identifier: traitmech:000431
label: DS-7 system
definition: A phage defense system in which an organism possesses the single-gene
  DefensePredictor-discovered system 7 locus cataloged with working_id SVIR 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-7
  synonym_type: EXACT_SYNONYM
  source: DOI:10.1126/science.adv7924
- synonym_text: SVIR
  synonym_type: RELATED_SYNONYM
  source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
- synonym_text: DS-7__DS-7
  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: "SVIR\tNZ_QOYF01000007.1\tGCF_003334585.1\t+\tTrue\tFalse\tFalse\tTrue\t\
    DefensePredictor hits\t310084\t311190\tDUF2634 domain-containing protein\tWP_225403053.1\t\
    5.785481186679323\t3.623314765621056\tTrue\tTrue\tPredicted novel defense gene\t\
    DS-7"
  notes: The final Science supplementary Table S6 maps working_id SVIR to DS_name
    DS-7, marks the cloned transcriptional unit as defensive, and records NZ_QOYF01000007.1
    positions 310084-311190 with product accession WP_225403053.1.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
  snippet: "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tSVIR\t24-03-12\t\
    24-03-12_SVIR_PIN8_NTTI_NADR.png\t2\t100\t\t10000\t2.6989700043360187\tTrue\t\t\
    \tLB\t37"
  notes: The final Science supplementary Table S7 reports an SVIR assay row with a
    Bas60 phage readout and a -log(EOP) value of 2.699.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
  snippet: "Bas60\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\t\
    SVIR\t\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t\
    4\t14\t\t140000\t1.330993219\nBas60\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t\
    3000000\tSVIR\tH52A\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t\
    5\t10\t\t1000000\t0.4771212547"
  notes: The final Science supplementary Table S7 System Mutants sheet pairs wild-type
    SVIR and SVIR H52A in a Bas60 assay panel, with -log(EOP) shifting from 1.331
    to 0.477 for the H52A mutant.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
  snippet: "Bas60\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tSVIR\t\t24-07-18\t\
    24-07-18_DISA-R468A_DISA_SVIR_DISA-D433A_SVIR-H52A.png\t0\t1\t\t1\t5.602059991\n\
    Bas60\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tSVIR\tH52A\t24-07-18\t\
    24-07-18_DISA-R468A_DISA_SVIR_DISA-D433A_SVIR-H52A.png\t4\t22\t\t220000\t0.2596373105"
  notes: The final Science supplementary Table S7 System Mutants sheet records a second
    SVIR versus SVIR H52A Bas60 panel, with -log(EOP) shifting from 5.602 to 0.260
    for the H52A mutant.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "SVIR\tDS-7\tTrue"
  notes: The final Science supplementary Table S8 maps SVIR to replicated display
    name DS-7.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "SVIR\t1.0\t368.0\tWP_225403053.1\tHNH endonuclease\t7RWK_A\tSAVED domain-containing\
    \ protein; DNA nuclease SAVED Sensor Effector\thhpred_1710432.hhr\t5.0\t122.0\t\
    0.99\t2024-04-17 00:00:00"
  notes: The final Science supplementary Table S8 reports an HNH endonuclease HHpred
    hit for WP_225403053.1 in SVIR.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "SVIR\t1.0\t368.0\tWP_225403053.1\tPhage baseplate\t8ENV_M\tSheath initiator\
    \ gp34; Pseudomonas, phage, baseplate\thhpred_1710432.hhr\t225.0\t350.0\t0.99\t\
    2024-04-17 00:00:00"
  notes: The final Science supplementary Table S8 reports a phage-baseplate-like HHpred
    hit for WP_225403053.1 in SVIR.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: '| DS-7 | 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-7 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-7__DS-7                                       |                                                  |
    DS-7                   | Custom                  | 200    |'
  notes: The pinned DefenseFinder HMM inventory records DS-7__DS-7 as a custom DS-7
    profile.
causal_graphs:
- graph_id: ds_7_locus_reduces_phage_plaquing
  title: DS-7 locus reduces bacteriophage plaquing
  description: Conservative system-level sketch linking the single-gene DS-7 locus
    to reduced bacteriophage plaquing without resolving DS-7 component function or
    effector activity.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures DS-7 as the validated SVIR transcriptional unit
    with one product accession and with a DefenseFinder DS-7 profile row. It does
    not assert native host breadth, exact profile-to-protein correspondence, the direct
    viral trigger or substrate, the exact HNH endonuclease activity, phage-baseplate-like
    domain relevance, phage target breadth, or DefenseFinder rule-level detection
    criteria.
  nodes:
  - node_id: ds_7_locus
    label: DS-7 locus
    node_type: GENETIC_ELEMENT
    description: A single-gene DefensePredictor-discovered system locus represented
      in the pinned DefenseFinder HMM inventory by one DS-7 custom profile.
  - node_id: reduced_phage_plaquing
    label: reduced bacteriophage plaquing
    node_type: BIOLOGICAL_PROCESS
    description: Reduced efficiency of plaquing by bacteriophage Bas60 in cells carrying
      cloned SVIR.
  - node_id: ds_7_system_trait
    label: DS-7 system
    node_type: TRAIT
    grounding: traitmech:000431
    description: Possession of a genome-encoded DS-7 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_7_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: reduced_phage_plaquing
    description: The DS-7/SVIR locus contributes to reduced bacteriophage plaquing
      when plasmid expressed.
    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 validate DefensePredictor-discovered systems
        by assaying cloned transcriptional units against E. coli phages.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
      snippet: "SVIR\tNZ_QOYF01000007.1\tGCF_003334585.1\t+\tTrue\tFalse\tFalse\t\
        True\tDefensePredictor hits\t310084\t311190\tDUF2634 domain-containing protein\t\
        WP_225403053.1\t5.785481186679323\t3.623314765621056\tTrue\tTrue\tPredicted\
        \ novel defense gene\tDS-7"
      notes: The final Science supplementary Table S6 maps working_id SVIR to DS_name
        DS-7, marks the cloned transcriptional unit as defensive, and records NZ_QOYF01000007.1
        positions 310084-311190 with product accession WP_225403053.1.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tSVIR\t\
        24-03-12\t24-03-12_SVIR_PIN8_NTTI_NADR.png\t2\t100\t\t10000\t2.6989700043360187\t\
        True\t\t\tLB\t37"
      notes: The final Science supplementary Table S7 reports an SVIR assay row with
        a Bas60 phage readout and a -log(EOP) value of 2.699.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas60\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t\
        3000000\tSVIR\t\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t\
        4\t14\t\t140000\t1.330993219\nBas60\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t\
        3000000\tSVIR\tH52A\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t\
        5\t10\t\t1000000\t0.4771212547"
      notes: The final Science supplementary Table S7 System Mutants sheet pairs wild-type
        SVIR and SVIR H52A in a Bas60 assay panel, with -log(EOP) shifting from 1.331
        to 0.477 for the H52A mutant.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas60\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tSVIR\t\
        \t24-07-18\t24-07-18_DISA-R468A_DISA_SVIR_DISA-D433A_SVIR-H52A.png\t0\t1\t\
        \t1\t5.602059991\nBas60\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\t\
        SVIR\tH52A\t24-07-18\t24-07-18_DISA-R468A_DISA_SVIR_DISA-D433A_SVIR-H52A.png\t\
        4\t22\t\t220000\t0.2596373105"
      notes: The final Science supplementary Table S7 System Mutants sheet records
        a second SVIR versus SVIR H52A Bas60 panel, with -log(EOP) shifting from 5.602
        to 0.260 for the H52A mutant.
  - subject: reduced_phage_plaquing
    predicate: confers
    predicate_id: METPO:2007700
    object: ds_7_system_trait
    description: DS-7-mediated phage plaquing reduction realizes the DS-7 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: "SVIR\tNZ_QOYF01000007.1\tGCF_003334585.1\t+\tTrue\tFalse\tFalse\t\
        True\tDefensePredictor hits\t310084\t311190\tDUF2634 domain-containing protein\t\
        WP_225403053.1\t5.785481186679323\t3.623314765621056\tTrue\tTrue\tPredicted\
        \ novel defense gene\tDS-7"
      notes: The final Science supplementary Table S6 maps working_id SVIR to DS_name
        DS-7, marks the cloned transcriptional unit as defensive, and records NZ_QOYF01000007.1
        positions 310084-311190 with product accession WP_225403053.1.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tSVIR\t\
        24-03-12\t24-03-12_SVIR_PIN8_NTTI_NADR.png\t2\t100\t\t10000\t2.6989700043360187\t\
        True\t\t\tLB\t37"
      notes: The final Science supplementary Table S7 reports an SVIR assay row with
        a Bas60 phage readout and a -log(EOP) value of 2.699.
  - subject: ds_7_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: DS-7 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-7 | 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-7 source key to
        the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has
        since been published in Science.
discussions:
- discussion_id: ds-7-defensefinder-model-gap
  prompt: Resolve DS-7 native host breadth, exact single-component activity, DS-7
    profile-to-protein mapping, sensitive-phage breadth, HNH endonuclease activity,
    the role of the H52 residue, the phage-baseplate-like hit, and rule-level detection
    criteria before minting narrower DS-7 mechanism children.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: DeWeirdt et al. support DS-7 as the defensive SVIR transcriptional unit
    that reduced Bas60 plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder
    HMM inventory records one DS-7 profile row. The pinned rules table has no DS-7
    row, and the first-pass record does not resolve native host breadth, exact profile-to-protein
    correspondence, HNH endonuclease activity, the function of the H52 residue, phage
    target breadth, or endogenous DS-7 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: "SVIR\tNZ_QOYF01000007.1\tGCF_003334585.1\t+\tTrue\tFalse\tFalse\tTrue\t\
      DefensePredictor hits\t310084\t311190\tDUF2634 domain-containing protein\tWP_225403053.1\t\
      5.785481186679323\t3.623314765621056\tTrue\tTrue\tPredicted novel defense gene\t\
      DS-7"
    notes: The final Science supplementary Table S6 maps working_id SVIR to DS_name
      DS-7, marks the cloned transcriptional unit as defensive, and records NZ_QOYF01000007.1
      positions 310084-311190 with product accession WP_225403053.1.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    snippet: "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tSVIR\t24-03-12\t\
      24-03-12_SVIR_PIN8_NTTI_NADR.png\t2\t100\t\t10000\t2.6989700043360187\tTrue\t\
      \t\tLB\t37"
    notes: The final Science supplementary Table S7 reports an SVIR assay row with
      a Bas60 phage readout and a -log(EOP) value of 2.699.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    snippet: "Bas60\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t\
      3000000\tSVIR\t\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t\
      4\t14\t\t140000\t1.330993219\nBas60\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t\
      3000000\tSVIR\tH52A\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t\
      5\t10\t\t1000000\t0.4771212547"
    notes: The final Science supplementary Table S7 System Mutants sheet pairs wild-type
      SVIR and SVIR H52A in a Bas60 assay panel, with -log(EOP) shifting from 1.331
      to 0.477 for the H52A mutant.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    snippet: "Bas60\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tSVIR\t\t\
      24-07-18\t24-07-18_DISA-R468A_DISA_SVIR_DISA-D433A_SVIR-H52A.png\t0\t1\t\t1\t\
      5.602059991\nBas60\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tSVIR\t\
      H52A\t24-07-18\t24-07-18_DISA-R468A_DISA_SVIR_DISA-D433A_SVIR-H52A.png\t4\t\
      22\t\t220000\t0.2596373105"
    notes: The final Science supplementary Table S7 System Mutants sheet records a
      second SVIR versus SVIR H52A Bas60 panel, with -log(EOP) shifting from 5.602
      to 0.260 for the H52A mutant.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "SVIR\tDS-7\tTrue"
    notes: The final Science supplementary Table S8 maps SVIR to replicated display
      name DS-7.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "SVIR\t1.0\t368.0\tWP_225403053.1\tHNH endonuclease\t7RWK_A\tSAVED domain-containing\
      \ protein; DNA nuclease SAVED Sensor Effector\thhpred_1710432.hhr\t5.0\t122.0\t\
      0.99\t2024-04-17 00:00:00"
    notes: The final Science supplementary Table S8 reports an HNH endonuclease HHpred
      hit for WP_225403053.1 in SVIR.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "SVIR\t1.0\t368.0\tWP_225403053.1\tPhage baseplate\t8ENV_M\tSheath initiator\
      \ gp34; Pseudomonas, phage, baseplate\thhpred_1710432.hhr\t225.0\t350.0\t0.99\t\
      2024-04-17 00:00:00"
    notes: The final Science supplementary Table S8 reports a phage-baseplate-like
      HHpred hit for WP_225403053.1 in SVIR.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    snippet: '| DS-7 | 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-7 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-7__DS-7                                       |                                                  |
      DS-7                   | Custom                  | 200    |'
    notes: The pinned DefenseFinder HMM inventory records DS-7__DS-7 as a custom DS-7
      profile.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    notes: The pinned DefenseFinder rules table does not list DS-7, leaving rule-level
      detection criteria unresolved.
  attaches_to:
  - causal_graphs#ds_7_locus_reduces_phage_plaquing
  posed_by: codex
  posed_date: '2026-09-28'
curation_history:
- timestamp: '2026-09-28T09:58:00Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted DS-7 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 SVIR transcriptional-unit
    level because the pinned DefenseFinder DS-7 HMM row is not backed by a rules row;
    proposals/metpo_traitmech_v308 reserves the replacement placeholder.
  llm_assisted: true
- timestamp: '2026-09-28T09:58:01Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed DS-7 system canonical_examples and left them empty because DeWeirdt
    et al. support cloned SVIR plaquing assays in E. coli MG1655 plus a DefenseFinder
    DS-7 model, but not a direct named native microbial isolate exemplar with experimentally
    verified endogenous DS-7 activity. No paid research was used.
  llm_assisted: true