Fitness for 5 genes in Pseudomonas putida KT2440

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500 ntPP_3944 and PP_3945 are separated by 321 nucleotidesPP_3945 and PP_3946 are separated by 70 nucleotidesPP_3946 and PP_3947 are separated by 441 nucleotidesPP_3947 and PP_3948 overlap by 4 nucleotides PP_3944: PP_3944 - 6-hydroxynicotinate 3-monooxygenase, at 4,446,416 to 4,447,564 _3944 PP_3945: PP_3945 - 2,5-dihydroxypyridine 5,6-dioxygenase, at 4,447,886 to 4,448,938 _3945 PP_3946: PP_3946 - HTH-type transcriptional repressor NicR, at 4,449,009 to 4,449,485 _3946 PP_3947: PP_3947 - nicotinate dehydrogenase subunit A, at 4,449,927 to 4,450,400 _3947 PP_3948: PP_3948 - nicotinate dehydrogenase subunit B (EC 1.17.2.1) (from data), at 4,450,397 to 4,453,960 _3948
Group Condition PP_3944 PP_3945 PP_3946 PP_3947 PP_3948
nitrogen source Nicotinic Acid (N) -1.5 -1.6 -0.2 -1.3 -1.3
nitrogen source Nicotinic Acid (N) -1.3 -1.6 -0.0 -1.3 -1.4
nitrogen source nitrate (N) -0.2 -0.2 -4.1 -0.8 +0.1
stress R2A with Fusaric 480 ug/mL +0.0 -0.1 -4.7 -0.0 -0.1
carbon source acetate (C) +0.1 +0.1 -4.1 -1.0 +0.1
carbon source 3-methyl-1-butanol (C) -0.1 -0.1 -3.7 -0.5 -0.0
temperature shift Temperature shift 30_to_25; with MOPS -0.0 -0.1 -3.9 -0.5 +0.0
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs -0.2 -0.0 -4.2 +0.0 -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 -3.9 -0.7 -0.1
temperature shift Temperature shift 30_to_25 -0.1 +0.1 -4.0 -0.5 +0.1
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs -0.2 +0.1 -4.1 -0.3 +0.1
agar plate interaction control Parafilmed volatile agar plate with no fungus -0.4 -0.0 -3.0 -0.5 -0.2
carbon source Trisodium citrate (C) +0.3 +0.1 -4.2 -0.2 -0.1
pH Growth at pH9 and (C) D-Glucose -0.0 +0.1 -4.0 -0.3 +0.1
carbon source L-Lysine (C) -0.3 +0.1 -3.9 +0.2 -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 -0.1 -3.9 -0.2 -0.0
pH Growth at pH6 and (C) Trisodium citrate +0.1 +0.0 -3.9 +0.2 -0.3
pH Growth at pH7 and (C) D-Glucose +0.0 -0.3 -4.2 +0.4 +0.3
temperature shift Temperature shift 30_to_25 +0.3 +0.1 -4.0 -0.1 -0.0
pH Growth at pH6 and (C) Trisodium citrate +0.1 +0.1 -4.2 +0.4 -0.1
carbon source D-Glucose (C) -0.2 +0.2 -4.0 +0.2 +0.0
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs -0.2 -0.2 -3.4 +0.4 -0.2
carbon source ferulate (C); with MOPS +0.3 +0.0 -3.8 +0.1 -0.0
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs -0.0 +0.1 -3.6 +0.4 -0.2
phage P. putida Sci small MOI 0.1 -0.2 -0.1 -3.1 +0.8 -0.8
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=72_hrs -0.1 +0.3 -3.6 -0.2 +0.3
carbon source butyrate (C) +0.3 +0.2 -2.9 -0.7 -0.1
stress R2A with Polymyxin B sulfate 0.002 mg/ml -0.0 +0.2 -3.8 +0.6 -0.1
nitrogen source nitrite (N) -0.2 +0.1 -3.4 +0.6 +0.1
carbon source Tween 20 (C) +0.2 +0.2 -3.6 +0.6 +0.0
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