Strain Fitness in Pseudomonas putida KT2440 around PP_5422

Experiment: Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=0_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_0027 and PP_0028 are separated by 32 nucleotidesPP_0028 and PP_5422 are separated by 198 nucleotidesPP_5422 and PP_0029 are separated by 317 nucleotidesPP_0029 and PP_0030 overlap by 4 nucleotides PP_0027: PP_0027 - conserved membrane protein of unknown function, at 31,404 to 31,844 _0027 PP_0028: PP_0028 - conserved hypothetical protein, at 31,877 to 32,203 _0028 PP_5422: PP_5422 - hypothetical protein, at 32,402 to 32,575 _5422 PP_0029: PP_0029 - two component heavy metal response regulator, at 32,893 to 33,567 _0029 PP_0030: PP_0030 - metal-sensor histidine kinase, at 33,564 to 34,982 _0030 Position (kb) 32 33Strain fitness (log2 ratio) -3 -2 -1 0 1 2 3at 31.515 kb on + strand, within PP_0027at 31.515 kb on + strand, within PP_0027at 31.515 kb on + strand, within PP_0027at 31.516 kb on - strand, within PP_0027at 31.516 kb on - strand, within PP_0027at 31.516 kb on - strand, within PP_0027at 31.516 kb on - strand, within PP_0027at 31.519 kb on + strand, within PP_0027at 31.519 kb on + strand, within PP_0027at 31.519 kb on + strand, within PP_0027at 31.519 kb on + strand, within PP_0027at 31.520 kb on - strand, within PP_0027at 31.534 kb on + strand, within PP_0027at 31.535 kb on - strand, within PP_0027at 31.633 kb on - strand, within PP_0027at 31.636 kb on + strand, within PP_0027at 31.677 kb on + strand, within PP_0027at 31.677 kb on + strand, within PP_0027at 31.678 kb on - strand, within PP_0027at 31.678 kb on - strand, within PP_0027at 31.689 kb on + strand, within PP_0027at 31.690 kb on - strand, within PP_0027at 31.715 kb on + strand, within PP_0027at 31.716 kb on - strand, within PP_0027at 31.716 kb on - strand, within PP_0027at 31.735 kb on + strand, within PP_0027at 31.735 kb on + strand, within PP_0027at 31.736 kb on - strand, within PP_0027at 31.739 kb on + strand, within PP_0027at 31.739 kb on + strand, within PP_0027at 31.739 kb on + strand, within PP_0027at 31.740 kb on - strand, within PP_0027at 31.740 kb on - strand, within PP_0027at 31.810 kb on + strandat 31.810 kb on + strandat 31.811 kb on - strandat 31.840 kb on + strandat 31.840 kb on + strandat 31.841 kb on - strandat 31.886 kb on - strandat 31.888 kb on + strandat 31.889 kb on - strandat 31.889 kb on - strandat 31.947 kb on + strand, within PP_0028at 31.964 kb on + strand, within PP_0028at 31.965 kb on - strand, within PP_0028at 31.965 kb on - strand, within PP_0028at 31.965 kb on - strand, within PP_0028at 31.965 kb on - strand, within PP_0028at 31.994 kb on + strand, within PP_0028at 31.994 kb on + strand, within PP_0028at 31.994 kb on + strand, within PP_0028at 31.995 kb on - strand, within PP_0028at 31.995 kb on - strand, within PP_0028at 31.995 kb on - strand, within PP_0028at 31.998 kb on + strand, within PP_0028at 31.998 kb on + strand, within PP_0028at 31.998 kb on + strand, within PP_0028at 31.998 kb on + strand, within PP_0028at 31.998 kb on + strand, within PP_0028at 31.998 kb on + strand, within PP_0028at 31.999 kb on - strand, within PP_0028at 31.999 kb on - strand, within PP_0028at 31.999 kb on - strand, within PP_0028at 32.009 kb on - strand, within PP_0028at 32.038 kb on - strand, within PP_0028at 32.079 kb on + strand, within PP_0028at 32.098 kb on + strand, within PP_0028at 32.099 kb on - strand, within PP_0028at 32.104 kb on + strand, within PP_0028at 32.105 kb on - strand, within PP_0028at 32.119 kb on + strand, within PP_0028at 32.119 kb on + strandat 32.190 kb on - strandat 32.204 kb on - strandat 32.204 kb on - strandat 32.255 kb on - strandat 32.268 kb on - strandat 32.268 kb on - strandat 32.440 kb on + strand, within PP_5422at 32.445 kb on + strand, within PP_5422at 32.556 kb on + strand, within PP_5422at 32.557 kb on - strand, within PP_5422at 32.573 kb on + strandat 32.573 kb on + strandat 32.574 kb on - strandat 32.629 kb on + strandat 32.629 kb on + strandat 32.630 kb on - strandat 32.630 kb on - strandat 32.701 kb on + strandat 32.702 kb on - strandat 32.844 kb on + strandat 32.859 kb on - strandat 32.904 kb on - strandat 32.922 kb on + strandat 32.936 kb on - strandat 32.965 kb on + strand, within PP_0029at 32.965 kb on + strand, within PP_0029at 32.965 kb on + strand, within PP_0029at 32.977 kb on - strand, within PP_0029at 32.994 kb on - strand, within PP_0029at 32.994 kb on - strand, within PP_0029at 32.994 kb on - strand, within PP_0029at 33.017 kb on + strand, within PP_0029at 33.018 kb on + strand, within PP_0029at 33.019 kb on - strand, within PP_0029at 33.093 kb on + strand, within PP_0029at 33.093 kb on + strand, within PP_0029at 33.094 kb on - strand, within PP_0029at 33.094 kb on - strand, within PP_0029at 33.094 kb on - strand, within PP_0029at 33.181 kb on + strand, within PP_0029at 33.181 kb on + strand, within PP_0029at 33.181 kb on + strand, within PP_0029at 33.182 kb on - strand, within PP_0029at 33.182 kb on - strand, within PP_0029at 33.182 kb on - strand, within PP_0029at 33.255 kb on - strand, within PP_0029at 33.255 kb on - strand, within PP_0029at 33.467 kb on + strand, within PP_0029at 33.467 kb on + strand, within PP_0029at 33.468 kb on - strand, within PP_0029at 33.468 kb on - strand, within PP_0029

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Per-strain Table

Position Strand Gene LocusTag Fraction Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=0_hrs
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31,515 + PP_0027 0.25 -0.2
31,515 + PP_0027 0.25 -0.7
31,515 + PP_0027 0.25 +0.2
31,516 - PP_0027 0.25 -0.3
31,516 - PP_0027 0.25 +0.8
31,516 - PP_0027 0.25 -0.9
31,516 - PP_0027 0.25 +1.0
31,519 + PP_0027 0.26 +0.8
31,519 + PP_0027 0.26 -1.4
31,519 + PP_0027 0.26 +1.0
31,519 + PP_0027 0.26 +0.6
31,520 - PP_0027 0.26 -0.1
31,534 + PP_0027 0.29 +0.2
31,535 - PP_0027 0.30 +0.2
31,633 - PP_0027 0.52 -0.6
31,636 + PP_0027 0.53 +0.7
31,677 + PP_0027 0.62 -3.2
31,677 + PP_0027 0.62 -0.6
31,678 - PP_0027 0.62 +0.8
31,678 - PP_0027 0.62 +1.0
31,689 + PP_0027 0.65 -1.4
31,690 - PP_0027 0.65 -0.6
31,715 + PP_0027 0.71 -0.0
31,716 - PP_0027 0.71 +0.4
31,716 - PP_0027 0.71 -0.6
31,735 + PP_0027 0.75 +0.6
31,735 + PP_0027 0.75 -0.3
31,736 - PP_0027 0.75 -0.3
31,739 + PP_0027 0.76 +0.7
31,739 + PP_0027 0.76 -0.3
31,739 + PP_0027 0.76 -1.4
31,740 - PP_0027 0.76 -1.4
31,740 - PP_0027 0.76 +0.2
31,810 + -0.8
31,810 + -0.5
31,811 - -0.2
31,840 + +1.2
31,840 + +0.5
31,841 - -0.2
31,886 - +0.6
31,888 + -0.4
31,889 - -0.8
31,889 - -0.6
31,947 + PP_0028 0.21 +0.5
31,964 + PP_0028 0.27 -1.6
31,965 - PP_0028 0.27 -2.3
31,965 - PP_0028 0.27 +0.4
31,965 - PP_0028 0.27 -0.1
31,965 - PP_0028 0.27 -0.4
31,994 + PP_0028 0.36 +0.6
31,994 + PP_0028 0.36 -0.1
31,994 + PP_0028 0.36 +0.9
31,995 - PP_0028 0.36 +0.2
31,995 - PP_0028 0.36 -1.1
31,995 - PP_0028 0.36 +0.1
31,998 + PP_0028 0.37 -0.3
31,998 + PP_0028 0.37 -0.5
31,998 + PP_0028 0.37 +0.4
31,998 + PP_0028 0.37 -0.9
31,998 + PP_0028 0.37 -3.2
31,998 + PP_0028 0.37 -0.1
31,999 - PP_0028 0.37 -0.3
31,999 - PP_0028 0.37 +0.8
31,999 - PP_0028 0.37 +0.1
32,009 - PP_0028 0.40 +2.4
32,038 - PP_0028 0.49 -0.8
32,079 + PP_0028 0.62 +2.2
32,098 + PP_0028 0.68 +0.2
32,099 - PP_0028 0.68 -0.5
32,104 + PP_0028 0.69 -1.0
32,105 - PP_0028 0.70 -1.1
32,119 + PP_0028 0.74 +0.4
32,119 + +1.1
32,190 - +1.0
32,204 - -0.2
32,204 - -0.0
32,255 - -1.6
32,268 - -1.5
32,268 - -0.3
32,440 + PP_5422 0.22 -1.5
32,445 + PP_5422 0.25 +0.1
32,556 + PP_5422 0.89 +0.5
32,557 - PP_5422 0.89 +1.4
32,573 + -0.5
32,573 + -0.5
32,574 - +2.1
32,629 + +0.3
32,629 + -1.9
32,630 - +1.1
32,630 - -1.2
32,701 + -0.4
32,702 - +1.1
32,844 + +0.5
32,859 - -0.5
32,904 - +0.3
32,922 + -0.0
32,936 - -1.9
32,965 + PP_0029 0.11 +0.3
32,965 + PP_0029 0.11 +0.4
32,965 + PP_0029 0.11 +0.2
32,977 - PP_0029 0.12 +0.0
32,994 - PP_0029 0.15 -0.4
32,994 - PP_0029 0.15 -0.4
32,994 - PP_0029 0.15 +0.0
33,017 + PP_0029 0.18 -0.8
33,018 + PP_0029 0.19 +0.8
33,019 - PP_0029 0.19 -0.1
33,093 + PP_0029 0.30 -1.8
33,093 + PP_0029 0.30 +0.2
33,094 - PP_0029 0.30 +0.4
33,094 - PP_0029 0.30 +0.3
33,094 - PP_0029 0.30 +0.6
33,181 + PP_0029 0.43 +0.7
33,181 + PP_0029 0.43 +0.4
33,181 + PP_0029 0.43 -0.5
33,182 - PP_0029 0.43 -1.1
33,182 - PP_0029 0.43 +0.7
33,182 - PP_0029 0.43 -0.9
33,255 - PP_0029 0.54 +0.4
33,255 - PP_0029 0.54 +0.8
33,467 + PP_0029 0.85 +3.1
33,467 + PP_0029 0.85 +0.2
33,468 - PP_0029 0.85 -0.4
33,468 - PP_0029 0.85 +0.6

Or see this region's nucleotide sequence