{"id":"W3017842490","doi":"10.1101/2020.04.22.056440","title":"Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism","year":2020,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Lethbridge","funders":"Marsden Fund; National Health and Medical Research Council; Biomolecular Interaction Centre, University of Canterbury; Göteborgs Universitet; State Government of Victoria; Massey University; Maurice Wilkins Centre for Molecular Biodiscovery; VINNOVA; Canterbury Medical Research Foundation; Australian Synchrotron; Ministry of Business, Innovation and Employment; Centre for Antibiotic Resistance Research, University of Gothenburg; University of Canterbury; National Institutes of Health; National Science Foundation","keywords":"Sialic acid; Repressor; DNA; Allosteric regulation; Biology; Psychological repression; Gene; Biochemistry; Escherichia coli; DNA-binding domain; Transcription (linguistics); Operator (biology); Transcription factor; Effector; Cell biology; Gene expression; Enzyme","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002160178,0.0002599353,0.0002454766,0.0001381429,0.0001770618,0.000310106,0.0003965867,0.0002713501,0.001703125],"category_scores_gemma":[0.0001475586,0.0001541154,0.0002257357,0.00005831834,0.0004315266,0.0001567154,0.0003632099,0.0004266406,0.0006264195],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003910677,"about_ca_system_score_gemma":0.0002047639,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003519742,"about_ca_topic_score_gemma":0.0002952545,"domain_scores_codex":[0.9998614,0.0000242615,0.000006325147,0.00003212138,0.00004488134,0.00003100948],"domain_scores_gemma":[0.9999108,0.00001456974,0.0000224613,0.00001773875,0.00001072647,0.00002373836],"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":[0.00007074984,0.000025539,0.0003802958,0.00002753621,0.000003544895,0.00008669271,0.00001521852,0.0001889066,0.9966213,0.001292811,0.00006928646,0.001218142],"study_design_scores_gemma":[0.00002979182,0.00008948484,0.003289062,0.000005560006,0.000003612324,0.0002193618,0.00003370946,0.006481831,0.9879382,0.0006412706,0.001259247,0.000008874364],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9793396,0.0008803613,0.01232081,0.0004205093,0.00004936173,0.00003445492,0.00009548783,0.0003816404,0.006477642],"genre_scores_gemma":[0.9948334,0.0001607963,0.002537128,0.00006631885,0.000008651775,0.00002151847,0.00006487693,0.00002022692,0.002287074],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001703125,"threshold_uncertainty_score":0.005697489,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01462206134485645,"score_gpt":0.2118157177713503,"score_spread":0.1971936564264939,"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."}}