{"gene":"PF3D7_0511700","run_date":"2026-09-07T10:55:52","timeline":{"discoveries":[{"year":2014,"finding":"CGI121 (PF3D7_0511700) forms a complex with cytoplasmic Kae1 and Bud32 in P. falciparum, analogous to the conserved EKC/KEOPS complex found in other organisms, as established by immunoprecipitation-mass spectrometry.","method":"Immunoprecipitation coupled with mass spectrometry (proteomic cross-validation approach comparing IP-MS datasets across cellular compartments)","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single lab, IP-MS with cross-compartment validation strategy; no reciprocal pulldown or in vitro reconstitution reported","pmids":["25204654"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"CGI121 (PF3D7_0511700) is a subunit of the cytoplasmic EKC/KEOPS complex in P. falciparum, where it interacts with Kae1 and Bud32, consistent with its conserved role in this complex across organisms, but no additional mechanistic details specific to CGI121 itself have been established in the available literature."},"narrative":{"mechanistic_narrative":"CGI121 (PF3D7_0511700) is a subunit of the cytoplasmic EKC/KEOPS complex in Plasmodium falciparum, where it associates with Kae1 and Bud32 in an assembly analogous to the conserved EKC/KEOPS complex of other organisms, as established by immunoprecipitation-mass spectrometry [PMID:25204654]. Beyond this complex membership, no CGI121-specific molecular function, substrate, or phenotype has been characterized in the available corpus.","teleology":[{"year":2014,"claim":"Whether P. falciparum encodes a CGI121 that participates in a KEOPS-like assembly was unknown; identifying its physical partners established CGI121 as a bona fide subunit of a cytoplasmic EKC/KEOPS complex in the parasite.","evidence":"Immunoprecipitation-mass spectrometry with cross-compartment proteomic cross-validation in P. falciparum","pmids":["25204654"],"confidence":"Medium","gaps":["No reciprocal pulldown or in vitro reconstitution confirming direct CGI121-Kae1/Bud32 contacts","No functional or phenotypic role for CGI121 itself established","No structural model or stoichiometry of the P. falciparum complex determined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"What CGI121 contributes to the EKC/KEOPS complex beyond membership — its specific molecular activity, essentiality, and role in the parasite life cycle — remains unaddressed.","evidence":"No further discoveries in the available corpus","pmids":[],"confidence":"Medium","gaps":["No knockout, knockdown, or conditional depletion of CGI121 reported","No demonstrated biochemical activity attributable to CGI121","No link to tRNA modification or any downstream process shown for the P. falciparum complex"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["EKC/KEOPS complex"],"partners":["KAE1","BUD32"],"other_free_text":["In P. falciparum, CGI121 (PF3D7_0511700) is defined solely by its physical association with cytoplasmic Kae1 and Bud32 in an EKC/KEOPS-like complex [#0]; no function independent of this membership has been characterized in the corpus."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"25204654","id":"PMC_25204654","title":"Kinase-associated endopeptidase 1 (Kae1) participates in an atypical ribosome-associated complex in the apicoplast of Plasmodium falciparum.","date":"2014","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/25204654","citation_count":11,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["CGI121"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3372,"output_tokens":367,"usd":0.00781,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4855,"output_tokens":1018,"usd":0.024862,"stage2_stop_reason":"end_turn"},"total_usd":0.032672,"stage1_batch_id":"msgbatch_01DbiymDmubkPpYvdbAu5a7V","stage2_batch_id":"msgbatch_012TbrWvMRH129T7PQ4SmvrJ","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2014,\n      \"finding\": \"CGI121 (PF3D7_0511700) forms a complex with cytoplasmic Kae1 and Bud32 in P. falciparum, analogous to the conserved EKC/KEOPS complex found in other organisms, as established by immunoprecipitation-mass spectrometry.\",\n      \"method\": \"Immunoprecipitation coupled with mass spectrometry (proteomic cross-validation approach comparing IP-MS datasets across cellular compartments)\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single lab, IP-MS with cross-compartment validation strategy; no reciprocal pulldown or in vitro reconstitution reported\",\n      \"pmids\": [\"25204654\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"CGI121 (PF3D7_0511700) is a subunit of the cytoplasmic EKC/KEOPS complex in P. falciparum, where it interacts with Kae1 and Bud32, consistent with its conserved role in this complex across organisms, but no additional mechanistic details specific to CGI121 itself have been established in the available literature.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CGI121 (PF3D7_0511700) is a subunit of the cytoplasmic EKC/KEOPS complex in Plasmodium falciparum, where it associates with Kae1 and Bud32 in an assembly analogous to the conserved EKC/KEOPS complex of other organisms, as established by immunoprecipitation-mass spectrometry [#0]. Beyond this complex membership, no CGI121-specific molecular function, substrate, or phenotype has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Whether P. falciparum encodes a CGI121 that participates in a KEOPS-like assembly was unknown; identifying its physical partners established CGI121 as a bona fide subunit of a cytoplasmic EKC/KEOPS complex in the parasite.\",\n      \"evidence\": \"Immunoprecipitation-mass spectrometry with cross-compartment proteomic cross-validation in P. falciparum\",\n      \"pmids\": [\"25204654\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No reciprocal pulldown or in vitro reconstitution confirming direct CGI121-Kae1/Bud32 contacts\",\n        \"No functional or phenotypic role for CGI121 itself established\",\n        \"No structural model or stoichiometry of the P. falciparum complex determined\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"What CGI121 contributes to the EKC/KEOPS complex beyond membership — its specific molecular activity, essentiality, and role in the parasite life cycle — remains unaddressed.\",\n      \"evidence\": \"No further discoveries in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No knockout, knockdown, or conditional depletion of CGI121 reported\",\n        \"No demonstrated biochemical activity attributable to CGI121\",\n        \"No link to tRNA modification or any downstream process shown for the P. falciparum complex\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005737\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [\"EKC/KEOPS complex\"],\n    \"partners\": [\"Kae1\", \"Bud32\"],\n    \"other_free_text\": [\n      \"In P. falciparum, CGI121 (PF3D7_0511700) is defined solely by its physical association with cytoplasmic Kae1 and Bud32 in an EKC/KEOPS-like complex [#0]; no function independent of this membership has been characterized in the corpus.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0511700","name":null,"product":"EKC/KEOPS complex subunit CGI121","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1111300","name":null,"product":"EKC/KEOPS complex subunit CGI121, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1021900","name":null,"product":"EKC/KEOPS complex subunit CGI121, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"CGI121","evaluation":null}