{"gene":"TG_224150","gene_symbol":"COG6","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2023,"finding":"The conserved oligomeric Golgi (COG) complex, which includes COG6, was identified and characterized in T. gondii tachyzoites and shown to be essential for protein transport; novel partners of the COG complex were also identified, suggesting T. gondii has broadened the role of conserved COG elements and reinvented missing trafficking machinery components.","method":"Genetic characterization and functional analysis of the COG complex in T. gondii tachyzoites (identification of complex components and novel partners, assessment of essentiality for protein transport)","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab, functional characterization with identification of partners, but abstract provides limited detail on specific methods used for COG6 individually","pmids":["37966241"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"COG6 is a subunit of the conserved oligomeric Golgi complex in Toxoplasma gondii tachyzoites, where the complex is essential for protein transport and glycosylation, with T. gondii having expanded its role and acquired novel interacting partners to meet parasite-specific trafficking needs."},"narrative":{"mechanistic_narrative":"COG6 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii tachyzoites, where the complex is essential for protein transport [PMID:37966241]. In T. gondii, the COG complex has broadened the role of its conserved elements and acquired novel interacting partners, apparently compensating for missing trafficking machinery components [PMID:37966241]. Beyond this complex-level characterization [PMID:37966241], no further mechanistic detail specific to COG6 has been characterized in the available corpus.","teleology":[{"year":2023,"claim":"Whether an apicomplexan parasite retains a functional COG complex and what role it plays was unknown; identifying the COG complex including COG6 in T. gondii and showing it is essential for protein transport established that this conserved Golgi machinery operates in tachyzoites and has been adapted with novel partners.","evidence":"Genetic characterization and functional analysis of the COG complex in T. gondii tachyzoites, including identification of components and novel partners and assessment of essentiality for protein transport","pmids":["37966241"],"confidence":"Medium","gaps":["The specific molecular activity and direct binding partners of COG6 individually within the complex are not defined","The identity and mechanism of the novel COG partners are not detailed","The precise cargo and glycosylation defects resulting from COG6 loss are not resolved"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Conserved oligomeric Golgi (COG) complex"],"partners":[],"other_free_text":["COG6 is a subunit of the T. gondii COG complex, which is essential for protein transport in tachyzoites [#0].","The T. gondii COG complex has acquired novel interacting partners, broadening the role of conserved COG elements [#0]."]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"37966241","id":"PMC_37966241","title":"Essential role of the conserved oligomeric Golgi complex in Toxoplasma gondii.","date":"2023","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/37966241","citation_count":7,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":2723,"output_tokens":343,"usd":0.006657,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4923,"output_tokens":1138,"usd":0.026533,"stage2_stop_reason":"end_turn"},"total_usd":0.067031,"stage1_batch_id":"msgbatch_01WokvBYTB6JLnYrpD4rXnyV","stage2_batch_id":"msgbatch_01M7hsQDvz6AqVC9DLVjQzzc","note":"batch pricing = 50% of standard","corrective_rerun":"2026-09-10 wrong-gene rerun (round-4 rules)","corrective_reason":"re-read with subject anchor"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2023,\n      \"finding\": \"The conserved oligomeric Golgi (COG) complex, which includes COG6, was identified and characterized in T. gondii tachyzoites and shown to be essential for protein transport; novel partners of the COG complex were also identified, suggesting T. gondii has broadened the role of conserved COG elements and reinvented missing trafficking machinery components.\",\n      \"method\": \"Genetic characterization and functional analysis of the COG complex in T. gondii tachyzoites (identification of complex components and novel partners, assessment of essentiality for protein transport)\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab, functional characterization with identification of partners, but abstract provides limited detail on specific methods used for COG6 individually\",\n      \"pmids\": [\"37966241\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"COG6 is a subunit of the conserved oligomeric Golgi complex in Toxoplasma gondii tachyzoites, where the complex is essential for protein transport and glycosylation, with T. gondii having expanded its role and acquired novel interacting partners to meet parasite-specific trafficking needs.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"COG6 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii tachyzoites, where the complex is essential for protein transport [#0]. In T. gondii, the COG complex has broadened the role of its conserved elements and acquired novel interacting partners, apparently compensating for missing trafficking machinery components [#0]. Beyond this complex-level characterization [#0], no further mechanistic detail specific to COG6 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2023,\n      \"claim\": \"Whether an apicomplexan parasite retains a functional COG complex and what role it plays was unknown; identifying the COG complex including COG6 in T. gondii and showing it is essential for protein transport established that this conserved Golgi machinery operates in tachyzoites and has been adapted with novel partners.\",\n      \"evidence\": \"Genetic characterization and functional analysis of the COG complex in T. gondii tachyzoites, including identification of components and novel partners and assessment of essentiality for protein transport\",\n      \"pmids\": [\"37966241\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The specific molecular activity and direct binding partners of COG6 individually within the complex are not defined\",\n        \"The identity and mechanism of the novel COG partners are not detailed\",\n        \"The precise cargo and glycosylation defects resulting from COG6 loss are not resolved\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How COG6 contributes individually to complex assembly, its direct interaction interfaces, and the mechanistic basis of the parasite-specific trafficking adaptations remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No structural or interaction map for COG6 within the T. gondii COG complex\",\n        \"No defined molecular activity attributable to COG6 alone\",\n        \"No characterization of the novel partners' function\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0015031\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\"Conserved oligomeric Golgi (COG) complex\"],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"COG6 is a subunit of the T. gondii COG complex, which is essential for protein transport in tachyzoites [#0].\",\n      \"The T. gondii COG complex has acquired novel interacting partners, broadening the role of conserved COG elements [#0].\"\n    ]\n  },\n  \"strain_conflicts\": []\n}\n```","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_224150","name":"COG6","product":"conserved oligomeric Golgi complex subunit 6","uniprot_acc":"S8F0D4","chromosome":"TGME49_chrX","start_pos":3302124},{"strain":"GT1","gene_id":"TGGT1_224150","name":null,"product":"hypothetical protein","uniprot_acc":null,"chromosome":"TGGT1_chrX","start_pos":3206396},{"strain":"RH88","gene_id":"TGRH88_043940","name":null,"product":"unspecified product","uniprot_acc":null,"chromosome":"CM023091","start_pos":4258381},{"strain":"VEG","gene_id":"TGVEG_224150","name":null,"product":"oligomeric complex protein COG6","uniprot_acc":"V4ZJ50","chromosome":"TGVEG_chrX","start_pos":3205920}]}