SDIC3 system

traitmech:000423 · CLASS · PROPOSED

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.

Trait evidence (9)

DOI:10.1016/j.celrep.2024.115055
Using this approach, we identified three candidate anti-phage systems/subtypes, which were renamed SDIC1–3

Cummins et al. identify SDIC3 as one of three Serratia defense-island candidate anti-phage systems or subtypes.
DOI:10.1016/j.celrep.2024.115055
In E. coli, SDIC1, SDIC2, and SDIC3 confer strong protection against several phages (R1,000-fold), including those from the Durham collection

Cummins et al. show that plasmid-expressed SDIC3 can strongly protect E. coli against several bacteriophages.
DOI:10.1016/j.celrep.2024.115055
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

Cummins et al. assayed the four SDIC candidates from low-copy plasmids under a constitutive promoter.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| SDIC3 | 10\.1016/j\.celrep\.2024\.115055 | Multi-conflict islands are a widespread trend within Serratia spp |

The pinned DefenseFinder article registry maps the SDIC3 source key to the Cummins et al. Serratia multi-conflict-island paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| SDIC3__SDIC3B | | SDIC3 | Custom | 20 |

The pinned DefenseFinder HMM inventory records SDIC3__SDIC3B as a custom SDIC3 profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| SDIC3__SDIC3C | | SDIC3 | Custom | 220 |

The pinned DefenseFinder HMM inventory records SDIC3__SDIC3C as a custom SDIC3 profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| SDIC3__SDIC3D | | SDIC3 | Custom | 40 |

The pinned DefenseFinder HMM inventory records SDIC3__SDIC3D as a custom SDIC3 profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| SDIC3__SDIC3E | | SDIC3 | Custom | 80 |

The pinned DefenseFinder HMM inventory records SDIC3__SDIC3E as a custom SDIC3 profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| SDIC3__SDIC3F | | SDIC3 | Custom | 600 |

The pinned DefenseFinder HMM inventory records SDIC3__SDIC3F as a custom SDIC3 profile.

SDIC3 loci confer bacterial phage defense

Conservative system-level sketch linking an SDIC3 locus to reduced bacteriophage propagation without resolving exact SDIC3 components or effector activity.

NONMECHANISTIC · 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.

Edge evidence

SDIC3 locus contributes to restricted phage propagation RO:0002326
The SDIC3 candidate locus contributes to strong restriction of bacteriophage propagation when plasmid expressed.
- DOI:10.1016/j.celrep.2024.115055 Using this approach, we identified three candidate anti-phage systems/subtypes, which were renamed SDIC1–3 Cummins et al. identify SDIC3 as an anti-phage candidate found in Serratia defense islands.
- DOI:10.1016/j.celrep.2024.115055 In E. coli, SDIC1, SDIC2, and SDIC3 confer strong protection against several phages (R1,000-fold), including those from the Durham collection Cummins et al. report strong SDIC3-mediated protection against multiple phages.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | SDIC3__SDIC3B | | SDIC3 | Custom | 20 | The pinned DefenseFinder HMM inventory records SDIC3__SDIC3B as a custom SDIC3 profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | SDIC3__SDIC3C | | SDIC3 | Custom | 220 | The pinned DefenseFinder HMM inventory records SDIC3__SDIC3C as a custom SDIC3 profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | SDIC3__SDIC3D | | SDIC3 | Custom | 40 | The pinned DefenseFinder HMM inventory records SDIC3__SDIC3D as a custom SDIC3 profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | SDIC3__SDIC3E | | SDIC3 | Custom | 80 | The pinned DefenseFinder HMM inventory records SDIC3__SDIC3E as a custom SDIC3 profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | SDIC3__SDIC3F | | SDIC3 | Custom | 600 | The pinned DefenseFinder HMM inventory records SDIC3__SDIC3F as a custom SDIC3 profile.
restricted phage propagation confers SDIC3 system METPO:2007700
SDIC3-mediated phage restriction realizes the SDIC3 system trait.
- DOI:10.1016/j.celrep.2024.115055 In E. coli, SDIC1, SDIC2, and SDIC3 confer strong protection against several phages (R1,000-fold), including those from the Durham collection Cummins et al. connect SDIC3 with strong phage protection.
SDIC3 system is a phage defense system rdfs:subClassOf
SDIC3 system possession is a phage-defense-system trait.
- DOI:10.1016/j.celrep.2024.115055 Using this approach, we identified three candidate anti-phage systems/subtypes, which were renamed SDIC1–3 Cummins et al. identify SDIC3 as an anti-phage candidate found in Serratia defense islands.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | SDIC3 | 10\.1016/j\.celrep\.2024\.115055 | Multi-conflict islands are a widespread trend within Serratia spp | The pinned DefenseFinder article registry maps the SDIC3 source key to the Cummins et al. Serratia multi-conflict-island paper.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1016/j.celrep.2024.115055

Parent traits (1)

phage defense system traitmech:000209

Synonyms (6)

SDIC3 EXACT_SYNONYM · DOI:10.1016/j.celrep.2024.115055
SDIC3__SDIC3B RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
SDIC3__SDIC3C RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
SDIC3__SDIC3D RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
SDIC3__SDIC3E RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
SDIC3__SDIC3F RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

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.

KNOWLEDGE GAP OPEN sdic3-defensefinder-model-gap · raised by codex · 2026-09-28

Attached to causal_graphs#sdic3_locus_restricts_phage

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

DOI:10.1016/j.celrep.2024.115055
Using this approach, we identified three candidate anti-phage systems/subtypes, which were renamed SDIC1–3
DOI:10.1016/j.celrep.2024.115055
In E. coli, SDIC1, SDIC2, and SDIC3 confer strong protection against several phages (R1,000-fold), including those from the Durham collection
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| SDIC3 | 10\.1016/j\.celrep\.2024\.115055 | Multi-conflict islands are a widespread trend within Serratia spp |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| SDIC3__SDIC3B | | SDIC3 | Custom | 20 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| SDIC3__SDIC3C | | SDIC3 | Custom | 220 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| SDIC3__SDIC3D | | SDIC3 | Custom | 40 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| SDIC3__SDIC3E | | SDIC3 | Custom | 80 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| SDIC3__SDIC3F | | SDIC3 | Custom | 600 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-28T01:42:00Z · MINTED_TRAITMECH_ID · codex
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.
2026-09-28T01:42:01Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
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.