{"id":"W2046017517","doi":"10.1074/jbc.m111682200","title":"Characterizing the DNA Contacts and Cooperative Binding of F Plasmid TraM to Its Cognate Sites at oriT","year":2002,"lang":"en","type":"article","venue":"Journal of Biological Chemistry","topic":"Bacterial Genetics and Biotechnology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":33,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"","keywords":"Inverted repeat; Footprinting; DNA; Biology; Deoxyribonuclease I; Direct repeat; Binding site; DNA footprinting; DNA binding site; Plasmid; Genetics; Molecular biology; DNA-binding protein; Gene; Promoter; Transcription factor; Genome; Gene expression","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":[],"consensus_categories":[],"category_scores_codex":[0.0001757828,0.000145189,0.0002592692,0.00001806283,0.0000734232,0.00001943801,0.0002274976,0.0003139442,0.0001161814],"category_scores_gemma":[0.0002562594,0.00008588516,0.00008108635,0.00007531411,0.0001400121,0.000003182905,0.000187312,0.0001388976,0.000003486041],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001358517,"about_ca_system_score_gemma":0.00001263301,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":2.577522e-7,"about_ca_topic_score_gemma":8.222803e-7,"domain_scores_codex":[0.9991615,0.00003444653,0.0003471532,0.0001839435,0.00008237047,0.0001905848],"domain_scores_gemma":[0.999338,0.00003666976,0.0002662909,0.0001180816,0.0001385775,0.0001024099],"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":[0.0001435915,0.00004619373,0.0008298553,0.00001385278,0.00004686344,0.000007560442,0.0000353848,0.00000113446,0.9981295,0.000004146911,0.0002355529,0.0005063599],"study_design_scores_gemma":[0.000384114,0.0006502784,0.001407265,0.00002652341,0.00001501936,0.0001842193,0.00005982493,0.000009083582,0.9842847,0.000003593351,0.01285985,0.0001155189],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9976386,0.000972888,0.000005521038,0.0009717179,0.00006935897,0.00007947833,0.00004200911,0.00000333926,0.0002171257],"genre_scores_gemma":[0.9978608,0.001348371,0.0001026163,0.0002428106,0.0002127796,0.000002259355,0.00001330659,0.000007081936,0.0002099212],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01384479,"threshold_uncertainty_score":0.3502295,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02747808273048558,"score_gpt":0.2377172634964831,"score_spread":0.2102391807659975,"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."}}