{"gene":"TG_251730","gene_symbol":"COG5","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2023,"finding":"The conserved oligomeric Golgi (COG) complex, which includes COG5, was identified and characterized in T. gondii tachyzoites and shown to be essential for protein transport; the study also identified novel COG-interacting partners critical for trafficking, suggesting T. gondii broadened the role of conserved COG elements and reinvented missing trafficking machinery components.","method":"Identification and functional characterization of the COG complex in T. gondii tachyzoites (genetic and biochemical approaches implied by context of study)","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab, single study characterizing the complex with implied loss-of-function and partner identification, but abstract lacks detail on specific methods used for COG5 individually","pmids":["37966241"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"In Toxoplasma gondii tachyzoites, COG5 is part of the essential conserved oligomeric Golgi complex, which functions in protein transport and interacts with novel parasite-specific partners, with T. gondii appearing to have broadened the role of conserved COG components to accommodate parasite-specific trafficking needs."},"narrative":{"mechanistic_narrative":"In Toxoplasma gondii tachyzoites, COG5 is a subunit of the conserved oligomeric Golgi (COG) complex, which is essential for protein transport and engages novel parasite-specific interacting partners critical for trafficking, indicating that T. gondii has broadened the role of conserved COG components to accommodate parasite-specific trafficking needs [PMID:37966241]. Beyond this characterization of the COG complex at the complex level, no further mechanistic detail specific to COG5 has been characterized in the available corpus.","teleology":[{"year":2023,"claim":"Whether T. gondii possesses a functional COG complex and what role it plays was unknown; identifying and characterizing the complex established that COG (including COG5) is essential for protein transport and recruits novel parasite-specific partners, revealing a broadened, reinvented trafficking machinery.","evidence":"Identification and functional characterization of the COG complex in T. gondii tachyzoites using genetic and biochemical approaches","pmids":["37966241"],"confidence":"Medium","gaps":["The specific molecular contribution of COG5 individually (versus the complex as a whole) is not resolved","The identity and binding mode of the novel COG-interacting partners are not detailed at the COG5 level","No structural or direct substrate/cargo information for COG5 is established"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Conserved oligomeric Golgi (COG) complex"],"partners":["NOVEL PARASITE-SPECIFIC COG-INTERACTING PARTNERS (UNNAMED)"],"other_free_text":["COG5 is part of the COG complex essential for protein transport in T. gondii tachyzoites [#0].","T. gondii appears to have broadened the role of conserved COG components to accommodate parasite-specific trafficking needs [#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":361,"usd":0.006792,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4948,"output_tokens":1076,"usd":0.02582,"stage2_stop_reason":"end_turn"},"total_usd":0.066425,"stage1_batch_id":"msgbatch_01TEPNZ4MCzJ7xtsNwosiDRk","stage2_batch_id":"msgbatch_01FQShM7n1sfCr4pWTDShmki","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 COG5, was identified and characterized in T. gondii tachyzoites and shown to be essential for protein transport; the study also identified novel COG-interacting partners critical for trafficking, suggesting T. gondii broadened the role of conserved COG elements and reinvented missing trafficking machinery components.\",\n      \"method\": \"Identification and functional characterization of the COG complex in T. gondii tachyzoites (genetic and biochemical approaches implied by context of study)\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab, single study characterizing the complex with implied loss-of-function and partner identification, but abstract lacks detail on specific methods used for COG5 individually\",\n      \"pmids\": [\"37966241\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"In Toxoplasma gondii tachyzoites, COG5 is part of the essential conserved oligomeric Golgi complex, which functions in protein transport and interacts with novel parasite-specific partners, with T. gondii appearing to have broadened the role of conserved COG components to accommodate parasite-specific trafficking needs.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"In Toxoplasma gondii tachyzoites, COG5 is a subunit of the conserved oligomeric Golgi (COG) complex, which is essential for protein transport and engages novel parasite-specific interacting partners critical for trafficking, indicating that T. gondii has broadened the role of conserved COG components to accommodate parasite-specific trafficking needs [#0]. Beyond this characterization of the COG complex at the complex level, no further mechanistic detail specific to COG5 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2023,\n      \"claim\": \"Whether T. gondii possesses a functional COG complex and what role it plays was unknown; identifying and characterizing the complex established that COG (including COG5) is essential for protein transport and recruits novel parasite-specific partners, revealing a broadened, reinvented trafficking machinery.\",\n      \"evidence\": \"Identification and functional characterization of the COG complex in T. gondii tachyzoites using genetic and biochemical approaches\",\n      \"pmids\": [\"37966241\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The specific molecular contribution of COG5 individually (versus the complex as a whole) is not resolved\",\n        \"The identity and binding mode of the novel COG-interacting partners are not detailed at the COG5 level\",\n        \"No structural or direct substrate/cargo information for COG5 is established\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How COG5 specifically contributes to COG complex assembly, cargo selection, and interaction with parasite-specific partners remains undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No COG5-specific loss-of-function phenotype reported\",\n        \"No direct interactors or structural model for COG5\",\n        \"No defined trafficking cargo dependent on COG5\"\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\": [\"Novel parasite-specific COG-interacting partners (unnamed)\"],\n    \"other_free_text\": [\n      \"COG5 is part of the COG complex essential for protein transport in T. gondii tachyzoites [#0].\",\n      \"T. gondii appears to have broadened the role of conserved COG components to accommodate parasite-specific trafficking needs [#0].\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_251730","name":"COG5","product":"conserved oligomeric Golgi complex subunit 5","uniprot_acc":"S8ESF4","chromosome":"TGME49_chrXII","start_pos":5540648},{"strain":"GT1","gene_id":"TGGT1_251730","name":null,"product":"hypothetical protein","uniprot_acc":null,"chromosome":"TGGT1_chrXII","start_pos":5462336},{"strain":"RH88","gene_id":"TGRH88_064580","name":null,"product":"unspecified product","uniprot_acc":null,"chromosome":"CM023093","start_pos":5621559},{"strain":"VEG","gene_id":"TGVEG_251730","name":null,"product":"hypothetical protein","uniprot_acc":"A0A125YRR0","chromosome":"TGVEG_chrXII","start_pos":5534388}]}