Fitness for 5 genes in Pseudomonas putida KT2440

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500 ntPP_4647 and PP_4648 are separated by 96 nucleotidesPP_4648 and PP_4649 are separated by 105 nucleotidesPP_4649 and PP_4650 are separated by 9 nucleotidesPP_4650 and PP_4651 are separated by 3 nucleotides PP_4647: PP_4647 - transcriptional regulator, LuxR family, at 5,272,050 to 5,272,757 _4647 PP_4648: PP_4648 - Ribosomal RNA large subunit methyltransferase G, at 5,272,854 to 5,273,978 _4648 PP_4649: PP_4649 - conserved protein of unknown function, at 5,274,084 to 5,274,239 _4649 PP_4650: PP_4650 - Ubiquinol oxidase subunit II, cyanide insensitive, at 5,274,249 to 5,275,256 _4650 PP_4651: PP_4651 - Ubiquinol oxidase subunit I, cyanide insensitive, at 5,275,260 to 5,276,696 _4651
Group Condition PP_4647 PP_4648 PP_4649 PP_4650 PP_4651
in planta Plant=Zea_mays-B73; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days -0.1 +0.3 N.D. -1.9 -3.3
in planta Plant=Zea_mays-bx1; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days -0.0 -0.1 N.D. -1.9 -2.3
in planta Plant=Zea_mays-bx1; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days -0.2 -0.1 N.D. -1.4 -1.1
in planta Plant=Zea_mays-B73; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days +0.1 +0.1 N.D. -1.0 -1.0
in planta Plant=Zea_mays-B73; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days -0.1 +0.1 N.D. -0.8 -0.8
reactor 48hr timepoint from 1L M9/1% dextrose BATCH fermentation in 2L Sartorius Biostat reactor kept at 10% DO. -0.0 -0.1 N.D. -1.2 -0.3
carbon source carbon source D-Xylose 66.6 mM and Glycerol 108.6 mM -0.7 +0.2 N.D. -0.1 -0.4
carbon source carbon source 2-Deoxy-D-glucose 10 mM -0.7 +0.3 N.D. -0.2 -0.4
carbon source carbon source 3-O-methyl-glucose 50 mM -0.5 +0.2 N.D. -0.5 -0.1
carbon source carbon source 4-vinylphenol 0.01 mM -0.8 +0.1 N.D. -0.2 -0.1
pH pH 6 -0.5 +0.2 N.D. -0.3 -0.2
carbon source carbon source 4-vinylphenol 0.1 mM -0.3 +0.4 N.D. -0.1 -0.7
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs -0.9 +0.1 N.D. +0.2 -0.1
pH pH 5 -0.3 +0.5 N.D. -0.5 -0.3
micoeukaryotes Tetrahymena sp., Mixed culture-2 +0.0 -0.7 N.D. +0.4 -0.2
micoeukaryotes Acanthamoeba sp., muxed culture-2 +0.4 -0.8 N.D. -0.0 -0.1
carbon source ferulate (C); with MOPS -0.4 +0.2 N.D. -0.5 +0.2
phage P. put PUT 10 MOI 10 -0.6 +0.6 N.D. -0.3 +0.1
phage P. putida South MOI 0.1 -0.4 +0.6 N.D. -0.4 -0.0
in planta Plant=Zea_mays; PlantTreatment=34_degrees_celsius; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16_outgrowth_LB; Time=7_days -0.4 +0.3 N.D. -0.3 +0.2
temperature shift Temperature shift 30_to_25; with MOPS -0.3 +0.3 N.D. -0.4 +0.2
stress R2A with Polymyxin B sulfate 0.002 mg/ml +0.3 -0.3 N.D. -0.4 +0.3
reactor 72hr timepoint from 1L M9/1% dextrose BATCH fermentation in 2L Sartorius Biostat reactor kept at 30% DO with 20% v/v oleyl alcohol overlay -0.6 -0.1 N.D. +0.6 +0.2
nitrogen source nitrate (N) -0.6 +0.1 N.D. +0.5 +0.2
carbon source butyrate (C) -0.5 +0.3 N.D. +0.2 +0.3
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 +0.3 +0.7 N.D. +0.0 -0.2
nitrogen source D-2-Aminobutyric (N) +0.8 +0.1 N.D. +0.3 -0.2
carbon source Trisodium citrate (C) +0.6 +0.2 N.D. -0.2 +0.5
carbon source D-Glucose (C) +0.4 +0.1 N.D. +0.5 +0.2
pH Growth at pH6 and (C) Trisodium citrate +0.2 +0.3 N.D. +0.5 +0.3
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