identifier: traitmech:000435
label: DS-11 system
definition: A phage defense system in which an organism possesses the single-gene
  DefensePredictor-discovered system 11 locus cataloged as working transcriptional
  unit IMPD 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-11
  synonym_type: EXACT_SYNONYM
  source: DOI:10.1126/science.adv7924
- synonym_text: IMPD
  synonym_type: RELATED_SYNONYM
  source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
- synonym_text: DS-11__DS-11
  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: "IMPD\tNZ_RRVY01000003.1\tGCF_003886375.1\t+\tTrue\tFalse\tFalse\tTrue\t\
    DefensePredictor hits\t365785\t366882\tCBS domain-containing protein\tWP_000257686.1\t\
    4.37610109478113\t1.840433765255303\tTrue\tTrue\tPredicted novel defense gene\t\
    DS-11"
  notes: The final Science supplementary Table S6 maps working_id IMPD to DS_name
    DS-11, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000003.1
    positions 365785-366882 with product accession WP_000257686.1.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
  snippet: "T3\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t300000000\tIMPD\t24-03-08\t\
    24-03-08_MNAC_GHOS_BRNT_IMPD.png\t5\t3\t\t300000\t3\tTrue\t\t\tLB\t37"
  notes: The final Science supplementary Table S7 reports an IMPD assay row with a
    T3 phage readout and a -log(EOP) value of 3.0.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
  snippet: "T3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t200000000\tIMPD\t\t24-07-18\t\
    24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t5\t4\t\t400000\t\
    2.698970004\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tIMPD\t\
    \t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t\
    5\t5\t\t500000\t1.602059991\nT3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t\
    200000000\tIMPD\tY157A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t\
    8\t2\t\t200000000\t0\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\t\
    IMPD\tY157A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t\
    7\t2\t\t20000000\t0\nT3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t200000000\t\
    IMPD\tR330A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t\
    8\t3\t\t300000000\t-0.1760912591\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t\
    20000000\tIMPD\tR330A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t\
    7\t3\t\t30000000\t-0.1760912591\nT3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t\
    200000000\tIMPD\tH335A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t\
    8\t1\t\t100000000\t0.3010299957\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t\
    20000000\tIMPD\tH335A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t\
    6\t6\t\t6000000\t0.5228787453"
  notes: The final Science supplementary Table S7 System Mutants sheet pairs wild-type
    IMPD with IMPD Y157A, R330A, and H335A rows in T3 and Bas67 assay panels.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "IMPD\tDS-11\tTrue"
  notes: The final Science supplementary Table S8 maps IMPD to replicated display
    name DS-11.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "IMPD\t1.0\t365.0\tWP_000257686.1\tHEPN\tPF18731.5\tHEPN_Swt1 ; Swt1-like\
    \ HEPN\thhpred_1021051.hhr\t252.0\t359.0\t0.98\t2024-04-16 00:00:00"
  notes: The final Science supplementary Table S8 reports a HEPN HHpred hit for WP_000257686.1
    in IMPD.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "IMPD\t1.0\t365.0\tWP_000257686.1\tCBS\tcd04614\tCBS_pair_arch2_repeat2;\
    \ Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present\
    \ in archaea\thhpred_1021051.hhr\t134.0\t241.0\t0.9916\t2024-04-16 00:00:00"
  notes: The final Science supplementary Table S8 reports a CBS HHpred hit for WP_000257686.1
    in IMPD.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: '| DS-11 | 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-11 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-11__DS-11                                     |                                                  |
    DS-11                  | Custom                  | 100    |'
  notes: The pinned DefenseFinder HMM inventory records DS-11__DS-11 as a custom DS-11
    profile.
causal_graphs:
- graph_id: ds_11_locus_reduces_phage_plaquing
  title: DS-11 locus reduces bacteriophage plaquing
  description: Conservative system-level sketch linking the single-gene DS-11 locus
    to reduced bacteriophage plaquing without resolving DS-11 component function or
    effector activity.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures DS-11 as the validated IMPD transcriptional unit
    with one product accession, final Table S8 HEPN and CBS HHpred-domain rows, and
    one DefenseFinder DS-11 profile row. It does not assert native host breadth, exact
    profile-to-protein correspondence, the direct viral trigger or ligand, the HEPN
    substrate, whether ATP binding or CBS-ligand binding activates the effector, phage
    target breadth, or DefenseFinder rule-level detection criteria.
  nodes:
  - node_id: ds_11_locus
    label: DS-11 locus
    node_type: GENETIC_ELEMENT
    description: A single-gene DefensePredictor-discovered system locus represented
      in the pinned DefenseFinder HMM inventory by one DS-11 custom profile.
  - node_id: reduced_phage_plaquing
    label: reduced bacteriophage plaquing
    node_type: BIOLOGICAL_PROCESS
    description: Reduced bacteriophage plaquing by cells carrying cloned IMPD.
  - node_id: ds_11_system_trait
    label: DS-11 system
    node_type: TRAIT
    grounding: traitmech:000435
    description: Possession of a genome-encoded DS-11 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_11_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: reduced_phage_plaquing
    description: The DS-11/IMPD locus contributes to reduced bacteriophage plaquing
      when plasmid expressed.
    evidence:
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
      snippet: "IMPD\tNZ_RRVY01000003.1\tGCF_003886375.1\t+\tTrue\tFalse\tFalse\t\
        True\tDefensePredictor hits\t365785\t366882\tCBS domain-containing protein\t\
        WP_000257686.1\t4.37610109478113\t1.840433765255303\tTrue\tTrue\tPredicted\
        \ novel defense gene\tDS-11"
      notes: The final Science supplementary Table S6 maps working_id IMPD to DS_name
        DS-11, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000003.1
        positions 365785-366882 with product accession WP_000257686.1.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "T3\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t300000000\tIMPD\t\
        24-03-08\t24-03-08_MNAC_GHOS_BRNT_IMPD.png\t5\t3\t\t300000\t3\tTrue\t\t\t\
        LB\t37"
      notes: The final Science supplementary Table S7 reports an IMPD assay row with
        a T3 phage readout and a -log(EOP) value of 3.0.
  - subject: reduced_phage_plaquing
    predicate: confers
    predicate_id: METPO:2007700
    object: ds_11_system_trait
    description: DS-11-mediated phage plaquing reduction realizes the DS-11 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 each validated transcriptional unit as a DefensePredictor
        discovered system.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
      snippet: "IMPD\tNZ_RRVY01000003.1\tGCF_003886375.1\t+\tTrue\tFalse\tFalse\t\
        True\tDefensePredictor hits\t365785\t366882\tCBS domain-containing protein\t\
        WP_000257686.1\t4.37610109478113\t1.840433765255303\tTrue\tTrue\tPredicted\
        \ novel defense gene\tDS-11"
      notes: The final Science supplementary Table S6 maps working_id IMPD to DS_name
        DS-11, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000003.1
        positions 365785-366882 with product accession WP_000257686.1.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "T3\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t300000000\tIMPD\t\
        24-03-08\t24-03-08_MNAC_GHOS_BRNT_IMPD.png\t5\t3\t\t300000\t3\tTrue\t\t\t\
        LB\t37"
      notes: The final Science supplementary Table S7 reports an IMPD assay row with
        a T3 phage readout and a -log(EOP) value of 3.0.
  - subject: ds_11_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: DS-11 system possession is a phage-defense-system trait.
    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. validate DSs as anti-phage systems.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: '| DS-11 | 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-11 source key to
        the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has
        since been published in Science.
discussions:
- discussion_id: ds-11-defensefinder-model-gap
  prompt: Resolve DS-11 native host breadth, profile-to-protein mapping, sensitive-phage
    breadth, direct viral trigger, direct HEPN-family nuclease substrate, CBS-ligand
    or ATP-dependent activation model, and rule-level detection criteria before minting
    narrower DS-11 mechanism children.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: DeWeirdt et al. support DS-11 as the defensive IMPD transcriptional unit
    that reduced T3 and Bas67 plaquing when cloned in E. coli MG1655, and the final
    Table S8 HHpred sheet reports HEPN and CBS hits for the single IMPD product. The
    pinned DefenseFinder HMM inventory records one DS-11 profile row, the pinned rules
    table has no DS-11 row, and the first-pass record does not resolve native host
    breadth, exact profile-to-protein correspondence, the direct HEPN substrate, the
    activation ligand, phage target breadth, or endogenous DS-11 activity.
  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. validate predicted transcriptional units by measuring plaquing
      relative to an empty vector control strain.
  - 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: "IMPD\tNZ_RRVY01000003.1\tGCF_003886375.1\t+\tTrue\tFalse\tFalse\tTrue\t\
      DefensePredictor hits\t365785\t366882\tCBS domain-containing protein\tWP_000257686.1\t\
      4.37610109478113\t1.840433765255303\tTrue\tTrue\tPredicted novel defense gene\t\
      DS-11"
    notes: The final Science supplementary Table S6 maps working_id IMPD to DS_name
      DS-11, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000003.1
      positions 365785-366882 with product accession WP_000257686.1.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    snippet: "T3\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t300000000\tIMPD\t24-03-08\t\
      24-03-08_MNAC_GHOS_BRNT_IMPD.png\t5\t3\t\t300000\t3\tTrue\t\t\tLB\t37"
    notes: The final Science supplementary Table S7 reports an IMPD assay row with
      a T3 phage readout and a -log(EOP) value of 3.0.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    snippet: "T3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t200000000\tIMPD\t\t\
      24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t\
      5\t4\t\t400000\t2.698970004\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t\
      20000000\tIMPD\t\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t\
      5\t5\t\t500000\t1.602059991\nT3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t\
      200000000\tIMPD\tY157A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t\
      8\t2\t\t200000000\t0\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\t\
      IMPD\tY157A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t\
      7\t2\t\t20000000\t0\nT3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t200000000\t\
      IMPD\tR330A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t\
      8\t3\t\t300000000\t-0.1760912591\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t\
      20000000\tIMPD\tR330A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t\
      7\t3\t\t30000000\t-0.1760912591\nT3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t\
      200000000\tIMPD\tH335A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t\
      8\t1\t\t100000000\t0.3010299957\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t\
      20000000\tIMPD\tH335A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t\
      6\t6\t\t6000000\t0.5228787453"
    notes: The final Science supplementary Table S7 System Mutants sheet pairs wild-type
      IMPD with IMPD Y157A, R330A, and H335A rows in T3 and Bas67 assay panels.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "IMPD\tDS-11\tTrue"
    notes: The final Science supplementary Table S8 maps IMPD to replicated display
      name DS-11.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "IMPD\t1.0\t365.0\tWP_000257686.1\tHEPN\tPF18731.5\tHEPN_Swt1 ; Swt1-like\
      \ HEPN\thhpred_1021051.hhr\t252.0\t359.0\t0.98\t2024-04-16 00:00:00"
    notes: The final Science supplementary Table S8 reports a HEPN HHpred hit for
      WP_000257686.1 in IMPD.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "IMPD\t1.0\t365.0\tWP_000257686.1\tCBS\tcd04614\tCBS_pair_arch2_repeat2;\
      \ Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present\
      \ in archaea\thhpred_1021051.hhr\t134.0\t241.0\t0.9916\t2024-04-16 00:00:00"
    notes: The final Science supplementary Table S8 reports a CBS HHpred hit for WP_000257686.1
      in IMPD.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    snippet: '| DS-11 | 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-11 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-11__DS-11                                     |                                                  |
      DS-11                  | Custom                  | 100    |'
    notes: The pinned DefenseFinder HMM inventory records DS-11__DS-11 as a custom
      DS-11 profile.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    notes: The pinned DefenseFinder rules table does not list DS-11, leaving rule-level
      detection criteria unresolved.
  attaches_to:
  - causal_graphs#ds_11_locus_reduces_phage_plaquing
  posed_by: codex
  posed_date: '2026-09-28'
curation_history:
- timestamp: '2026-09-28T13:46:45Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted DS-11 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 cloned IMPD transcriptional-unit
    level because HEPN/CBS domain and mutant readouts do not resolve native DS-11
    activation or effector chemistry and proposals/metpo_traitmech_v312 reserves the
    replacement placeholder.
  llm_assisted: true
- timestamp: '2026-09-28T13:46:46Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed DS-11 system canonical_examples and left them empty because DeWeirdt
    et al. support cloned IMPD plaquing assays in E. coli MG1655 plus a DefenseFinder
    DS-11 model, but not a direct named native microbial isolate exemplar with experimentally
    verified endogenous DS-11 activity. No paid research was used.
  llm_assisted: true
- timestamp: '2026-09-28T14:33:00Z'
  curator: codex
  action: ADDRESSED_PR_REVIEW
  changes: 'Resolved PR #1403 review issue #1404 by broadening the DS-11 reduced-phage-plaquing
    node description so it no longer names only T3 while the evidence bundle includes
    Bas67 rows.'
  llm_assisted: true