Gao-Her-SIR system

traitmech:000362 · CLASS · PROPOSED

A phage defense system in which an organism possesses a Gao_Her_SIR locus represented by DefenseFinder as a two-profile model requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2.

Trait evidence (5)

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 the broader Gao_Her family key 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_SIR 2 2 Gao_Her_SIR__HerA_SIR2, Gao_Her_SIR__SIR2

The DefenseFinder rules table models Gao_Her_SIR as a two-profile system requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Gao_Her_SIR__HerA_SIR2 | Gao_Her_SIR__HerA_SIR2 | Gao_Her_SIR | Custom | 43 |

The DefenseFinder HMM inventory records Gao_Her_SIR__HerA_SIR2 under Gao_Her_SIR.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Gao_Her_SIR__SIR2 | Gao_Her_SIR__SIR2 | Gao_Her_SIR | Custom | 34 |

The DefenseFinder HMM inventory records Gao_Her_SIR__SIR2 under Gao_Her_SIR.

Gao-Her-SIR loci confer bacterial phage defense

Conservative system-level sketch linking possession of a Gao_Her_SIR locus to Gao et al. antiviral cassette defense without asserting the unresolved Her-SIR component activities.

NONMECHANISTIC · The graph captures Gao-Her-SIR as a named DefenseFinder two-profile Gao-family system while leaving natural hosts, HerA_SIR2/SIR2 protein functions, phage triggers, and direct effector activity unresolved.

Edge evidence

Gao_Her_SIR locus contributes to Gao 2020 antiviral cassette defense RO:0002326
DefenseFinder maps the broader Gao_Her family key to the Gao et al. systematic antiphage-system discovery paper and models Gao_Her_SIR as a two-profile system requiring HerA_SIR2 and SIR2.
- 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 bacteriophage protection by 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 the broader Gao_Her family key 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_SIR 2 2 Gao_Her_SIR__HerA_SIR2, Gao_Her_SIR__SIR2 The DefenseFinder rules table models Gao_Her_SIR as a two-profile system requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | Gao_Her_SIR__HerA_SIR2 | Gao_Her_SIR__HerA_SIR2 | Gao_Her_SIR | Custom | 43 | The DefenseFinder HMM inventory records Gao_Her_SIR__HerA_SIR2 under Gao_Her_SIR.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | Gao_Her_SIR__SIR2 | Gao_Her_SIR__SIR2 | Gao_Her_SIR | Custom | 34 | The DefenseFinder HMM inventory records Gao_Her_SIR__SIR2 under Gao_Her_SIR.
Gao 2020 antiviral cassette defense confers Gao-Her-SIR system METPO:2007700
Gao_Her_SIR-associated antiviral cassette defense realizes the Gao-Her-SIR 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 bacteriophage protection by widespread antiviral gene cassettes.
Gao-Her-SIR system is a Gao-Her system rdfs:subClassOf
Gao-Her-SIR system possession is a Gao-Her family phage-defense-system trait.
- 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)

Gao-Her system traitmech:000409

Synonyms (3)

Gao_Her_SIR RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Gao_Her_SIR__HerA_SIR2 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Gao_Her_SIR__SIR2 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 Gao_Her_SIR natural hosts, HerA_SIR2/SIR2 component functions, phage triggers, and effector activity before minting narrower Gao_Her_SIR mechanism children.

KNOWLEDGE GAP OPEN gao-her-sir-mechanism-gap · raised by codex · 2026-09-22

Attached to causal_graphs#gao_her_sir_locus_restricts_phage

Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_Her_SIR as a two-profile system under the Gao_Her family key. The exact natural host breadth, HerA_SIR2/SIR2 component identities, phage trigger, and profile-to-activity mapping remain unresolved.

Curation history

2026-09-22T10:04:44Z · MINTED_TRAITMECH_ID · codex
Minted Gao-Her-SIR system as a DOI-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_v239.
2026-09-27T13:51:19Z · EDIT · codex
Reparented the record under traitmech:000409 Gao-Her system and added a Gao-Her parent node plus subclass edge to the causal graph.
2026-09-27T13:56:56Z · EDIT · codex
Removed the redundant Gao-Her-to-phage subclass edge from the child graph; the Gao-Her parent record now carries that edge.