Strain Fitness in Pseudomonas putida KT2440 around PP_4906

Experiment: Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs

Add experiment(s):

Zoom: Pan:

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.

download SVG
500 ntPP_4904 and PP_4905 are separated by 3 nucleotidesPP_4905 and PP_4906 are separated by 130 nucleotidesPP_4906 and PP_4907 are separated by 44 nucleotidesPP_4907 and PP_4908 are separated by 9 nucleotides PP_4904: PP_4904 - Flagellar motor rotation protein, at 5,574,253 to 5,575,293 _4904 PP_4905: PP_4905 - Flagellar motor rotation protein, at 5,575,297 to 5,576,148 _4905 PP_4906: PP_4906 - conserved protein of unknown function, at 5,576,279 to 5,577,814 _4906 PP_4907: PP_4907 - Thiosulfate sulfurtransferase, at 5,577,859 to 5,578,668 _4907 PP_4908: PP_4908 - phosphatidylserine decarboxylase, at 5,578,678 to 5,579,541 _4908 Position (kb) 5576 5577 5578Strain fitness (log2 ratio) -4 -3 -2 -1 0 1 2at 5575.353 kb on - strandat 5575.499 kb on + strand, within PP_4905at 5575.500 kb on - strand, within PP_4905at 5575.512 kb on + strand, within PP_4905at 5575.525 kb on - strand, within PP_4905at 5575.543 kb on + strand, within PP_4905at 5575.543 kb on + strand, within PP_4905at 5575.543 kb on + strand, within PP_4905at 5575.543 kb on + strand, within PP_4905at 5575.544 kb on - strand, within PP_4905at 5575.544 kb on - strand, within PP_4905at 5575.638 kb on + strandat 5575.766 kb on + strand, within PP_4905at 5575.815 kb on - strand, within PP_4905at 5575.929 kb on - strand, within PP_4905at 5576.120 kb on - strandat 5576.142 kb on + strandat 5576.142 kb on + strandat 5576.142 kb on + strandat 5576.148 kb on + strandat 5576.148 kb on + strandat 5576.148 kb on + strandat 5576.149 kb on - strandat 5576.149 kb on - strandat 5576.149 kb on - strandat 5576.180 kb on + strandat 5576.196 kb on + strandat 5576.197 kb on - strandat 5576.211 kb on - strandat 5576.211 kb on - strandat 5576.211 kb on - strandat 5576.214 kb on + strandat 5576.215 kb on - strandat 5576.236 kb on + strandat 5576.236 kb on + strandat 5576.236 kb on + strandat 5576.237 kb on - strandat 5576.237 kb on - strandat 5576.239 kb on - strandat 5576.239 kb on - strandat 5576.322 kb on + strandat 5576.322 kb on + strandat 5576.379 kb on - strandat 5576.379 kb on - strandat 5576.379 kb on - strandat 5576.379 kb on - strandat 5576.620 kb on - strand, within PP_4906at 5576.883 kb on - strand, within PP_4906at 5576.883 kb on - strand, within PP_4906at 5577.054 kb on + strand, within PP_4906at 5577.054 kb on + strand, within PP_4906at 5577.054 kb on + strand, within PP_4906at 5577.126 kb on + strand, within PP_4906at 5577.126 kb on + strand, within PP_4906at 5577.126 kb on + strand, within PP_4906at 5577.126 kb on + strand, within PP_4906at 5577.127 kb on - strand, within PP_4906at 5577.166 kb on - strand, within PP_4906at 5577.468 kb on - strand, within PP_4906at 5577.528 kb on + strand, within PP_4906at 5577.529 kb on - strand, within PP_4906at 5577.657 kb on + strand, within PP_4906at 5577.657 kb on + strand, within PP_4906at 5577.658 kb on - strand, within PP_4906at 5577.658 kb on - strand, within PP_4906at 5577.660 kb on + strand, within PP_4906at 5577.660 kb on + strand, within PP_4906at 5577.660 kb on + strand, within PP_4906at 5577.660 kb on + strand, within PP_4906at 5577.661 kb on - strandat 5577.661 kb on - strandat 5577.661 kb on - strandat 5577.661 kb on - strandat 5577.796 kb on + strandat 5577.797 kb on - strandat 5577.824 kb on + strandat 5578.108 kb on + strand, within PP_4907at 5578.108 kb on + strand, within PP_4907at 5578.108 kb on + strand, within PP_4907at 5578.108 kb on + strand, within PP_4907at 5578.117 kb on + strand, within PP_4907at 5578.186 kb on + strand, within PP_4907at 5578.186 kb on + strand, within PP_4907at 5578.186 kb on + strand, within PP_4907at 5578.192 kb on + strand, within PP_4907at 5578.192 kb on + strand, within PP_4907at 5578.280 kb on + strand, within PP_4907at 5578.570 kb on + strand, within PP_4907at 5578.570 kb on + strand, within PP_4907at 5578.612 kb on + strand

download strain data

Per-strain Table

Position Strand Gene LocusTag Fraction Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs
remove
5,575,353 - +0.9
5,575,499 + PP_4905 0.24 -2.3
5,575,500 - PP_4905 0.24 -0.2
5,575,512 + PP_4905 0.25 -1.2
5,575,525 - PP_4905 0.27 +0.2
5,575,543 + PP_4905 0.29 -2.5
5,575,543 + PP_4905 0.29 +2.0
5,575,543 + PP_4905 0.29 +0.4
5,575,543 + PP_4905 0.29 -0.8
5,575,544 - PP_4905 0.29 +0.2
5,575,544 - PP_4905 0.29 -0.2
5,575,638 + +2.4
5,575,766 + PP_4905 0.55 -0.3
5,575,815 - PP_4905 0.61 -1.5
5,575,929 - PP_4905 0.74 +0.1
5,576,120 - +0.9
5,576,142 + -1.9
5,576,142 + -2.8
5,576,142 + -2.0
5,576,148 + -1.2
5,576,148 + -2.2
5,576,148 + +0.2
5,576,149 - +0.3
5,576,149 - -0.1
5,576,149 - -2.5
5,576,180 + -0.6
5,576,196 + -2.4
5,576,197 - +1.5
5,576,211 - -0.0
5,576,211 - -0.3
5,576,211 - +2.1
5,576,214 + -3.9
5,576,215 - +2.1
5,576,236 + -0.4
5,576,236 + -1.9
5,576,236 + -1.1
5,576,237 - -2.0
5,576,237 - -2.6
5,576,239 - +0.6
5,576,239 - -2.2
5,576,322 + -1.8
5,576,322 + +0.3
5,576,379 - -1.1
5,576,379 - +0.1
5,576,379 - -0.9
5,576,379 - +0.9
5,576,620 - PP_4906 0.22 +0.3
5,576,883 - PP_4906 0.39 +0.8
5,576,883 - PP_4906 0.39 -0.2
5,577,054 + PP_4906 0.50 -2.8
5,577,054 + PP_4906 0.50 -0.3
5,577,054 + PP_4906 0.50 +0.5
5,577,126 + PP_4906 0.55 -1.0
5,577,126 + PP_4906 0.55 -1.3
5,577,126 + PP_4906 0.55 +0.5
5,577,126 + PP_4906 0.55 -0.8
5,577,127 - PP_4906 0.55 -3.6
5,577,166 - PP_4906 0.58 -0.7
5,577,468 - PP_4906 0.77 -0.6
5,577,528 + PP_4906 0.81 +0.3
5,577,529 - PP_4906 0.81 -0.7
5,577,657 + PP_4906 0.90 -0.4
5,577,657 + PP_4906 0.90 -0.1
5,577,658 - PP_4906 0.90 -2.9
5,577,658 - PP_4906 0.90 +0.2
5,577,660 + PP_4906 0.90 -0.3
5,577,660 + PP_4906 0.90 -0.1
5,577,660 + PP_4906 0.90 -2.5
5,577,660 + PP_4906 0.90 +0.1
5,577,661 - -0.0
5,577,661 - -2.8
5,577,661 - +0.0
5,577,661 - +1.0
5,577,796 + +0.9
5,577,797 - -1.0
5,577,824 + -0.3
5,578,108 + PP_4907 0.31 +1.2
5,578,108 + PP_4907 0.31 -1.8
5,578,108 + PP_4907 0.31 -0.2
5,578,108 + PP_4907 0.31 +1.6
5,578,117 + PP_4907 0.32 +0.1
5,578,186 + PP_4907 0.40 -0.3
5,578,186 + PP_4907 0.40 +0.5
5,578,186 + PP_4907 0.40 -1.8
5,578,192 + PP_4907 0.41 -3.5
5,578,192 + PP_4907 0.41 -3.0
5,578,280 + PP_4907 0.52 -1.9
5,578,570 + PP_4907 0.88 +0.8
5,578,570 + PP_4907 0.88 -0.5
5,578,612 + -1.8

Or see this region's nucleotide sequence