Fitness for 5 genes in Pseudomonas putida KT2440

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500 ntPP_2608 and PP_2609 are separated by 156 nucleotidesPP_2609 and PP_2610 are separated by 150 nucleotidesPP_2610 and PP_2611 overlap by 4 nucleotidesPP_2611 and PP_2612 are separated by 4 nucleotides PP_2608: PP_2608 - Shikimate dehydrogenase family protein, at 2,982,369 to 2,983,178 _2608 PP_2609: PP_2609 - Transcriptional regulator, IclR family, at 2,983,335 to 2,984,105 _2609 PP_2610: PP_2610 - conserved protein of unknown function, at 2,984,256 to 2,984,513 _2610 PP_2611: PP_2611 - membrane protein of unknown function, at 2,984,510 to 2,985,403 _2611 PP_2612: PP_2612 - conserved membrane protein of unknown function, at 2,985,408 to 2,988,398 _2612
Group Condition PP_2608 PP_2609 PP_2610 PP_2611 PP_2612
nitrogen source Ammonium chloride (N) -0.3 -0.1 -0.2 -1.8 -0.1
carbon source ferulate (C); with MOPS -0.7 -0.2 +0.2 -1.7 -0.1
carbon source D-Glucose (C) -0.0 -0.2 -0.4 -0.9 -0.6
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=0_hrs -0.1 -0.2 -0.4 -1.3 -0.1
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=144_hrs -0.2 +0.2 -0.4 -1.2 -0.4
phage P. put South MOI 10 -0.7 +0.2 -0.5 -0.5 -0.3
carbon source acetate (C) -0.7 +0.1 -0.8 -0.5 +0.1
carbon source carbon source D-Glucose 55.5 mM -0.3 -0.1 +0.2 -1.6 +0.1
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI ago3mutant -0.3 -0.0 +0.3 -0.3 -1.0
nitrogen source no extra (N); with MOPS -0.6 +0.2 -0.1 -0.8 -0.1
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI +0.3 -0.1 -0.8 -0.9 +0.3
nitrogen source Urea (N) +0.1 -0.0 -0.8 -0.7 +0.4
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI dcr2mutant -0.5 -0.1 -0.4 +0.5 -0.3
mixed carbon source mixed (C)s Trisodium citrate 10 mM and Parachlorophenylalanine 10 mM +0.3 -0.3 -0.5 -0.5 +0.3
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI tmk3mutant +0.4 -0.2 -0.2 +0.5 -0.7
phage P. putida Sci small MOI 0.1 -0.8 +0.1 -0.4 +0.6 +0.3
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs +0.6 -0.0 +0.6 -0.6 -0.6
in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=no_outgrowth_LB; Time=7_days +0.5 -0.2 -0.7 +0.4 +0.0
carbon source butyrate (C) -0.5 -0.1 -0.3 +0.6 +0.5
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=0_hrs +0.1 +0.3 +0.6 -0.2 -0.6
nitrogen source nitrogen source nitrate 5mM -0.2 -0.2 +0.7 +0.6 -0.4
nitrogen source nitrogen source nitrite 0.5mM -0.3 -0.1 +0.5 +1.0 -0.1
in planta Plant=Zea_mays; PlantTreatment=34_degrees_celsius_and_Fusarium; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16_outgrowth_LB; Time=7_days +0.0 -0.2 +0.8 +0.9 -0.2
phage P. putida Sci small MOI 0.1 -0.5 +0.3 +0.0 +1.1 +0.4
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs +0.8 +0.4 +0.3 -0.5 +0.3
nitrogen source nitrogen source Ammonium chloride 20mM -0.2 -0.0 +0.6 +0.6 +0.5
phage PUT8 MOI 10 +0.3 -0.1 -0.4 +1.4 +0.4
phage PUT8 MOI 10 +0.1 -0.2 -0.0 +1.4 +0.9
phage PUT8 MOI 0.1 +0.0 -0.2 -0.1 +1.4 +1.1
phage PUT8 MOI 0.1 +0.1 -0.2 +0.4 +1.7 +0.3
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