Strain Fitness in Pseudomonas putida KT2440 around PP_0088

Experiment: 48hr timepoint from 1L M9/1% dextrose BATCH fermentation in 2L Sartorius Biostat reactor kept at 10% DO.

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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_0085 and PP_0086 overlap by 15 nucleotidesPP_0086 and PP_0087 are separated by 58 nucleotidesPP_0087 and PP_0088 are separated by 71 nucleotidesPP_0088 and PP_0089 are separated by 152 nucleotidesPP_0089 and PP_0090 are separated by 12 nucleotidesPP_0090 and PP_0091 are separated by 35 nucleotides PP_0085: PP_0085 - conserved protein of unknown function, at 94,597 to 95,085 _0085 PP_0086: PP_0086 - conserved protein of unknown function, at 95,071 to 95,286 _0086 PP_0087: PP_0087 - conserved exported protein of unknown function, at 95,345 to 95,608 _0087 PP_0088: PP_0088 - putative alkanal monooxygenase, at 95,680 to 96,684 _0088 PP_0089: PP_0089 - stress-induced peroxiredoxin, lipoyl-dependent peroxidase, at 96,837 to 97,262 _0089 PP_0090: PP_0090 - conserved exported protein of unknown function, at 97,275 to 97,571 _0090 PP_0091: PP_0091 - putative lipoprotein, at 97,607 to 98,020 _0091 Position (kb) 95 96 97Strain fitness (log2 ratio) -3 -2 -1 0 1 2at 94.736 kb on + strand, within PP_0085at 94.737 kb on - strand, within PP_0085at 94.750 kb on + strand, within PP_0085at 94.900 kb on - strand, within PP_0085at 94.900 kb on - strand, within PP_0085at 94.939 kb on + strand, within PP_0085at 94.940 kb on - strand, within PP_0085at 94.940 kb on - strand, within PP_0085at 95.016 kb on + strand, within PP_0085at 95.017 kb on - strand, within PP_0085at 95.035 kb on + strand, within PP_0085at 95.036 kb on - strand, within PP_0085at 95.089 kb on + strandat 95.090 kb on - strandat 95.142 kb on + strand, within PP_0086at 95.142 kb on + strand, within PP_0086at 95.142 kb on + strand, within PP_0086at 95.280 kb on + strandat 95.280 kb on + strandat 95.280 kb on + strandat 95.302 kb on + strandat 95.303 kb on - strandat 95.303 kb on - strandat 95.303 kb on - strandat 95.303 kb on - strandat 95.303 kb on - strandat 95.323 kb on + strandat 95.324 kb on - strandat 95.514 kb on - strand, within PP_0087at 95.563 kb on + strand, within PP_0087at 95.563 kb on + strand, within PP_0087at 95.564 kb on - strand, within PP_0087at 95.606 kb on + strandat 95.607 kb on - strandat 95.651 kb on + strandat 95.651 kb on + strandat 95.651 kb on + strandat 95.651 kb on + strandat 95.651 kb on + strandat 95.651 kb on + strandat 95.652 kb on - strandat 95.652 kb on - strandat 95.714 kb on + strandat 95.714 kb on + strandat 95.714 kb on + strandat 95.714 kb on + strandat 95.715 kb on - strandat 95.741 kb on + strandat 95.741 kb on + strandat 95.741 kb on + strandat 95.742 kb on - strandat 95.742 kb on - strandat 95.742 kb on - strandat 95.742 kb on - strandat 95.754 kb on + strandat 95.754 kb on + strandat 95.755 kb on - strandat 95.755 kb on - strandat 95.797 kb on + strand, within PP_0088at 95.798 kb on - strand, within PP_0088at 95.798 kb on - strand, within PP_0088at 95.798 kb on - strand, within PP_0088at 95.809 kb on + strand, within PP_0088at 95.810 kb on - strand, within PP_0088at 95.810 kb on - strand, within PP_0088at 95.955 kb on - strand, within PP_0088at 95.973 kb on - strand, within PP_0088at 95.973 kb on - strand, within PP_0088at 96.026 kb on + strand, within PP_0088at 96.026 kb on + strand, within PP_0088at 96.026 kb on + strand, within PP_0088at 96.026 kb on + strand, within PP_0088at 96.026 kb on + strand, within PP_0088at 96.093 kb on - strand, within PP_0088at 96.123 kb on - strand, within PP_0088at 96.200 kb on + strand, within PP_0088at 96.249 kb on - strand, within PP_0088at 96.317 kb on + strand, within PP_0088at 96.317 kb on + strand, within PP_0088at 96.318 kb on - strand, within PP_0088at 96.318 kb on - strand, within PP_0088at 96.462 kb on + strand, within PP_0088at 96.462 kb on + strandat 96.463 kb on - strand, within PP_0088at 96.463 kb on - strand, within PP_0088at 96.486 kb on - strand, within PP_0088at 96.730 kb on - strandat 96.765 kb on + strandat 96.765 kb on + strandat 96.765 kb on + strandat 96.766 kb on - strandat 96.766 kb on - strandat 96.766 kb on - strandat 96.766 kb on - strandat 96.766 kb on - strandat 96.766 kb on - strandat 96.806 kb on + strandat 96.811 kb on - strandat 96.811 kb on - strandat 96.811 kb on - strandat 96.811 kb on - strandat 96.811 kb on - strandat 96.811 kb on - strandat 96.811 kb on - strandat 96.899 kb on + strand, within PP_0089at 96.930 kb on + strand, within PP_0089at 97.049 kb on + strand, within PP_0089at 97.049 kb on + strand, within PP_0089at 97.050 kb on - strand, within PP_0089at 97.147 kb on + strand, within PP_0089at 97.147 kb on + strand, within PP_0089at 97.147 kb on + strand, within PP_0089at 97.147 kb on + strand, within PP_0089at 97.290 kb on - strandat 97.294 kb on + strandat 97.294 kb on + strandat 97.294 kb on + strandat 97.295 kb on - strandat 97.348 kb on + strand, within PP_0090at 97.348 kb on + strand, within PP_0090at 97.348 kb on + strand, within PP_0090at 97.349 kb on - strand, within PP_0090at 97.349 kb on - strand, within PP_0090at 97.349 kb on - strand, within PP_0090at 97.349 kb on - strand, within PP_0090at 97.352 kb on + strand, within PP_0090at 97.353 kb on - strand, within PP_0090at 97.551 kb on + strandat 97.551 kb on + strandat 97.552 kb on - strandat 97.552 kb on - strandat 97.626 kb on + strandat 97.630 kb on + strandat 97.631 kb on - strandat 97.665 kb on + strand, within PP_0091at 97.665 kb on + strand, within PP_0091at 97.666 kb on - strand, within PP_0091at 97.666 kb on - strand, within PP_0091at 97.666 kb on - strand, within PP_0091at 97.667 kb on + strand, within PP_0091at 97.667 kb on + strand, within PP_0091at 97.667 kb on + strand, within PP_0091at 97.667 kb on + strand, within PP_0091at 97.667 kb on + strand, within PP_0091at 97.668 kb on - strand, within PP_0091at 97.668 kb on - strand, within PP_0091at 97.668 kb on - strand, within PP_0091at 97.668 kb on - strand, within PP_0091at 97.668 kb on - strand, within PP_0091at 97.668 kb on - strand, within PP_0091at 97.668 kb on - strand, within PP_0091at 97.668 kb on - strand, within PP_0091

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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 10% DO.
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94,736 + PP_0085 0.28 -1.6
94,737 - PP_0085 0.29 +0.4
94,750 + PP_0085 0.31 -0.0
94,900 - PP_0085 0.62 -0.8
94,900 - PP_0085 0.62 -0.3
94,939 + PP_0085 0.70 +1.0
94,940 - PP_0085 0.70 -0.1
94,940 - PP_0085 0.70 -0.8
95,016 + PP_0085 0.86 -0.3
95,017 - PP_0085 0.86 -0.2
95,035 + PP_0085 0.90 -0.2
95,036 - PP_0085 0.90 +1.4
95,089 + -0.6
95,090 - -0.1
95,142 + PP_0086 0.33 -2.3
95,142 + PP_0086 0.33 +2.3
95,142 + PP_0086 0.33 -0.2
95,280 + -0.1
95,280 + -0.7
95,280 + -0.6
95,302 + -0.1
95,303 - +0.5
95,303 - +1.5
95,303 - +0.1
95,303 - -0.8
95,303 - +0.7
95,323 + -2.3
95,324 - -1.1
95,514 - PP_0087 0.64 +0.9
95,563 + PP_0087 0.83 +0.7
95,563 + PP_0087 0.83 -2.2
95,564 - PP_0087 0.83 -1.8
95,606 + +0.1
95,607 - +0.4
95,651 + +1.1
95,651 + +0.7
95,651 + -1.1
95,651 + -2.2
95,651 + +2.7
95,651 + +0.0
95,652 - -1.7
95,652 - +0.4
95,714 + +0.8
95,714 + -0.1
95,714 + -1.2
95,714 + -0.1
95,715 - -1.7
95,741 + +1.4
95,741 + +0.8
95,741 + -0.9
95,742 - +2.1
95,742 - +0.4
95,742 - +0.9
95,742 - +0.5
95,754 + +0.6
95,754 + -1.2
95,755 - +1.4
95,755 - -1.4
95,797 + PP_0088 0.12 -0.5
95,798 - PP_0088 0.12 +1.1
95,798 - PP_0088 0.12 -1.1
95,798 - PP_0088 0.12 +1.4
95,809 + PP_0088 0.13 -0.7
95,810 - PP_0088 0.13 +1.1
95,810 - PP_0088 0.13 -0.7
95,955 - PP_0088 0.27 -2.8
95,973 - PP_0088 0.29 -0.2
95,973 - PP_0088 0.29 -0.5
96,026 + PP_0088 0.34 -0.8
96,026 + PP_0088 0.34 +0.5
96,026 + PP_0088 0.34 -0.5
96,026 + PP_0088 0.34 -2.2
96,026 + PP_0088 0.34 -0.2
96,093 - PP_0088 0.41 +0.4
96,123 - PP_0088 0.44 -0.6
96,200 + PP_0088 0.52 -0.4
96,249 - PP_0088 0.57 -0.5
96,317 + PP_0088 0.63 -1.0
96,317 + PP_0088 0.63 -0.9
96,318 - PP_0088 0.63 -1.3
96,318 - PP_0088 0.63 -1.3
96,462 + PP_0088 0.78 +0.2
96,462 + +0.9
96,463 - PP_0088 0.78 +0.9
96,463 - PP_0088 0.78 -0.0
96,486 - PP_0088 0.80 +1.1
96,730 - -0.3
96,765 + -1.1
96,765 + +0.0
96,765 + -0.0
96,766 - -2.0
96,766 - -1.4
96,766 - -0.6
96,766 - -0.3
96,766 - -0.9
96,766 - -0.2
96,806 + +0.8
96,811 - -0.7
96,811 - +0.7
96,811 - +0.3
96,811 - +0.2
96,811 - +1.2
96,811 - -0.2
96,811 - +0.1
96,899 + PP_0089 0.15 -0.0
96,930 + PP_0089 0.22 +0.2
97,049 + PP_0089 0.50 +0.4
97,049 + PP_0089 0.50 -0.1
97,050 - PP_0089 0.50 -1.2
97,147 + PP_0089 0.73 +0.2
97,147 + PP_0089 0.73 -1.3
97,147 + PP_0089 0.73 -0.5
97,147 + PP_0089 0.73 +0.2
97,290 - +0.9
97,294 + +2.1
97,294 + -0.1
97,294 + +0.0
97,295 - -0.4
97,348 + PP_0090 0.25 -3.0
97,348 + PP_0090 0.25 +0.3
97,348 + PP_0090 0.25 -0.2
97,349 - PP_0090 0.25 +0.5
97,349 - PP_0090 0.25 +1.6
97,349 - PP_0090 0.25 +0.4
97,349 - PP_0090 0.25 -0.2
97,352 + PP_0090 0.26 -0.0
97,353 - PP_0090 0.26 -0.3
97,551 + -0.8
97,551 + +0.4
97,552 - +0.0
97,552 - -0.3
97,626 + +0.2
97,630 + +0.4
97,631 - -0.1
97,665 + PP_0091 0.14 +0.1
97,665 + PP_0091 0.14 -0.7
97,666 - PP_0091 0.14 -1.1
97,666 - PP_0091 0.14 -0.1
97,666 - PP_0091 0.14 +0.4
97,667 + PP_0091 0.14 -0.7
97,667 + PP_0091 0.14 -0.6
97,667 + PP_0091 0.14 +1.1
97,667 + PP_0091 0.14 -0.2
97,667 + PP_0091 0.14 -0.9
97,668 - PP_0091 0.15 -1.4
97,668 - PP_0091 0.15 -1.0
97,668 - PP_0091 0.15 -1.8
97,668 - PP_0091 0.15 +2.4
97,668 - PP_0091 0.15 -1.0
97,668 - PP_0091 0.15 -0.5
97,668 - PP_0091 0.15 -0.1
97,668 - PP_0091 0.15 -0.4

Or see this region's nucleotide sequence