identifier: traitmech:000341 label: AbiN system definition: An abortive infection system in which an organism possesses a single-component AbiN-family locus represented by DefenseFinder as a mandatory AbiN__AbiN profile. definition_source: DOI:10.1111/j.1574-6968.1998.tb12879.x trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 synonyms: - synonym_text: AbiN synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: AbiN__AbiN synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1111/j.1574-6968.1998.tb12879.x snippet: Nucleotide sequence and analysis of the new chromosomal abortive infection gene abiN of Lactococcus lactis subsp. cremoris S114 notes: Crossref metadata verifies the Prevots et al. 1998 AbiN primary paper title and DOI. - reference: DOI:10.1093/femsre/fuag009 snippet: the majority (18 systems) are each represented by single protein-coding genes notes: The FEMS review lists AbiN among the 34 confirmed lactococcal Abi-like systems in Table 1 and omits AbiN from the named two- and three-component exception lists. - reference: DOI:10.1093/femsre/fuag009 snippet: The structure of AbiN is predicted with high confidence by AlphaFold and resembles a putative periplasmic ligand-binding sensor domain protein notes: The FEMS review summarizes a predicted AbiN sensor-like fold but does not establish a molecular trigger or effector activity. - reference: DOI:10.1093/femsre/fuag009 snippet: further research is needed to clarify the mechanism of AbiN and if it functions via abortive infection notes: The FEMS review explicitly leaves the AbiN mechanism unresolved, so this record does not mint a more specific sensor or effector trait. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiN | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiN 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: "AbiN\tAbiN\t1\t1\tAbiN__AbiN\t\t\t" notes: The DefenseFinder rules table models AbiN as a one-component system requiring the AbiN__AbiN profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiN__AbiN | AbiN__AbiN | AbiN | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiN__AbiN under the AbiN model namespace. causal_graphs: - graph_id: abin_locus_restricts_lactococcal_phage title: AbiN loci confer abortive-infection phage defense description: Conservative system-level sketch linking possession of a DefenseFinder AbiN locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, predicted ligand-binding sensor role, or molecular effector activity. scope_status: NONMECHANISTIC scope_notes: The graph captures AbiN as a named single-profile lactococcal Abi-like system with the DefenseFinder AbiN__AbiN HMM while leaving its direct phage trigger, ligand-sensor interpretation, exact molecular activity, phage-cycle step, phage escape routes, and growth-arrest or cell-death route unresolved. nodes: - node_id: abin_locus label: AbiN locus node_type: GENETIC_ELEMENT description: An AbiN-family abortive-infection locus represented by the DefenseFinder AbiN__AbiN profile. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced bacteriophage propagation in cells carrying an AbiN-family abortive-infection system. - node_id: abin_system_trait label: AbiN system node_type: TRAIT grounding: traitmech:000341 description: Possession of a genome-encoded AbiN 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: abin_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: The DefenseFinder AbiN namespace is modeled as a one-profile AbiN__AbiN system. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiN\tAbiN\t1\t1\tAbiN__AbiN\t\t\t" notes: The DefenseFinder rules table models AbiN as a one-component system requiring the AbiN__AbiN profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiN__AbiN | AbiN__AbiN | AbiN | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiN__AbiN under the AbiN model namespace. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: abin_system_trait description: Restriction of phage propagation realizes the AbiN abortive-infection system possession trait. evidence: - reference: DOI:10.1111/j.1574-6968.1998.tb12879.x snippet: Nucleotide sequence and analysis of the new chromosomal abortive infection gene abiN of Lactococcus lactis subsp. cremoris S114 notes: Crossref metadata verifies the Prevots et al. 1998 AbiN primary paper title and DOI. - reference: DOI:10.1093/femsre/fuag009 snippet: the majority (18 systems) are each represented by single protein-coding genes notes: The FEMS review lists AbiN among the 34 confirmed lactococcal Abi-like systems in Table 1 and omits AbiN from the named two- and three-component exception lists. - subject: abin_system_trait predicate: is a predicate_id: rdfs:subClassOf object: abortive_infection_system_trait description: AbiN system possession is an abortive-infection-system trait. evidence: - reference: DOI:10.1111/j.1574-6968.1998.tb12879.x snippet: Nucleotide sequence and analysis of the new chromosomal abortive infection gene abiN of Lactococcus lactis subsp. cremoris S114 notes: Crossref metadata verifies the Prevots et al. 1998 AbiN primary paper title and DOI. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiN | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiN model namespace to the Chopin et al. lactococcal abortive-infection review. discussions: - discussion_id: abin-trigger-and-effector-gap prompt: Resolve the AbiN phage trigger, molecular activity, predicted ligand-binding sensor interpretation, and growth-arrest or cell-death route before minting narrower AbiN mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Prevots et al. support AbiN as a chromosomal lactococcal abortive infection gene, the FEMS review retains AbiN among confirmed lactococcal Abi-like systems, and DefenseFinder represents AbiN with a mandatory AbiN__AbiN profile. The FEMS table leaves the affected phage lytic-cycle step, phage escape mutants, and mechanism of cell arrest or death unknown, and the FEMS structural discussion predicts a putative ligand-binding sensor fold while explicitly calling for further research on the AbiN mechanism. This first system-level record therefore leaves the direct phage trigger, sensor ligand, exact molecular activity, growth-arrest or cell-death route, and phage escape routes unresolved. evidence: - reference: DOI:10.1093/femsre/fuag009 snippet: The structure of AbiN is predicted with high confidence by AlphaFold and resembles a putative periplasmic ligand-binding sensor domain protein notes: The FEMS review summarizes a predicted AbiN sensor-like fold but does not establish a molecular trigger or effector activity. - reference: DOI:10.1093/femsre/fuag009 snippet: further research is needed to clarify the mechanism of AbiN and if it functions via abortive infection notes: The FEMS review explicitly leaves the AbiN mechanism unresolved, so this record does not mint a more specific sensor or effector trait. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiN\tAbiN\t1\t1\tAbiN__AbiN\t\t\t" notes: The DefenseFinder rules table models AbiN as a one-component system requiring the AbiN__AbiN profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiN__AbiN | AbiN__AbiN | AbiN | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiN__AbiN under the AbiN model namespace. attaches_to: - causal_graphs#abin_locus_restricts_lactococcal_phage posed_by: codex posed_date: '2026-09-21' curation_history: - timestamp: '2026-09-21T17:52:22Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted AbiN 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_v218. llm_assisted: true