Gao-Her system

traitmech:000409 · CLASS · PROPOSED

A phage defense system in which an organism possesses a Gao_Her locus represented by DefenseFinder as either a Gao_Her_DUF or Gao_Her_SIR two-profile subsystem.

Trait evidence (4)

PMID:32855333
By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.

Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Gao_Her | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes

The DefenseFinder article registry maps Gao_Her to the Gao et al. prokaryotic antiviral-immunity paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Gao_Her Gao_Her_DUF 2 2 Gao_Her_DUF__DUF4297, Gao_Her_DUF__HerA_DUF

The DefenseFinder rules table models Gao_Her_DUF as a two-profile Gao_Her subsystem requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Gao_Her Gao_Her_SIR 2 2 Gao_Her_SIR__HerA_SIR2, Gao_Her_SIR__SIR2

The DefenseFinder rules table models Gao_Her_SIR as a two-profile Gao_Her subsystem requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2.

Gao-Her loci confer bacterial phage defense

Conservative family-level sketch linking Gao_Her loci to Gao et al. antiviral cassette defense without asserting the unresolved Her-DUF or Her-SIR component activities.

NONMECHANISTIC · The graph captures Gao-Her as the DefenseFinder Gao_Her family containing Gao_Her_DUF and Gao_Her_SIR subsystems while leaving natural hosts, subtype-specific phage triggers, and DUF4297, HerA_DUF, HerA_SIR2, and SIR2 molecular functions unresolved.

Edge evidence

Gao_Her locus contributes to Gao 2020 antiviral cassette defense RO:0002326
DefenseFinder maps Gao_Her to the Gao et al. systematic antiphage-system discovery paper and models two Gao_Her subsystems, Gao_Her_DUF and Gao_Her_SIR.
- PMID:32855333 By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Gao_Her | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes The DefenseFinder article registry maps Gao_Her to the Gao et al. prokaryotic antiviral-immunity paper.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Gao_Her Gao_Her_DUF 2 2 Gao_Her_DUF__DUF4297, Gao_Her_DUF__HerA_DUF The DefenseFinder rules table models Gao_Her_DUF as a two-profile Gao_Her subsystem requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Gao_Her Gao_Her_SIR 2 2 Gao_Her_SIR__HerA_SIR2, Gao_Her_SIR__SIR2 The DefenseFinder rules table models Gao_Her_SIR as a two-profile Gao_Her subsystem requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2.
Gao 2020 antiviral cassette defense confers Gao-Her system METPO:2007700
Gao_Her-associated antiviral cassette defense realizes the Gao-Her system trait.
- PMID:32855333 By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes.
Gao-Her system is a phage defense system rdfs:subClassOf
Gao-Her system possession is a phage-defense-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Gao_Her | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes The DefenseFinder article registry maps Gao_Her to the Gao et al. prokaryotic antiviral-immunity paper.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Gao_Her Gao_Her_DUF 2 2 Gao_Her_DUF__DUF4297, Gao_Her_DUF__HerA_DUF The DefenseFinder rules table models Gao_Her_DUF as a two-profile Gao_Her subsystem requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Gao_Her Gao_Her_SIR 2 2 Gao_Her_SIR__HerA_SIR2, Gao_Her_SIR__SIR2 The DefenseFinder rules table models Gao_Her_SIR as a two-profile Gao_Her subsystem requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1126/science.aba0372

Parent traits (1)

phage defense system traitmech:000209

Children (2)

Synonyms (1)

Gao_Her RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.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 Gao_Her natural host breadth, subtype boundaries, phage triggers, and the effector outputs of Gao_Her_DUF and Gao_Her_SIR before minting narrower Gao-Her mechanism children.

KNOWLEDGE GAP OPEN gao-her-family-mechanism-gap · raised by codex · 2026-09-27

Attached to causal_graphs#gao_her_locus_restricts_phage

Gao et al. support bacteriophage protection by widespread antiviral gene cassettes, and DefenseFinder models Gao_Her_DUF and Gao_Her_SIR as two-profile subsystems under the Gao_Her family key. This first parent record captures the Gao_Her family while leaving subtype-specific triggers, natural host breadth, and direct effector activities unresolved.

Curation history

2026-09-27T13:51:19Z · MINTED_TRAITMECH_ID · codex
Minted Gao-Her system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system 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_v286.
2026-09-27T13:56:56Z · EDIT · codex
Removed a repeated DefenseFinder article-row citation from the Gao-Her confers edge so no graph reuses the same snippet more than twice.