Strain Fitness in Pseudomonas putida KT2440 around PP_0546

Experiment: Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=144_hrs

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Only strains with sufficient reads to estimate fitness are shown, but the strain fitness values are still rather noisy and may be biased towards zero. Strains near the edge of a gene are not shown as being associated with that gene (they are in grey). Strains in the central 10-90% of a gene are color coded by the insertion's strand. Usually, "+" means that the selectable marker is encoded on the forward strand, i.e., transcribed rightward.

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500 ntPP_0545 and PP_0546 are separated by 254 nucleotidesPP_0546 and PP_0547 are separated by 66 nucleotides PP_0545: PP_0545 - aldehyde dehydrogenase, at 631,920 to 633,440 _0545 PP_0546: PP_0546 - sigma-54 dependent transcriptional regulator, at 633,695 to 635,710 _0546 PP_0547: PP_0547 - UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase, at 635,777 to 637,126 _0547 Position (kb) 633 634 635 636Strain fitness (log2 ratio) -2 -1 0 1at 632.717 kb on + strand, within PP_0545at 632.785 kb on + strand, within PP_0545at 632.796 kb on + strand, within PP_0545at 632.797 kb on - strand, within PP_0545at 632.844 kb on + strand, within PP_0545at 632.845 kb on - strand, within PP_0545at 632.996 kb on - strand, within PP_0545at 633.281 kb on + strand, within PP_0545at 633.281 kb on + strand, within PP_0545at 633.281 kb on + strand, within PP_0545at 633.282 kb on - strand, within PP_0545at 633.326 kb on + strandat 633.356 kb on + strandat 633.356 kb on + strandat 633.356 kb on + strandat 633.357 kb on - strandat 633.357 kb on - strandat 633.376 kb on + strandat 633.377 kb on - strandat 633.377 kb on - strandat 633.377 kb on - strandat 633.377 kb on - strandat 633.377 kb on - strandat 633.385 kb on + strandat 633.434 kb on - strandat 633.456 kb on + strandat 633.456 kb on + strandat 633.675 kb on - strandat 633.689 kb on - strandat 633.736 kb on + strandat 633.815 kb on + strandat 633.816 kb on - strandat 634.252 kb on - strand, within PP_0546at 634.319 kb on + strand, within PP_0546at 634.319 kb on + strand, within PP_0546at 634.320 kb on - strand, within PP_0546at 634.320 kb on - strand, within PP_0546at 634.470 kb on + strand, within PP_0546at 634.864 kb on + strand, within PP_0546at 634.865 kb on - strand, within PP_0546at 634.865 kb on - strand, within PP_0546at 635.000 kb on + strand, within PP_0546at 635.000 kb on - strand, within PP_0546at 635.104 kb on + strand, within PP_0546at 635.159 kb on + strand, within PP_0546at 635.159 kb on + strand, within PP_0546at 635.160 kb on - strand, within PP_0546at 635.160 kb on - strand, within PP_0546at 635.160 kb on - strand, within PP_0546at 635.160 kb on - strand, within PP_0546at 635.160 kb on - strand, within PP_0546at 635.160 kb on - strand, within PP_0546at 635.162 kb on + strand, within PP_0546at 635.268 kb on + strand, within PP_0546at 635.269 kb on - strand, within PP_0546at 635.269 kb on - strand, within PP_0546at 635.269 kb on - strand, within PP_0546at 635.308 kb on + strand, within PP_0546at 635.383 kb on + strand, within PP_0546at 635.383 kb on + strand, within PP_0546at 635.662 kb on + strandat 635.663 kb on - strandat 635.663 kb on - strandat 635.696 kb on - strandat 635.782 kb on + strandat 635.782 kb on + strandat 635.782 kb on + strandat 635.879 kb on + strandat 636.014 kb on + strand, within PP_0547at 636.038 kb on + strand, within PP_0547at 636.038 kb on + strand, within PP_0547at 636.038 kb on + strand, within PP_0547at 636.657 kb on + strand, within PP_0547at 636.657 kb on + strand, within PP_0547at 636.657 kb on + strand, within PP_0547

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Per-strain Table

Position Strand Gene LocusTag Fraction Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=144_hrs
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632,717 + PP_0545 0.52 +0.4
632,785 + PP_0545 0.57 +0.5
632,796 + PP_0545 0.58 -0.7
632,797 - PP_0545 0.58 +0.2
632,844 + PP_0545 0.61 +1.7
632,845 - PP_0545 0.61 -0.6
632,996 - PP_0545 0.71 +1.6
633,281 + PP_0545 0.89 +0.5
633,281 + PP_0545 0.89 +0.9
633,281 + PP_0545 0.89 -0.2
633,282 - PP_0545 0.90 -0.0
633,326 + +0.7
633,356 + -1.0
633,356 + +1.0
633,356 + +0.6
633,357 - -0.9
633,357 - +0.1
633,376 + -0.4
633,377 - +1.3
633,377 - -0.7
633,377 - -0.2
633,377 - -0.6
633,377 - -0.3
633,385 + -1.1
633,434 - -0.5
633,456 + +0.8
633,456 + -1.3
633,675 - +0.3
633,689 - -0.0
633,736 + +0.4
633,815 + +0.4
633,816 - -0.7
634,252 - PP_0546 0.28 -0.4
634,319 + PP_0546 0.31 +0.6
634,319 + PP_0546 0.31 +1.0
634,320 - PP_0546 0.31 +1.0
634,320 - PP_0546 0.31 +1.2
634,470 + PP_0546 0.38 -1.4
634,864 + PP_0546 0.58 -0.0
634,865 - PP_0546 0.58 +0.0
634,865 - PP_0546 0.58 +1.4
635,000 + PP_0546 0.65 +0.9
635,000 - PP_0546 0.65 +1.2
635,104 + PP_0546 0.70 +0.7
635,159 + PP_0546 0.73 +0.2
635,159 + PP_0546 0.73 -0.9
635,160 - PP_0546 0.73 +0.1
635,160 - PP_0546 0.73 +1.2
635,160 - PP_0546 0.73 -1.2
635,160 - PP_0546 0.73 -1.0
635,160 - PP_0546 0.73 +0.5
635,160 - PP_0546 0.73 +1.5
635,162 + PP_0546 0.73 +0.9
635,268 + PP_0546 0.78 +0.6
635,269 - PP_0546 0.78 +0.6
635,269 - PP_0546 0.78 +1.3
635,269 - PP_0546 0.78 +0.1
635,308 + PP_0546 0.80 +0.6
635,383 + PP_0546 0.84 +0.3
635,383 + PP_0546 0.84 -0.5
635,662 + -1.1
635,663 - -0.7
635,663 - -0.3
635,696 - +0.5
635,782 + -2.4
635,782 + -1.3
635,782 + -1.4
635,879 + -0.8
636,014 + PP_0547 0.18 -0.3
636,038 + PP_0547 0.19 -0.6
636,038 + PP_0547 0.19 -1.5
636,038 + PP_0547 0.19 -0.7
636,657 + PP_0547 0.65 -2.5
636,657 + PP_0547 0.65 +0.4
636,657 + PP_0547 0.65 +0.2

Or see this region's nucleotide sequence