{"gene":"PF3D7_1438100","run_date":"2026-09-08T14:19:07","timeline":{"discoveries":[{"year":2007,"finding":"Bioinformatics analysis identified a homologue of Sec62 in the P. falciparum genome, placing PF3D7_1438100 (SEC62) as a predicted component of the Sec translocation complex (Sec61αβγ/Sec62/Sec63) involved in post- and co-translational protein translocation across the ER membrane.","method":"Bioinformatics/computational genome analysis","journal":"Archives of biochemistry and biophysics","confidence":"Low","confidence_rationale":"Tier 4 / Weak — purely computational prediction with no experimental validation of the protein's function or interactions in P. falciparum","pmids":["17919451"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2019,"finding":"Computational peptide-protein docking and molecular dynamics simulations identified autophagy-interacting motifs (AIMs/LIR motifs) in PF3D7_1438100 (SEC62/PfSec62) that are predicted to interact with PfAtg8, suggesting SEC62 may act as an ER-resident autophagy receptor mediating recovER-phagy in P. falciparum; however, no experimental validation was performed.","method":"Computational peptide-protein docking, molecular dynamics simulations, steered MD simulations, free energy calculations","journal":"Frontiers in bioengineering and biotechnology","confidence":"Low","confidence_rationale":"Tier 4 / Weak — entirely computational study with no in vitro or in vivo experimental confirmation of the predicted SEC62–PfAtg8 interaction","pmids":["31608276"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1438100 (SEC62) is a predicted ER membrane component of the Sec translocation complex in P. falciparum, and computational analyses further propose it harbors AIM/LIR motifs enabling interaction with PfAtg8 as an autophagy receptor for recovER-phagy, but neither its translocation function nor its autophagy receptor role has been experimentally validated in the parasite."},"narrative":{"mechanistic_narrative":"PF3D7_1438100 (SEC62) is a P. falciparum protein known in the available corpus only through computational prediction. Bioinformatic analysis of the parasite genome identified it as a homologue of Sec62, placing it as a predicted component of the ER Sec translocation complex (Sec61αβγ/Sec62/Sec63) implicated in post- and co-translational protein translocation across the ER membrane [PMID:17919451]. A subsequent computational study identified predicted autophagy-interacting motifs (AIM/LIR motifs) in SEC62 that dock with PfAtg8, raising the possibility of a role as an ER-resident autophagy receptor for recovER-phagy [PMID:31608276]. Beyond these two computational predictions [PMID:17919451, PMID:31608276], no experimental validation of SEC62's translocation function, interactions, or autophagy receptor role in the parasite has been reported in the available corpus.","teleology":[{"year":2007,"claim":"Before any parasite-specific study, it was unknown whether P. falciparum encodes a Sec62 component of the ER translocation machinery; genome analysis established SEC62 as a predicted member of the Sec translocation complex.","evidence":"Bioinformatics/computational genome analysis of the P. falciparum genome","pmids":["17919451"],"confidence":"Low","gaps":["Purely computational homology prediction; no experimental confirmation of expression, localization, or translocation function in the parasite","Membership in the Sec61/Sec62/Sec63 complex not demonstrated biochemically","No evidence distinguishing SEC62 from sibling Sec-family members"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2019,"claim":"It was unknown whether SEC62 could link the ER to autophagy in P. falciparum; in silico docking predicted AIM/LIR motifs mediating an interaction with PfAtg8, proposing SEC62 as a candidate recovER-phagy receptor.","evidence":"Computational peptide-protein docking, molecular dynamics and steered MD simulations, and free energy calculations","pmids":["31608276"],"confidence":"Low","gaps":["Entirely computational; predicted SEC62–PfAtg8 interaction not tested in vitro or in vivo","No demonstration that SEC62 functions as an autophagy receptor in the parasite","recovER-phagy pathway in P. falciparum not experimentally established"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether SEC62 physically participates in the P. falciparum Sec translocation complex and/or acts as a PfAtg8-binding autophagy receptor remains experimentally unaddressed.","evidence":"No experimental study of SEC62 exists in the available corpus","pmids":[],"confidence":"Low","gaps":["No biochemical or genetic validation of translocation function","No experimental confirmation of the predicted PfAtg8 interaction","No localization, interaction, or knockout data for the endogenous protein"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Predicted component of the Sec translocation complex (Sec61αβγ/Sec62/Sec63) [#0]"],"partners":["PFATG8 (PREDICTED AIM/LIR-MEDIATED INTERACTION, COMPUTATIONAL ONLY) [#1]"],"other_free_text":["All available evidence for PF3D7_1438100 (SEC62) is computational; its ER translocation function and proposed recovER-phagy autophagy receptor role are unvalidated predictions [#0, #1]."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"17919451","id":"PMC_17919451","title":"Unraveling the components of protein translocation pathway in human malaria parasite Plasmodium falciparum.","date":"2007","source":"Archives of biochemistry and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/17919451","citation_count":25,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SEC62"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"31608276","id":"PMC_31608276","title":"Structural Analysis of PfSec62-Autophagy Interacting Motifs (AIM) and PfAtg8 Interactions for Its Implications in RecovER-phagy in Plasmodium falciparum.","date":"2019","source":"Frontiers in bioengineering and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/31608276","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SEC62","PfSEC62"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40396048","id":"PMC_40396048","title":"The ART of Resistance.","date":"2022","source":"Autophagy reports","url":"https://pubmed.ncbi.nlm.nih.gov/40396048","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SEC62","translocation protein SEC62","PfSEC62"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4438,"output_tokens":641,"usd":0.011465,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5250,"output_tokens":1501,"usd":0.031887,"stage2_stop_reason":"end_turn"},"total_usd":0.043352,"stage1_batch_id":"msgbatch_011BPjN2BL33F8cJXD1r7V7T","stage2_batch_id":"msgbatch_01Qwg6vP7qxkpL6Gsc7tajsb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"Bioinformatics analysis identified a homologue of Sec62 in the P. falciparum genome, placing PF3D7_1438100 (SEC62) as a predicted component of the Sec translocation complex (Sec61αβγ/Sec62/Sec63) involved in post- and co-translational protein translocation across the ER membrane.\",\n      \"method\": \"Bioinformatics/computational genome analysis\",\n      \"journal\": \"Archives of biochemistry and biophysics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — purely computational prediction with no experimental validation of the protein's function or interactions in P. falciparum\",\n      \"pmids\": [\"17919451\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Computational peptide-protein docking and molecular dynamics simulations identified autophagy-interacting motifs (AIMs/LIR motifs) in PF3D7_1438100 (SEC62/PfSec62) that are predicted to interact with PfAtg8, suggesting SEC62 may act as an ER-resident autophagy receptor mediating recovER-phagy in P. falciparum; however, no experimental validation was performed.\",\n      \"method\": \"Computational peptide-protein docking, molecular dynamics simulations, steered MD simulations, free energy calculations\",\n      \"journal\": \"Frontiers in bioengineering and biotechnology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — entirely computational study with no in vitro or in vivo experimental confirmation of the predicted SEC62–PfAtg8 interaction\",\n      \"pmids\": [\"31608276\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_1438100 (SEC62) is a predicted ER membrane component of the Sec translocation complex in P. falciparum, and computational analyses further propose it harbors AIM/LIR motifs enabling interaction with PfAtg8 as an autophagy receptor for recovER-phagy, but neither its translocation function nor its autophagy receptor role has been experimentally validated in the parasite.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1438100 (SEC62) is a P. falciparum protein known in the available corpus only through computational prediction. Bioinformatic analysis of the parasite genome identified it as a homologue of Sec62, placing it as a predicted component of the ER Sec translocation complex (Sec61\\u03b1\\u03b2\\u03b3/Sec62/Sec63) implicated in post- and co-translational protein translocation across the ER membrane [#0]. A subsequent computational study identified predicted autophagy-interacting motifs (AIM/LIR motifs) in SEC62 that dock with PfAtg8, raising the possibility of a role as an ER-resident autophagy receptor for recovER-phagy [#1]. Beyond these two computational predictions [#0, #1], no experimental validation of SEC62's translocation function, interactions, or autophagy receptor role in the parasite has been reported in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Before any parasite-specific study, it was unknown whether P. falciparum encodes a Sec62 component of the ER translocation machinery; genome analysis established SEC62 as a predicted member of the Sec translocation complex.\",\n      \"evidence\": \"Bioinformatics/computational genome analysis of the P. falciparum genome\",\n      \"pmids\": [\n        \"17919451\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Purely computational homology prediction; no experimental confirmation of expression, localization, or translocation function in the parasite\",\n        \"Membership in the Sec61/Sec62/Sec63 complex not demonstrated biochemically\",\n        \"No evidence distinguishing SEC62 from sibling Sec-family members\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"It was unknown whether SEC62 could link the ER to autophagy in P. falciparum; in silico docking predicted AIM/LIR motifs mediating an interaction with PfAtg8, proposing SEC62 as a candidate recovER-phagy receptor.\",\n      \"evidence\": \"Computational peptide-protein docking, molecular dynamics and steered MD simulations, and free energy calculations\",\n      \"pmids\": [\n        \"31608276\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Entirely computational; predicted SEC62\\u2013PfAtg8 interaction not tested in vitro or in vivo\",\n        \"No demonstration that SEC62 functions as an autophagy receptor in the parasite\",\n        \"recovER-phagy pathway in P. falciparum not experimentally established\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether SEC62 physically participates in the P. falciparum Sec translocation complex and/or acts as a PfAtg8-binding autophagy receptor remains experimentally unaddressed.\",\n      \"evidence\": \"No experimental study of SEC62 exists in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No biochemical or genetic validation of translocation function\",\n        \"No experimental confirmation of the predicted PfAtg8 interaction\",\n        \"No localization, interaction, or knockout data for the endogenous protein\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [\n      \"Predicted component of the Sec translocation complex (Sec61\\u03b1\\u03b2\\u03b3/Sec62/Sec63) [#0]\"\n    ],\n    \"partners\": [\n      \"PfAtg8 (predicted AIM/LIR-mediated interaction, computational only) [#1]\"\n    ],\n    \"other_free_text\": [\n      \"All available evidence for PF3D7_1438100 (SEC62) is computational; its ER translocation function and proposed recovER-phagy autophagy receptor role are unvalidated predictions [#0, #1].\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1438100","name":null,"product":"translocation protein SEC62, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1302200","name":null,"product":"translocation protein SEC62, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1244300","name":null,"product":"translocation protein SEC62, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"SEC62","evaluation":null}