme assay. DOI10.1007/s00425-010-1222-x access hold remains; no primary claim. Transit1..25 is ECO:0000255 prediction; chain26..472 and predicted NAD binding62..90 are not experimentally verified processing or constructs. Exact reference/CDS correspondence is CURATOR_INFERENCE, not assay-stock identity, experimental processing, genomic exon structure, native production or functional proof.
beta-carotene biosynthetic process has_ontology_defined_primary_output beta-carotene Process-class output definition only; not an enzyme-specific reaction experiment.
http://purl.obolibrary.org/obo/GO_1901812
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    http://purl.obolibrary.org/obo/GO_1901812
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Existing local OAK GO cache version2026-07-26 inspected2026-10-10: GO:1901812 has the RO:0004008 has primary output restriction to CHEBI:17579. This is an ontology-level process definition, not an enzyme-specific terminal reaction, assayed product, measured stereoselectivity or proof of native production. AmiGO timed out on the attempted open; no retry or fresh ontology download.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 3 nodes, 2 edges

LCY-B (Nicotiana tabacum reference): Deliberately selected canonical protein reference for a database-proposed biosynthetic process, not an independently inspected assay construct. GROUNDED denotes reference identity, not experimental function. These organism-specific alternatives are not a shared pathway or physical assembly and are not BGC0000646/FJ151553.1 assignments. No producer, occurrence, BGC, taxonomy or origin upgrade. No exact substrate, intermediate, reaction order, cofactor or measured stereoselectivity is adopted; the earlier lycopene chemical-representation hold remains.

SubjectPredicateObjectNotesEvidence
LCY-B (Nicotiana tabacum reference) is_database_proposed_participant_in beta-carotene biosynthetic process Deliberately selected canonical protein reference for a database-proposed biosynthetic process, not an independently inspected assay construct. GROUNDED denotes reference identity, not experimental function. These organism-specific alternatives are not a shared pathway or physical assembly and are not BGC0000646/FJ151553.1 assignments. No producer, occurrence, BGC, taxonomy or origin upgrade. No exact substrate, intermediate, reaction order, cofactor or measured stereoselectivity is adopted; the earlier lycopene chemical-representation hold remains.
https://www.uniprot.org/uniprotkb/Q43578
http://purl.obolibrary.org/obo/GO_1901812
https://www.ncbi.nlm.nih.gov/protein/CAA57386.1
https://www.ncbi.nlm.nih.gov/nuccore/X81787.1?from=61&to=1563
  • reference
    https://www.uniprot.org/uniprotkb/Q43578
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Reviewed UniProt entry105/sequence1, 500aa, 1: Evidence at protein level. PATHWAY has no explicit evidence tag. FUNCTION also names beta-carotene formation; no independent assay claim is made. Generic reaction carries ECO:0000269/PMID:8624411 in UniProt. Only generic RHEA:55620 (CHEBI:139114 to CHEBI:139120) is annotated, not RHEA:32239. The graph represents process participation, not an exact terminal reaction or substrate; the separate beta-zeacarotene PATHWAY annotation is not adopted for this owner. GO:1901812 is a curator mapping of PATHWAY wording, not a retrieved GO gene-product annotation. Functional evidence remains DATABASE_ASSERTION; primary assays were not independently inspected. Native CrtL-1, cultivar Samsun NN, leaf. DOI10.1007/bf00019013 and DOI10.1105/tpc.8.9.1613 access holds remain; no independently inspected primary assay. Transit1..81 is ECO:0000255 prediction; chain82..500 is not a verified assay construct. RefSeq NP_001311716.1 remains uninspected.
    snippet
    Carotenoid biosynthesis; beta-carotene biosynthesis
  • reference
    http://purl.obolibrary.org/obo/GO_1901812
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Curator maps the explicit UniProt beta-carotene biosynthesis PATHWAY wording to GO:1901812, not to an exact reaction. This is not a GO gene-product annotation. Existing local OAK GO cache version2026-07-26 inspected2026-10-10; term label and definition denote beta-carotene biosynthesis. AmiGO timed out; no fresh ontology download is claimed.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/CAA57386.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete plus-strand mRNA CDS X81787.1:61..1563, 1503nt including stop, ATG/codon_start1/standard code1, independently translates to CAA57386.1 and canonical UniProtKB:Q43578, all 500aa. Native taxon4097. TGA stop. Native CrtL-1, cultivar Samsun NN, leaf. DOI10.1007/bf00019013 and DOI10.1105/tpc.8.9.1613 access holds remain; no independently inspected primary assay. Transit1..81 is ECO:0000255 prediction; chain82..500 is not a verified assay construct. RefSeq NP_001311716.1 remains uninspected. Exact reference/CDS correspondence is CURATOR_INFERENCE, not assay-stock identity, experimental processing, genomic exon structure, native production or functional proof.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/X81787.1?from=61&to=1563
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete plus-strand mRNA CDS X81787.1:61..1563, 1503nt including stop, ATG/codon_start1/standard code1, independently translates to CAA57386.1 and canonical UniProtKB:Q43578, all 500aa. Native taxon4097. TGA stop. Native CrtL-1, cultivar Samsun NN, leaf. DOI10.1007/bf00019013 and DOI10.1105/tpc.8.9.1613 access holds remain; no independently inspected primary assay. Transit1..81 is ECO:0000255 prediction; chain82..500 is not a verified assay construct. RefSeq NP_001311716.1 remains uninspected. Exact reference/CDS correspondence is CURATOR_INFERENCE, not assay-stock identity, experimental processing, genomic exon structure, native production or functional proof.
beta-carotene biosynthetic process has_ontology_defined_primary_output beta-carotene Process-class output definition only; not an enzyme-specific reaction experiment.
http://purl.obolibrary.org/obo/GO_1901812
https://www.ebi.ac.uk/chebi/CHEBI:17579
  • reference
    http://purl.obolibrary.org/obo/GO_1901812
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    Existing local OAK GO cache version2026-07-26 inspected2026-10-10: GO:1901812 has the RO:0004008 has primary output restriction to CHEBI:17579. This is an ontology-level process definition, not an enzyme-specific terminal reaction, assayed product, measured stereoselectivity or proof of native production. AmiGO timed out on the attempted open; no retry or fresh ontology download.
  • reference
    https://www.ebi.ac.uk/chebi/CHEBI:17579
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-09
    notes
    Inspected ChEBI255 beta-carotene: neutral C40H56, Standard InChIKeyOENHQHLEOONYIE-JLTXGRSLSA-N. Independent RDKit2026.03.5 parsing of cached SMILES and InChI reproduces the full key. The existing MIBiG-derived owner SMILES and InChI independently give this same key. This is exact database chemical-identity correspondence, not an independent experimental structure or stereoselectivity measurement.

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

Causal graph — biosynthesis 4 nodes, 3 edges

DcLCYB1 complementation and a separately identified sequence reference. No BGC0000646 assignment, exact substrate/reaction, cofactor, assembly, native-producer, origin, taxonomy or bioactivity upgrade. Existing chemical and access holds remain.

SubjectPredicateObjectNotesEvidence
DcLCYB1 (Nantaise assay; sequence unresolved) is_expressed_in DcLCYB1 heterologous complementation Assay participation, not purified-enzyme kinetics or canonical-reference activity.
DOI:10.1371/journal.pone.0058144
  • reference
    DOI:10.1371/journal.pone.0058144
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-10
    notes
    Methods and Fig.4: Nantaise-derived pET-Blue1/Lcyb1 in E. coli BL21 gold carrying pDS1B-delta-crtY; IPTG induction, empty-vector control.
DcLCYB1 heterologous complementation has_reported_product beta-carotene Reported HPLC assignment; no isomer-purity or stereoselectivity measurement.
DOI:10.1371/journal.pone.0058144
  • reference
    DOI:10.1371/journal.pone.0058144
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-10
    notes
    Fig.4: complemented cells show the assigned beta-carotene peak; control lacks it. Methods use retention, absorption spectra and pigment standards.
    snippet
    leading to β-carotene production.
LCYB (B493 reference; not verified assay sequence) is_cited_sequence_reference_for DcLCYB1 (Nantaise assay; sequence unresolved) Reference correspondence only, not sequence equality; see curator-dclcyb1-construct-reference.
DOI:10.1371/journal.pone.0058144
https://www.uniprot.org/uniprotkb/Q2VEX7
https://www.ebi.ac.uk/ena/browser/view/DQ192190.1
  • reference
    DOI:10.1371/journal.pone.0058144
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Paper cites DQ192190 but Fig.2 ends at residue521. Table1 reverse primers map beyond the reference stop, including the purported stopless fusion primer. Complete assay-construct sequence remains unresolved.
  • reference
    https://www.uniprot.org/uniprotkb/Q2VEX7
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    UniProt2026_03, unreviewed entry61/sequence1; taxon79200, 508aa, LCYB, DQ192190/ABB52071.1. GROUNDED identifies this reference only. Automatic ARBA pathway annotations are not experimental evidence; RefSeq NP_001316089.1 was not inspected.
  • reference
    https://www.ebi.ac.uk/ena/browser/view/DQ192190.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete B493 mRNA CDS408..1934, 1527nt, ATG, codon_start1, standard code1 (no explicit transl_table), TAG stop; independent translation matches ABB52071.1 and Q2VEX7, all508aa. Table1 forward primer matches408..428; reverse-primer annealing spans1994..2013 (complete) or1997..2013 (localization). Predicted amplicon408..2013 is1606nt and retains TAG. This reference calculation does not establish the actual Nantaise clone, readthrough, processing or a corrected construct.

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

Causal graph — biosynthesis 3 nodes, 2 edges

KRD DcLcyB2 heterologous expression with a printed protein sequence matching Q2VEX6. Reference equivalence does not establish a deposited complete expression construct. No exact substrate/reaction, purified-enzyme kinetics, measured affinity, physical assembly, BGC0000646 assignment, native-producer, taxonomy, origin or bioactivity upgrade. The separate Nantaise DcLCYB1 construct discussion and prior chemical/access holds remain.

SubjectPredicateObjectNotesEvidence
DcLcyB2 (KRD printed-sequence match) is_expressed_in DcLcyB2 heterologous expression Protein-insert sequence correspondence, not complete fusion/vector sequence or B493 assay-stock equality. Vector junctions, tag retention/cleavage and native processing were not independently established.
DOI:10.1186/s43897-026-00232-z
DOI:10.1186/s43897-026-00232-z
https://www.uniprot.org/uniprotkb/Q2VEX6
https://www.ebi.ac.uk/ena/browser/view/DQ192191.1
  • reference
    DOI:10.1186/s43897-026-00232-z
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-10
    notes
    Methods and Fig.2: Kurodagosun (KRD) supplied the cloned full coding region; pGEX-5X-1 DcLcyB2 was co-transformed with pACCRT-EIB (crtE/crtI/crtB) in E. coli BL21(DE3), cultured in dark LB with antibiotics. The Fig.2 control is pACCRT-EIB alone, not a stated empty-pGEX control. No induction protocol is inferred.
  • reference
    DOI:10.1186/s43897-026-00232-z
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Supplement1 Fig.S2: the complete manually transcribed KRD row (492aa) equals Q2VEX6 sequence1; its five variable alignment positions are I7/L25/E92/R338/H423. This is printed protein correspondence, not deposited KRD nucleotide or sequenced expression-construct identity. Supplement2 TableS1 full-F/pGEX-F anneal to DQ192191.1:96..118, full-R/pGEX-R reverse-anneal to1552..1574. With nonannealing cloning tails excluded, the reference amplicon96..1574 is1479nt and retains TGA. This calculation does not establish actual vector junctions.
  • reference
    https://www.uniprot.org/uniprotkb/Q2VEX6
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-10
    notes
    UniProt2026_03, unreviewed entry58/sequence1, tax79200,492aa, geneCCS; DQ192191/ABB52072.1. GROUNDED denotes the matching protein reference. Putative capsanthin-capsorubin-synthase naming and automatic ARBA/IEA carotenoid annotations are not the experimental support for this edge. RefSeq NP_001316108.1/NM_001329179.1 were not inspected.
  • reference
    https://www.ebi.ac.uk/ena/browser/view/DQ192191.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-10
    notes
    Complete B493 mRNA,1730nt,tax79200. CDS96..1574,1479nt including TGA stop, ATG/codon_start1 and standard code1 (no explicit transl_table), independently translates to ABB52072.1 and Q2VEX6, all492aa. The B493 source is a sequence reference, not the KRD experimental stock.
DcLcyB2 heterologous expression has_reported_product beta-carotene Reported chromatographic assignment, not independently demonstrated isomer purity, stereoselectivity, conversion efficiency or a terminal reaction. Other detected carotenes and DcLcyE coexpression are separate claims.
DOI:10.1186/s43897-026-00232-z
  • reference
    DOI:10.1186/s43897-026-00232-z
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-10
    notes
    Fig.2A/B and Results report a beta-carotene peak in the pACCRT-EIB + DcLcyB2 condition, compared with pACCRT-EIB alone. Methods describe UPLC and LC-MS/MS carotenoid identification using standards and a standard curve; standard isomer purity is not specified. No quantitative catalytic-rate comparison or native carrot production claim is adopted.
    snippet
    The chromatogram displayed the significant peaks representing β-carotene

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

Bioactivities 25

Entries preserve source qualifiers, targets and evidence. Repeated assay names or values are not independent replications; inspect source detail for differences.

AssayResultTarget enzymeSource detail
A quantitative high throughput screen for small molecules that induce DNA re-replication in SW480 colon adenocarcinoma cells.OTHER 2.6609 uM; INACTIVENot recorded
pubchem.aid:624297
assay
A quantitative high throughput screen for small molecules that induce DNA re-replication in SW480 colon adenocarcinoma cells.
evidence
  • reference
    pubchem.aid:624297
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 624297, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency. Target accession NP_056979 was left ungrounded because PubChem did not provide a UniProtKB accession.
call
INACTIVE
measurement type
OTHER
value
2.6609
units
uM
BET inhibitor-based combinations targeting novel dependencies in MECOM-rearranged (r) AML: HNT-34 cell lineOTHER 37.1975 uM; NOT_DETERMINEDNot recorded
pubchem.aid:2202234
assay
BET inhibitor-based combinations targeting novel dependencies in MECOM-rearranged (r) AML: HNT-34 cell line
evidence
  • reference
    pubchem.aid:2202234
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 2202234, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency.
call
NOT_DETERMINED
measurement type
OTHER
value
37.1975
units
uM
BET inhibitor-based combinations targeting novel dependencies in MECOM-rearranged (r) AML: MV-4-11 cell lineOTHER 23.47 uM; ACTIVENot recorded
pubchem.aid:2202233
assay
BET inhibitor-based combinations targeting novel dependencies in MECOM-rearranged (r) AML: MV-4-11 cell line
evidence
  • reference
    pubchem.aid:2202233
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 2202233, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency.
call
ACTIVE
measurement type
OTHER
value
23.47
units
uM
BET inhibitor-based combinations targeting novel dependencies in MECOM-rearranged (r) AML: OCI-AML3 cell lineOTHER 18.6429 uM; NOT_DETERMINEDNot recorded
pubchem.aid:2202232
assay
BET inhibitor-based combinations targeting novel dependencies in MECOM-rearranged (r) AML: OCI-AML3 cell line
evidence
  • reference
    pubchem.aid:2202232
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 2202232, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency.
call
NOT_DETERMINED
measurement type
OTHER
value
18.6429
units
uM
Cellular viability qHTS for anaplastic thyroid cancer (ATC) cell line THJ-16TOTHER 5.5059 uM; NOT_DETERMINEDNot recorded
pubchem.aid:2202551
assay
Cellular viability qHTS for anaplastic thyroid cancer (ATC) cell line THJ-16T
evidence
  • reference
    pubchem.aid:2202551
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 2202551, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency.
call
NOT_DETERMINED
measurement type
OTHER
value
5.5059
units
uM
Confirmatory qHTS for inhibitors of NSP2Pro chikungunya virus (CHIKV)OTHER 8.9552 uM; NOT_DETERMINEDNot recorded
pubchem.aid:1964105
assay
Confirmatory qHTS for inhibitors of NSP2Pro chikungunya virus (CHIKV)
evidence
  • reference
    pubchem.aid:1964105
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1964105, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency.
call
NOT_DETERMINED
measurement type
OTHER
value
8.9552
units
uM
High Throughput Screening for Foot and Mouth Disease Virus AntiviralsOTHER 5.0119 uM; ACTIVENot recorded
pubchem.aid:1159524
assay
High Throughput Screening for Foot and Mouth Disease Virus Antivirals
evidence
  • reference
    pubchem.aid:1159524
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1159524, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency.
call
ACTIVE
measurement type
OTHER
value
5.0119
units
uM
activity class
ANTIVIRAL
Late stage assay provider counterscreen results for the probe development effort to identify inhibitors of Hepatitis C Virus (HCV) core protein dimerization: Absorbance-based cell-based assay to identify compounds that are cytotoxic to Huh-7.5 cellsOTHER 24.7 uM; INACTIVENot recorded
pubchem.aid:485280
assay
Late stage assay provider counterscreen results for the probe development effort to identify inhibitors of Hepatitis C Virus (HCV) core protein dimerization: Absorbance-based cell-based assay to identify compounds that are cytotoxic to Huh-7.5 cells
evidence
  • reference
    pubchem.aid:485280
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 485280, deposited by The Scripps Research Institute Molecular Screening Center; assay type Confirmatory. Source endpoint: CC50.
call
INACTIVE
measurement type
OTHER
value
24.7
units
uM
Late stage assay provider counterscreen results for the probe development effort to identify inhibitors of Hepatitis C Virus (HCV) core protein dimerization: Luminescence-based biochemical AlphaScreen assay to identify inhibitors of HCV core dimerizationIC50 34.8 uM; INACTIVENot recorded
pubchem.aid:463085
assay
Late stage assay provider counterscreen results for the probe development effort to identify inhibitors of Hepatitis C Virus (HCV) core protein dimerization: Luminescence-based biochemical AlphaScreen assay to identify inhibitors of HCV core dimerization
evidence
  • reference
    pubchem.aid:463085
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 463085, deposited by The Scripps Research Institute Molecular Screening Center; assay type Confirmatory. Target accession ABC47431 was left ungrounded because PubChem did not provide a UniProtKB accession.
call
INACTIVE
measurement type
IC50
value
34.8
units
uM
Late stage results for the probe development effort to identify inhibitors of Hepatitis C Virus (HCV) core protein dimerization: TR-FRET-based biochemical dose response assay for HCV core inhibitorsIC50 49.751 uM; INACTIVENot recorded
pubchem.aid:2488
assay
Late stage results for the probe development effort to identify inhibitors of Hepatitis C Virus (HCV) core protein dimerization: TR-FRET-based biochemical dose response assay for HCV core inhibitors
evidence
  • reference
    pubchem.aid:2488
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 2488, deposited by The Scripps Research Institute Molecular Screening Center; assay type Confirmatory. Target accession ABC47431 was left ungrounded because PubChem did not provide a UniProtKB accession.
call
INACTIVE
measurement type
IC50
value
49.751
units
uM
Primary qHTS for inhibitors of NSP2Pro chikungunya virus (CHIKV)OTHER 6.2365 uM; NOT_DETERMINEDUniProtKB:Q8JUX6
pubchem.aid:1964107
assay
Primary qHTS for inhibitors of NSP2Pro chikungunya virus (CHIKV)
evidence
  • reference
    pubchem.aid:1964107
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1964107, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency.
call
NOT_DETERMINED
measurement type
OTHER
value
6.2365
units
uM
target enzyme
UniProtKB:Q8JUX6
Primary qHTS for inhibitors of nuclear receptor binding SET domain protein 2 (NSD2) in an RCH-ACV wild type WT cells (2C)OTHER 18.6429 uM; ACTIVENot recorded
pubchem.aid:1645877
assay
Primary qHTS for inhibitors of nuclear receptor binding SET domain protein 2 (NSD2) in an RCH-ACV wild type WT cells (2C)
evidence
  • reference
    pubchem.aid:1645877
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1645877, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency.
call
ACTIVE
measurement type
OTHER
value
18.6429
units
uM
activity class
ENZYME_INHIBITOR
Primary qHTS for inhibitors of nuclear receptor binding SET domain protein 2 (NSD2) in an RCH-ACV wild type WT cells (2C)OTHER 18.6429 uM; ACTIVEUniProtKB:O96028
pubchem.aid:1645877
assay
Primary qHTS for inhibitors of nuclear receptor binding SET domain protein 2 (NSD2) in an RCH-ACV wild type WT cells (2C)
evidence
  • reference
    pubchem.aid:1645877
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1645877, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency.
call
ACTIVE
measurement type
OTHER
value
18.6429
units
uM
target enzyme
UniProtKB:O96028
activity class
ENZYME_INHIBITOR
Primary qHTS for inhibitors of nuclear receptor binding SET domain protein 2 (NSD2) in an isogenic RCH-ACV NSD2 p.E1099K mutant (9B)OTHER 23.47 uM; NOT_DETERMINEDNot recorded
pubchem.aid:1645876
assay
Primary qHTS for inhibitors of nuclear receptor binding SET domain protein 2 (NSD2) in an isogenic RCH-ACV NSD2 p.E1099K mutant (9B)
evidence
  • reference
    pubchem.aid:1645876
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1645876, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency.
call
NOT_DETERMINED
measurement type
OTHER
value
23.47
units
uM
Primary qHTS for inhibitors of nuclear receptor binding SET domain protein 2 (NSD2) in an isogenic RCH-ACV NSD2 p.E1099K mutant (9B)OTHER 23.47 uM; NOT_DETERMINEDUniProtKB:O96028
pubchem.aid:1645876
assay
Primary qHTS for inhibitors of nuclear receptor binding SET domain protein 2 (NSD2) in an isogenic RCH-ACV NSD2 p.E1099K mutant (9B)
evidence
  • reference
    pubchem.aid:1645876
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1645876, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency.
call
NOT_DETERMINED
measurement type
OTHER
value
23.47
units
uM
target enzyme
UniProtKB:O96028
Primary qHTS to identify anti-liver cancer compounds using libraries of approved drugs and bioactive compoundsOTHER 35.4813 uM; NOT_DETERMINEDNot recorded
pubchem.aid:2202548
assay
Primary qHTS to identify anti-liver cancer compounds using libraries of approved drugs and bioactive compounds
evidence
  • reference
    pubchem.aid:2202548
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 2202548, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency.
call
NOT_DETERMINED
measurement type
OTHER
value
35.4813
units
uM
S16 Schwann cell PMP22 intronic element beta-lactamase assayOTHER 12.5797 uM; NOT_DETERMINEDNot recorded
pubchem.aid:624044
assay
S16 Schwann cell PMP22 intronic element beta-lactamase assay
evidence
  • reference
    pubchem.aid:624044
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 624044, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. Target accession NP_058733 was left ungrounded because PubChem did not provide a UniProtKB accession.
call
NOT_DETERMINED
measurement type
OTHER
value
12.5797
units
uM
Selectivity profile for inhibitors of NSP2Pro chikungunya virus (CHIKV): Full length NSP2 enzyme counterscreen (CHIKV-NSP2)OTHER 18.3362 uM; NOT_DETERMINEDUniProtKB:Q8JUX6
pubchem.aid:1964101
assay
Selectivity profile for inhibitors of NSP2Pro chikungunya virus (CHIKV): Full length NSP2 enzyme counterscreen (CHIKV-NSP2)
evidence
  • reference
    pubchem.aid:1964101
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1964101, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency.
call
NOT_DETERMINED
measurement type
OTHER
value
18.3362
units
uM
target enzyme
UniProtKB:Q8JUX6
Selectivity profile for inhibitors of NSP2Pro chikungunya virus (CHIKV): Papain CounterscreenOTHER 18.3362 uM; NOT_DETERMINEDUniProtKB:P00784
pubchem.aid:1964104
assay
Selectivity profile for inhibitors of NSP2Pro chikungunya virus (CHIKV): Papain Counterscreen
evidence
  • reference
    pubchem.aid:1964104
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1964104, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency.
call
NOT_DETERMINED
measurement type
OTHER
value
18.3362
units
uM
target enzyme
UniProtKB:P00784
TR-FRET-based biochemical high-throughput dose response assay to identify inhibitors of Hepatitis C Virus (HCV) core protein dimerization.IC50 29.693 uM; INACTIVENot recorded
pubchem.aid:2159
assay
TR-FRET-based biochemical high-throughput dose response assay to identify inhibitors of Hepatitis C Virus (HCV) core protein dimerization.
evidence
  • reference
    pubchem.aid:2159
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 2159, deposited by The Scripps Research Institute Molecular Screening Center; assay type Confirmatory. Target accession ABC47431 was left ungrounded because PubChem did not provide a UniProtKB accession.
call
INACTIVE
measurement type
IC50
value
29.693
units
uM
Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) drug resistant MV4-11 cellsOTHER 18.6429 uM; NOT_DETERMINEDNot recorded
pubchem.aid:1963824
assay
Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) drug resistant MV4-11 cells
evidence
  • reference
    pubchem.aid:1963824
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1963824, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency.
call
NOT_DETERMINED
measurement type
OTHER
value
18.6429
units
uM
Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) drug resistant MV4-11 cellsOTHER 18.6429 uM; NOT_DETERMINEDUniProtKB:P43405
pubchem.aid:1963824
assay
Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) drug resistant MV4-11 cells
evidence
  • reference
    pubchem.aid:1963824
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1963824, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency.
call
NOT_DETERMINED
measurement type
OTHER
value
18.6429
units
uM
target enzyme
UniProtKB:P43405
Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) naive MV4-11 cellsOTHER 23.47 uM; ACTIVENot recorded
pubchem.aid:1963823
assay
Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) naive MV4-11 cells
evidence
  • reference
    pubchem.aid:1963823
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1963823, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency.
call
ACTIVE
measurement type
OTHER
value
23.47
units
uM
Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) naive MV4-11 cellsOTHER 23.47 uM; ACTIVEUniProtKB:P43405
pubchem.aid:1963823
assay
Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) naive MV4-11 cells
evidence
  • reference
    pubchem.aid:1963823
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1963823, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency.
call
ACTIVE
measurement type
OTHER
value
23.47
units
uM
target enzyme
UniProtKB:P43405
qHTS Assay for Inhibitors of Aldehyde Dehydrogenase 1 (ALDH1A1)OTHER 35.4813 uM; NOT_DETERMINEDNot recorded
pubchem.aid:1030
assay
qHTS Assay for Inhibitors of Aldehyde Dehydrogenase 1 (ALDH1A1)
evidence
  • reference
    pubchem.aid:1030
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1030, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. Target accession AAP35567 was left ungrounded because PubChem did not provide a UniProtKB accession.
call
NOT_DETERMINED
measurement type
OTHER
value
35.4813
units
uM
notes
14 further PubChem assay results are in data/raw/pubchem_bioassay.tsv but not written here.

Explore across X-Mech

AntibioticMech (β-carotene) ↗ MediaIngredientMech (CHEBI:17579) ↗ PathwayMech (mibig:BGC0000646) ↗

Open questions 6

name-disagreement — ChEBI calls this structure 'β-carotene' and MIBiG calls it 'β-carotein'. They share a Standard InChIKey, so if the names denote different compounds then one upstream record has the wrong structure. Check which.

unnamed-producer — No producer claim is written from BGC0000646, which gives NCBITaxon:77133 (uncultured bacterium — shared by every unplaced bacterium), because the taxon names no single organism. The cluster is kept: a characterized locus is an origin assertion whether or not its host has a name, and for a compound from an uncultured symbiont that is the honest state. Name the producer if the primary literature does.

curator-q7z859-assay-reference — Which CrtYB sequence and isoform were assayed for terminal cyclization, and can that assay be mapped to canonical Q7Z859 E307 rather than CBS6938 K307?

curator-p37295-assay-reference — Which al-2 coding model was used in terminal-cyclization assays, and does it match canonical P37295 602aa rather than the historical partial601aa model?

curator-q43415-assay-reference — Which LCY1 sequence and construct were assayed, and does it match canonical Q43415 498aa rather than Lamuyo T146A/N152K or a processed chain?

curator-dclcyb1-construct-reference — What is the complete Nantaise assay sequence, and how does it map to the B493 reference?

Provenance

Source conceptSourceVersion
BGC0000646MIBIG5
CHEBI:17579CHEBI3-star

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