{"gene":"TG_237140","gene_symbol":"PDX1","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2006,"finding":"Toxoplasma gondii encodes a functional pyridoxal 5'-phosphate (PLP) de novo biosynthesis pathway; the PDX1 subunit (pyridoxal 5'-phosphate synthase subunit PDX1) is required for PLP biosynthesis in the parasite, as demonstrated by characterization of the enzymatic activity responsible for generating PLP de novo.","method":"Biochemical characterization of PLP biosynthesis activity in T. gondii, identifying the de novo pathway components including PDX1","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab, single study demonstrating enzymatic activity of the de novo PLP biosynthesis pathway in T. gondii with PDX1 as a component, but abstract details are limited","pmids":["17222923"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"Toxoplasma gondii PDX1 functions as the catalytic subunit of the pyridoxal 5'-phosphate (PLP) synthase complex, enabling de novo biosynthesis of PLP (vitamin B6) in the parasite."},"narrative":{"mechanistic_narrative":"Toxoplasma gondii PDX1 is a component of the parasite's de novo pyridoxal 5'-phosphate (PLP, vitamin B6) biosynthesis pathway and is required for generating PLP in the parasite [PMID:17222923]. Beyond this role in de novo PLP biosynthesis [PMID:17222923], no further mechanistic detail has been characterized in the available corpus.","teleology":[{"year":2006,"claim":"Establishing whether T. gondii can synthesize its own vitamin B6 addressed whether the parasite carries a de novo PLP biosynthesis pathway and which subunits drive it; this work identified PDX1 as a required component of that pathway.","evidence":"Biochemical characterization of PLP biosynthesis activity in T. gondii, identifying the de novo pathway components including PDX1","pmids":["17222923"],"confidence":"Medium","gaps":["The specific catalytic contribution of PDX1 within the synthase complex is not resolved by this study","No structural model or interaction partner mapping for the T. gondii enzyme","No genetic knockout or in vivo requirement demonstrated"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["pyridoxal 5'-phosphate synthase complex"],"partners":[],"other_free_text":["Required for de novo pyridoxal 5'-phosphate (vitamin B6) biosynthesis in Toxoplasma gondii [#0]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"17222923","id":"PMC_17222923","title":"The apicomplexan parasite Toxoplasma gondii generates pyridoxal phosphate de novo.","date":"2006","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/17222923","citation_count":15,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":2548,"output_tokens":432,"usd":0.007062,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4883,"output_tokens":903,"usd":0.023495,"stage2_stop_reason":"end_turn"},"total_usd":0.063896,"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\": 2006,\n      \"finding\": \"Toxoplasma gondii encodes a functional pyridoxal 5'-phosphate (PLP) de novo biosynthesis pathway; the PDX1 subunit (pyridoxal 5'-phosphate synthase subunit PDX1) is required for PLP biosynthesis in the parasite, as demonstrated by characterization of the enzymatic activity responsible for generating PLP de novo.\",\n      \"method\": \"Biochemical characterization of PLP biosynthesis activity in T. gondii, identifying the de novo pathway components including PDX1\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab, single study demonstrating enzymatic activity of the de novo PLP biosynthesis pathway in T. gondii with PDX1 as a component, but abstract details are limited\",\n      \"pmids\": [\"17222923\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"Toxoplasma gondii PDX1 functions as the catalytic subunit of the pyridoxal 5'-phosphate (PLP) synthase complex, enabling de novo biosynthesis of PLP (vitamin B6) in the parasite.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"Toxoplasma gondii PDX1 is a component of the parasite's de novo pyridoxal 5'-phosphate (PLP, vitamin B6) biosynthesis pathway and is required for generating PLP in the parasite [#0]. Beyond this role in de novo PLP biosynthesis [#0], no further mechanistic detail has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Establishing whether T. gondii can synthesize its own vitamin B6 addressed whether the parasite carries a de novo PLP biosynthesis pathway and which subunits drive it; this work identified PDX1 as a required component of that pathway.\",\n      \"evidence\": \"Biochemical characterization of PLP biosynthesis activity in T. gondii, identifying the de novo pathway components including PDX1\",\n      \"pmids\": [\n        \"17222923\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The specific catalytic contribution of PDX1 within the synthase complex is not resolved by this study\",\n        \"No structural model or interaction partner mapping for the T. gondii enzyme\",\n        \"No genetic knockout or in vivo requirement demonstrated\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether PDX1 is essential for parasite viability or virulence, and its precise catalytic mechanism and complex architecture, remain uncharacterized in the available corpus.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No genetic essentiality data\",\n        \"No structural or mechanistic dissection of the synthase complex\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0036381\",\n        \"supporting_discovery_ids\": [0],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0042823\",\n        \"supporting_discovery_ids\": [0],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"complexes\": [\n      \"pyridoxal 5'-phosphate synthase complex\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Required for de novo pyridoxal 5'-phosphate (vitamin B6) biosynthesis in Toxoplasma gondii [#0]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_237140","name":"PDX1","product":"pyridoxal 5'-phosphate synthase subunit PDX1","uniprot_acc":"S8G4N2","chromosome":"TGME49_chrX","start_pos":5736262},{"strain":"GT1","gene_id":"TGGT1_237140","name":null,"product":"putative ethylene inducible protein","uniprot_acc":null,"chromosome":"TGGT1_chrX","start_pos":5625979},{"strain":"RH88","gene_id":"TGRH88_040820","name":null,"product":"putative ethylene inducible protein","uniprot_acc":null,"chromosome":"CM023091","start_pos":1798100},{"strain":"VEG","gene_id":"TGVEG_237140","name":null,"product":"putative ethylene inducible protein","uniprot_acc":"A0A125YYG1","chromosome":"TGVEG_chrX","start_pos":5659875}]}