DS-13 system

traitmech:000437 · CLASS · PROPOSED

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.

Trait evidence (6)

DOI:10.1101/2025.01.08.631726
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

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.
DOI:10.1101/2025.01.08.631726
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.

DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered Systems.
DOI:10.1101/2025.01.08.631726
To begin elucidating the function of the 45 validated TUs, we further annotated their protein domains (see Methods; table S6).

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.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-13 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems |

The pinned DefenseFinder article registry maps the DS-13 source key to the DeWeirdt et al. DefensePredictor preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-13__DS-13A | | DS-13 | Custom | 20 |

The pinned DefenseFinder HMM inventory records DS-13__DS-13A as a custom DS-13 profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-13__DS-13B | | DS-13 | Custom | 50 |

The pinned DefenseFinder HMM inventory records DS-13__DS-13B as a custom DS-13 profile.

DS-13 locus profile model

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.

NONMECHANISTIC · 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.

Edge evidence

DS-13 locus contributes to DS-13 system RO:0002326
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.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | DS-13 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | The pinned DefenseFinder article registry maps the DS-13 source key to the DeWeirdt et al. DefensePredictor preprint.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-13__DS-13A | | DS-13 | Custom | 20 | The pinned DefenseFinder HMM inventory records DS-13__DS-13A as a custom DS-13 profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-13__DS-13B | | DS-13 | Custom | 50 | The pinned DefenseFinder HMM inventory records DS-13__DS-13B as a custom DS-13 profile.
DS-13 system is a phage defense system rdfs:subClassOf
DS-13 system possession is a phage-defense-system trait.
- DOI:10.1101/2025.01.08.631726 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. DeWeirdt et al. name validated TUs as DefensePredictor discovered Systems.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | DS-13 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | The pinned DefenseFinder article registry maps the DS-13 source key to the DeWeirdt et al. DefensePredictor preprint.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1101/2025.01.08.631726

Parent traits (1)

phage defense system traitmech:000209

Synonyms (3)

DS-13 EXACT_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
DS-13__DS-13A RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
DS-13__DS-13B 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 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.

KNOWLEDGE GAP OPEN ds-13-defensefinder-model-gap · raised by codex · 2026-09-28

Attached to causal_graphs#ds_13_locus_profile_model

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

DOI:10.1101/2025.01.08.631726
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
DOI:10.1101/2025.01.08.631726
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.
DOI:10.1101/2025.01.08.631726
To begin elucidating the function of the 45 validated TUs, we further annotated their protein domains (see Methods; table S6).
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-13 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-13__DS-13A | | DS-13 | Custom | 20 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-13__DS-13B | | DS-13 | Custom | 50 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-28T16:05:54Z · MINTED_TRAITMECH_ID · codex
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.
2026-09-28T16:05:55Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
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.