{"id":"W1995141949","doi":"10.1038/nature03306","title":"A universal trend of amino acid gain and loss in protein evolution","year":2005,"lang":"en","type":"article","venue":"Nature","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":309,"is_retracted":false,"has_abstract":false,"ca_institutions":"","funders":"Genome Canada; Rural Industries Research and Development Corporation; Rockefeller Foundation","keywords":"Amino acid; Genetic code; Archaea; Genome; Biology; Taxon; Genetics; Evolutionary biology; Biochemistry; Bacteria; Gene; Ecology","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00004614972,0.00005798263,0.00006670583,0.00002740507,0.00001437804,0.0000019473,0.00004699166,0.000306649,0.000001975089],"category_scores_gemma":[0.000013797,0.00005438965,0.00001928045,0.00004303962,0.00004129974,4.426482e-7,0.00004378168,0.0001502184,3.012193e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001022274,"about_ca_system_score_gemma":0.0000162471,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009217612,"about_ca_topic_score_gemma":0.000264169,"domain_scores_codex":[0.9996746,0.00001413769,0.00006531618,0.0001250012,0.00003817445,0.00008283162],"domain_scores_gemma":[0.9998547,0.000001853487,0.00002700509,0.0000825055,0.00001714342,0.00001677453],"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":[0.0000487965,0.0000247469,0.01014125,0.000009675524,0.00001462481,0.000001043905,0.00008154268,0.00002533437,0.9866285,0.0004767978,0.0001767075,0.002371028],"study_design_scores_gemma":[0.001620842,0.0003253423,0.2041786,0.00002889548,0.00001610645,0.00001177212,0.0002290093,0.0001119899,0.7523077,0.0004239764,0.04049761,0.0002482018],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9917275,0.007347853,0.00002122334,0.0002261093,0.00001862481,0.00007920847,0.00001782759,7.889496e-7,0.0005608773],"genre_scores_gemma":[0.9990138,0.0001049654,0.0005561281,0.00004678618,0.00006954624,0.000002982687,0.000008822288,0.000004226955,0.000192717],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2343208,"threshold_uncertainty_score":0.2365158,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.003406457256667582,"score_gpt":0.2108089839968793,"score_spread":0.2074025267402117,"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."}}