{"id":"W2903760456","doi":"10.3389/fmicb.2018.03162","title":"Phylogenomic Analysis of the Gammaproteobacterial Methanotrophs (Order Methylococcales) Calls for the Reclassification of Members at the Genus and Species Levels","year":2018,"lang":"en","type":"article","venue":"Frontiers in Microbiology","topic":"Microbial metabolism and enzyme function","field":"Biochemistry, Genetics and Molecular Biology","cited_by":160,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"Natural Sciences and Engineering Research Council of Canada; Deutsche Forschungsgemeinschaft","keywords":"Biology; Gammaproteobacteria; Methanotroph; Alphaproteobacteria; Phylogenetic tree; Genome; Gene; Evolutionary biology; Ecology; Genetics; 16S ribosomal RNA; Anaerobic oxidation of methane","routes":{"ca_aff":true,"ca_fund":true,"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":[],"consensus_categories":[],"category_scores_codex":[0.0004823314,0.0001229779,0.0002782748,0.00007041379,0.000116956,0.000004842052,0.0002918309,0.0001728557,0.00004129645],"category_scores_gemma":[0.0001467786,0.00006653148,0.0001498854,0.0002788842,0.0008751053,0.000002451836,0.00014377,0.00006158838,4.851365e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002269818,"about_ca_system_score_gemma":0.00004021369,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006227054,"about_ca_topic_score_gemma":0.0003766568,"domain_scores_codex":[0.9989899,0.0002356189,0.0003002973,0.0002695378,0.00002799012,0.0001767027],"domain_scores_gemma":[0.9991348,0.00004722374,0.0002469627,0.000438916,0.0001184009,0.00001369833],"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":[0.0003108824,0.00001287973,0.002169384,0.000009124521,0.0004889502,1.744053e-8,0.0001640404,0.00006247603,0.9895384,0.00002464423,0.005908334,0.001310872],"study_design_scores_gemma":[0.0003853825,0.00006964786,0.02165401,0.000002786257,0.0004164492,0.000002147465,0.000130105,0.00005942351,0.817007,0.00002162241,0.1601728,0.00007860251],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9819489,0.001844918,0.01357575,0.0003151572,0.001236551,0.0005055007,0.0005470826,0.000001569447,0.00002460008],"genre_scores_gemma":[0.9946853,0.0003982524,0.003324098,0.0001881083,0.0002827166,0.00004779145,0.0001323376,0.00001436172,0.0009270583],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1725314,"threshold_uncertainty_score":0.3224362,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01497253944684816,"score_gpt":0.2324465001275679,"score_spread":0.2174739606807198,"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."}}