Experiment set24IT059 for Pseudomonas putida KT2440

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Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=72_hrs

200 most important genes:

  gene name fitness t score description  
PP_1623 -5.7 -6.9 RNA polymerase, sigma S (sigma 38) factor compare
PP_0164 -5.3 -6.3 conserved protein of unknown function compare
PP_1215 -4.3 -3.6 Crossover junction endodeoxyribonuclease RuvC compare
PP_5185 -3.8 -6.7 acetylglutamate kinase-like protein (regulatory domain)/amino acid N-acetyltransferase compare
PP_4994 -3.4 -6.0 conserved protein of unknown function compare
PP_0406 -3.0 -3.5 Nucleotidyltransferase family protein compare
PP_0846 -2.9 -1.8 DnaK-like molecular chaperone specific for IscU compare
PP_1898 -2.9 -3.8 MotA/TolQ/ExbB proton channel family protein compare
PP_0547 -2.8 -5.2 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase compare
PP_1733 -2.7 -4.1 membrane ATPase of the MinC-MinD-MinE system compare
PP_5289 -2.7 -3.9 Acetylglutamate kinase compare
PP_4902 -2.7 -3.7 Oligoribonuclease compare
PP_4004 -2.7 -5.7 DNA translocase FtsK compare
PP_4726 -2.6 -3.8 Chaperone protein DnaJ compare
PP_4008 -2.5 -7.8 ATP-dependent serine protease compare
PP_1088 -2.5 -10.0 Argininosuccinate synthase compare
PP_0022 -2.4 -1.6 hypothetical protein compare
PP_5328 -2.4 -1.7 putative phosphate transport system permease protein compare
PP_4058 -2.4 -10.5 1,4-alpha-glucan branching enzyme compare
PP_2378 -2.4 -2.3 Fe/S biogenesis protein NfuA compare
PP_1097 -2.4 -2.1 Methionine--tRNA ligase compare
PP_4942 -2.4 -3.6 conserved protein of unknown function compare
PP_0218 -2.3 -8.6 Sensory box protein compare
PP_1779 -2.3 -5.1 Lipopolysaccharide ABC export system, ATP-binding protein compare
PP_5338 -2.2 -3.6 aspartate ammonia-lyase compare
PP_1778 -2.2 -4.7 Lipopolysaccharide ABC export system, permease protein compare
PP_0377 -2.2 -2.6 coenzyme PQQ synthesis protein D compare
PP_2402 -2.2 -2.6 putative Sensor histidine kinase compare
PP_1734 -2.2 -4.6 Probable septum site-determining protein MinC compare
PP_4696 -2.1 -4.8 Nitrogen regulation protein NR(I) compare
PP_5309 -2.1 -6.4 oxidative and nitrosative stress transcriptional dual regulator compare
PP_0276 -2.0 -1.5 Transcriptional regulator, Cro/CI family compare
PP_1428 -2.0 -1.9 Sigma factor AlgU negative regulatory protein compare
PP_0184 -2.0 -5.0 Argininosuccinate lyase compare
PP_4262 -2.0 -2.6 Cytochrome oxidase maturation protein, cbb3-type compare
PP_1468 -2.0 -2.2 Tyrosine recombinase XerD compare
PP_1055 -1.9 -1.7 Type II secretion pathway protein GspN compare
PP_5337 -1.9 -5.5 LysR family transcriptional regulator compare
PP_1217 -1.9 -4.7 Holliday junction ATP-dependent DNA helicase RuvB compare
PP_4369 -1.9 -7.4 Flagellar M-ring protein compare
PP_3926 -1.9 -1.7 short-chain dehydrogenase compare
PP_1319 -1.8 -4.5 Ubiquinol--cytochrome c reductase, cytochrome c1 compare
PP_5095 -1.8 -1.2 pyrroline-5-carboxylate reductase compare
PP_0949 -1.7 -4.4 putative ATP-binding protein UPF0042 compare
PP_4941 -1.7 -6.0 conserved exported protein of unknown function compare
PP_4370 -1.7 -2.7 Flagellar hook-basal body complex protein FliE compare
PP_1198 -1.6 -1.9 transcriptional regulator, Cro/CI family (higA antitoxin like) compare
PP_1912 -1.6 -4.9 Phosphate acyltransferase compare
PP_4124 -1.6 -2.9 NADH-quinone oxidoreductase subunit G compare
PP_5279 -1.6 -3.3 conserved protein of unknown function compare
PP_0435 -1.6 -6.4 Peptidase, M23/M37 family compare
PP_5310 -1.6 -5.7 junction-specific ATP-dependent DNA helicase compare
PP_1208 -1.6 -1.8 conserved protein of unknown function, SlyX family compare
PP_5114 -1.6 -2.5 putative adenine methyltransferase compare
PP_2214 -1.5 -3.2 3-hydroxyacyl-CoA dehydrogenase type-2 compare
PP_4261 -1.5 -3.4 cation-transporting P-type ATPase compare
PP_0290 -1.5 -3.6 Imidazole glycerol phosphate synthase subunit HisH compare
PP_4131 -1.5 -3.6 NADH-quinone oxidoreductase subunit N compare
PP_5230 -1.5 -3.0 Tyrosine recombinase XerC compare
PP_1232 -1.5 -5.3 conserved exported protein of unknown function compare
PP_4120 -1.5 -3.0 NADH-quinone oxidoreductase subunit B compare
PP_0405 -1.5 -6.6 conserved protein of unknown function compare
PP_1036 -1.5 -7.0 membrane-bound lytic murein transglycosylase F compare
PP_4379 -1.5 -2.9 Beta-ketoacyl-acyl-carrier-protein synthase I compare
PP_2044 -1.5 -2.4 conserved inner membrane protein of unknown function compare
PP_4471 -1.5 -4.1 Magnesium transporter compare
PP_4909 -1.4 -5.0 phosphoserine phosphatase compare
PP_4824 -1.4 -5.2 Sensor histidine kinase/response regulator compare
PP_5216 -1.4 -1.7 exopolyphosphatase compare
PP_2433 -1.4 -1.9 conserved protein of unknown function compare
PP_1994 -1.4 -1.8 tRNA pseudouridine (38-40)synthase compare
PP_4528 -1.4 -2.1 conserved protein of unknown function compare
PP_1224 -1.4 -4.1 periplasmic subunit of the TolQRA transport system compare
PP_3449 -1.4 -2.0 conserved exported protein of unknown function compare
PP_4358 -1.4 -5.9 flagellar synthesis, switching and energizing component compare
PP_4368 -1.3 -3.7 flagellar motor switch protein compare
PP_3484 -1.3 -3.1 Response regulator receiver protein compare
PP_5073 -1.3 -1.9 conserved exported protein of unknown function compare
PP_0789 -1.3 -3.0 N-acetyl-anhydromuramyl-L-alanine-amidase compare
PP_2302 -1.3 -3.9 DNA-binding, ATP-dependent protease compare
PP_4937 -1.3 -3.1 toluene tolerance protein compare
PP_4122 -1.3 -1.2 proton-pumping NADH:ubiquinone oxidoreductase, respiratory complex I, subunit E compare
PP_3649 -1.3 -3.5 Transcriptional regulator, GntR family compare
PP_2107 -1.3 -1.5 conserved protein of unknown function compare
PP_5350 -1.3 -2.3 Transcriptional regulator, RpiR family compare
PP_2322 -1.3 -4.3 Major outer membrane lipoprotein compare
PP_1493 -1.3 -1.8 chemotaxis response regulator protein-glutamate methylesterase of group 3 operon compare
PP_4880 -1.3 -6.4 exoribonuclease R compare
PP_4340 -1.3 -2.9 response regulator for chemotactic signal transduction compare
PP_2883 -1.3 -1.9 conserved protein of unknown function compare
PP_4343 -1.2 -3.9 Flagellar biosynthesis protein FlhF compare
PP_4964 -1.2 -2.6 D-erythrose 4-phosphate dehydrogenase compare
PP_1186 -1.2 -1.4 two component system DNA-binding transcriptional dual regulator compare
PP_0395 -1.2 -8.0 putative type IV piliation protein compare
PP_4700 -1.2 -1.2 pantothenate synthetase compare
PP_4362 -1.2 -4.2 conserved protein of unknown function compare
PP_2650 -1.2 -2.9 putative 4-hydroxybutyrate dehydrogenase compare
PP_1317 -1.2 -2.5 Ubiquinol-cytochrome c reductase iron-sulfur subunit compare
PP_4917 -1.2 -2.8 3',5'-cyclic-nucleotide phosphodiesterase compare
PP_2820 -1.2 -2.8 HTH-type transcriptional regulator nfxB compare
PP_4944 -1.2 -2.5 Carbamoyltransferase compare
PP_4383 -1.2 -3.5 Flagellar P-ring protein compare
PP_4344 -1.2 -6.9 flagellar export pore protein compare
PP_5039 -1.2 -2.4 conserved protein of unknown function compare
PP_4251 -1.2 -2.7 cytochrome c oxidase subunit, cbb3-type compare
PP_2145 -1.2 -2.3 beta-N-acetylglucosaminidase compare
PP_4121 -1.2 -2.7 NADH-quinone oxidoreductase subunit C/D compare
PP_4337 -1.2 -3.1 chemotaxis response regulator protein-glutamate methylesterase of group 1 operon compare
PP_2718 -1.2 -1.8 arsenic resistance transcriptional regulator compare
PP_4808 -1.2 -1.1 23S rRNA m3psi1915 methyltransferase compare
PP_1128 -1.2 -2.7 OmpA family protein compare
PP_0063 -1.2 -3.3 putative Lipid A biosynthesis lauroyl acyltransferase compare
PP_0397 -1.1 -7.2 protein kinase compare
PP_3541 -1.1 -2.0 Transporter, MgtC family compare
PP_0995 -1.1 -4.1 conserved membrane protein of unknown function compare
PP_4356 -1.1 -3.1 Flagellar protein FliO compare
PP_1268 -1.1 -2.1 putative HtrA suppressor protein sohA compare
PP_4943 -1.1 -1.6 putative Glycosyl transferase compare
PP_0393 -1.1 -0.8 putative 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase compare
PP_0914 -1.1 -5.4 GGDEF domain protein compare
PP_3519 -1.1 -1.0 putative Lipoprotein compare
PP_4381 -1.1 -6.9 Flagellar hook-associated protein FlgK compare
PP_4392 -1.1 -5.3 chemotaxis protein methyltransferase compare
PP_5327 -1.1 -2.4 putative phosphate ABC transporter, permease subunit compare
PP_4375 -1.1 -4.2 flagellar chaperone, inhibits premature FliC assembly compare
PP_1999 -1.1 -1.9 membrane protein required for colicin V production compare
PP_4332 -1.1 -4.1 Chemotaxis protein CheW compare
PP_5253 -1.0 -2.0 Arylesterase compare
PP_4354 -1.0 -3.1 flagellar export apparatus subunit compare
PP_5346 -1.0 -4.7 pyruvate carboxylase subunit B compare
PP_4380 -1.0 -6.5 Flagellar hook-associated protein FlgL compare
PP_4378 -1.0 -7.4 flagellin, filament structural protein compare
PP_4376 -1.0 -5.5 flagellar filament capping protein compare
PP_2088 -1.0 -1.5 RNA polymerase sigma factor SigX compare
PP_0293 -1.0 -1.1 Imidazole glycerol phosphate synthase subunit HisF compare
PP_5100 -1.0 -2.0 dITP/XTP pyrophosphatase compare
PP_4875 -1.0 -2.3 conserved membrane protein of unknown function compare
PP_0082 -1.0 -3.4 tryptophan synthase alpha chain compare
PP_1216 -1.0 -1.9 Holliday junction ATP-dependent DNA helicase RuvA compare
PP_4353 -1.0 -3.1 Flagellar biosynthetic protein fliR compare
PP_4130 -1.0 -2.6 NADH:ubiquinone oxidoreductase, membrane subunit M compare
PP_1513 -1.0 -2.8 Ribosomal RNA small subunit methyltransferase J compare
PP_2203 -1.0 -2.4 conserved protein of unknown function compare
PP_3614 -1.0 -2.3 conserved membrane protein of unknown function compare
PP_0346 -0.9 -4.6 putative Heptose kinase WapQ compare
PP_2337 -0.9 -1.3 aconitate isomerase compare
PP_0025 -0.9 -1.0 hypothetical protein compare
PP_2027 -0.9 -4.0 conserved exported protein of unknown function compare
PP_4361 -0.9 -4.0 Flagellar hook-length control protein FliK compare
PP_4065 -0.9 -4.6 methylcrotonyl-CoA carboxylase biotin-containing subunit beta compare
PP_3105 -0.9 -1.5 conserved membrane protein of unknown function compare
PP_4532 -0.9 -1.7 ATP-dependent DEAD-box RNA helicase require for 50S ribosomal subunit biogenesis compare
PP_2032 -0.9 -2.9 putative ATPase compare
PP_4359 -0.9 -3.5 Flagellar protein FliL compare
PP_1355 -0.9 -4.6 Muropeptide permease AmpG compare
PP_1834 -0.9 -2.7 conserved protein of unknown function compare
PP_1328 -0.9 -1.5 Protein MraZ compare
PP_3307 -0.9 -1.7 conserved protein of unknown function compare
PP_1318 -0.9 -3.6 Cytochrome b compare
PP_4067 -0.9 -3.8 methylcrotonyl-CoA carboxylase biotin-containing subunit alpha compare
PP_4793 -0.9 -1.6 conserved protein of unknown function compare
PP_3052 -0.9 -1.2 conserved protein of unknown function compare
PP_4382 -0.9 -3.8 Peptidoglycan hydrolase FlgJ compare
PP_0725 -0.9 -2.8 conserved hypothetical TPR repeat protein compare
PP_0127 -0.9 -3.1 Thiol:disulfide interchange protein compare
PP_0484 -0.9 -3.2 transporter of an unknown substrate compare
PP_3999 -0.9 -3.3 Uroporphyrinogen-III C-methyltransferase/Precorrin-2 dehydrogenase/Sirohydrochlorin ferrochelatase compare
PP_4470 -0.9 -1.5 putative transcriptional regulator (Arc domain-containing) compare
PP_4338 -0.9 -3.8 Chemotaxis histidine kinase CheA compare
PP_4341 -0.9 -3.8 RNA polymerase sigma 28 (sigma F) factor for class III flagellar operons compare
PP_1322 -0.9 -1.7 putative Lipoprotein compare
PP_1079 -0.9 -3.4 Ornithine carbamoyltransferase compare
PP_3359 -0.9 -1.6 putative Hydroxycinnamic acid degradation regulator compare
PP_1629 -0.9 -2.9 Protein RecA compare
PP_5146 -0.9 -3.9 RNA pyrophosphohydrolase compare
PP_0396 -0.9 -5.2 conserved protein of unknown function compare
PP_2582 -0.9 -2.0 putative Heme oxygenase compare
PP_5000 -0.8 -1.3 peptidase component of the ATP-dependent HslVU protease compare
PP_1523 -0.8 -1.4 conserved protein of unknown function compare
PP_4389 -0.8 -3.7 Flagellar basal-body rod modification protein FlgD compare
PP_5121 -0.8 -3.0 conserved exported protein of unknown function compare
PP_0951 -0.8 -3.7 Ribosome hibernation promoting factor compare
PP_4366 -0.8 -5.1 flagellum-specific ATP synthase compare
PP_4581 -0.8 -1.7 putative amidotransferase compare
PP_4352 -0.8 -4.9 flagellin export apparatus, substrate specificity protein compare
PP_5525 -0.8 -1.7 conserved exported protein of unknown function compare
PP_1381 -0.8 -0.8 4-carboxymuconolactone decarboxylase compare
PP_4391 -0.8 -3.1 flagellar basal-body rod protein FlgB compare
PP_5486 -0.8 -1.3 conserved protein of unknown function compare
PP_4388 -0.8 -5.4 Flagellar hook protein FlgE compare
PP_2144 -0.8 -1.8 Transcriptional regulator, TetR family compare
PP_3891 -0.8 -1.7 conserved protein of unknown function compare
PP_4129 -0.8 -1.6 NADH:ubiquinone oxidoreductase, membrane subunit L compare
PP_0065 -0.8 -1.9 NAD-binding component of TrK potassium transporter compare
PP_1028 -0.8 -2.6 Transcriptional regulator, LysR family compare
PP_2122 -0.8 -1.6 molybdenum cofactor biosynthesis protein B compare
PP_5145 -0.8 -6.4 phosphoenolpyruvate-dependent regulator (with NPR and NTR proteins) compare
PP_0888 -0.8 -1.0 Photosynthetic apparatus regulatory protein RegA compare
PP_2136 -0.8 -2.7 enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase compare
PP_4505 -0.8 -3.1 Sensor histidine kinase compare


Specific Phenotypes

None in this experiment

For Pseudomonas putida KT2440 in soil experiments

For soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=72_hrs across organisms