identifier: traitmech:000437 label: DS-13 system definition: A phage defense system in which an organism possesses a genome-encoded DefensePredictor-discovered system 13 locus represented in the pinned DefenseFinder model inventory by DS-13A and DS-13B custom HMM profiles. definition_source: DOI:10.1101/2025.01.08.631726 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: DS-13 synonym_type: EXACT_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: DS-13__DS-13A synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: DS-13__DS-13B synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1101/2025.01.08.631726 snippet: To test for anti-phage defense, we placed each TU with its native promoter region on a low-copy number plasmid in E. coli MG1655 and then challenged these strains with a panel of 24 diverse E. coli phages (fig. S2). In total, 45 (42% of 106) 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 45 predicted transcriptional units as phage-defense systems in E. coli; the first-pass DS-13 record uses this source only for the DefensePredictor DS naming context, not for an exact DS-13 phage readout. - reference: DOI:10.1101/2025.01.08.631726 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: DOI:10.1101/2025.01.08.631726 snippet: To begin elucidating the function of the 45 validated TUs, we further annotated their protein domains (see Methods; table S6). notes: DeWeirdt et al. describe Table S6 as a protein-domain annotation table for the validated DS transcriptional units; the exact preprint DS-13 row was not recovered in this curation pass. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-13 | 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-13 source key to the DeWeirdt et al. DefensePredictor preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-13__DS-13A | | DS-13 | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records DS-13__DS-13A as a custom DS-13 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-13__DS-13B | | DS-13 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records DS-13__DS-13B as a custom DS-13 profile. causal_graphs: - graph_id: ds_13_locus_profile_model title: DS-13 locus profile model description: Conservative system-level sketch linking the DS-13 DefensePredictor-discovered system key to DS-13 system possession and the broader phage-defense-system trait without resolving DS-13 component function or a phage activity readout. scope_status: NONMECHANISTIC scope_notes: The graph captures DS-13 as a DefensePredictor-discovered system with DS-13A and DS-13B custom HMM rows in the pinned DefenseFinder HMM inventory. It does not assert the preprint working identifier, preprint Table S5/S6 rows, final Science supplement rows, native host breadth, profile-to-protein correspondence, DS-13A or DS-13B molecular activity, exact phage target breadth, or DefenseFinder rule-level detection criteria. nodes: - node_id: ds_13_locus label: DS-13 locus node_type: GENETIC_ELEMENT description: A DefensePredictor-discovered system 13 locus represented in the pinned DefenseFinder HMM inventory by DS-13A and DS-13B custom profiles. - node_id: ds_13_system_trait label: DS-13 system node_type: TRAIT grounding: traitmech:000437 description: Possession of a genome-encoded DS-13 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_13_locus predicate: contributes to predicate_id: RO:0002326 object: ds_13_system_trait description: DefenseFinder links the DS-13 source key to the DefensePredictor preprint and represents DS-13 in the HMM inventory with DS-13A and DS-13B custom profiles. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-13 | 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-13 source key to the DeWeirdt et al. DefensePredictor preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-13__DS-13A | | DS-13 | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records DS-13__DS-13A as a custom DS-13 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-13__DS-13B | | DS-13 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records DS-13__DS-13B as a custom DS-13 profile. - subject: ds_13_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: DS-13 system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1101/2025.01.08.631726 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-13 | 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-13 source key to the DeWeirdt et al. DefensePredictor preprint. discussions: - discussion_id: ds-13-defensefinder-model-gap prompt: Resolve DS-13 working-identifier rows, preprint Table S5 and S6 context, final Science supplement omission, native host breadth, DS-13A/DS-13B profile-to-protein mapping, sensitive-phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-13 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: The DeWeirdt et al. preprint supports the DefensePredictor discovered System naming convention, the pinned DefenseFinder article registry names DS-13 and maps it to that preprint, and the pinned HMM inventory records DS-13A and DS-13B custom profile rows. DS-13 is absent from the final Science Table S6, S7, and S8 files checked during this curation pass, the exact preprint per-TU rows were not recovered, the pinned DefenseFinder rules table has no DS-13 row, and the first-pass record does not resolve the working identifier, assayed phages, phage readout, native host, profile-to-component mapping, component activities, or complete detection criteria. evidence: - reference: DOI:10.1101/2025.01.08.631726 snippet: To test for anti-phage defense, we placed each TU with its native promoter region on a low-copy number plasmid in E. coli MG1655 and then challenged these strains with a panel of 24 diverse E. coli phages (fig. S2). In total, 45 (42% of 106) 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:10.1101/2025.01.08.631726 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: DOI:10.1101/2025.01.08.631726 snippet: To begin elucidating the function of the 45 validated TUs, we further annotated their protein domains (see Methods; table S6). notes: DeWeirdt et al. describe Table S6 as further protein-domain annotation of validated TUs. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-13 | 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-13 source key to the DeWeirdt et al. DefensePredictor preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-13__DS-13A | | DS-13 | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records DS-13__DS-13A as a custom DS-13 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-13__DS-13B | | DS-13 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records DS-13__DS-13B as a custom DS-13 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list DS-13, DS-13A, or DS-13B, leaving complete component coverage and rule-level detection criteria unresolved. attaches_to: - causal_graphs#ds_13_locus_profile_model posed_by: codex posed_date: '2026-09-28' curation_history: - timestamp: '2026-09-28T16:05:54Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted DS-13 system as a DOI- and DefenseFinder-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 DS-13 source-key and HMM-profile level because preprint Table S5/S6 rows, final Science supplement rows, and rule rows remain unresolved, and proposals/metpo_traitmech_v314 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-28T16:05:55Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed DS-13 system canonical_examples and left them empty because the pinned DefenseFinder registries support DS-13 system identity and custom HMM coverage but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-13 activity. No paid research was used. llm_assisted: true