identifier: traitmech:000287 label: Geb system definition: A phage defense system in which an organism possesses a Geb locus that can protect bacteria from bacteriophage infection. definition_source: DOI:10.1101/2025.01.08.631966 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Geb synonym_type: EXACT_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: GebA1 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: GebA2 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1101/2025.01.08.631966 snippet: Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun). notes: Mordret et al. directly name Geb among six Streptomyces systems that increased resistance to at least one phage. - reference: DOI:10.1101/2025.01.08.631966 snippet: The bacterial pangenome encodes an immense array of antiphage systems, yet much of their diversity remains uncharted notes: Mordret et al. motivate a conservative system-level record that does not assert a resolved Geb trigger, effector output, or universal pathway. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Geb | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses notes: The DefenseFinder model registry maps the named Geb system to the Mordret et al. antiphage-system discovery preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Geb__GebA1 | | Geb notes: The DefenseFinder HMM inventory records GebA1 in the Geb model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Geb__GebA2 | | Geb notes: The DefenseFinder HMM inventory records GebA2 in the Geb model namespace. causal_graphs: - graph_id: geb_locus_restricts_phage title: Geb loci confer bacterial phage defense description: Conservative system-level sketch linking possession of a Geb locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures Geb as a named anti-phage system with GebA1 and GebA2 DefenseFinder HMM profile entries while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved. nodes: - node_id: geb_locus label: Geb locus node_type: GENETIC_ELEMENT description: A Geb anti-phage defense locus cataloged in DefenseFinder with GebA1 and GebA2 HMM profile entries. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced propagation of bacteriophage in cells carrying the Geb system. - node_id: geb_system_trait label: Geb system node_type: TRAIT grounding: traitmech:000287 description: Possession of a genome-encoded Geb phage-defense system. - node_id: phage_defense_system label: phage defense system node_type: TRAIT grounding: traitmech:000209 description: Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection. edges: - subject: geb_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: DefenseFinder maps Geb to a protein- and genomic-language-model antiphage-system discovery preprint and catalogs GebA1 and GebA2 HMM profile entries in the Geb model namespace. evidence: - reference: DOI:10.1101/2025.01.08.631966 snippet: Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun). notes: Mordret et al. directly name Geb among six Streptomyces systems that restricted at least one phage. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Geb | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses notes: The DefenseFinder registry maps Geb itself to the Mordret et al. bacterial antiphage-system discovery preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Geb__GebA1 | | Geb notes: The DefenseFinder HMM inventory records GebA1 in the Geb model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Geb__GebA2 | | Geb notes: The DefenseFinder HMM inventory records GebA2 in the Geb model namespace. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: geb_system_trait description: Geb-mediated phage restriction realizes the Geb system trait. evidence: - reference: DOI:10.1101/2025.01.08.631966 snippet: Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun). notes: Mordret et al. directly name Geb among six systems that increased resistance to at least one phage. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Geb | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses notes: DefenseFinder records Geb as a named system from the Mordret et al. antiphage discovery preprint. - subject: geb_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Geb system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Geb | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses |' notes: DefenseFinder associates Geb with the Mordret et al. bacterial antiphage-system discovery preprint. discussions: - discussion_id: geb-mechanism-gap prompt: Resolve Geb phage triggers and effector outputs before minting narrower Geb mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Mordret et al. and DefenseFinder support Geb as a named anti-phage system with GebA1 and GebA2 HMM profile entries, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait. attaches_to: - causal_graphs#geb_locus_restricts_phage posed_by: codex posed_date: '2026-09-19' curation_history: - timestamp: '2026-09-19T17:00:41Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Geb system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v164. llm_assisted: true - timestamp: '2026-09-19T17:39:40Z' curator: codex action: ADDRESSED_PR_REVIEW changes: 'Resolved PR #1073 review issues #1074 and #1075 by making the Geb subclass evidence snippet self-supporting and replacing unsupported GebA1-or-GebA2 profile-choice wording with wording limited to the DefenseFinder HMM inventory.' llm_assisted: true - timestamp: '2026-09-19T18:00:25Z' curator: codex action: ADDRESSED_PR_REVIEW changes: 'Resolved PR #1073 review issue #1076 by replacing abstract-only Geb validation support with Mordret full-text snippets that directly name Geb among the six phage-restricting systems.' llm_assisted: true