{"id":"W4415757368","doi":"10.1101/2025.10.30.685691","title":"Evolutionary Adaptation of Prephenate Dehydrogenases: A regulatory ACT domain acquisition in ecological niche specialization","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Biochemical and biochemical processes","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"National Institute of General Medical Sciences","keywords":"Allosteric regulation; Tyrosine; Amino acid; Phylogenetic tree; Metabolic pathway; Enzyme; Protein domain; Domain (mathematical analysis)","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0003813765,0.0004238504,0.0004518672,0.0001765987,0.00006454508,0.00003016373,0.0004539083,0.001184158,0.00002897308],"category_scores_gemma":[0.0003114629,0.0004370582,0.0001928266,0.0004469264,0.0002125453,0.00001323981,0.0005629963,0.0003641561,0.000004282795],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001738549,"about_ca_system_score_gemma":0.0007124027,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002429839,"about_ca_topic_score_gemma":0.000006114041,"domain_scores_codex":[0.997444,0.0001729827,0.0007098045,0.001001674,0.000302996,0.0003685263],"domain_scores_gemma":[0.9982668,0.00003472585,0.0004375434,0.0006949797,0.0004401492,0.0001258138],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0002199247,0.0004123281,0.006500617,0.0005900022,0.00008385176,0.000005825262,0.000005692218,0.0003928542,0.9910904,0.0002374104,0.0004572967,0.000003791585],"study_design_scores_gemma":[0.0006050732,0.0001050412,0.03599178,0.0003841253,0.00005858142,3.123107e-8,0.000006240131,0.0004608654,0.9605017,0.00006674173,0.001320373,0.0004994394],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9933813,0.003469345,0.00183683,0.000101075,0.0002592074,0.0005913699,0.0002683637,0.00005964426,0.00003292711],"genre_scores_gemma":[0.9948961,0.000524779,0.003814165,0.0001780226,0.0003683166,0.0001506008,0.0000256796,0.00003325331,0.000009117938],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0305887,"threshold_uncertainty_score":0.9998081,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.008810119855118561,"score_gpt":0.2167017687471085,"score_spread":0.2078916488919899,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}