{"id":"W4414413882","doi":"10.1101/2025.09.22.677880","title":"Mining thermophile photosynthesis genes: a synthetic operon expressing <i>Chloroflexota</i> species reaction center genes in <i>Rhodobacter sphaeroides</i>","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Photosynthetic Processes and Mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"Basic Energy Sciences; National Institute of Allergy and Infectious Diseases; Natural Sciences and Engineering Research Council of Canada; University of California, San Francisco; Office of Science; National Institutes of Health; Goddard Space Flight Center; Joint Genome Institute; U.S. Department of Energy","keywords":"Anoxygenic photosynthesis; Operon; Photosynthesis; Gene; Thermophile; Metagenomics; Photosynthetic reaction centre; Cyanobacteria","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":[0.000386235,0.0006231293,0.0006932195,0.0005226966,0.0003119138,0.0007045779,0.0004436782,0.0005466728,0.0004543211],"category_scores_gemma":[0.0005986118,0.0002938742,0.0007195755,0.0007512788,0.0002232596,0.0002989167,0.0004927006,0.0006927238,0.0004140301],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005110952,"about_ca_system_score_gemma":0.0005471154,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002223722,"about_ca_topic_score_gemma":0.003141127,"domain_scores_codex":[0.9995209,0.00005380626,0.0000622517,0.0001311393,0.0001630581,0.00006891337],"domain_scores_gemma":[0.999661,0.0000806077,0.0001109447,0.00003999251,0.00004913401,0.00005838743],"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":[0.000073672,0.00003892837,0.0005804137,0.00004161035,0.000007006221,0.00006117352,0.00003798574,0.0003058965,0.9974726,0.00002596826,0.00003348917,0.001321226],"study_design_scores_gemma":[0.00002096372,0.000201054,0.004406569,0.00001008403,0.00003889924,0.0002822569,0.0001149897,0.002433521,0.9909654,0.00004015838,0.001467549,0.00001875262],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9793732,0.0002561001,0.01589598,0.0002170345,0.00002194951,0.0001868247,0.003182274,0.0003354178,0.0005311124],"genre_scores_gemma":[0.9049112,0.0005309837,0.07660142,0.0001290593,0.00001909607,0.0002010056,0.01544815,0.0004432301,0.001715888],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002223722,"threshold_uncertainty_score":0.004421592,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01418606571278953,"score_gpt":0.219908786635862,"score_spread":0.2057227209230724,"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."}}