Fitness for 5 genes in Pseudomonas putida KT2440

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500 ntPP_0074 and PP_0075 are separated by 129 nucleotidesPP_0075 and PP_0076 are separated by 144 nucleotidesPP_0076 and PP_0077 are separated by 14 nucleotidesPP_0077 and PP_0079 are separated by 108 nucleotides PP_0074: PP_0074 - shikimate 5-dehydrogenase, at 84,198 to 85,022 _0074 PP_0075: PP_0075 - putative choline sulfate transporter, at 85,152 to 86,717 _0075 PP_0076: PP_0076 - putative choline betaine-binding protein, at 86,862 to 87,785 _0076 PP_0077: PP_0077 - choline-sulfatase, at 87,800 to 89,317 _0077 PP_0079: PP_0079 - putative transcriptional regulator, at 89,426 to 90,325 _0079
Group Condition PP_0074 PP_0075 PP_0076 PP_0077 PP_0079
nitrogen source 2,6-diaminopimelic (N) N.D. +0.1 -0.3 -0.3 -1.0
nitrogen source nitrate (N) N.D. -0.0 -0.6 +0.0 -0.7
nitrogen source nitrate (N) N.D. -0.3 -0.5 -0.4 -0.0
temperature shift Temperature shift 10_to_25; with MOPS N.D. -0.1 -0.3 -0.2 -0.5
phage P. putida Sci Big MOI 0.1 N.D. -0.3 -0.2 -0.2 -0.4
temperature shift Temperature shift 10_to_25; with MOPS N.D. -0.1 -0.4 -0.3 -0.2
carbon source DL-3-Hydroxybutyric (C) N.D. +0.1 -0.4 -0.2 -0.5
carbon source Valerolactone (C) N.D. -0.2 -0.3 -0.1 -0.2
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=72_hrs N.D. -0.3 -0.3 +0.1 -0.3
carbon source 2,3-Butanediol (C) N.D. -0.1 -0.3 +0.1 -0.5
in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16h_outgrowth_LB; Time=7_days N.D. -0.2 -0.6 +0.1 +0.1
phage P. putida PUT 7 MOI 1 N.D. -0.1 -0.2 +0.2 -0.6
phage P. putida Sci small MOI 0.1 N.D. -0.3 -0.3 +0.3 -0.3
reactor 40hr timepoint of 1L M9/1% dextrose CONTINUOUS FED BATCH fermentation in 2L Sartorius Biostat, feed rate 2.15g/hr dextrose, set to 30% DO. N.D. +0.2 -0.3 -0.2 -0.2
carbon source D-Glucose (C) N.D. +0.1 -0.3 -0.4 +0.1
nitrogen source NAG (N); with MOPS N.D. -0.3 +0.3 -0.5 +0.1
pH pH 7 N.D. -0.4 +0.3 +0.1 -0.3
micoeukaryotes Acanthamoeba sp., muxed culture-1 N.D. -0.2 -0.1 +0.3 -0.3
micoeukaryotes Tetrahymena sp., Mixed culture-2 N.D. -0.0 -0.6 +0.1 +0.3
nitrogen source nitrogen source nitrite 1mM N.D. -0.2 -0.3 -0.1 +0.4
carbon source L-Lysine (C) N.D. -0.3 -0.3 +0.1 +0.2
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=144_hrs N.D. +0.1 -0.3 -0.3 +0.4
temperature shift Temperature shift 30_to_25 N.D. -0.2 +0.1 -0.3 +0.4
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=72_hrs N.D. -0.0 -0.4 +0.3 +0.2
carbon source Myristic (C) N.D. -0.4 +0.3 +0.0 +0.3
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI N.D. -0.1 +0.1 -0.2 +0.5
in planta Plant=Zea_mays; PlantTreatment=34_degrees_celsius; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16_outgrowth_LB; Time=7_days N.D. +0.1 +0.0 -0.2 +0.5
nitrogen source D-2-Aminobutyric (N) N.D. +0.1 +0.7 +0.0 -0.3
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI ago3mutant N.D. +0.4 -0.1 -0.0 +0.4
micoeukaryotes C.elegans, mixed culture-2 N.D. -0.0 +0.1 +0.3 +0.4
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