identifier: traitmech:000412 label: TgvAB system definition: A restriction-modification system in which an organism possesses a two-gene TgvAB locus embedded in the Vibrio cholerae VPI-2 type I R-M cluster, encoding TgvA and TgvB modification-dependent restriction proteins related to GmrSD type IV restriction enzymes that restrict glucosylated hmC-containing T-even-like phage DNA. definition_source: DOI:10.1128/jb.00145-24 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000095 synonyms: - synonym_text: TgvAB synonym_type: EXACT_SYNONYM source: DOI:10.1128/jb.00145-24 - synonym_text: TgvAB__TgvA synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: TgvAB__TgvB synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1128/jb.00145-24 snippet: the two genes embedded within the T1RM system encode a novel two-protein modification-dependent restriction system related to the GmrSD family of type IV restriction enzymes notes: Vizzarro et al. define TgvAB as a modification-dependent restriction system related to GmrSD-family type IV restriction enzymes. - reference: DOI:10.1128/jb.00145-24 snippet: potent anti-phage activity against diverse members of the Tevenvirinae notes: Vizzarro et al. support TgvAB anti-phage activity against phages with hypermodified genomes. - reference: DOI:10.1128/jb.00143-24 snippet: both TgvA and TgvB are required for defense against T2, T4, and T6 notes: Gomez and Waters independently report that both TgvA and TgvB are required for TgvAB-mediated anti-phage activity. - reference: DOI:10.1128/jb.00143-24 snippet: TgvAB targets phage DNA with glucosylated 5-hydroxymethylcytosine (5hmC) bases notes: Gomez and Waters support TgvAB as a type IV restriction system targeting glucosylated 5-hydroxymethylcytosine in T-even phage genomes. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| TgvAB | 10\.1128/jb\.00145-24 | Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems |' notes: The pinned DefenseFinder article registry maps the named TgvAB system to the Vizzarro et al. VPI-2 restriction-systems paper. The pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) does not list TgvAB, so the registry and HMM rows support a named system-possession trait rather than complete DefenseFinder detection criteria. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| TgvAB__TgvA | | TgvAB | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records TgvAB__TgvA as a custom TgvAB profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| TgvAB__TgvB | | TgvAB | Custom | 400 |' notes: The pinned DefenseFinder HMM inventory records TgvAB__TgvB as a custom TgvAB profile. causal_graphs: - graph_id: tgvab_type_iv_restriction title: TgvAB restricts glucosylated T-even-like phage DNA description: Conservative system-level sketch linking a two-gene TgvAB locus to modification-dependent type IV restriction of glucosylated hmC-containing T-even-like phage DNA and TgvAB system possession. scope_status: NONMECHANISTIC scope_notes: The graph captures TgvAB at VPI-2, T-even-like-phage, and type-IV-restriction level without asserting complete native host breadth, exact TgvA/TgvB subunit stoichiometry, or a DefenseFinder rule-level profile combination. nodes: - node_id: tgvab_locus label: TgvAB locus node_type: GENETIC_ELEMENT description: A two-gene locus encoding TgvA and TgvB GmrSD-related modification-dependent restriction proteins. - node_id: glucosylated_hmc_phage_dna label: glucosylated hmC phage DNA node_type: ENVIRONMENTAL_FACTOR description: T-even-like bacteriophage DNA carrying glucosylated 5-hydroxymethylcytosine modifications. - node_id: tgvab_dependent_type_iv_restriction label: TgvAB-dependent type IV restriction node_type: BIOLOGICAL_PROCESS description: Modification-dependent restriction of hypermodified phage DNA by TgvAB. - node_id: t_even_like_phage_propagation label: T-even-like phage propagation node_type: BIOLOGICAL_PROCESS description: Productive propagation of T-even-like phages whose genomes carry glucosylated hmC. - node_id: tgvab_system_trait label: TgvAB system node_type: TRAIT grounding: traitmech:000412 description: Possession of a genome-encoded TgvAB modification-dependent restriction system. - node_id: restriction_modification_system label: restriction-modification system node_type: TRAIT grounding: traitmech:000095 description: Possession of a methyltransferase and restriction endonuclease system for self/non-self DNA discrimination. edges: - subject: tgvab_locus predicate: enables predicate_id: RO:0002327 object: tgvab_dependent_type_iv_restriction description: A TgvAB locus encodes both proteins required for modification-dependent restriction of T-even phage DNA. evidence: - reference: DOI:10.1128/jb.00145-24 snippet: the two genes embedded within the T1RM system encode a novel two-protein modification-dependent restriction system related to the GmrSD family of type IV restriction enzymes notes: Vizzarro et al. define the embedded VPI-2 TgvAB locus as a GmrSD-related type IV restriction system. - reference: DOI:10.1128/jb.00143-24 snippet: both TgvA and TgvB are required for defense against T2, T4, and T6 notes: Gomez and Waters show that anti-phage activity requires both TgvA and TgvB. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| TgvAB | 10\.1128/jb\.00145-24 | Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems |' notes: The pinned DefenseFinder article registry maps the named TgvAB system to the Vizzarro et al. VPI-2 restriction-systems paper. The pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) does not list TgvAB, so the registry and HMM rows support a named system-possession trait rather than complete DefenseFinder detection criteria. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| TgvAB__TgvA | | TgvAB | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records TgvAB__TgvA as a custom TgvAB profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| TgvAB__TgvB | | TgvAB | Custom | 400 |' notes: The pinned DefenseFinder HMM inventory records TgvAB__TgvB as a custom TgvAB profile. - subject: tgvab_dependent_type_iv_restriction predicate: mitigates predicate_id: METPO:2007407 object: glucosylated_hmc_phage_dna description: TgvAB-dependent type IV restriction targets T-even-like phage DNA bearing glucosylated 5-hydroxymethylcytosine. evidence: - reference: DOI:10.1128/jb.00143-24 snippet: TgvAB targets phage DNA with glucosylated 5-hydroxymethylcytosine (5hmC) bases notes: Gomez and Waters directly connect the TgvAB system to targeting glucosylated 5-hydroxymethylcytosine during phage defense. - subject: tgvab_dependent_type_iv_restriction predicate: mitigates predicate_id: METPO:2007407 object: t_even_like_phage_propagation description: Restriction of hypermodified T-even-like phage DNA inhibits productive phage propagation. evidence: - reference: DOI:10.1128/jb.00145-24 snippet: potent anti-phage activity against diverse members of the Tevenvirinae notes: Vizzarro et al. support TgvAB anti-phage activity against hypermodified phages. - reference: DOI:10.1128/jb.00143-24 snippet: TgvAB targets phage DNA with glucosylated 5-hydroxymethylcytosine (5hmC) bases notes: Gomez and Waters identify glucosylated 5-hydroxymethylcytosine as the phage-DNA modification targeted by TgvAB. - subject: tgvab_dependent_type_iv_restriction predicate: confers predicate_id: METPO:2007700 object: tgvab_system_trait description: TgvAB-dependent type IV restriction realizes the TgvAB system trait. evidence: - reference: DOI:10.1128/jb.00145-24 snippet: novel modification-dependent type IV restriction system that recognizes hypermodified cytosines notes: Vizzarro et al. frame TgvAB as a type IV restriction system recognizing hypermodified cytosines. - reference: DOI:10.1128/jb.00143-24 snippet: both TgvA and TgvB are required for defense against T2, T4, and T6 notes: Gomez and Waters report that both encoded TgvAB components are required for anti-phage activity. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| TgvAB | 10\.1128/jb\.00145-24 | Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems |' notes: The pinned DefenseFinder article registry maps the named TgvAB system to the Vizzarro et al. VPI-2 restriction-systems paper. The pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) does not list TgvAB, so the registry and HMM rows support a named system-possession trait rather than complete DefenseFinder detection criteria. - subject: tgvab_system_trait predicate: is a predicate_id: rdfs:subClassOf object: restriction_modification_system description: TgvAB is a GmrSD-related type IV restriction system in the broader restriction-modification family. evidence: - reference: DOI:10.1128/jb.00145-24 snippet: the two genes embedded within the T1RM system encode a novel two-protein modification-dependent restriction system related to the GmrSD family of type IV restriction enzymes notes: Vizzarro et al. place TgvAB among GmrSD-family type IV restriction enzymes. discussions: - discussion_id: tgvab-defensefinder-rule-gap prompt: Resolve TgvAB native host breadth, TgvA/TgvB biochemical roles, phage substrate breadth, and DefenseFinder rule or model coverage before minting narrower TgvAB mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Vizzarro et al. and Gomez and Waters support TgvAB as a two-component VPI-2 type IV restriction system that restricts glucosylated hmC-containing T-even phage DNA, and the pinned DefenseFinder HMM inventory carries TgvA and TgvB custom profiles. The pinned DefenseFinder rules table has no TgvAB row, and the evidence does not yet resolve native host breadth, the individual TgvA versus TgvB biochemical roles, full phage substrate breadth, or a rule-level profile combination. evidence: - reference: DOI:10.1128/jb.00145-24 snippet: the two genes embedded within the T1RM system encode a novel two-protein modification-dependent restriction system related to the GmrSD family of type IV restriction enzymes notes: Vizzarro et al. name TgvAB as the GmrSD-related modification-dependent restriction system. - reference: DOI:10.1128/jb.00143-24 snippet: TgvAB targets phage DNA with glucosylated 5-hydroxymethylcytosine (5hmC) bases notes: Gomez and Waters support the glucosylated hmC substrate class while leaving broader phage substrate limits open. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| TgvAB__TgvA | | TgvAB | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records TgvAB__TgvA as a custom TgvAB profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| TgvAB__TgvB | | TgvAB | Custom | 400 |' notes: The pinned DefenseFinder HMM inventory records TgvAB__TgvB as a custom TgvAB profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list a TgvAB row, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#tgvab_type_iv_restriction posed_by: codex posed_date: '2026-09-27' curation_history: - timestamp: '2026-09-27T16:50:26Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted TgvAB system as a DOI-backed GENOMICS TraitRecord under restriction-modification system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at two-component TgvAB/type-IV-restriction level because the pinned DefenseFinder HMM rows are not backed by a pinned rules row; the replacement placeholder is reserved in proposals/metpo_traitmech_v289. llm_assisted: true