{"gene":"TG_208370","gene_symbol":"GRA46","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2018,"finding":"GRA46 is a dense granule protein identified as a substrate of the Golgi-associated aspartyl protease ASP5; it contains an RRL motif that is cleaved by ASP5, and mutation of the motif from RRL to ARL abolishes processing, confirming direct maturation by ASP5.","method":"TAILS (Terminal Amine Isotopic Labeling of Substrates) N-terminal peptide enrichment and quantitative proteomics comparing wild-type and Δasp5 parasites, with RRL→ARL motif mutagenesis validation","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — quantitative proteomics with orthogonal motif mutagenesis validation in a single study; single lab","pmids":["30377279"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2018,"finding":"GRA46, as an ASP5 substrate, resides within the parasitophorous vacuole (PV) or its membrane (PVM) and is not exported into the host cell, distinguishing it from the analogous exported substrates in Plasmodium spp.","method":"Subcellular localization inferred from N-terminal peptide mapping and proteomics of wild-type vs. Δasp5 parasites; localization assessed at the host-parasite interface","journal":"mBio","confidence":"Low","confidence_rationale":"Tier 3 / Weak — localization inferred from proteomics without direct imaging or fractionation confirmation specifically for GRA46; single lab, single method","pmids":["30377279"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"GRA46 is a dense granule protein that resides at the parasitophorous vacuole and is directly matured by the Golgi-associated aspartyl protease ASP5, which cleaves at an RRL motif; unlike the analogous Plasmodium system, GRA46 is not exported into the host cell."},"narrative":{"mechanistic_narrative":"GRA46 is a dense granule protein of Toxoplasma gondii that is a direct maturation substrate of the Golgi-associated aspartyl protease ASP5, which cleaves an RRL motif within GRA46; mutation of this motif from RRL to ARL abolishes processing, establishing GRA46 as a bona fide ASP5 substrate [PMID:30377279]. Beyond its identification and ASP5-dependent maturation [PMID:30377279], nothing further has been characterized about GRA46 in the available corpus.","teleology":[{"year":2018,"claim":"Establishing that GRA46 is a genuine ASP5 substrate answered whether it undergoes ASP5-dependent processing and defined the molecular determinant of that cleavage.","evidence":"TAILS N-terminal peptide enrichment and quantitative proteomics comparing wild-type and Δasp5 parasites, with RRL→ARL motif mutagenesis validation","pmids":["30377279"],"confidence":"Medium","gaps":["The functional consequence of ASP5 cleavage for GRA46 activity or trafficking is not defined","No molecular activity or interaction partners of GRA46 are identified","No structural model of the GRA46 cleavage site or mature protein is available"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2018,"claim":"Assigning GRA46 to the parasitophorous vacuole and showing it is not exported clarified where the ASP5-matured protein resides relative to the host-parasite interface.","evidence":"Subcellular localization inferred from N-terminal peptide mapping and proteomics of wild-type vs. Δasp5 parasites at the host-parasite interface","pmids":["30377279"],"confidence":"Low","gaps":["Localization was inferred from proteomics without direct imaging or fractionation confirmation specifically for GRA46","Whether GRA46 sits in the PV lumen or the PVM is not resolved","No functional role at the PV/PVM is established"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["ASP5 (GOLGI-ASSOCIATED ASPARTYL PROTEASE THAT CLEAVES THE GRA46 RRL MOTIF)"],"other_free_text":["GRA46 is a dense granule protein whose RRL motif is directly cleaved by ASP5; RRL→ARL mutation abolishes processing [#0].","Unlike the analogous exported ASP5 substrates in Plasmodium, GRA46 is not exported into the host cell and remains at the PV/PVM [#1]."]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"30377279","id":"PMC_30377279","title":"Aspartyl Protease 5 Matures Dense Granule Proteins That Reside at the Host-Parasite Interface in Toxoplasma gondii.","date":"2018","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/30377279","citation_count":45,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3197,"output_tokens":625,"usd":0.009483,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5308,"output_tokens":1488,"usd":0.03187,"stage2_stop_reason":"end_turn"},"total_usd":0.083121,"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\": 2018,\n      \"finding\": \"GRA46 is a dense granule protein identified as a substrate of the Golgi-associated aspartyl protease ASP5; it contains an RRL motif that is cleaved by ASP5, and mutation of the motif from RRL to ARL abolishes processing, confirming direct maturation by ASP5.\",\n      \"method\": \"TAILS (Terminal Amine Isotopic Labeling of Substrates) N-terminal peptide enrichment and quantitative proteomics comparing wild-type and Δasp5 parasites, with RRL→ARL motif mutagenesis validation\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — quantitative proteomics with orthogonal motif mutagenesis validation in a single study; single lab\",\n      \"pmids\": [\"30377279\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"GRA46, as an ASP5 substrate, resides within the parasitophorous vacuole (PV) or its membrane (PVM) and is not exported into the host cell, distinguishing it from the analogous exported substrates in Plasmodium spp.\",\n      \"method\": \"Subcellular localization inferred from N-terminal peptide mapping and proteomics of wild-type vs. Δasp5 parasites; localization assessed at the host-parasite interface\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — localization inferred from proteomics without direct imaging or fractionation confirmation specifically for GRA46; single lab, single method\",\n      \"pmids\": [\"30377279\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"GRA46 is a dense granule protein that resides at the parasitophorous vacuole and is directly matured by the Golgi-associated aspartyl protease ASP5, which cleaves at an RRL motif; unlike the analogous Plasmodium system, GRA46 is not exported into the host cell.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"GRA46 is a dense granule protein of Toxoplasma gondii that is a direct maturation substrate of the Golgi-associated aspartyl protease ASP5, which cleaves an RRL motif within GRA46; mutation of this motif from RRL to ARL abolishes processing, establishing GRA46 as a bona fide ASP5 substrate [#0]. Beyond its identification and ASP5-dependent maturation [#0], nothing further has been characterized about GRA46 in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"Establishing that GRA46 is a genuine ASP5 substrate answered whether it undergoes ASP5-dependent processing and defined the molecular determinant of that cleavage.\",\n      \"evidence\": \"TAILS N-terminal peptide enrichment and quantitative proteomics comparing wild-type and \\u0394asp5 parasites, with RRL\\u2192ARL motif mutagenesis validation\",\n      \"pmids\": [\n        \"30377279\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The functional consequence of ASP5 cleavage for GRA46 activity or trafficking is not defined\",\n        \"No molecular activity or interaction partners of GRA46 are identified\",\n        \"No structural model of the GRA46 cleavage site or mature protein is available\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Assigning GRA46 to the parasitophorous vacuole and showing it is not exported clarified where the ASP5-matured protein resides relative to the host-parasite interface.\",\n      \"evidence\": \"Subcellular localization inferred from N-terminal peptide mapping and proteomics of wild-type vs. \\u0394asp5 parasites at the host-parasite interface\",\n      \"pmids\": [\n        \"30377279\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Localization was inferred from proteomics without direct imaging or fractionation confirmation specifically for GRA46\",\n        \"Whether GRA46 sits in the PV lumen or the PVM is not resolved\",\n        \"No functional role at the PV/PVM is established\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular function, interaction partners, and biological role of GRA46 at the parasitophorous vacuole remain unknown.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No enzymatic or binding activity assigned to GRA46\",\n        \"No phenotype from GRA46 loss-of-function reported\",\n        \"No direct imaging confirming PV lumen vs. PVM residence\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\n        \"term_id\": \"GO:0020003\",\n        \"supporting_discovery_ids\": [\n          1\n        ],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [\n      \"ASP5 (Golgi-associated aspartyl protease that cleaves the GRA46 RRL motif)\"\n    ],\n    \"other_free_text\": [\n      \"GRA46 is a dense granule protein whose RRL motif is directly cleaved by ASP5; RRL\\u2192ARL mutation abolishes processing [#0].\",\n      \"Unlike the analogous exported ASP5 substrates in Plasmodium, GRA46 is not exported into the host cell and remains at the PV/PVM [#1].\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_208370","name":"GRA46","product":"dense granule protein GRA46","uniprot_acc":"S8FC47","chromosome":"TGME49_chrIb","start_pos":635939},{"strain":"GT1","gene_id":"TGGT1_208370","name":null,"product":"putative myosin heavy chain","uniprot_acc":null,"chromosome":"TGGT1_chrIb","start_pos":652389},{"strain":"RH88","gene_id":"TGRH88_022490","name":null,"product":"putative myosin heavy chain","uniprot_acc":null,"chromosome":"CM023082","start_pos":1371010},{"strain":"VEG","gene_id":"TGVEG_208370","name":null,"product":"putative myosin heavy chain","uniprot_acc":"B9QL03","chromosome":"TGVEG_chrIb","start_pos":634619}]}