{"id":"W4416202233","doi":"10.1264/jsme2.me25018","title":"Using Phylogeny and a Conserved Genomic Neighborhood Analysis to Extract and Visualize Gene Sets Involved in Target Gene Function: The Case of [NiFe]-hydrogenase and Succinate Dehydrogenase","year":2025,"lang":"en","type":"article","venue":"Microbes and Environments","topic":"Metalloenzymes and iron-sulfur proteins","field":"Energy","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; Japan Society for the Promotion of Science; Institute for Fermentation, Osaka","keywords":"Phylogenetic tree; Gene; Phylogenetics; Clade; Genome; Function (biology); Conserved sequence; Gene cluster","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":[0.0004101412,0.0004392812,0.0004609078,0.002690738,0.0005701352,0.0005890959,0.0003598975,0.0003564215,0.0007844492],"category_scores_gemma":[0.001100143,0.0002399331,0.0005289382,0.002159991,0.0002574744,0.0004357371,0.0004779983,0.0003466645,0.0003124135],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002820168,"about_ca_system_score_gemma":0.0004148307,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002089065,"about_ca_topic_score_gemma":0.00312616,"domain_scores_codex":[0.9996676,0.00008728423,0.00002238929,0.0001373805,0.00005378943,0.00003154726],"domain_scores_gemma":[0.9997441,0.00007589109,0.00005468718,0.00004723366,0.00005224371,0.00002581092],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0008650609,0.0003987945,0.05068839,0.0005596277,0.0003544754,0.0008002676,0.001228377,0.02041494,0.7045323,0.005896692,0.001286089,0.2129749],"study_design_scores_gemma":[0.0001134041,0.000541864,0.259789,0.0001109642,0.0003365521,0.002280349,0.001363732,0.5540407,0.1486802,0.01169254,0.0209115,0.000139212],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6934816,0.0005744502,0.300467,0.00009784946,0.00001920472,0.0001762611,0.001800223,0.001308,0.002075415],"genre_scores_gemma":[0.630482,0.000232149,0.3648147,0.00002158498,0.000008919707,0.0001978655,0.003397492,0.0001954898,0.0006496585],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002690738,"threshold_uncertainty_score":0.004153848,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01579878632172171,"score_gpt":0.2477394889052571,"score_spread":0.2319407025835354,"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."}}