{"id":"W2050730005","doi":"10.1016/j.jmb.2014.09.018","title":"Mechanistic Basis of Plasmid-Specific DNA Binding of the F Plasmid Regulatory Protein, TraM","year":2014,"lang":"en","type":"article","venue":"Journal of Molecular Biology","topic":"Bacterial Genetics and Biotechnology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":11,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Alberta","funders":"Canadian Institutes of Health Research; Canadian HIV Trials Network, Canadian Institutes of Health Research","keywords":"Biology; Plasmid; Genetics; DNA; Base pair; Binding site; Conserved sequence; Peptide sequence; DNA-binding domain; DNA binding site; Gene; Transcription factor; Promoter","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000428196,0.0004880371,0.000452919,0.0003185691,0.0008258113,0.0007789194,0.0009820688,0.001104122,0.004106439],"category_scores_gemma":[0.0007818372,0.0003541145,0.0005595517,0.0001332567,0.0006437632,0.0007056792,0.000599575,0.001555099,0.0009809419],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001134445,"about_ca_system_score_gemma":0.0009243182,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002053119,"about_ca_topic_score_gemma":0.001998149,"domain_scores_codex":[0.999745,0.0000295433,0.000009228997,0.00006179458,0.00006750021,0.00008709241],"domain_scores_gemma":[0.9996881,0.0001232941,0.0000413092,0.00004159128,0.0000409362,0.00006459237],"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":[0.0002303147,0.0001071857,0.0004829482,0.0001563481,0.00001168868,0.0003975642,0.0000759214,0.0009943368,0.9808037,0.01363429,0.0004144493,0.002691152],"study_design_scores_gemma":[0.00004875285,0.000186514,0.006375062,0.00003005771,0.00001626529,0.0009962051,0.000235587,0.02059442,0.9631265,0.003139587,0.00522256,0.00002834891],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9415627,0.002236514,0.0402072,0.002168425,0.0002036828,0.0001426989,0.0004845813,0.0006442333,0.01234991],"genre_scores_gemma":[0.9914131,0.0004069009,0.004471718,0.0001974942,0.00001391228,0.00004529048,0.0002404727,0.00002767155,0.003183473],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.004106439,"threshold_uncertainty_score":0.01373738,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00596701209496756,"score_gpt":0.2112951237383915,"score_spread":0.205328111643424,"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."}}