{"id":"W3129416664","doi":"10.1101/2021.02.18.431926","title":"Investigating the chemolithoautotrophic and formate metabolism of <i>Nitrospira moscoviensis</i> by constraint-based metabolic modeling and <sup>13</sup> C-tracer analysis","year":2021,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Wastewater Treatment and Nitrogen Removal","field":"Environmental Science","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Division of Graduate Education; Division of Chemical, Bioengineering, Environmental, and Transport Systems; Natural Sciences and Engineering Research Council of Canada; National Science Foundation","keywords":"Nitrospira; Autotroph; Nitrogen cycle; Formate; Metabolic network; Nitrification; Metabolic pathway; Environmental chemistry; Nitrite; Biogeochemical cycle; Chemistry; Biology; Metabolism; Biochemistry; Nitrate; Ecology; Bacteria; Nitrogen; Organic chemistry","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":[0.0001575893,0.000754337,0.0004374353,0.0002166068,0.0002991474,0.0004725712,0.0005395231,0.0005142919,0.0005797357],"category_scores_gemma":[0.0002906357,0.000180814,0.0005222905,0.0003215206,0.0002363964,0.0002521942,0.0003187332,0.0003418112,0.0001245242],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008122296,"about_ca_system_score_gemma":0.0006804675,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0174347,"about_ca_topic_score_gemma":0.01240534,"domain_scores_codex":[0.9999347,0.000008790554,0.000003715005,0.00002921632,0.0000151845,0.000008518854],"domain_scores_gemma":[0.9999084,0.00002755896,0.00002337958,0.00001028601,0.00001790849,0.00001250981],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0001620163,0.0001170637,0.02104942,0.0001911138,0.0001075389,0.0001991201,0.0000555437,0.6155685,0.3558316,0.001446687,0.000124026,0.005147467],"study_design_scores_gemma":[0.00001792951,0.0001282312,0.008888106,0.000006435895,0.00002706875,0.00003522608,0.00006287392,0.9552586,0.0342899,0.0006806651,0.0005849436,0.00002002938],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9924548,0.00009947135,0.005842363,0.00004468618,0.00000383431,0.00001244974,0.0007804741,0.00005416339,0.0007077256],"genre_scores_gemma":[0.9894321,0.0001887549,0.009016909,0.0000096358,0.000001806708,0.0000325643,0.0010719,0.00002467555,0.0002217744],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0174347,"threshold_uncertainty_score":0.03466642,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009964503048522304,"score_gpt":0.1941758317595054,"score_spread":0.1842113287109831,"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."}}