identifier: traitmech:000421 label: SDIC4 system definition: A phage defense system in which an organism possesses an SDIC4 locus encoding an SDIC4A component and a VasI-like SDIC4B component that can reduce adsorption of invading 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: SDIC4 synonym_type: EXACT_SYNONYM source: DOI:10.1016/j.celrep.2024.115055 - synonym_text: SDIC4__SDIC4A synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: SDIC4__SDIC4B 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: SDIC4 comprises SDIC4A, a protein of unknown function, and SDIC4B, harboring the VasI-like domain notes: Cummins et al. describe the SDIC4 locus as encoding an SDIC4A component of unknown function and a VasI-like SDIC4B component. - reference: DOI:10.1016/j.celrep.2024.115055 snippet: SDIC4-mediated anti-phage activity is more modest (R10- to 200-fold) but still significant notes: Cummins et al. report significant SDIC4-mediated anti-phage activity when SDIC4 was expressed in E. coli. - reference: DOI:10.1016/j.celrep.2024.115055 snippet: In the presence of full-length SDIC4 or SDIC4B, we observed a decrease in the adsorption rate notes: Cummins et al. connect full-length SDIC4 and SDIC4B with a decreased bacteriophage adsorption rate. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: SDIC4 | 10\.1016/j\.celrep\.2024\.115055 | Multi-conflict islands are a widespread trend within Serratia spp notes: The pinned DefenseFinder article registry maps the SDIC4 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: '| SDIC4__SDIC4A | | SDIC4 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records SDIC4__SDIC4A as a custom SDIC4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC4__SDIC4B | | SDIC4 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records SDIC4__SDIC4B as a custom SDIC4 profile. causal_graphs: - graph_id: sdic4_locus_reduces_phage_adsorption title: SDIC4 loci reduce bacterial phage adsorption description: Conservative system-level sketch linking the SDIC4 locus to reduced adsorption of invading bacteriophages. scope_status: NONMECHANISTIC scope_notes: The graph captures SDIC4 as a named anti-phage system with SDIC4A and SDIC4B DefenseFinder profiles while leaving natural host breadth, sensitive-phage breadth, the SDIC4 type I versus type II boundary, the exact SDIC4A/SDIC4B profile-to-protein correspondence, the receptor or phage target, and rule-level detection criteria unresolved. nodes: - node_id: sdic4_locus label: SDIC4 locus node_type: GENETIC_ELEMENT description: An SDIC4 anti-phage defense locus represented in the pinned DefenseFinder HMM inventory by SDIC4A and SDIC4B custom profiles. - node_id: phage_adsorption_reduction label: reduced phage adsorption rate node_type: BIOLOGICAL_PROCESS description: Reduction of the rate at which invading bacteriophages adsorb to bacterial cells. - node_id: sdic4_system_trait label: SDIC4 system node_type: TRAIT grounding: traitmech:000421 description: Possession of a genome-encoded SDIC4 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: sdic4_locus predicate: contributes to predicate_id: RO:0002326 object: phage_adsorption_reduction description: The SDIC4 locus contributes to reduced adsorption of invading bacteriophages. evidence: - reference: DOI:10.1016/j.celrep.2024.115055 snippet: In the presence of full-length SDIC4 or SDIC4B, we observed a decrease in the adsorption rate notes: Cummins et al. report decreased phage adsorption for full-length SDIC4 and SDIC4B. - reference: DOI:10.1016/j.celrep.2024.115055 snippet: SDIC4 type I and type II elicit protection against phage infection by reducing the adsorption rate of invading phages notes: Cummins et al. connect both tested SDIC4 subtypes with reduced phage adsorption. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC4__SDIC4A | | SDIC4 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records SDIC4__SDIC4A as a custom SDIC4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC4__SDIC4B | | SDIC4 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records SDIC4__SDIC4B as a custom SDIC4 profile. - subject: phage_adsorption_reduction predicate: confers predicate_id: METPO:2007700 object: sdic4_system_trait description: Reduced phage adsorption realizes the SDIC4 system trait. evidence: - reference: DOI:10.1016/j.celrep.2024.115055 snippet: SDIC4-mediated anti-phage activity is more modest (R10- to 200-fold) but still significant notes: Cummins et al. report significant SDIC4-mediated anti-phage activity. - subject: sdic4_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: SDIC4 system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1016/j.celrep.2024.115055 snippet: SDIC4-mediated anti-phage activity is more modest (R10- to 200-fold) but still significant notes: Cummins et al. report SDIC4-mediated anti-phage activity. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: SDIC4 | 10\.1016/j\.celrep\.2024\.115055 | Multi-conflict islands are a widespread trend within Serratia spp notes: The pinned DefenseFinder article registry maps the SDIC4 source key to the Cummins et al. Serratia multi-conflict-island paper. discussions: - discussion_id: sdic4-defensefinder-model-gap prompt: Resolve SDIC4 natural host breadth, sensitive-phage breadth, type I versus type II component scope, SDIC4A/SDIC4B component functions, receptor or phage target, and rule-level detection criteria before minting narrower SDIC4 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Cummins et al. support SDIC4 as a VasI-like anti-phage system that reduces phage adsorption, and the pinned DefenseFinder HMM inventory records SDIC4A and SDIC4B profile rows. The pinned rules table has no SDIC4 row, and the first-pass record does not resolve natural host breadth, sensitive-phage breadth, type I versus type II system boundaries, the exact profile-to-component mapping, the SDIC4A/SDIC4B relationship, or the phage-adsorption target. evidence: - reference: DOI:10.1016/j.celrep.2024.115055 snippet: SDIC4 comprises SDIC4A, a protein of unknown function, and SDIC4B, harboring the VasI-like domain notes: Cummins et al. describe the initially named SDIC4 candidate as an SDIC4A/SDIC4B system. - reference: DOI:10.1016/j.celrep.2024.115055 snippet: SDIC4 type I and type II elicit protection against phage infection by reducing the adsorption rate of invading phages notes: Cummins et al. later add a second SDIC4 subtype and connect both tested types with reduced adsorption. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: SDIC4 | 10\.1016/j\.celrep\.2024\.115055 | Multi-conflict islands are a widespread trend within Serratia spp notes: The pinned DefenseFinder article registry maps the SDIC4 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: '| SDIC4__SDIC4A | | SDIC4 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records SDIC4__SDIC4A as a custom SDIC4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| SDIC4__SDIC4B | | SDIC4 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records SDIC4__SDIC4B as a custom SDIC4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list SDIC4, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#sdic4_locus_reduces_phage_adsorption posed_by: codex posed_date: '2026-09-27' curation_history: - timestamp: '2026-09-27T23:47:56Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted SDIC4 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 SDIC4 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v298 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-27T23:47:57Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed SDIC4 system canonical_examples and left them empty because Cummins et al. support plasmid-expressed E. coli and S. marcescens phage-challenge and phage-adsorption assays plus a DefenseFinder SDIC4 system model, but not a direct native microbial isolate exemplar with experimentally verified endogenous SDIC4 activity. No paid research was used. llm_assisted: true