{"gene":"PF3D7_1021900","run_date":"2026-09-08T12:51:28","timeline":{"discoveries":[{"year":2021,"finding":"The PHAX domain-containing protein (PF3D7_1021900 ortholog in P. berghei) was identified as an interacting partner of GBP2 by immunoprecipitation coupled to mass spectrometry (IP-MS), implicating it as an adaptor protein for exportin-1 in the mRNA export pathway of malaria parasites.","method":"Immunoprecipitation coupled to mass spectrometry (IP-MS)","journal":"Frontiers in cellular and infection microbiology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/MS experiment in a study focused on GBP2, not PF3D7_1021900; no direct functional validation of the PHAX domain-containing protein itself","pmids":["34604117"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"current_model":"The PHAX domain-containing protein (PF3D7_1021900) interacts with GBP2 in Plasmodium berghei blood-stage parasites, suggesting a role as an exportin-1 adaptor in mRNA nuclear export, but no direct functional or structural characterization of the protein itself has been reported."},"narrative":{"mechanistic_narrative":"The PHAX domain-containing protein encoded by PF3D7_1021900 has been characterized in the available corpus only through its physical association with GBP2 in Plasmodium berghei blood-stage parasites, where it was recovered as a GBP2 interacting partner by immunoprecipitation-mass spectrometry, implicating it as a candidate exportin-1 adaptor in the parasite mRNA nuclear export pathway [PMID:34604117]. Beyond this single interaction, no direct functional, biochemical, or structural characterization of PF3D7_1021900 itself has been reported in the available corpus, and its role is inferred from the biology of the GBP2 complex rather than established for the protein directly.","teleology":[{"year":2021,"claim":"To place PF3D7_1021900 in a pathway, its physical partners were unknown; identifying it in a GBP2 pulldown established a candidate link to the mRNA nuclear export machinery.","evidence":"Immunoprecipitation coupled to mass spectrometry of GBP2 in P. berghei blood-stage parasites","pmids":["34604117"],"confidence":"Low","gaps":["Single Co-IP/MS in a study focused on GBP2, with no reciprocal pulldown or direct validation of the interaction from the PF3D7_1021900 side","No functional evidence that PF3D7_1021900 acts as an exportin-1 adaptor or participates in mRNA export","The interaction was shown for the P. berghei ortholog, not directly for PF3D7_1021900 in P. falciparum"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":null,"claim":"Whether PF3D7_1021900 has any intrinsic activity, direct binding to exportin-1 or RNA, essential function, or a defined subcellular localization remains entirely unestablished.","evidence":"No further experimental characterization present in the corpus","pmids":[],"confidence":"Low","gaps":["No genetic knockout, knockdown, or complementation data for PF3D7_1021900","No structural model or PHAX-domain function validated for this protein","No demonstrated role in mRNA export beyond guilt-by-association with GBP2"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["GBP2 (PLASMODIUM BERGHEI, BY IP-MS) [#0]"],"other_free_text":["PF3D7_1021900 (P. berghei ortholog) co-purifies with GBP2, implicating it as a putative exportin-1 adaptor in the malaria parasite mRNA nuclear export pathway; this is the only characterization of the protein in the corpus [#0].","Beyond membership as a candidate partner in the GBP2 interactome, the corpus establishes nothing directly about PF3D7_1021900's own function, localization, or activity."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"34604117","id":"PMC_34604117","title":"Roles and Cellular Localization of GBP2 and NAB2 During the Blood Stage of Malaria Parasites.","date":"2021","source":"Frontiers in cellular and infection microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/34604117","citation_count":6,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PHAX"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3493,"output_tokens":367,"usd":0.007992,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4798,"output_tokens":1108,"usd":0.025845,"stage2_stop_reason":"end_turn"},"total_usd":0.033837,"stage1_batch_id":"msgbatch_01DisAaTypwmC8QwdMBuePHo","stage2_batch_id":"msgbatch_0184zxZTqxiEfdYYfPMfkqjb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2021,\n      \"finding\": \"The PHAX domain-containing protein (PF3D7_1021900 ortholog in P. berghei) was identified as an interacting partner of GBP2 by immunoprecipitation coupled to mass spectrometry (IP-MS), implicating it as an adaptor protein for exportin-1 in the mRNA export pathway of malaria parasites.\",\n      \"method\": \"Immunoprecipitation coupled to mass spectrometry (IP-MS)\",\n      \"journal\": \"Frontiers in cellular and infection microbiology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/MS experiment in a study focused on GBP2, not PF3D7_1021900; no direct functional validation of the PHAX domain-containing protein itself\",\n      \"pmids\": [\"34604117\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"The PHAX domain-containing protein (PF3D7_1021900) interacts with GBP2 in Plasmodium berghei blood-stage parasites, suggesting a role as an exportin-1 adaptor in mRNA nuclear export, but no direct functional or structural characterization of the protein itself has been reported.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"The PHAX domain-containing protein encoded by PF3D7_1021900 has been characterized in the available corpus only through its physical association with GBP2 in Plasmodium berghei blood-stage parasites, where it was recovered as a GBP2 interacting partner by immunoprecipitation-mass spectrometry, implicating it as a candidate exportin-1 adaptor in the parasite mRNA nuclear export pathway [#0]. Beyond this single interaction, no direct functional, biochemical, or structural characterization of PF3D7_1021900 itself has been reported in the available corpus, and its role is inferred from the biology of the GBP2 complex rather than established for the protein directly.\",\n  \"teleology\": [\n    {\n      \"year\": 2021,\n      \"claim\": \"To place PF3D7_1021900 in a pathway, its physical partners were unknown; identifying it in a GBP2 pulldown established a candidate link to the mRNA nuclear export machinery.\",\n      \"evidence\": \"Immunoprecipitation coupled to mass spectrometry of GBP2 in P. berghei blood-stage parasites\",\n      \"pmids\": [\"34604117\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single Co-IP/MS in a study focused on GBP2, with no reciprocal pulldown or direct validation of the interaction from the PF3D7_1021900 side\",\n        \"No functional evidence that PF3D7_1021900 acts as an exportin-1 adaptor or participates in mRNA export\",\n        \"The interaction was shown for the P. berghei ortholog, not directly for PF3D7_1021900 in P. falciparum\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether PF3D7_1021900 has any intrinsic activity, direct binding to exportin-1 or RNA, essential function, or a defined subcellular localization remains entirely unestablished.\",\n      \"evidence\": \"No further experimental characterization present in the corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No genetic knockout, knockdown, or complementation data for PF3D7_1021900\",\n        \"No structural model or PHAX-domain function validated for this protein\",\n        \"No demonstrated role in mRNA export beyond guilt-by-association with GBP2\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [\"GBP2 (Plasmodium berghei, by IP-MS) [#0]\"],\n    \"other_free_text\": [\n      \"PF3D7_1021900 (P. berghei ortholog) co-purifies with GBP2, implicating it as a putative exportin-1 adaptor in the malaria parasite mRNA nuclear export pathway; this is the only characterization of the protein in the corpus [#0].\",\n      \"Beyond membership as a candidate partner in the GBP2 interactome, the corpus establishes nothing directly about PF3D7_1021900's own function, localization, or activity.\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_1021900","tier":"IDENTITY_CHECK","verdict":"identity unverified","subtype":"names_other_cards","uniprot_band":"","rules_fired":"R12","issue":"No cited paper names this card; 1 of 1 cited papers name other catalogue genes (PF3D7_0320800, PF3D7_0623100, PF3D7_1006800). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1021900","name":null,"product":"PHAX domain-containing protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0606200","name":null,"product":"PHAX domain-containing protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}