TraitMech

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DS-36 system

traitmech:000474 · CLASS · PROPOSED

A phage defense system in which an organism possesses a genome-encoded DefensePredictor-discovered system 36 locus represented in the pinned DefenseFinder model inventory by the DS-36 custom HMM profile.

Trait evidence (5)

  • 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-36 record uses this source only for the DefensePredictor DS naming context, not for an exact DS-36 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-36 row was not recovered in this curation pass.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    | DS-36 | 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-36 source key to the DeWeirdt et al. DefensePredictor preprint.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    | DS-36__DS-36 | | DS-36 | Custom | 200 |

    The pinned DefenseFinder HMM inventory records DS-36__DS-36 as a custom DS-36 profile.

DS-36 locus profile model

Conservative system-level sketch linking the DS-36 DefensePredictor-discovered system key to DS-36 system possession and the broader phage-defense-system trait without resolving DS-36 component function or a phage activity readout.

NONMECHANISTIC · The graph captures DS-36 as a DefensePredictor-discovered system with a DS-36 custom HMM row 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-36 molecular activity, exact phage target breadth, or DefenseFinder rule-level detection criteria.

DS-36 locus profile model Interactive directed graph showing evidence-backed causal relationships for DS-36 system.

Edge evidence

Provenance

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

Parent traits (1)

Synonyms (2)

  • DS-36 EXACT_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  • DS-36__DS-36 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-36 working-identifier rows, preprint Table S5 and S6 context, final Science supplement omission, native host breadth, DS-36 profile-to-protein mapping, sensitive-phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-36 mechanism children.

KNOWLEDGE GAP OPEN ds-36-defensefinder-model-gap · raised by codex · 2026-09-29

Attached to causal_graphs#ds_36_locus_profile_model

The DeWeirdt et al. preprint supports the DefensePredictor discovered System naming convention, the pinned DefenseFinder article registry names DS-36 and maps it to that preprint, and the pinned HMM inventory records a DS-36 custom profile row. DS-36 is absent from the final Science Table S6, S7, and S8 files checked during this curation pass, the exact preprint per-TU row was not recovered, the pinned DefenseFinder rules table has no DS-36 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

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted DS-36 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-36 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_v351 reserves the replacement placeholder.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed DS-36 system canonical_examples and left them empty because the pinned DefenseFinder registries support DS-36 system identity and custom HMM coverage but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-36 activity. No paid research was used.