identifier: traitmech:000423 label: SDIC3 system definition: A phage defense system in which an organism possesses an SDIC3 Serratia defense-island candidate locus that can confer strong protection against several bacteriophages when plasmid expressed. 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: SDIC3 synonym_type: EXACT_SYNONYM source: DOI:10.1016/j.celrep.2024.115055 - synonym_text: SDIC3__SDIC3B synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: SDIC3__SDIC3C synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: SDIC3__SDIC3D synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: SDIC3__SDIC3E synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: SDIC3__SDIC3F 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: Using this approach, we identified three candidate anti-phage systems/subtypes, which were renamed SDIC1–3 notes: Cummins et al. identify SDIC3 as one of three Serratia defense-island candidate anti-phage systems or subtypes. - reference: DOI:10.1016/j.celrep.2024.115055 snippet: In E. coli, SDIC1, SDIC2, and SDIC3 confer strong protection against several phages (R1,000-fold), including those from the Durham collection notes: Cummins et al. show that plasmid-expressed SDIC3 can strongly protect E. coli against several bacteriophages. - reference: DOI:10.1016/j.celrep.2024.115055 snippet: The four candidates were cloned into a low-copy plasmid under the control of a constitutive promoter compatible with expression in E. coli and S. marcescens notes: Cummins et al. assayed the four SDIC candidates from low-copy plasmids under a constitutive promoter. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| SDIC3 | 10\.1016/j\.celrep\.2024\.115055 | Multi-conflict islands are a widespread trend within Serratia spp |' notes: The pinned DefenseFinder article registry maps the SDIC3 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: '| SDIC3__SDIC3B | | SDIC3 | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records SDIC3__SDIC3B as a custom SDIC3 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC3__SDIC3C | | SDIC3 | Custom | 220 |' notes: The pinned DefenseFinder HMM inventory records SDIC3__SDIC3C as a custom SDIC3 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC3__SDIC3D | | SDIC3 | Custom | 40 |' notes: The pinned DefenseFinder HMM inventory records SDIC3__SDIC3D as a custom SDIC3 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC3__SDIC3E | | SDIC3 | Custom | 80 |' notes: The pinned DefenseFinder HMM inventory records SDIC3__SDIC3E as a custom SDIC3 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC3__SDIC3F | | SDIC3 | Custom | 600 |' notes: The pinned DefenseFinder HMM inventory records SDIC3__SDIC3F as a custom SDIC3 profile. causal_graphs: - graph_id: sdic3_locus_restricts_phage title: SDIC3 loci confer bacterial phage defense description: Conservative system-level sketch linking an SDIC3 locus to reduced bacteriophage propagation without resolving exact SDIC3 components or effector activity. scope_status: NONMECHANISTIC scope_notes: The graph captures SDIC3 as a named anti-phage system with DefenseFinder SDIC3B, SDIC3C, SDIC3D, SDIC3E, and SDIC3F profile rows. It does not assert native host breadth, SDIC3A status, exact profile-to-protein correspondence, whether SDIC3 is a distinct ECOR61-system subtype, sensitive-phage breadth, the direct trigger, the molecular output, or DefenseFinder rule-level detection criteria. nodes: - node_id: sdic3_locus label: SDIC3 locus node_type: GENETIC_ELEMENT description: An SDIC3 candidate anti-phage locus represented in the pinned DefenseFinder HMM inventory by custom SDIC3B, SDIC3C, SDIC3D, SDIC3E, and SDIC3F profiles. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced bacteriophage propagation in cells carrying a plasmid-expressed SDIC3 candidate anti-phage system. - node_id: sdic3_system_trait label: SDIC3 system node_type: TRAIT grounding: traitmech:000423 description: Possession of a genome-encoded SDIC3 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: sdic3_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: The SDIC3 candidate locus contributes to strong restriction of bacteriophage propagation when plasmid expressed. evidence: - reference: DOI:10.1016/j.celrep.2024.115055 snippet: Using this approach, we identified three candidate anti-phage systems/subtypes, which were renamed SDIC1–3 notes: Cummins et al. identify SDIC3 as an anti-phage candidate found in Serratia defense islands. - reference: DOI:10.1016/j.celrep.2024.115055 snippet: In E. coli, SDIC1, SDIC2, and SDIC3 confer strong protection against several phages (R1,000-fold), including those from the Durham collection notes: Cummins et al. report strong SDIC3-mediated protection against multiple phages. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC3__SDIC3B | | SDIC3 | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records SDIC3__SDIC3B as a custom SDIC3 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC3__SDIC3C | | SDIC3 | Custom | 220 |' notes: The pinned DefenseFinder HMM inventory records SDIC3__SDIC3C as a custom SDIC3 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC3__SDIC3D | | SDIC3 | Custom | 40 |' notes: The pinned DefenseFinder HMM inventory records SDIC3__SDIC3D as a custom SDIC3 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC3__SDIC3E | | SDIC3 | Custom | 80 |' notes: The pinned DefenseFinder HMM inventory records SDIC3__SDIC3E as a custom SDIC3 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC3__SDIC3F | | SDIC3 | Custom | 600 |' notes: The pinned DefenseFinder HMM inventory records SDIC3__SDIC3F as a custom SDIC3 profile. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: sdic3_system_trait description: SDIC3-mediated phage restriction realizes the SDIC3 system trait. evidence: - reference: DOI:10.1016/j.celrep.2024.115055 snippet: In E. coli, SDIC1, SDIC2, and SDIC3 confer strong protection against several phages (R1,000-fold), including those from the Durham collection notes: Cummins et al. connect SDIC3 with strong phage protection. - subject: sdic3_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: SDIC3 system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1016/j.celrep.2024.115055 snippet: Using this approach, we identified three candidate anti-phage systems/subtypes, which were renamed SDIC1–3 notes: Cummins et al. identify SDIC3 as an anti-phage candidate found in Serratia defense islands. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| SDIC3 | 10\.1016/j\.celrep\.2024\.115055 | Multi-conflict islands are a widespread trend within Serratia spp |' notes: The pinned DefenseFinder article registry maps the SDIC3 source key to the Cummins et al. Serratia multi-conflict-island paper. discussions: - discussion_id: sdic3-defensefinder-model-gap prompt: Resolve SDIC3 natural host breadth, SDIC3A status, exact SDIC3B/SDIC3C/SDIC3D/SDIC3E/SDIC3F component functions, sensitive-phage breadth, ECOR61-system subtype scope, the direct trigger and molecular output, and rule-level detection criteria before minting narrower SDIC3 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Cummins et al. support SDIC3 as a Serratia defense-island candidate anti-phage system that can strongly protect E. coli when plasmid expressed, and the pinned DefenseFinder HMM inventory records SDIC3B, SDIC3C, SDIC3D, SDIC3E, and SDIC3F profile rows. The pinned rules table has no SDIC3 row, and the first-pass record does not resolve natural host breadth, whether SDIC3A is part of the DefenseFinder-detectable system, phage target breadth, ECOR61 anti-phage-system boundaries, or the direct molecular output. evidence: - reference: DOI:10.1016/j.celrep.2024.115055 snippet: Using this approach, we identified three candidate anti-phage systems/subtypes, which were renamed SDIC1–3 notes: Cummins et al. identify SDIC3 as a Serratia defense-island candidate. - reference: DOI:10.1016/j.celrep.2024.115055 snippet: In E. coli, SDIC1, SDIC2, and SDIC3 confer strong protection against several phages (R1,000-fold), including those from the Durham collection notes: Cummins et al. report strong phage protection in E. coli. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| SDIC3 | 10\.1016/j\.celrep\.2024\.115055 | Multi-conflict islands are a widespread trend within Serratia spp |' notes: The pinned DefenseFinder article registry maps the SDIC3 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: '| SDIC3__SDIC3B | | SDIC3 | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records SDIC3__SDIC3B as a custom SDIC3 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC3__SDIC3C | | SDIC3 | Custom | 220 |' notes: The pinned DefenseFinder HMM inventory records SDIC3__SDIC3C as a custom SDIC3 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC3__SDIC3D | | SDIC3 | Custom | 40 |' notes: The pinned DefenseFinder HMM inventory records SDIC3__SDIC3D as a custom SDIC3 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC3__SDIC3E | | SDIC3 | Custom | 80 |' notes: The pinned DefenseFinder HMM inventory records SDIC3__SDIC3E as a custom SDIC3 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC3__SDIC3F | | SDIC3 | Custom | 600 |' notes: The pinned DefenseFinder HMM inventory records SDIC3__SDIC3F as a custom SDIC3 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list SDIC3, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#sdic3_locus_restricts_phage posed_by: codex posed_date: '2026-09-28' curation_history: - timestamp: '2026-09-28T01:42:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted SDIC3 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 SDIC3 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v300 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-28T01:42:01Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed SDIC3 system canonical_examples and left them empty because Cummins et al. support plasmid-expressed E. coli and S. marcescens phage-challenge assays plus a DefenseFinder SDIC3 system model, but not a direct native microbial isolate exemplar with experimentally verified endogenous SDIC3 activity. No paid research was used. llm_assisted: true