{"gene":"PF3D7_0110800","run_date":"2026-09-07T10:55:51","timeline":{"discoveries":[{"year":2005,"finding":"Computational sequence analysis (HCA and PSI-BLAST) predicted PF3D7_0110800 as a putative ortholog of the general transcription factor TFIIB in P. falciparum, placing it in the basal RNA polymerase II transcription machinery.","method":"Computational sequence analysis (Hydrophobic Cluster Analysis, PSI-BLAST profile-based search)","journal":"BMC genomics","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational prediction only, no experimental validation of protein function or interactions","pmids":["16042788"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2005,"finding":"A homology-based structural model of the P. falciparum TBP–TFIIB complex (pfTBP–pfTFIIB) was built and energetically optimized; interface analysis identified conserved and species-specific residues at the TBP–TFIIB binding interface, establishing that PF3D7_0110800 (pfTFIIB) interacts with pfTBP in a manner analogous to eukaryotic homologs but with distinct residues compared to the human complex.","method":"Comparative homology modelling with energy minimization and interface residue analysis; comparison with available experimental TBP/TFIIB mutant data from other organisms","journal":"Archives of medical research","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational modelling only with no direct experimental validation in P. falciparum; interaction inferred from model, not Co-IP or in vitro assay","pmids":["15950069"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0110800 is computationally predicted to be the P. falciparum ortholog of transcription initiation factor TFIIB, a component of the basal RNA polymerase II machinery, and homology modelling suggests it forms an interface with pfTBP analogous to that seen in other eukaryotes, but no direct experimental validation of its function, interactions, or structure has been reported."},"narrative":{"mechanistic_narrative":"PF3D7_0110800 is computationally predicted to be the P. falciparum ortholog of the general transcription initiation factor TFIIB, a component of the basal RNA polymerase II machinery, based on sequence analysis (Hydrophobic Cluster Analysis and PSI-BLAST) [PMID:16042788]. A homology-based structural model of the P. falciparum TBP–TFIIB complex places PF3D7_0110800 at an interface with pfTBP analogous to that of other eukaryotic homologs, while identifying species-specific interface residues distinct from the human complex [PMID:15950069]. Beyond these computational predictions [PMID:16042788, PMID:15950069], no direct experimental validation of the function, interactions, localization, or structure of PF3D7_0110800 has been reported in the available corpus.","teleology":[{"year":2005,"claim":"Before this work the identity of the P. falciparum basal transcription machinery was unclear; sequence analysis assigned PF3D7_0110800 as a candidate TFIIB ortholog, establishing a first hypothesis for its place in RNA polymerase II transcription.","evidence":"Computational sequence analysis (Hydrophobic Cluster Analysis, PSI-BLAST profile-based search) in P. falciparum","pmids":["16042788"],"confidence":"Low","gaps":["Prediction is computational only; no experimental confirmation of TFIIB function or RNA Pol II association","No demonstration that the protein is expressed or participates in transcription in vivo","No biochemical or genetic validation of the ortholog assignment"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2005,"claim":"To ask how the predicted factor might engage the transcription machinery, a homology model of the pfTBP–pfTFIIB complex was built, inferring that PF3D7_0110800 binds pfTBP through an interface with conserved architecture but species-specific residues relative to humans.","evidence":"Comparative homology modelling with energy minimization and interface residue analysis, benchmarked against TBP/TFIIB mutant data from other organisms, in P. falciparum","pmids":["15950069"],"confidence":"Low","gaps":["Interaction is inferred from a model, not from Co-IP, pulldown, or an in vitro binding assay","The distinct interface residues are not experimentally tested for their effect on binding","No experimental structure of the P. falciparum complex exists"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether PF3D7_0110800 functions as a TFIIB in vivo, physically associates with pfTBP and RNA polymerase II, and drives transcription initiation in P. falciparum remains experimentally unestablished.","evidence":"No direct experimental study of the protein is present in the corpus","pmids":[],"confidence":"Low","gaps":["No experimental confirmation of the pfTBP–pfTFIIB interaction","No functional, genetic, or localization data for the protein","No experimentally determined structure"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["pfTBP–pfTFIIB complex (homology-modelled) [#1]"],"partners":["PFTBP (TATA-BINDING PROTEIN, PREDICTED INTERFACE PARTNER) [#1]"],"other_free_text":["Assignment of PF3D7_0110800 as P. falciparum TFIIB and its interaction with pfTBP rest entirely on computational sequence analysis and homology modelling; no direct experimental validation of function, interaction, or structure has been reported [#0, #1]."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"16042788","id":"PMC_16042788","title":"Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eukaryotes.","date":"2005","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/16042788","citation_count":101,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"15950069","id":"PMC_15950069","title":"Model of the TBP-TFIIB complex from Plasmodium falciparum: interface analysis and perspectives as a new target for antimalarial design.","date":"2005","source":"Archives of medical research","url":"https://pubmed.ncbi.nlm.nih.gov/15950069","citation_count":7,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["TFIIB","PfTFIIB"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3917,"output_tokens":631,"usd":0.010608,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5183,"output_tokens":1519,"usd":0.031945,"stage2_stop_reason":"end_turn"},"total_usd":0.042553,"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\": 2005,\n      \"finding\": \"Computational sequence analysis (HCA and PSI-BLAST) predicted PF3D7_0110800 as a putative ortholog of the general transcription factor TFIIB in P. falciparum, placing it in the basal RNA polymerase II transcription machinery.\",\n      \"method\": \"Computational sequence analysis (Hydrophobic Cluster Analysis, PSI-BLAST profile-based search)\",\n      \"journal\": \"BMC genomics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational prediction only, no experimental validation of protein function or interactions\",\n      \"pmids\": [\"16042788\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"A homology-based structural model of the P. falciparum TBP–TFIIB complex (pfTBP–pfTFIIB) was built and energetically optimized; interface analysis identified conserved and species-specific residues at the TBP–TFIIB binding interface, establishing that PF3D7_0110800 (pfTFIIB) interacts with pfTBP in a manner analogous to eukaryotic homologs but with distinct residues compared to the human complex.\",\n      \"method\": \"Comparative homology modelling with energy minimization and interface residue analysis; comparison with available experimental TBP/TFIIB mutant data from other organisms\",\n      \"journal\": \"Archives of medical research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational modelling only with no direct experimental validation in P. falciparum; interaction inferred from model, not Co-IP or in vitro assay\",\n      \"pmids\": [\"15950069\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_0110800 is computationally predicted to be the P. falciparum ortholog of transcription initiation factor TFIIB, a component of the basal RNA polymerase II machinery, and homology modelling suggests it forms an interface with pfTBP analogous to that seen in other eukaryotes, but no direct experimental validation of its function, interactions, or structure has been reported.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0110800 is computationally predicted to be the P. falciparum ortholog of the general transcription initiation factor TFIIB, a component of the basal RNA polymerase II machinery, based on sequence analysis (Hydrophobic Cluster Analysis and PSI-BLAST) [#0]. A homology-based structural model of the P. falciparum TBP–TFIIB complex places PF3D7_0110800 at an interface with pfTBP analogous to that of other eukaryotic homologs, while identifying species-specific interface residues distinct from the human complex [#1]. Beyond these computational predictions [#0, #1], no direct experimental validation of the function, interactions, localization, or structure of PF3D7_0110800 has been reported in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Before this work the identity of the P. falciparum basal transcription machinery was unclear; sequence analysis assigned PF3D7_0110800 as a candidate TFIIB ortholog, establishing a first hypothesis for its place in RNA polymerase II transcription.\",\n      \"evidence\": \"Computational sequence analysis (Hydrophobic Cluster Analysis, PSI-BLAST profile-based search) in P. falciparum\",\n      \"pmids\": [\"16042788\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Prediction is computational only; no experimental confirmation of TFIIB function or RNA Pol II association\",\n        \"No demonstration that the protein is expressed or participates in transcription in vivo\",\n        \"No biochemical or genetic validation of the ortholog assignment\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"To ask how the predicted factor might engage the transcription machinery, a homology model of the pfTBP–pfTFIIB complex was built, inferring that PF3D7_0110800 binds pfTBP through an interface with conserved architecture but species-specific residues relative to humans.\",\n      \"evidence\": \"Comparative homology modelling with energy minimization and interface residue analysis, benchmarked against TBP/TFIIB mutant data from other organisms, in P. falciparum\",\n      \"pmids\": [\"15950069\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Interaction is inferred from a model, not from Co-IP, pulldown, or an in vitro binding assay\",\n        \"The distinct interface residues are not experimentally tested for their effect on binding\",\n        \"No experimental structure of the P. falciparum complex exists\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether PF3D7_0110800 functions as a TFIIB in vivo, physically associates with pfTBP and RNA polymerase II, and drives transcription initiation in P. falciparum remains experimentally unestablished.\",\n      \"evidence\": \"No direct experimental study of the protein is present in the corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No experimental confirmation of the pfTBP–pfTFIIB interaction\",\n        \"No functional, genetic, or localization data for the protein\",\n        \"No experimentally determined structure\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0017025\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006367\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\n      \"pfTBP–pfTFIIB complex (homology-modelled) [#1]\"\n    ],\n    \"partners\": [\n      \"pfTBP (TATA-binding protein, predicted interface partner) [#1]\"\n    ],\n    \"other_free_text\": [\n      \"Assignment of PF3D7_0110800 as P. falciparum TFIIB and its interaction with pfTBP rest entirely on computational sequence analysis and homology modelling; no direct experimental validation of function, interaction, or structure has been reported [#0, #1].\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_0110800","tier":"IDENTITY_CHECK","verdict":"identity unverified","subtype":"names_other_cards","uniprot_band":"","rules_fired":"R12","issue":"No cited paper names this card; 2 of 2 cited papers name other catalogue genes (PF3D7_0522200, PF3D7_0506200). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0110800","name":null,"product":"transcription initiation factor TFIIB, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0202900","name":null,"product":"transcription initiation factor TFIIB, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0203100","name":null,"product":"transcription initiation factor TFIIB, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}