{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0008980668,0.0002870513,0.0004989469,0.0009696956,0.0005510033,0.0008404668,0.0003461963,0.000690448,0.001791768],"category_scores_gemma":[0.001580315,0.0002538065,0.000265308,0.00105265,0.001219721,0.001299207,0.0006806338,0.000870907,0.0005561405],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005236416,"about_ca_system_score_gemma":0.0006269454,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007591784,"about_ca_topic_score_gemma":0.0008829083,"domain_scores_codex":[0.9993809,0.00006574407,0.00005078051,0.0003045959,0.0001306505,0.00006724412],"domain_scores_gemma":[0.9986647,0.000295975,0.0002978804,0.000298735,0.0002590427,0.0001836822],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.001770637,0.0001323406,0.1472712,0.0005799824,0.0002909624,0.0004413773,0.0005041469,0.001383162,0.7326123,0.00968662,0.0008860208,0.1044412],"study_design_scores_gemma":[0.00009032214,0.001484049,0.8002419,0.000134246,0.0002495984,0.005732618,0.0007418191,0.006648321,0.1537978,0.01504553,0.01570528,0.0001285371],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9779473,0.00558464,0.009135015,0.000622034,0.0001117377,0.0000369805,0.0006618273,0.0002820717,0.005618447],"genre_scores_gemma":[0.9910519,0.002425896,0.003968161,0.0003882663,0.0001006825,0.00001885562,0.0003078366,0.00006876673,0.00166964],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001791768,"threshold_uncertainty_score":0.005994081,"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."}}