Lamassu-Cap4 nuclease system

traitmech:000557 · CLASS · PROPOSED

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Cap4_nuclease subtype locus represented by the Lamassu-Cap4_nuclease rule row requiring the Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

Trait evidence (6)

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_Cap4_nuclease_II | Lamassu-Fam__LmuA_effector_Cap4_nuclease_II | Lamassu-Fam | Custom | 20 |

The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Cap4_nuclease 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 listed as mandatory by the Lamassu-Cap4_nuclease 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-Cap4_nuclease rule row.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Lamassu-Fam Lamassu-Cap4_nuclease 2 2 Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II Lamassu-Fam__LmuC_acc_Lipase Lamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical

The pinned DefenseFinder rules table models Lamassu-Cap4_nuclease as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile.

Lamassu-Cap4 nuclease loci mark a Lamassu antiphage subtype

Conservative subtype-level sketch linking a DefenseFinder Lamassu-Cap4_nuclease locus to Lamassu antiphage activity and Lamassu-Cap4 nuclease system possession.

NONMECHANISTIC · The graph captures the Lamassu-Cap4_nuclease subtype at DefenseFinder rule-row level without asserting exact phage-triggered substrate chemistry, viral-DNA trigger, LmuC requirement, native host breadth, cell-death output, or whether every DefenseFinder Lamassu-Cap4_nuclease prediction is a complete experimentally active locus.

Edge evidence

Lamassu-Cap4 nuclease locus contributes to Lamassu subtype antiphage activity RO:0002326
Lamassu-Cap4 nuclease loci are modeled in DefenseFinder by LmuA Cap4 nuclease and LmuB SMC mandatory profiles plus an LmuC accessory profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | Lamassu-Fam__LmuA_effector_Cap4_nuclease_II | Lamassu-Fam__LmuA_effector_Cap4_nuclease_II | Lamassu-Fam | Custom | 20 | The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Cap4_nuclease 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 listed as mandatory by the Lamassu-Cap4_nuclease 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-Cap4_nuclease rule row.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Lamassu-Fam Lamassu-Cap4_nuclease 2 2 Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II Lamassu-Fam__LmuC_acc_Lipase Lamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical The pinned DefenseFinder rules table models Lamassu-Cap4_nuclease as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile.
Lamassu subtype antiphage activity confers Lamassu-Cap4 nuclease system METPO:2007700
The first-pass Lamassu-Cap4 nuclease system trait is realized by a DefenseFinder Lamassu-Cap4_nuclease subtype locus.
- 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/DefenseFinder_rules.tsv Lamassu-Cap4_nuclease 2 2 Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II Lamassu-Fam__LmuC_acc_Lipase The pinned DefenseFinder rules table models Lamassu-Cap4_nuclease as requiring LmuA Cap4 nuclease and LmuB SMC profiles with LmuC as an accessory profile.
Lamassu-Cap4 nuclease system is a Lamassu system rdfs:subClassOf
Lamassu-Cap4 nuclease 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-Cap4_nuclease 2 2 The pinned DefenseFinder rules table places the Lamassu-Cap4_nuclease 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 (4)

Lamassu-Cap4_nuclease RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Lamassu-Fam__LmuA_effector_Cap4_nuclease_II RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Lamassu-Fam__LmuC_acc_Lipase 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-Cap4 nuclease phage triggers, native hosts, Cap4 nuclease substrates, LmuC usage, and profile-to-activity criteria before minting enzyme, trigger, or component children.

KNOWLEDGE GAP OPEN lamassu-cap4-nuclease-activity-gap · raised by codex · 2026-10-02

Attached to causal_graphs#lamassu_cap4_nuclease_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-Cap4_nuclease as a Lamassu-Fam subtype whose rule row requires Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II. This first-pass record leaves exact Cap4 nuclease substrates, LmuC requirement, native hosts, phage triggers, cell-death output, profile-to-activity criteria, and the relationship between the DefenseFinder _II row and the structurally characterized Lamassu Vc-Cap4 branch unresolved.

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_Cap4_nuclease_II | Lamassu-Fam__LmuA_effector_Cap4_nuclease_II | Lamassu-Fam | Custom | 20 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Lamassu-Fam Lamassu-Cap4_nuclease 2 2 Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II Lamassu-Fam__LmuC_acc_Lipase Lamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical

Curation history

2026-10-02T22:16:24Z · MINTED_TRAITMECH_ID · codex
Minted Lamassu-Cap4 nuclease 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; the replacement placeholder is reserved in proposals/metpo_traitmech_v434. Exact Cap4 effector profile hits were limited to evidence and forbidden-profile strings on the neighboring Lamassu-Amidase record.
2026-10-02T22:16:26Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed Lamassu-Cap4 nuclease 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-Cap4_nuclease profiles and experimentally verified endogenous activity. No paid research was used.