AbiN system

traitmech:000341 · CLASS · PROPOSED

An abortive infection system in which an organism possesses a single-component AbiN-family locus represented by DefenseFinder as a mandatory AbiN__AbiN profile.

Trait evidence (7)

DOI:10.1111/j.1574-6968.1998.tb12879.x
Nucleotide sequence and analysis of the new chromosomal abortive infection gene abiN of Lactococcus lactis subsp. cremoris S114

Crossref metadata verifies the Prevots et al. 1998 AbiN primary paper title and DOI.
DOI:10.1093/femsre/fuag009
the majority (18 systems) are each represented by single protein-coding genes

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.
DOI:10.1093/femsre/fuag009
The structure of AbiN is predicted with high confidence by AlphaFold and resembles a putative periplasmic ligand-binding sensor domain protein

The FEMS review summarizes a predicted AbiN sensor-like fold but does not establish a molecular trigger or effector activity.
DOI:10.1093/femsre/fuag009
further research is needed to clarify the mechanism of AbiN and if it functions via abortive infection

The FEMS review explicitly leaves the AbiN mechanism unresolved, so this record does not mint a more specific sensor or effector trait.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
AbiN | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme

The DefenseFinder article registry maps the named AbiN model namespace to the Chopin et al. lactococcal abortive-infection review.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
AbiN AbiN 1 1 AbiN__AbiN

The DefenseFinder rules table models AbiN as a one-component system requiring the AbiN__AbiN profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiN__AbiN | AbiN__AbiN | AbiN | Custom | 20 |

The DefenseFinder HMM inventory records AbiN__AbiN under the AbiN model namespace.

AbiN loci confer abortive-infection phage defense

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.

NONMECHANISTIC · 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.

Edge evidence

AbiN locus contributes to restricted phage propagation RO:0002326
The DefenseFinder AbiN namespace is modeled as a one-profile AbiN__AbiN system.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv AbiN AbiN 1 1 AbiN__AbiN The DefenseFinder rules table models AbiN as a one-component system requiring the AbiN__AbiN profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | AbiN__AbiN | AbiN__AbiN | AbiN | Custom | 20 | The DefenseFinder HMM inventory records AbiN__AbiN under the AbiN model namespace.
restricted phage propagation confers AbiN system METPO:2007700
Restriction of phage propagation realizes the AbiN abortive-infection system possession trait.
- DOI:10.1111/j.1574-6968.1998.tb12879.x Nucleotide sequence and analysis of the new chromosomal abortive infection gene abiN of Lactococcus lactis subsp. cremoris S114 Crossref metadata verifies the Prevots et al. 1998 AbiN primary paper title and DOI.
- DOI:10.1093/femsre/fuag009 the majority (18 systems) are each represented by single protein-coding genes 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.
AbiN system is a abortive infection system rdfs:subClassOf
AbiN system possession is an abortive-infection-system trait.
- DOI:10.1111/j.1574-6968.1998.tb12879.x Nucleotide sequence and analysis of the new chromosomal abortive infection gene abiN of Lactococcus lactis subsp. cremoris S114 Crossref metadata verifies the Prevots et al. 1998 AbiN primary paper title and DOI.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md AbiN | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme The DefenseFinder article registry maps the named AbiN model namespace to the Chopin et al. lactococcal abortive-infection review.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1111/j.1574-6968.1998.tb12879.x

Parent traits (1)

abortive infection system traitmech:000214

Synonyms (2)

AbiN RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
AbiN__AbiN 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 the AbiN phage trigger, molecular activity, predicted ligand-binding sensor interpretation, and growth-arrest or cell-death route before minting narrower AbiN mechanism children.

KNOWLEDGE GAP OPEN abin-trigger-and-effector-gap · raised by codex · 2026-09-21

Attached to causal_graphs#abin_locus_restricts_lactococcal_phage

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

DOI:10.1093/femsre/fuag009
The structure of AbiN is predicted with high confidence by AlphaFold and resembles a putative periplasmic ligand-binding sensor domain protein
DOI:10.1093/femsre/fuag009
further research is needed to clarify the mechanism of AbiN and if it functions via abortive infection
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
AbiN AbiN 1 1 AbiN__AbiN
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiN__AbiN | AbiN__AbiN | AbiN | Custom | 20 |

Curation history

2026-09-21T17:52:22Z · MINTED_TRAITMECH_ID · codex
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.