Lamassu-PDDEXK system

traitmech:000564 · CLASS · PROPOSED

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-PDDEXK subtype locus represented by the Lamassu-PDDEXK rule row requiring the Lamassu-Fam__LmuA_effector_PDDEXK and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

Trait evidence (8)

DOI:10.1073/pnas.2519643122
a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor

Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| Lamassu-Fam | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages |

The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__LmuA_effector_PDDEXK | Lamassu-Fam__LmuA_effector_PDDEXK | Lamassu-Fam | Custom | 20 |

The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_PDDEXK custom profile listed as mandatory by the Lamassu-PDDEXK rule row.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II | Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II | Lamassu-Fam | Custom | 20 |

The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II custom profile, which the Lamassu-PDDEXK rule row lists as mandatory despite the HMM inventory also carrying a PDDEXK-scoped LmuB SMC profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__LmuB_SMC_PDDEXK | Lamassu-Fam__LmuB_SMC_PDDEXK | Lamassu-Fam | Custom | 20 |

The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuB_SMC_PDDEXK custom profile that is not the LmuB SMC profile named by the pinned Lamassu-PDDEXK rule row.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__LmuC_acc_Lipase | Lamassu-Fam__LmuC_acc_Lipase | Lamassu-Fam | Custom | 20 |

The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile listed as accessory by the Lamassu-PDDEXK rule row.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__LmuC_acc_PDDEXK | Lamassu-Fam__LmuC_acc_PDDEXK | Lamassu-Fam | Custom | 20 |

The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuC_acc_PDDEXK custom profile that is not the LmuC accessory profile named by the pinned Lamassu-PDDEXK rule row.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Lamassu-Fam Lamassu-PDDEXK 2 2 Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II Lamassu-Fam__LmuC_acc_Lipase Lamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical

The pinned DefenseFinder rules table models Lamassu-PDDEXK as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_PDDEXK and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile.

Lamassu-PDDEXK is a DefenseFinder Lamassu subtype

Conservative subtype-level classification linking the DefenseFinder Lamassu-PDDEXK rule-row definition to Lamassu-PDDEXK system possession and its Lamassu parent.

NONMECHANISTIC · The graph captures Lamassu-PDDEXK as a DefenseFinder rule-row subtype of Lamassu system possession without asserting a Lamassu-PDDEXK-specific antiphage process, selecting between the rule-row LmuB/LmuC profile names and the PDDEXK-scoped LmuB/LmuC HMM rows, or resolving exact phage-triggered PDDEXK effector activity, viral-DNA trigger, LmuC requirement, native host breadth, cell-death output, or whether every DefenseFinder Lamassu-PDDEXK prediction is a complete experimentally active locus.

Edge evidence

Lamassu-PDDEXK system is a Lamassu system rdfs:subClassOf
Lamassu-PDDEXK system possession is a Lamassu-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | Lamassu-Fam | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Lamassu-Fam Lamassu-PDDEXK 2 2 The pinned DefenseFinder rules table places the Lamassu-PDDEXK subsystem under the Lamassu-Fam system key with 2 mandatory matches and 2 genes required.

Provenance

Identifier source: TraitMech local identifier
Definition source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Parent traits (1)

Lamassu system traitmech:000232

Synonyms (2)

Lamassu-PDDEXK RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Lamassu-Fam__LmuA_effector_PDDEXK 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 Lamassu-PDDEXK phage triggers, native hosts, PDDEXK effector activity, LmuB/LmuC model rows, LmuC usage, and profile-to-activity criteria before minting enzyme, trigger, or component children.

KNOWLEDGE GAP OPEN lamassu-pddexk-activity-gap · raised by codex · 2026-10-03

Attached to causal_graphs#lamassu_pddexk_locus_subtype_defense

Haudiquet et al. support a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor, and the pinned DefenseFinder HMM inventory and rules table support Lamassu-PDDEXK as a Lamassu-Fam subtype whose rule row requires Lamassu-Fam__LmuA_effector_PDDEXK and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II. This first-pass record follows the rule row but leaves the relationship between its LmuB Cap4-nuclease and LmuC Lipase profile names and the PDDEXK-scoped Lamassu-Fam__LmuB_SMC_PDDEXK and Lamassu-Fam__LmuC_acc_PDDEXK HMM rows unresolved, along with exact PDDEXK effector activity, LmuC requirement, native hosts, phage triggers, cell-death output, and profile-to-activity criteria.

Evidence

DOI:10.1073/pnas.2519643122
a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__LmuA_effector_PDDEXK | Lamassu-Fam__LmuA_effector_PDDEXK | Lamassu-Fam | Custom | 20 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__LmuB_SMC_PDDEXK | Lamassu-Fam__LmuB_SMC_PDDEXK | Lamassu-Fam | Custom | 20 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__LmuC_acc_PDDEXK | Lamassu-Fam__LmuC_acc_PDDEXK | Lamassu-Fam | Custom | 20 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Lamassu-Fam Lamassu-PDDEXK 2 2 Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II Lamassu-Fam__LmuC_acc_Lipase Lamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical

Curation history

2026-10-03T05:05:00Z · MINTED_TRAITMECH_ID · codex
Minted Lamassu-PDDEXK system as a DefenseFinder-backed GENOMICS TraitRecord under the Lamassu system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, human label, or DefenseFinder subsystem; existing Lamassu-Fam__LmuA_effector_PDDEXK mentions were limited to forbidden-profile evidence on neighboring Lamassu-Fam subtypes, their earlier writer scripts, and rendered pages, and the replacement placeholder is reserved in proposals/metpo_traitmech_v441.
2026-10-03T05:05:02Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed Lamassu-PDDEXK system during initial curation and left canonical_examples empty because the pinned DefenseFinder tables support a rule-row subtype but not an accession-backed native microbial taxon exemplar tied to the Lamassu-PDDEXK profiles and experimentally verified endogenous activity. No paid research was used.