identifier: traitmech:000461
label: DS-39 system
definition: A phage defense system in which an organism possesses the single-gene
  DefensePredictor-discovered system 39 locus cataloged as working transcriptional
  unit AAA5 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.
definition_source: DOI:10.1126/science.adv7924
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: DS-39
  synonym_type: EXACT_SYNONYM
  source: DOI:10.1126/science.adv7924
- synonym_text: AAA5
  synonym_type: RELATED_SYNONYM
  source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
- synonym_text: DS-39__DS-39
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
evidence:
- reference: DOI:10.1126/science.adv7924
  snippet: To test for anti-phage defense, we placed each TU with its predicted native
    promoter region on a low-copy number plasmid in E. coli MG1655 and challenged
    these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In
    total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced
    the efficiency of plating (EOP) at least ten-fold relative to an empty vector
    control strain
  notes: DeWeirdt et al. experimentally validated 42 predicted transcriptional units
    as phage-defense systems in E. coli.
- reference: DOI:10.1126/science.adv7924
  snippet: We refer to these validated TUs as DefensePredictor discovered systems
    (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A
    is the first gene of DS-8.
  notes: DeWeirdt et al. name validated transcriptional units as DefensePredictor
    discovered systems.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
  snippet: "AAA5\tNZ_RRWS01000024.1\tGCF_003892555.1\t+\tTrue\tFalse\tTrue\tTrue\t\
    DefensePredictor hits\t12586\t14718\tMarR family transcriptional regulator\tWP_042346724.1\t\
    9.53722790980957\t3.842009204807092\tTrue\tTrue\tPredicted novel defense gene\t\
    DS-39"
  notes: The final Science supplementary Table S6 maps working_id AAA5 to DS_name
    DS-39, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000024.1
    positions 12586-14718 with product accession WP_042346724.1.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
  snippet: "Bas1\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t5000000\tAAA5\t24-04-10\t\
    24-04-10_HTHO_AAA5.png\t0\t1\t\t1\t6.698970004336019\t\tTrue\t\tLB\t37"
  notes: The final Science supplementary Table S7 Systems sheet reports an AAA5 assay
    row with a Bas1 phage readout and a -log(EOP) value of 6.699.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
  snippet: "Bas3\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t200000000\tAAA5\t24-04-10\t\
    24-04-10_HTHO_AAA5.png\t3\t7\tY\t7000\t4.455931955649724\t\tTrue\t\tLB\t37"
  notes: The final Science supplementary Table S7 Systems sheet reports an AAA5 assay
    row with a Bas3 phage readout and a -log(EOP) value of 4.456.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "AAA5\tDS-39\tTrue"
  notes: The final Science supplementary Table S8 maps AAA5 to replicated display
    name DS-39.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "AAA5\t1.0\t710.0\tWP_042346724.1\tAAA+ ATPase\t7MCA_I\tCell division control\
    \ protein 6; replication initiation, REPLICATION\thhpred_6053627.hhr\t53.0\t540.0\t\
    0.9852\t2024-04-15 00:00:00\t\t"
  notes: The final Science supplementary Table S8 reports a high-probability AAA+
    ATPase HHpred hit for WP_042346724.1 in AAA5.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "AAA5\t1.0\t710.0\tWP_042346724.1\tZF\tPF18256.5\tHscB_4_cys ; Co-chaperone\
    \ HscB tetracysteine metal binding motif\thhpred_6053627.hhr\t583.0\t615.0\t0.87\t\
    2024-04-15 00:00:00\t\t"
  notes: The final Science supplementary Table S8 reports a moderate-probability zinc-finger
    HHpred hit for WP_042346724.1 in AAA5.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "AAA5\t1.0\t710.0\tWP_042346724.1\tHTH\t5HS5_B\tHTH-type transcriptional\
    \ regulator SarX\thhpred_6053627.hhr\t623.0\t706.0\t0.98\t2024-04-15 00:00:00\t\
    \t"
  notes: The final Science supplementary Table S8 reports a high-probability HTH HHpred
    hit for WP_042346724.1 in AAA5.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: '| DS-39 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine
    learning model to discover novel prokaryotic immune systems | '
  notes: The pinned DefenseFinder article registry maps the DS-39 source key to the
    preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been
    published in Science.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| DS-39__DS-39                                     |                                                  |
    DS-39                  | Custom                  | 200    |'
  notes: The pinned DefenseFinder HMM inventory records DS-39__DS-39 as a custom DS-39
    profile.
causal_graphs:
- graph_id: ds_39_locus_reduces_phage_plaquing
  title: DS-39 locus reduces bacteriophage plaquing
  description: Conservative system-level sketch linking the single-gene DS-39 locus
    to reduced bacteriophage plaquing without resolving DS-39 component function or
    molecular output.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures DS-39 as the validated AAA5 transcriptional unit
    with one product accession, high-probability AAA+ ATPase and HTH HHpred rows for
    WP_042346724.1, a moderate-probability zinc-finger HHpred row for WP_042346724.1,
    and one DefenseFinder DS-39 profile row. It does not assert exact profile-to-protein
    correspondence, AAA+ ATPase activity, HTH DNA-binding activity, zinc-finger metal-binding
    activity, native host breadth, DS-39 molecular output, complete phage breadth,
    or DefenseFinder rule-level detection criteria.
  nodes:
  - node_id: ds_39_locus
    label: DS-39 locus
    node_type: GENETIC_ELEMENT
    description: A single-gene DefensePredictor-discovered system 39 locus represented
      in the pinned DefenseFinder HMM inventory by one DS-39 custom profile.
  - node_id: reduced_phage_plaquing
    label: reduced bacteriophage plaquing
    node_type: BIOLOGICAL_PROCESS
    description: Reduced bacteriophage plaquing in cells carrying cloned AAA5.
  - node_id: ds_39_system_trait
    label: DS-39 system
    node_type: TRAIT
    grounding: traitmech:000461
    description: Possession of a genome-encoded DS-39 phage-defense system.
  - node_id: phage_defense_system
    label: phage defense system
    node_type: TRAIT
    grounding: traitmech:000209
    description: Possession of one or more genome-encoded immune systems that inhibit
      bacteriophage infection.
  edges:
  - subject: ds_39_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: reduced_phage_plaquing
    description: The DS-39/AAA5 locus contributes to reduced bacteriophage plaquing
      in heterologous E. coli MG1655 plasmid-expression assays.
    evidence:
    - reference: DOI:10.1126/science.adv7924
      snippet: To test for anti-phage defense, we placed each TU with its predicted
        native promoter region on a low-copy number plasmid in E. coli MG1655 and
        challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3;
        fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque
        sizes or reduced the efficiency of plating (EOP) at least ten-fold relative
        to an empty vector control strain
      notes: DeWeirdt et al. describe the plasmid-based phage challenge used to validate
        predicted transcriptional units.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
      snippet: "AAA5\tNZ_RRWS01000024.1\tGCF_003892555.1\t+\tTrue\tFalse\tTrue\tTrue\t\
        DefensePredictor hits\t12586\t14718\tMarR family transcriptional regulator\t\
        WP_042346724.1\t9.53722790980957\t3.842009204807092\tTrue\tTrue\tPredicted\
        \ novel defense gene\tDS-39"
      notes: The final Science supplementary Table S6 maps working_id AAA5 to DS_name
        DS-39, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000024.1
        positions 12586-14718 with product accession WP_042346724.1.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas1\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t5000000\tAAA5\t\
        24-04-10\t24-04-10_HTHO_AAA5.png\t0\t1\t\t1\t6.698970004336019\t\tTrue\t\t\
        LB\t37"
      notes: The final Science supplementary Table S7 Systems sheet reports an AAA5
        assay row with a Bas1 phage readout and a -log(EOP) value of 6.699.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas3\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t200000000\tAAA5\t\
        24-04-10\t24-04-10_HTHO_AAA5.png\t3\t7\tY\t7000\t4.455931955649724\t\tTrue\t\
        \tLB\t37"
      notes: The final Science supplementary Table S7 Systems sheet reports an AAA5
        assay row with a Bas3 phage readout and a -log(EOP) value of 4.456.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
      snippet: "AAA5\tDS-39\tTrue"
      notes: The final Science supplementary Table S8 maps AAA5 to replicated display
        name DS-39.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
      snippet: "AAA5\t1.0\t710.0\tWP_042346724.1\tAAA+ ATPase\t7MCA_I\tCell division\
        \ control protein 6; replication initiation, REPLICATION\thhpred_6053627.hhr\t\
        53.0\t540.0\t0.9852\t2024-04-15 00:00:00\t\t"
      notes: The final Science supplementary Table S8 reports a high-probability AAA+
        ATPase HHpred hit for WP_042346724.1 in AAA5.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
      snippet: "AAA5\t1.0\t710.0\tWP_042346724.1\tZF\tPF18256.5\tHscB_4_cys ; Co-chaperone\
        \ HscB tetracysteine metal binding motif\thhpred_6053627.hhr\t583.0\t615.0\t\
        0.87\t2024-04-15 00:00:00\t\t"
      notes: The final Science supplementary Table S8 reports a moderate-probability
        zinc-finger HHpred hit for WP_042346724.1 in AAA5.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
      snippet: "AAA5\t1.0\t710.0\tWP_042346724.1\tHTH\t5HS5_B\tHTH-type transcriptional\
        \ regulator SarX\thhpred_6053627.hhr\t623.0\t706.0\t0.98\t2024-04-15 00:00:00\t\
        \t"
      notes: The final Science supplementary Table S8 reports a high-probability HTH
        HHpred hit for WP_042346724.1 in AAA5.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| DS-39__DS-39                                     |                                                  |
        DS-39                  | Custom                  | 200    |'
      notes: The pinned DefenseFinder HMM inventory records DS-39__DS-39 as a custom
        DS-39 profile.
  - subject: reduced_phage_plaquing
    predicate: confers
    predicate_id: METPO:2007700
    object: ds_39_system_trait
    description: DS-39-mediated phage plaquing reduction realizes the DS-39 system
      trait.
    evidence:
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
      snippet: "AAA5\tNZ_RRWS01000024.1\tGCF_003892555.1\t+\tTrue\tFalse\tTrue\tTrue\t\
        DefensePredictor hits\t12586\t14718\tMarR family transcriptional regulator\t\
        WP_042346724.1\t9.53722790980957\t3.842009204807092\tTrue\tTrue\tPredicted\
        \ novel defense gene\tDS-39"
      notes: The final Science supplementary Table S6 maps working_id AAA5 to DS_name
        DS-39, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000024.1
        positions 12586-14718 with product accession WP_042346724.1.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas1\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t5000000\tAAA5\t\
        24-04-10\t24-04-10_HTHO_AAA5.png\t0\t1\t\t1\t6.698970004336019\t\tTrue\t\t\
        LB\t37"
      notes: The final Science supplementary Table S7 Systems sheet reports an AAA5
        assay row with a Bas1 phage readout and a -log(EOP) value of 6.699.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas3\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t200000000\tAAA5\t\
        24-04-10\t24-04-10_HTHO_AAA5.png\t3\t7\tY\t7000\t4.455931955649724\t\tTrue\t\
        \tLB\t37"
      notes: The final Science supplementary Table S7 Systems sheet reports an AAA5
        assay row with a Bas3 phage readout and a -log(EOP) value of 4.456.
    - reference: DOI:10.1126/science.adv7924
      snippet: We refer to these validated TUs as DefensePredictor discovered systems
        (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g.,
        DS-8A is the first gene of DS-8.
      notes: The DS nomenclature is used for DefensePredictor discovered systems.
  - subject: ds_39_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: DS-39 system possession is a phage-defense-system trait.
    evidence:
    - reference: DOI:10.1126/science.adv7924
      snippet: We refer to these validated TUs as DefensePredictor discovered systems
        (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g.,
        DS-8A is the first gene of DS-8.
      notes: DeWeirdt et al. name validated TUs as DefensePredictor discovered systems.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: '| DS-39 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine
        learning model to discover novel prokaryotic immune systems | '
      notes: The pinned DefenseFinder article registry maps the DS-39 source key to
        the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has
        since been published in Science.
discussions:
- discussion_id: ds-39-defensefinder-model-gap
  prompt: Resolve DS-39 native host breadth, exact component activity, profile-to-protein
    mapping, AAA+ ATPase interpretation, HTH/zinc-finger interpretation, complete
    phage breadth, molecular output, and rule-level DefenseFinder criteria before
    minting narrower DS-39 mechanism children.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: DeWeirdt et al. support DS-39 as the defensive AAA5 transcriptional unit
    and final Science Tables S6/S7/S8 map it to one product accession, Bas1 and Bas3
    phage readouts, display name DS-39, high-probability AAA+ ATPase and HTH HHpred
    rows, and a moderate-probability zinc-finger HHpred row. The pinned DefenseFinder
    HMM inventory records one DS-39 custom profile row. The pinned rules table has
    no DS-39 row, and the first-pass record does not resolve native host breadth,
    complete phage breadth, direct profile-to-protein correspondence, AAA+ ATPase
    activity, HTH or zinc-finger interpretation, molecular output, or endogenous DS-39
    activity.
  evidence:
  - reference: DOI:10.1126/science.adv7924
    snippet: We refer to these validated TUs as DefensePredictor discovered systems
      (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g.,
      DS-8A is the first gene of DS-8.
    notes: DeWeirdt et al. name validated TUs as DSs.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
    snippet: "AAA5\tNZ_RRWS01000024.1\tGCF_003892555.1\t+\tTrue\tFalse\tTrue\tTrue\t\
      DefensePredictor hits\t12586\t14718\tMarR family transcriptional regulator\t\
      WP_042346724.1\t9.53722790980957\t3.842009204807092\tTrue\tTrue\tPredicted novel\
      \ defense gene\tDS-39"
    notes: The final Science supplementary Table S6 maps working_id AAA5 to DS_name
      DS-39, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000024.1
      positions 12586-14718 with product accession WP_042346724.1.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    snippet: "Bas1\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t5000000\tAAA5\t24-04-10\t\
      24-04-10_HTHO_AAA5.png\t0\t1\t\t1\t6.698970004336019\t\tTrue\t\tLB\t37"
    notes: The final Science supplementary Table S7 Systems sheet reports an AAA5
      assay row with a Bas1 phage readout and a -log(EOP) value of 6.699.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    snippet: "Bas3\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t200000000\tAAA5\t\
      24-04-10\t24-04-10_HTHO_AAA5.png\t3\t7\tY\t7000\t4.455931955649724\t\tTrue\t\
      \tLB\t37"
    notes: The final Science supplementary Table S7 Systems sheet reports an AAA5
      assay row with a Bas3 phage readout and a -log(EOP) value of 4.456.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "AAA5\tDS-39\tTrue"
    notes: The final Science supplementary Table S8 maps AAA5 to replicated display
      name DS-39.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "AAA5\t1.0\t710.0\tWP_042346724.1\tAAA+ ATPase\t7MCA_I\tCell division\
      \ control protein 6; replication initiation, REPLICATION\thhpred_6053627.hhr\t\
      53.0\t540.0\t0.9852\t2024-04-15 00:00:00\t\t"
    notes: The final Science supplementary Table S8 reports a high-probability AAA+
      ATPase HHpred hit for WP_042346724.1 in AAA5.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "AAA5\t1.0\t710.0\tWP_042346724.1\tZF\tPF18256.5\tHscB_4_cys ; Co-chaperone\
      \ HscB tetracysteine metal binding motif\thhpred_6053627.hhr\t583.0\t615.0\t\
      0.87\t2024-04-15 00:00:00\t\t"
    notes: The final Science supplementary Table S8 reports a moderate-probability
      zinc-finger HHpred hit for WP_042346724.1 in AAA5.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "AAA5\t1.0\t710.0\tWP_042346724.1\tHTH\t5HS5_B\tHTH-type transcriptional\
      \ regulator SarX\thhpred_6053627.hhr\t623.0\t706.0\t0.98\t2024-04-15 00:00:00\t\
      \t"
    notes: The final Science supplementary Table S8 reports a high-probability HTH
      HHpred hit for WP_042346724.1 in AAA5.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    snippet: '| DS-39 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine
      learning model to discover novel prokaryotic immune systems | '
    notes: The pinned DefenseFinder article registry maps the DS-39 source key to
      the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since
      been published in Science.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| DS-39__DS-39                                     |                                                  |
      DS-39                  | Custom                  | 200    |'
    notes: The pinned DefenseFinder HMM inventory records DS-39__DS-39 as a custom
      DS-39 profile.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    notes: The pinned DefenseFinder rules table does not list DS-39, leaving rule-level
      detection criteria unresolved.
  attaches_to:
  - causal_graphs#ds_39_locus_reduces_phage_plaquing
  posed_by: codex
  posed_date: '2026-09-29'
curation_history:
- timestamp: '2026-09-29T11:35:06Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted DS-39 system as a DOI-backed GENOMICS TraitRecord under phage defense
    system after an ignored-and-hidden duplicate review found no exact live TraitMech,
    METPO, history, or prior proposal record; kept the graph at AAA5 transcriptional-unit
    level because the AAA+ ATPase, HTH, zinc-finger, and rule rows remain unresolved,
    and proposals/metpo_traitmech_v338 reserves the replacement placeholder.
  llm_assisted: true
- timestamp: '2026-09-29T11:35:07Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed DS-39 system canonical_examples and left them empty because DeWeirdt
    et al. directly support cloned AAA5 assays in E. coli MG1655 and a DefenseFinder
    DS-39 model, but not a direct named native microbial isolate exemplar with experimentally
    verified endogenous DS-39 activity. No paid research was used.
  llm_assisted: true