Strain Fitness in Pseudomonas putida KT2440 around PP_0096

Experiment: 48hr timepoint from 1L M9/1% dextrose BATCH fermentation in 2L Sartorius Biostat reactor kept at 30% DO with 20% v/v dodecane overlay

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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_0094 and PP_0095 are separated by 121 nucleotidesPP_0095 and PP_0096 are separated by 102 nucleotidesPP_0096 and PP_0097 overlap by 4 nucleotidesPP_0097 and PP_0098 are separated by 18 nucleotidesPP_0098 and PP_0099 are separated by 139 nucleotides PP_0094: PP_0094 - 5'-nucleotidase, at 99,758 to 100,408 _0094 PP_0095: PP_0095 - putative enzyme of unknown function, at 100,530 to 101,078 _0095 PP_0096: PP_0096 - oligopeptidase A, at 101,181 to 103,232 _0096 PP_0097: PP_0097 - conserved protein of unknown function, at 103,229 to 103,510 _0097 PP_0098: PP_0098 - conserved protein of unknown function, at 103,529 to 103,702 _0098 PP_0099: PP_0099 - conserved protein of unknown function, at 103,842 to 104,900 _0099 Position (kb) 101 102 103 104Strain fitness (log2 ratio) -2 -1 0 1 2 3at 100.237 kb on - strand, within PP_0094at 100.410 kb on + strandat 100.411 kb on - strandat 100.411 kb on - strandat 100.411 kb on - strandat 100.411 kb on - strandat 100.411 kb on - strandat 100.411 kb on - strandat 100.469 kb on + strandat 100.469 kb on + strandat 100.470 kb on - strandat 100.546 kb on + strandat 100.582 kb on + strandat 100.582 kb on + strandat 100.582 kb on + strandat 100.583 kb on - strandat 100.583 kb on - strandat 100.597 kb on + strand, within PP_0095at 100.598 kb on - strand, within PP_0095at 100.660 kb on + strand, within PP_0095at 100.660 kb on + strand, within PP_0095at 100.660 kb on + strand, within PP_0095at 100.661 kb on - strand, within PP_0095at 100.661 kb on - strand, within PP_0095at 100.661 kb on - strand, within PP_0095at 100.661 kb on - strand, within PP_0095at 100.661 kb on - strand, within PP_0095at 100.661 kb on - strand, within PP_0095at 100.667 kb on - strand, within PP_0095at 100.719 kb on + strand, within PP_0095at 100.719 kb on + strand, within PP_0095at 100.720 kb on - strand, within PP_0095at 100.720 kb on - strand, within PP_0095at 100.764 kb on - strand, within PP_0095at 100.881 kb on - strand, within PP_0095at 101.081 kb on + strandat 101.082 kb on - strandat 101.082 kb on - strandat 101.082 kb on - strandat 101.138 kb on - strandat 101.138 kb on - strandat 101.141 kb on + strandat 101.141 kb on + strandat 101.141 kb on + strandat 101.141 kb on + strandat 101.289 kb on - strandat 101.330 kb on + strandat 101.330 kb on + strandat 101.330 kb on + strandat 101.330 kb on + strandat 101.330 kb on + strandat 101.331 kb on - strandat 101.331 kb on - strandat 101.331 kb on - strandat 101.331 kb on - strandat 101.445 kb on + strand, within PP_0096at 101.445 kb on + strand, within PP_0096at 101.445 kb on + strand, within PP_0096at 101.445 kb on + strand, within PP_0096at 101.445 kb on + strand, within PP_0096at 101.446 kb on - strand, within PP_0096at 101.475 kb on + strand, within PP_0096at 101.476 kb on - strand, within PP_0096at 101.476 kb on - strand, within PP_0096at 101.517 kb on + strand, within PP_0096at 101.518 kb on - strand, within PP_0096at 101.518 kb on - strand, within PP_0096at 101.574 kb on - strand, within PP_0096at 101.844 kb on + strand, within PP_0096at 101.844 kb on + strand, within PP_0096at 101.845 kb on - strand, within PP_0096at 101.845 kb on - strand, within PP_0096at 101.862 kb on + strand, within PP_0096at 101.863 kb on - strand, within PP_0096at 101.893 kb on + strand, within PP_0096at 101.893 kb on + strand, within PP_0096at 101.894 kb on - strand, within PP_0096at 101.894 kb on - strand, within PP_0096at 101.894 kb on - strand, within PP_0096at 101.894 kb on - strand, within PP_0096at 101.895 kb on + strand, within PP_0096at 101.895 kb on + strand, within PP_0096at 101.896 kb on - strand, within PP_0096at 102.144 kb on + strand, within PP_0096at 102.144 kb on + strand, within PP_0096at 102.144 kb on + strand, within PP_0096at 102.193 kb on - strand, within PP_0096at 102.222 kb on + strand, within PP_0096at 102.222 kb on + strand, within PP_0096at 102.223 kb on - strand, within PP_0096at 102.223 kb on - strand, within PP_0096at 102.223 kb on - strand, within PP_0096at 102.358 kb on + strand, within PP_0096at 102.358 kb on + strandat 102.358 kb on + strand, within PP_0096at 102.358 kb on + strand, within PP_0096at 102.359 kb on - strand, within PP_0096at 102.359 kb on - strand, within PP_0096at 102.417 kb on + strand, within PP_0096at 102.417 kb on + strandat 102.747 kb on + strand, within PP_0096at 102.748 kb on - strand, within PP_0096at 102.895 kb on + strand, within PP_0096at 102.895 kb on + strand, within PP_0096at 102.895 kb on + strand, within PP_0096at 102.896 kb on - strand, within PP_0096at 102.951 kb on + strand, within PP_0096at 102.951 kb on + strand, within PP_0096at 102.951 kb on + strand, within PP_0096at 102.952 kb on - strand, within PP_0096at 103.011 kb on + strand, within PP_0096at 103.012 kb on - strand, within PP_0096at 103.012 kb on - strand, within PP_0096at 103.012 kb on - strand, within PP_0096at 103.012 kb on - strand, within PP_0096at 103.012 kb on - strand, within PP_0096at 103.017 kb on + strand, within PP_0096at 103.017 kb on + strand, within PP_0096at 103.017 kb on + strandat 103.018 kb on - strand, within PP_0096at 103.018 kb on - strand, within PP_0096at 103.018 kb on - strand, within PP_0096at 103.018 kb on - strand, within PP_0096at 103.018 kb on - strandat 103.239 kb on + strandat 103.239 kb on + strandat 103.239 kb on + strandat 103.240 kb on - strandat 103.240 kb on - strandat 103.240 kb on - strandat 103.367 kb on - strand, within PP_0097at 103.508 kb on + strandat 103.509 kb on - strandat 103.511 kb on + strandat 103.511 kb on + strandat 103.511 kb on + strandat 103.511 kb on + strandat 103.512 kb on - strandat 103.512 kb on - strandat 103.701 kb on - strandat 103.701 kb on - strandat 103.745 kb on + strandat 103.745 kb on + strandat 103.745 kb on + strandat 103.745 kb on + strandat 103.745 kb on + strandat 103.745 kb on + strandat 103.746 kb on - strandat 103.746 kb on - strandat 103.746 kb on - strandat 103.746 kb on - strandat 103.746 kb on - strandat 103.770 kb on - strandat 103.939 kb on - strandat 103.939 kb on - strandat 103.964 kb on + strand, within PP_0099at 104.076 kb on + strand, within PP_0099at 104.076 kb on + strand, within PP_0099at 104.076 kb on + strand, within PP_0099at 104.076 kb on + strand, within PP_0099at 104.076 kb on + strand, within PP_0099at 104.077 kb on - strand, within PP_0099at 104.077 kb on - strand, within PP_0099at 104.077 kb on - strand, within PP_0099at 104.077 kb on - strand, within PP_0099at 104.077 kb on - strand, within PP_0099at 104.077 kb on - strand, within PP_0099at 104.082 kb on + strand, within PP_0099at 104.082 kb on + strand, within PP_0099at 104.082 kb on + strand, within PP_0099at 104.083 kb on - strand, within PP_0099at 104.083 kb on - strand, within PP_0099at 104.083 kb on - strand, within PP_0099at 104.083 kb on - strand, within PP_0099at 104.083 kb on - strand, within PP_0099at 104.200 kb on - strand, within PP_0099

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Per-strain Table

Position Strand Gene LocusTag Fraction 48hr timepoint from 1L M9/1% dextrose BATCH fermentation in 2L Sartorius Biostat reactor kept at 30% DO with 20% v/v dodecane overlay
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100,237 - PP_0094 0.74 +0.6
100,410 + +0.6
100,411 - -0.4
100,411 - +0.9
100,411 - +1.2
100,411 - -0.8
100,411 - +1.1
100,411 - -1.0
100,469 + -0.1
100,469 + -0.1
100,470 - -1.0
100,546 + -0.7
100,582 + +1.4
100,582 + +0.6
100,582 + +0.1
100,583 - -1.0
100,583 - +1.0
100,597 + PP_0095 0.12 +0.6
100,598 - PP_0095 0.12 -0.6
100,660 + PP_0095 0.24 -0.8
100,660 + PP_0095 0.24 -0.4
100,660 + PP_0095 0.24 -0.7
100,661 - PP_0095 0.24 +1.0
100,661 - PP_0095 0.24 -0.2
100,661 - PP_0095 0.24 -1.3
100,661 - PP_0095 0.24 +0.2
100,661 - PP_0095 0.24 -0.3
100,661 - PP_0095 0.24 -0.2
100,667 - PP_0095 0.25 -0.2
100,719 + PP_0095 0.34 +0.6
100,719 + PP_0095 0.34 -0.8
100,720 - PP_0095 0.35 +0.6
100,720 - PP_0095 0.35 -0.7
100,764 - PP_0095 0.43 +0.6
100,881 - PP_0095 0.64 +0.2
101,081 + -0.4
101,082 - -0.6
101,082 - -0.2
101,082 - +1.1
101,138 - +0.6
101,138 - -0.4
101,141 + -0.3
101,141 + -0.2
101,141 + -0.8
101,141 + -0.9
101,289 - -0.8
101,330 + +0.1
101,330 + -1.0
101,330 + +1.6
101,330 + -1.3
101,330 + -0.2
101,331 - -1.0
101,331 - -1.2
101,331 - -1.4
101,331 - +0.6
101,445 + PP_0096 0.13 +0.6
101,445 + PP_0096 0.13 -2.1
101,445 + PP_0096 0.13 -0.4
101,445 + PP_0096 0.13 +0.6
101,445 + PP_0096 0.13 +0.1
101,446 - PP_0096 0.13 -0.8
101,475 + PP_0096 0.14 +0.2
101,476 - PP_0096 0.14 +1.6
101,476 - PP_0096 0.14 -1.8
101,517 + PP_0096 0.16 +1.6
101,518 - PP_0096 0.16 +0.0
101,518 - PP_0096 0.16 +0.6
101,574 - PP_0096 0.19 -0.3
101,844 + PP_0096 0.32 -0.4
101,844 + PP_0096 0.32 -0.5
101,845 - PP_0096 0.32 +0.6
101,845 - PP_0096 0.32 -0.4
101,862 + PP_0096 0.33 +0.6
101,863 - PP_0096 0.33 -0.7
101,893 + PP_0096 0.35 -0.0
101,893 + PP_0096 0.35 -0.2
101,894 - PP_0096 0.35 -0.8
101,894 - PP_0096 0.35 +1.6
101,894 - PP_0096 0.35 +0.6
101,894 - PP_0096 0.35 -0.4
101,895 + PP_0096 0.35 -1.0
101,895 + PP_0096 0.35 +0.6
101,896 - PP_0096 0.35 -1.4
102,144 + PP_0096 0.47 -1.2
102,144 + PP_0096 0.47 -0.7
102,144 + PP_0096 0.47 -0.2
102,193 - PP_0096 0.49 -1.0
102,222 + PP_0096 0.51 +1.1
102,222 + PP_0096 0.51 +0.6
102,223 - PP_0096 0.51 +0.6
102,223 - PP_0096 0.51 -1.0
102,223 - PP_0096 0.51 +0.3
102,358 + PP_0096 0.57 +0.6
102,358 + +0.6
102,358 + PP_0096 0.57 +2.1
102,358 + PP_0096 0.57 -0.8
102,359 - PP_0096 0.57 -1.0
102,359 - PP_0096 0.57 +0.6
102,417 + PP_0096 0.60 +2.9
102,417 + +0.6
102,747 + PP_0096 0.76 -0.2
102,748 - PP_0096 0.76 -0.8
102,895 + PP_0096 0.84 +0.9
102,895 + PP_0096 0.84 +0.6
102,895 + PP_0096 0.84 +0.1
102,896 - PP_0096 0.84 +0.6
102,951 + PP_0096 0.86 -1.3
102,951 + PP_0096 0.86 -1.0
102,951 + PP_0096 0.86 +2.1
102,952 - PP_0096 0.86 -0.4
103,011 + PP_0096 0.89 +0.6
103,012 - PP_0096 0.89 -0.4
103,012 - PP_0096 0.89 +1.1
103,012 - PP_0096 0.89 -0.4
103,012 - PP_0096 0.89 +1.6
103,012 - PP_0096 0.89 -0.4
103,017 + PP_0096 0.89 -0.0
103,017 + PP_0096 0.89 +0.0
103,017 + -0.4
103,018 - PP_0096 0.90 +1.6
103,018 - PP_0096 0.90 -0.2
103,018 - PP_0096 0.90 +0.6
103,018 - PP_0096 0.90 -0.4
103,018 - +1.6
103,239 + +1.0
103,239 + -0.8
103,239 + -0.4
103,240 - +1.6
103,240 - +0.6
103,240 - -1.4
103,367 - PP_0097 0.49 +0.6
103,508 + -1.4
103,509 - -1.1
103,511 + +1.0
103,511 + -0.0
103,511 + +0.6
103,511 + -0.3
103,512 - +1.0
103,512 - -1.8
103,701 - -1.8
103,701 - +0.7
103,745 + -2.2
103,745 + +0.4
103,745 + +0.4
103,745 + -0.3
103,745 + +0.4
103,745 + +2.3
103,746 - +0.2
103,746 - +0.9
103,746 - +0.3
103,746 - -0.4
103,746 - +0.7
103,770 - +0.6
103,939 - +0.4
103,939 - -0.1
103,964 + PP_0099 0.12 +0.6
104,076 + PP_0099 0.22 +0.0
104,076 + PP_0099 0.22 -1.1
104,076 + PP_0099 0.22 +0.6
104,076 + PP_0099 0.22 +0.2
104,076 + PP_0099 0.22 +0.0
104,077 - PP_0099 0.22 -1.0
104,077 - PP_0099 0.22 +0.6
104,077 - PP_0099 0.22 +0.3
104,077 - PP_0099 0.22 +0.6
104,077 - PP_0099 0.22 -1.2
104,077 - PP_0099 0.22 +1.8
104,082 + PP_0099 0.23 -1.0
104,082 + PP_0099 0.23 +0.0
104,082 + PP_0099 0.23 +0.3
104,083 - PP_0099 0.23 +0.2
104,083 - PP_0099 0.23 +0.4
104,083 - PP_0099 0.23 +0.2
104,083 - PP_0099 0.23 +0.1
104,083 - PP_0099 0.23 +1.4
104,200 - PP_0099 0.34 +1.0

Or see this region's nucleotide sequence