Avs II system

traitmech:000535 · CLASS · PROPOSED

An AVAST system in which an organism possesses a genome-encoded subtype II locus represented by DefenseFinder with an Avs2A profile.

Trait evidence (6)

DOI:10.1126/science.aba0372
AVAST, antiviral ATPase/NTPase of the STAND superfamily

Gao et al. coined AVAST as an antiviral STAND ATPase/NTPase defense-system family.
DOI:10.1126/science.abm4096
Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal

Gao et al. support Avs2 as a phage-protein-sensing member of the AVAST receptor family.
DOI:10.1126/science.abm4096
In all four cases, target recognition led to Avs protein activation and antiviral activity

Gao et al. connect Avs1 through Avs4 target recognition to Avs activation and antiviral activity.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| Avs | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes |

The pinned DefenseFinder article registry maps the Avs source key to the Gao et al. pangenome-scale antiviral-immunity paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Avs_II__Avs2A | Avs_II__Avs2A | Avs_II | Custom | 100 |

The pinned DefenseFinder HMM inventory records Avs_II__Avs2A under the Avs_II model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Avs Avs_II 1 1 Avs_II__Avs2A

The pinned DefenseFinder rules table models Avs_II as an Avs subsystem with an Avs2A profile.

Avs II loci support phage protein recognition

Conservative system-level sketch linking an Avs_II locus to Avs2-mediated phage protein recognition and Avs II system possession.

NONMECHANISTIC · The graph captures Avs_II at locus and Avs2 phage-protein recognition level without asserting the exact Avs2A component role, direct effector activity, native host breadth, sensitive-phage breadth, or whether every DefenseFinder Avs_II prediction is a complete experimentally active Avs II locus.

Edge evidence

Avs II locus contributes to Avs2 phage protein recognition RO:0002326
Avs II loci encode Avs2 components, and Avs2 belongs to the AVAST receptors that recognize the phage large terminase subunit.
- DOI:10.1126/science.abm4096 Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal Gao et al. support Avs2 as a phage-protein-sensing member of the AVAST receptor family.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | Avs_II__Avs2A | Avs_II__Avs2A | Avs_II | Custom | 100 | The pinned DefenseFinder HMM inventory records Avs_II__Avs2A under the Avs_II model namespace.
Avs2 phage protein recognition confers Avs II system METPO:2007700
The first-pass Avs II system trait is realized by Avs2 target recognition and downstream antiviral activity.
- DOI:10.1126/science.abm4096 Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal Gao et al. support Avs2 as a phage-protein-sensing member of the AVAST receptor family.
- DOI:10.1126/science.abm4096 In all four cases, target recognition led to Avs protein activation and antiviral activity Gao et al. connect Avs1 through Avs4 target recognition to Avs activation and antiviral activity.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Avs Avs_II 1 1 Avs_II__Avs2A The pinned DefenseFinder rules table models Avs_II as an Avs subsystem with an Avs2A profile.
Avs II system is a AVAST system rdfs:subClassOf
Avs II system possession is an AVAST-system trait.
- DOI:10.1126/science.aba0372 AVAST, antiviral ATPase/NTPase of the STAND superfamily Gao et al. coined AVAST as an antiviral STAND ATPase/NTPase defense-system family.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | Avs | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | The pinned DefenseFinder article registry maps the Avs source key to the Gao et al. pangenome-scale antiviral-immunity paper.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Avs Avs_II 1 1 Avs_II__Avs2A The pinned DefenseFinder rules table models Avs_II as an Avs subsystem with an Avs2A profile.

Provenance

Identifier source: TraitMech local identifier
Definition source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Parent traits (1)

AVAST system traitmech:000239

Synonyms (2)

Avs_II RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Avs_II__Avs2A 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 Avs2A component role, direct effector chemistry, exact phage-trigger mapping, native host breadth, and sensitive-phage breadth before minting Avs II mechanism or component children.

KNOWLEDGE GAP OPEN avs-ii-component-and-effector-gap · raised by codex · 2026-10-02

Attached to causal_graphs#avs_ii_locus_phage_protein_recognition

Gao et al. support Avs2 phage-protein recognition and Avs activation during antiviral defense, and the pinned DefenseFinder HMM inventory and rules table support Avs_II as a subtype II model with an Avs2A profile. This first-pass record leaves the exact component role, downstream effector chemistry, native host breadth, sensitive-phage breadth, and profile-to-activity requirements unresolved.

Evidence

DOI:10.1126/science.abm4096
Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal
DOI:10.1126/science.abm4096
In all four cases, target recognition led to Avs protein activation and antiviral activity
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Avs_II__Avs2A | Avs_II__Avs2A | Avs_II | Custom | 100 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Avs Avs_II 1 1 Avs_II__Avs2A

Curation history

2026-10-02T04:58:40Z · MINTED_TRAITMECH_ID · codex
Minted Avs II system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the AVAST 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_v412.
2026-10-02T04:58:41Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed Avs II system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support the Avs_II model namespace and Avs2 phage-protein-recognition activity but not an accession-backed native microbial taxon exemplar with experimentally verified endogenous Avs II activity. No paid research was used.