{"gene":"TG_319900","gene_symbol":"AAP5","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2019,"finding":"AAP5 was identified as a component of the apical annuli structures in Toxoplasma gondii by reciprocal proximity biotinylation (BioID) proteomics and validated as one of five apical annuli proteins (AAP1–5) residing within the inner membrane complex (IMC) sutures.","method":"Reciprocal proximity biotinylation (BioID) proteomics; super-resolution microscopy","journal":"Cellular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal BioID with super-resolution microscopy validation in a single lab; two orthogonal methods but no functional rescue or mutagenesis for AAP5 specifically","pmids":["31470470"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"finding":"The apical annuli complex, which includes AAP5, is organized as a concentric pore-like structure with four rings of 200–400 nm diameter, embedded in the IMC sutures, and is composed of coiled-coil and signalling domain-containing proteins together with Centrin2.","method":"Super-resolution microscopy; BioID proteomics; domain analysis","journal":"Cellular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — super-resolution microscopy plus BioID in a single lab; structural organization established at the complex level","pmids":["31470470"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"finding":"Phylogenetic analysis showed that AAP5 is conserved narrowly within coccidian apicomplexans that multiply by internal budding, suggesting a functional role linked to internal budding replication.","method":"Phylogenetic analysis","journal":"Cellular microbiology","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational phylogenetic inference only, no direct functional experiment on AAP5","pmids":["31470470"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"AAP5 is a validated component of the apical annuli of Toxoplasma gondii, localizing within the inner membrane complex sutures as part of a concentric, pore-like ring structure (200–400 nm) composed of coiled-coil and signalling domain proteins alongside Centrin2; its narrow conservation in internally budding coccidians suggests a role in replication, but no direct functional mechanism for AAP5 specifically has been experimentally defined."},"narrative":{"mechanistic_narrative":"AAP5 is a component of the apical annuli of Toxoplasma gondii, a set of structures embedded within the inner membrane complex (IMC) sutures, where it was identified and validated by reciprocal proximity biotinylation (BioID) proteomics and super-resolution microscopy as one of five apical annuli proteins (AAP1–5) [PMID:31470470]. Within this structure, AAP5 forms part of a concentric, pore-like ring assembly of 200–400 nm diameter built from coiled-coil and signalling domain-containing proteins together with Centrin2 [PMID:31470470]. No direct functional mechanism for AAP5 itself has been experimentally defined in the available corpus; its narrow conservation among internally budding coccidians is the only basis for an inferred role.","teleology":[{"year":2019,"claim":"Establishing what proteins constitute the apical annuli answered where AAP5 resides in the parasite, placing it as a bona fide structural component of the IMC sutures rather than a diffuse cytoplasmic factor.","evidence":"Reciprocal BioID proteomics with super-resolution microscopy validation in Toxoplasma gondii","pmids":["31470470"],"confidence":"Medium","gaps":["No functional rescue or mutagenesis of AAP5 specifically","Molecular activity of AAP5 within the complex not defined"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"claim":"Resolving the architecture of the apical annuli showed AAP5 sits within a concentric pore-like ring, defining the structural context in which it operates alongside Centrin2 and coiled-coil/signalling proteins.","evidence":"Super-resolution microscopy, BioID, and domain analysis in Toxoplasma gondii","pmids":["31470470"],"confidence":"Medium","gaps":["AAP5's specific contribution to ring assembly or integrity untested","Function of the pore-like structure unknown"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"claim":"Phylogenetic restriction of AAP5 to internally budding coccidians offered a first hypothesis linking the protein to replication by internal budding, though without direct functional testing.","evidence":"Phylogenetic analysis","pmids":["31470470"],"confidence":"Low","gaps":["Computational inference only, no functional experiment","Connection to internal budding untested experimentally"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Apical annuli complex (AAP1–5 with Centrin2)"],"partners":["AAP1","AAP2","AAP3","AAP4","CENTRIN2"],"other_free_text":["AAP5 is one of five apical annuli proteins organized as a concentric pore-like ring of 200–400 nm diameter [#1].","AAP5 is narrowly conserved among internally budding coccidian apicomplexans, an inferred link to internal budding replication [#2]."]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"31470470","id":"PMC_31470470","title":"The apical annuli of Toxoplasma gondii are composed of coiled-coil and signalling proteins embedded in the inner membrane complex sutures.","date":"2019","source":"Cellular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/31470470","citation_count":38,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":2950,"output_tokens":758,"usd":0.01011,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5535,"output_tokens":1609,"usd":0.03395,"stage2_stop_reason":"end_turn"},"total_usd":0.088906,"stage1_batch_id":"msgbatch_01S6GjoYQm8LTPUsdhASdqag","stage2_batch_id":"msgbatch_01VX63RTMdBJqsG6gQMqoCjz","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\": 2019,\n      \"finding\": \"AAP5 was identified as a component of the apical annuli structures in Toxoplasma gondii by reciprocal proximity biotinylation (BioID) proteomics and validated as one of five apical annuli proteins (AAP1–5) residing within the inner membrane complex (IMC) sutures.\",\n      \"method\": \"Reciprocal proximity biotinylation (BioID) proteomics; super-resolution microscopy\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal BioID with super-resolution microscopy validation in a single lab; two orthogonal methods but no functional rescue or mutagenesis for AAP5 specifically\",\n      \"pmids\": [\"31470470\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"finding\": \"The apical annuli complex, which includes AAP5, is organized as a concentric pore-like structure with four rings of 200–400 nm diameter, embedded in the IMC sutures, and is composed of coiled-coil and signalling domain-containing proteins together with Centrin2.\",\n      \"year\": 2019,\n      \"method\": \"Super-resolution microscopy; BioID proteomics; domain analysis\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — super-resolution microscopy plus BioID in a single lab; structural organization established at the complex level\",\n      \"pmids\": [\"31470470\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"finding\": \"Phylogenetic analysis showed that AAP5 is conserved narrowly within coccidian apicomplexans that multiply by internal budding, suggesting a functional role linked to internal budding replication.\",\n      \"year\": 2019,\n      \"method\": \"Phylogenetic analysis\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational phylogenetic inference only, no direct functional experiment on AAP5\",\n      \"pmids\": [\"31470470\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"AAP5 is a validated component of the apical annuli of Toxoplasma gondii, localizing within the inner membrane complex sutures as part of a concentric, pore-like ring structure (200–400 nm) composed of coiled-coil and signalling domain proteins alongside Centrin2; its narrow conservation in internally budding coccidians suggests a role in replication, but no direct functional mechanism for AAP5 specifically has been experimentally defined.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"AAP5 is a component of the apical annuli of Toxoplasma gondii, a set of structures embedded within the inner membrane complex (IMC) sutures, where it was identified and validated by reciprocal proximity biotinylation (BioID) proteomics and super-resolution microscopy as one of five apical annuli proteins (AAP1–5) [#0]. Within this structure, AAP5 forms part of a concentric, pore-like ring assembly of 200–400 nm diameter built from coiled-coil and signalling domain-containing proteins together with Centrin2 [#1]. No direct functional mechanism for AAP5 itself has been experimentally defined in the available corpus; its narrow conservation among internally budding coccidians is the only basis for an inferred role.\",\n  \"teleology\": [\n    {\n      \"year\": 2019,\n      \"claim\": \"Establishing what proteins constitute the apical annuli answered where AAP5 resides in the parasite, placing it as a bona fide structural component of the IMC sutures rather than a diffuse cytoplasmic factor.\",\n      \"evidence\": \"Reciprocal BioID proteomics with super-resolution microscopy validation in Toxoplasma gondii\",\n      \"pmids\": [\"31470470\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional rescue or mutagenesis of AAP5 specifically\", \"Molecular activity of AAP5 within the complex not defined\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Resolving the architecture of the apical annuli showed AAP5 sits within a concentric pore-like ring, defining the structural context in which it operates alongside Centrin2 and coiled-coil/signalling proteins.\",\n      \"evidence\": \"Super-resolution microscopy, BioID, and domain analysis in Toxoplasma gondii\",\n      \"pmids\": [\"31470470\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"AAP5's specific contribution to ring assembly or integrity untested\", \"Function of the pore-like structure unknown\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Phylogenetic restriction of AAP5 to internally budding coccidians offered a first hypothesis linking the protein to replication by internal budding, though without direct functional testing.\",\n      \"evidence\": \"Phylogenetic analysis\",\n      \"pmids\": [\"31470470\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Computational inference only, no functional experiment\", \"Connection to internal budding untested experimentally\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular activity of AAP5, its direct binding partners within the annuli, and its causal role in internal budding replication remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No knockout or knockdown phenotype for AAP5\", \"No direct biochemical activity assigned\", \"No reciprocal partner validation beyond complex-level BioID\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"apical annuli\", \"supporting_discovery_ids\": [0, 1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"inner membrane complex sutures\", \"supporting_discovery_ids\": [0, 1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [\"Apical annuli complex (AAP1–5 with Centrin2)\"],\n    \"partners\": [\"AAP1\", \"AAP2\", \"AAP3\", \"AAP4\", \"Centrin2\"],\n    \"other_free_text\": [\n      \"AAP5 is one of five apical annuli proteins organized as a concentric pore-like ring of 200–400 nm diameter [#1].\",\n      \"AAP5 is narrowly conserved among internally budding coccidian apicomplexans, an inferred link to internal budding replication [#2].\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_319900","name":"AAP5","product":"apical annuli protein AAP5","uniprot_acc":"S8F9P9","chromosome":"TGME49_chrIV","start_pos":678305},{"strain":"GT1","gene_id":"TGGT1_319900","name":null,"product":"hypothetical protein","uniprot_acc":null,"chromosome":"TGGT1_chrIV","start_pos":622899},{"strain":"RH88","gene_id":"TGRH88_007290","name":null,"product":"unspecified product","uniprot_acc":null,"chromosome":"CM023085","start_pos":689277},{"strain":"VEG","gene_id":"TGVEG_319900","name":null,"product":"hypothetical protein","uniprot_acc":"V4Z2T9","chromosome":"TGVEG_chrIV","start_pos":678012}]}