identifier: traitmech:000420 label: SDIC1 system definition: A phage defense system in which an organism possesses an SDIC1 locus encoding a TIR-domain SDIC1A component and a ubiquitin-ligase-like SDIC1B component that can provide population-wide immunity against bacteriophages. definition_source: DOI:10.1016/j.celrep.2024.115055 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: SDIC1 synonym_type: EXACT_SYNONYM source: DOI:10.1016/j.celrep.2024.115055 - synonym_text: SDIC1__SDIC1A synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: SDIC1__SDIC1B synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1016/j.celrep.2024.115055 snippet: four newly identified anti-phage systems notes: Cummins et al. identify SDIC1 in a cohort of Serratia defense-island candidate systems with anti-phage activity. - reference: DOI:10.1016/j.celrep.2024.115055 snippet: previously unreported Toll/interleukin (IL)-1 receptor (TIR)-domain-containing system with population-wide immunity notes: Cummins et al. support SDIC1 as a TIR-domain-containing phage-defense system with a population-wide immunity phenotype. - reference: DOI:10.1016/j.celrep.2024.115055 snippet: SDIC1 combines TIR and ubiquitin ligase notes: Cummins et al. connect the SDIC1 system with TIR and ubiquitin-ligase-like components. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: SDIC1 | 10\.1016/j\.celrep\.2024\.115055 | Multi-conflict islands are a widespread trend within Serratia spp notes: The pinned DefenseFinder article registry maps the SDIC1 source key to the Cummins et al. Serratia multi-conflict-island paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC1__SDIC1A | | SDIC1 | Custom | 350 |' notes: The pinned DefenseFinder HMM inventory records SDIC1__SDIC1A as a custom SDIC1 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC1__SDIC1B | | SDIC1 | Custom | 130 |' notes: The pinned DefenseFinder HMM inventory records SDIC1__SDIC1B as a custom SDIC1 profile. causal_graphs: - graph_id: sdic1_locus_restricts_phage title: SDIC1 loci confer bacterial phage defense description: Conservative system-level sketch linking the SDIC1 locus to population-wide immunity against bacteriophages. scope_status: NONMECHANISTIC scope_notes: The graph captures SDIC1 as a named anti-phage system with SDIC1A and SDIC1B DefenseFinder profiles while leaving natural host breadth, sensitive-phage breadth, the exact SDIC1A/SDIC1B profile-to-protein correspondence, the direct trigger, the ubiquitination substrate, and rule-level detection criteria unresolved. nodes: - node_id: sdic1_locus label: SDIC1 locus node_type: GENETIC_ELEMENT description: An SDIC1 anti-phage defense locus represented in the pinned DefenseFinder HMM inventory by SDIC1A and SDIC1B custom profiles. - node_id: population_wide_antiphage_immunity label: population-wide anti-phage immunity node_type: BIOLOGICAL_PROCESS description: Protection of a bacterial population against bacteriophage infection by SDIC1 activity. - node_id: sdic1_system_trait label: SDIC1 system node_type: TRAIT grounding: traitmech:000420 description: Possession of a genome-encoded SDIC1 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: sdic1_locus predicate: contributes to predicate_id: RO:0002326 object: population_wide_antiphage_immunity description: The SDIC1 locus contributes to population-wide immunity against bacteriophages. evidence: - reference: DOI:10.1016/j.celrep.2024.115055 snippet: previously unreported Toll/interleukin (IL)-1 receptor (TIR)-domain-containing system with population-wide immunity notes: Cummins et al. report population-wide immunity for the SDIC1 TIR-domain system. - reference: DOI:10.1016/j.celrep.2024.115055 snippet: SDIC1 combines TIR and ubiquitin ligase notes: Cummins et al. place TIR and ubiquitin-ligase-like activities in the SDIC1 system. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC1__SDIC1A | | SDIC1 | Custom | 350 |' notes: The pinned DefenseFinder HMM inventory records SDIC1__SDIC1A as a custom SDIC1 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC1__SDIC1B | | SDIC1 | Custom | 130 |' notes: The pinned DefenseFinder HMM inventory records SDIC1__SDIC1B as a custom SDIC1 profile. - subject: population_wide_antiphage_immunity predicate: confers predicate_id: METPO:2007700 object: sdic1_system_trait description: SDIC1-mediated anti-phage immunity realizes the SDIC1 system trait. evidence: - reference: DOI:10.1016/j.celrep.2024.115055 snippet: four newly identified anti-phage systems notes: Cummins et al. identify SDIC1 in the newly reported anti-phage system cohort. - subject: sdic1_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: SDIC1 system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1016/j.celrep.2024.115055 snippet: four newly identified anti-phage systems notes: Cummins et al. identify SDIC1 among anti-phage systems. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: SDIC1 | 10\.1016/j\.celrep\.2024\.115055 | Multi-conflict islands are a widespread trend within Serratia spp notes: The pinned DefenseFinder article registry maps the SDIC1 source key to the Cummins et al. Serratia multi-conflict-island paper. discussions: - discussion_id: sdic1-defensefinder-model-gap prompt: Resolve SDIC1 natural host breadth, SDIC1A/SDIC1B component functions, phage triggers, ubiquitination substrates, population-immunity mechanism, and rule-level detection criteria before minting narrower SDIC1 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Cummins et al. support SDIC1 as a TIR-domain-containing anti-phage system with a ubiquitin-ligase-like component, and the pinned DefenseFinder HMM inventory records SDIC1A and SDIC1B profile rows. The pinned rules table has no SDIC1 row, and the first-pass record does not resolve natural host breadth, sensitive-phage breadth, the exact profile-to-component mapping, phage triggers, the direct TIR-dependent output, or the ubiquitination substrate. evidence: - reference: DOI:10.1016/j.celrep.2024.115055 snippet: previously unreported Toll/interleukin (IL)-1 receptor (TIR)-domain-containing system with population-wide immunity notes: Cummins et al. support SDIC1 as a TIR-domain anti-phage system with a population-level output. - reference: DOI:10.1016/j.celrep.2024.115055 snippet: SDIC1 combines TIR and ubiquitin ligase notes: Cummins et al. connect SDIC1 with a TIR domain and a ubiquitin-ligase-like component. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: SDIC1 | 10\.1016/j\.celrep\.2024\.115055 | Multi-conflict islands are a widespread trend within Serratia spp notes: The pinned DefenseFinder article registry maps the SDIC1 source key to the Cummins et al. Serratia multi-conflict-island paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC1__SDIC1A | | SDIC1 | Custom | 350 |' notes: The pinned DefenseFinder HMM inventory records SDIC1__SDIC1A as a custom SDIC1 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC1__SDIC1B | | SDIC1 | Custom | 130 |' notes: The pinned DefenseFinder HMM inventory records SDIC1__SDIC1B as a custom SDIC1 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list SDIC1, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#sdic1_locus_restricts_phage posed_by: codex posed_date: '2026-09-27' curation_history: - timestamp: '2026-09-27T22:49:28Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted SDIC1 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 candidate-locus level because the pinned DefenseFinder SDIC1 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v297 reserves the replacement placeholder. llm_assisted: true