identifier: traitmech:000338 label: Abi2 system definition: An abortive infection system in which an organism possesses a single-component Abi-like locus represented by the DefenseFinder Abi2 model namespace and mandatory Abi2__Abi_2/PF07751 profile. definition_source: DOI:10.1016/j.mib.2005.06.006 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 synonyms: - synonym_text: Abi2 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: Abi2__Abi_2 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: Abi_2 synonym_type: RELATED_SYNONYM source: https://www.ebi.ac.uk/interpro/entry/pfam/PF07751/ evidence: - reference: DOI:10.1016/j.mib.2005.06.006 snippet: Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. notes: Chopin et al. define the abortive-infection class of phage exclusion systems used by the DefenseFinder Abi2 registry row. - reference: DOI:10.1128/jb.177.13.3818-3823.1995 snippet: Lactococcal phage abortive infection (AbiD1) determined by plasmid pIL105 is active on both prolate- and small-isometric-head phages notes: Anba et al. characterize AbiD1 as a plasmid-encoded lactococcal abortive-infection determinant active on multiple phage morphotypes. - reference: DOI:10.1128/jb.177.13.3818-3823.1995 snippet: The Abi phenotype was found to be encoded by a single gene, designated abiD1. notes: Anba et al. support a single-gene AbiD1 locus used as family-level background for Abi-like abortive-infection systems. - reference: DOI:10.1128/jb.177.13.3824-3829.1995 snippet: Phage bIL66 is unable to grow on Lactococcus lactis cells harboring the abortive infection gene abiD1. notes: Bidnenko et al. connect abiD1 carriage to restriction of bIL66 phage growth in Lactococcus lactis. - reference: https://www.ebi.ac.uk/interpro/entry/pfam/PF07751/ snippet: This family, found in various bacterial species, contains sequences that are similar to the Abi group of proteins notes: EBI InterPro resolves PF07751 as the reviewed Pfam Abi-like protein family with short name Abi_2. - reference: https://rest.uniprot.org/uniprotkb/Q48717.tsv?fields=accession,id,gene_names,protein_name,xref_pfam,organism_name snippet: "Q48717\tQ48717_9LACT\tabiD1\tAbiD1\tPF07751;\tLactococcus lactis" notes: UniProt maps the Lactococcus lactis abiD1/AbiD1 entry to Pfam PF07751, bridging primary AbiD1 papers to the Abi_2 HMM family without making DefenseFinder Abi2 exactly equivalent to AbiD1. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'Abi2 | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named Abi2 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: "Abi2\tAbi2\t1\t1\tAbi2__Abi_2\t\t\t" notes: The DefenseFinder rules table models Abi2 as a one-component system requiring the Abi2__Abi_2 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Abi2__Abi_2 | Abi2__Abi_2 | Abi2 | PF07751.12 | 60 |' notes: The DefenseFinder HMM inventory records Abi2__Abi_2 under the Abi2 model namespace, backed by the Pfam PF07751.12 Abi_2 profile. causal_graphs: - graph_id: abi2_locus_restricts_phage title: Abi2 loci confer abortive-infection phage defense description: Conservative system-level sketch linking possession of a DefenseFinder Abi2 locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, small-RNA component, or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures Abi2 as a named DefenseFinder single-profile abortive-infection system with an Abi2__Abi_2/PF07751 HMM profile while leaving its natural locus boundaries, AbiD/F-group breadth, upstream regulatory RNA relationships, phage trigger, and direct effector activity unresolved. nodes: - node_id: abi2_locus label: Abi2 locus node_type: GENETIC_ELEMENT description: A single-component Abi2 abortive-infection locus represented by the DefenseFinder Abi2__Abi_2 profile. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced propagation of bacteriophage in cells carrying an Abi2-family abortive-infection system. - node_id: abi2_system_trait label: Abi2 system node_type: TRAIT grounding: traitmech:000338 description: Possession of a genome-encoded Abi2 abortive-infection 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: abi2_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: DefenseFinder represents Abi2 with the Abi2__Abi_2 Pfam profile, and Abi-like loci mediate abortive-infection phage restriction. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Abi2\tAbi2\t1\t1\tAbi2__Abi_2\t\t\t" notes: The DefenseFinder rules table models Abi2 as a one-component system requiring the Abi2__Abi_2 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Abi2__Abi_2 | Abi2__Abi_2 | Abi2 | PF07751.12 | 60 |' notes: The DefenseFinder HMM inventory records Abi2__Abi_2 under the Abi2 model namespace, backed by the Pfam PF07751.12 Abi_2 profile. - reference: DOI:10.1128/jb.177.13.3818-3823.1995 snippet: Lactococcal phage abortive infection (AbiD1) determined by plasmid pIL105 is active on both prolate- and small-isometric-head phages notes: Anba et al. support abortive-infection antiphage activity in the Abi-like family. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: abi2_system_trait description: Restriction of phage propagation realizes the Abi2 abortive-infection system possession trait. evidence: - reference: DOI:10.1128/jb.177.13.3824-3829.1995 snippet: Phage bIL66 is unable to grow on Lactococcus lactis cells harboring the abortive infection gene abiD1. notes: Bidnenko et al. connect AbiD1-family carriage to blocked phage growth. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'Abi2 | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named Abi2 model namespace to the Chopin et al. lactococcal abortive-infection review. - subject: abi2_system_trait predicate: is a predicate_id: rdfs:subClassOf object: abortive_infection_system_trait description: Abi2 system possession is an abortive-infection-system trait. evidence: - reference: DOI:10.1016/j.mib.2005.06.006 snippet: Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. notes: Chopin et al. place Abi systems in the abortive-infection class of phage defense. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'Abi2 | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named Abi2 model namespace to the Chopin et al. lactococcal abortive-infection review. discussions: - discussion_id: abi2-family-boundary-gap prompt: Resolve the natural Abi2 locus breadth, phage trigger, and AbiD/F-group mapping before minting narrower Abi2 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: The DefenseFinder Abi2 model namespace requires the Abi2__Abi_2 PF07751 profile; InterPro treats PF07751 as an Abi-like family, and UniProt maps the AbiD1 protein onto the same Pfam family. This first record leaves unresolved whether DefenseFinder Abi2 exactly corresponds to AbiD1, the broader AbiD/F group, or a different subset of Abi-like loci; it therefore avoids protein-level chemistry and records only the genome-level model namespace. attaches_to: - causal_graphs#abi2_locus_restricts_phage posed_by: codex posed_date: '2026-09-21' curation_history: - timestamp: '2026-09-21T14:52:53Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Abi2 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_v215. llm_assisted: true