identifier: traitmech:000340 label: AbiL system definition: An abortive infection system in which an organism possesses a two-component AbiL-family locus represented by DefenseFinder as mandatory AbiL__AbiLi and AbiL__AbiLii profiles. definition_source: DOI:10.1016/S0168-1656(98)00175-8 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 synonyms: - synonym_text: AbiL synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: AbiL__AbiLi synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: AbiL__AbiLii synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1016/S0168-1656(98)00175-8 snippet: Genetic organization and functional analysis of a novel phage abortive infection system, AbiL, from Lactococcus lactis notes: Crossref metadata verifies the Deng et al. 1999 AbiL primary paper title and DOI. - reference: DOI:10.1093/femsre/fuag009 snippet: 13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu notes: The FEMS review counts AbiL among the confirmed two-component lactococcal Abi-like systems. - reference: DOI:10.1093/femsre/fuag009 snippet: AbiL has been included among systems such as PARIS, which feature an ABC ATPase and a TOPRIM nuclease notes: The FEMS review places AbiL among predicted ATPase-plus-TOPRIM systems but does not resolve the AbiLi and AbiLii molecular activities. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiL | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiL model namespace to the Chopin et al. lactococcal abortive-infection review. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiL\tAbiL\t2\t2\tAbiL__AbiLi, AbiL__AbiLii\t\t\t" notes: The DefenseFinder rules table models AbiL as a two-component system requiring the AbiL__AbiLi and AbiL__AbiLii profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiL__AbiLi | AbiL__AbiLi | AbiL | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiL__AbiLi under the AbiL model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiL__AbiLii | AbiL__AbiLii | AbiL | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiL__AbiLii under the AbiL model namespace. causal_graphs: - graph_id: abil_locus_restricts_lactococcal_phage title: AbiL loci confer abortive-infection phage defense description: Conservative system-level sketch linking possession of a DefenseFinder AbiL locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, AbiLi or AbiLii molecular activity, or AbiL-to-PARIS mechanistic correspondence. scope_status: NONMECHANISTIC scope_notes: The graph captures AbiL as a named lactococcal abortive-infection system with DefenseFinder AbiL__AbiLi and AbiL__AbiLii HMM profiles while leaving its direct phage trigger, the exact AbiLi and AbiLii activities, the relationship between the mandatory and suffixed HMM rows, and the similarity of its route to PARIS unresolved. nodes: - node_id: abil_locus label: AbiL locus node_type: GENETIC_ELEMENT description: An AbiL-family abortive-infection locus represented by the DefenseFinder AbiL__AbiLi and AbiL__AbiLii profiles. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced bacteriophage propagation in cells carrying an AbiL-family abortive-infection system. - node_id: abil_system_trait label: AbiL system node_type: TRAIT grounding: traitmech:000340 description: Possession of a genome-encoded AbiL abortive-infection phage-defense system. - node_id: abortive_infection_system_trait label: abortive infection system node_type: TRAIT grounding: traitmech:000214 description: Possession of a genome-encoded abortive-infection phage-defense system. edges: - subject: abil_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: The DefenseFinder AbiL namespace is modeled as a two-profile AbiL__AbiLi plus AbiL__AbiLii system, and AbiL is a confirmed lactococcal Abi-like system. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiL\tAbiL\t2\t2\tAbiL__AbiLi, AbiL__AbiLii\t\t\t" notes: The DefenseFinder rules table models AbiL as a two-component system requiring the AbiL__AbiLi and AbiL__AbiLii profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiL__AbiLi | AbiL__AbiLi | AbiL | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiL__AbiLi under the AbiL model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiL__AbiLii | AbiL__AbiLii | AbiL | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiL__AbiLii under the AbiL model namespace. - reference: DOI:10.1093/femsre/fuag009 snippet: 13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu notes: The FEMS review counts AbiL among the confirmed two-component lactococcal Abi-like systems. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: abil_system_trait description: Restriction of phage propagation realizes the AbiL abortive-infection system possession trait. evidence: - reference: DOI:10.1016/S0168-1656(98)00175-8 snippet: Genetic organization and functional analysis of a novel phage abortive infection system, AbiL, from Lactococcus lactis notes: Crossref metadata verifies the Deng et al. 1999 AbiL primary paper title and DOI. - reference: DOI:10.1093/femsre/fuag009 snippet: 13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu notes: The FEMS review counts AbiL among the confirmed two-component lactococcal Abi-like systems. - subject: abil_system_trait predicate: is a predicate_id: rdfs:subClassOf object: abortive_infection_system_trait description: AbiL system possession is an abortive-infection-system trait. evidence: - reference: DOI:10.1016/S0168-1656(98)00175-8 snippet: Genetic organization and functional analysis of a novel phage abortive infection system, AbiL, from Lactococcus lactis notes: Crossref metadata verifies the Deng et al. 1999 AbiL primary paper title and DOI. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiL | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiL model namespace to the Chopin et al. lactococcal abortive-infection review. discussions: - discussion_id: abil-trigger-and-effector-gap prompt: Resolve the AbiL phage trigger, AbiLi and AbiLii activities, AbiLi2 and AbiLii2 HMM row relationships, and ATPase-plus-TOPRIM mechanism before minting narrower AbiL mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Deng et al. support AbiL as a lactococcal phage abortive infection system, the FEMS review lists AbiL among confirmed two-component lactococcal Abi-like systems, and DefenseFinder represents AbiL with mandatory AbiL__AbiLi and AbiL__AbiLii profiles. The same pinned HMM inventory also contains AbiL__AbiLi2 and AbiL__AbiLii2 rows that are not in the pinned two-profile rule, and the FEMS review summarizes unresolved ATPase and TOPRIM predictions. This first system-level record therefore leaves the direct phage trigger, exact AbiLi and AbiLii molecular activities, accessory-model interpretation, AbiL-to-PARIS similarity, growth-arrest or cell-death route, and phage escape routes unresolved. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiL__AbiLi2 | AbiL__AbiLi2 | AbiL | Custom | 20 |' notes: The DefenseFinder HMM inventory also records AbiL__AbiLi2 under the AbiL model namespace, but this profile is not listed in the two mandatory profiles in the pinned AbiL rule. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiL__AbiLii2 | AbiL__AbiLii2 | AbiL | Custom | 20 |' notes: The DefenseFinder HMM inventory also records AbiL__AbiLii2 under the AbiL model namespace, but this profile is not listed in the two mandatory profiles in the pinned AbiL rule. - reference: DOI:10.1093/femsre/fuag009 snippet: AbiL has been included among systems such as PARIS, which feature an ABC ATPase and a TOPRIM nuclease notes: The FEMS review places AbiL among predicted ATPase-plus-TOPRIM systems but does not resolve the AbiLi and AbiLii molecular activities. - reference: DOI:10.1093/femsre/fuag009 snippet: No significant sequence similarity was found between the second components of AbiL and PARIS notes: The AbiL-to-PARIS comparison remains indirect for the second component, so this record does not copy the PARIS mechanism onto AbiL. attaches_to: - causal_graphs#abil_locus_restricts_lactococcal_phage posed_by: codex posed_date: '2026-09-21' curation_history: - timestamp: '2026-09-21T17:17:22Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted AbiL system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v217. llm_assisted: true