Strain Fitness in Pseudomonas putida KT2440 around PP_5374

Experiment: Parafilmed volatile agar plate with Trichoderma atroviridae IMI tmk3mutant

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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_5373 and PP_5374 are separated by 397 nucleotidesPP_5374 and PP_5375 are separated by 66 nucleotides PP_5373: PP_5373 - Rieske 2Fe-2S family protein, at 6,123,618 to 6,124,808 _5373 PP_5374: PP_5374 - Choline/carnitine/betaine transporter family protein, at 6,125,206 to 6,126,909 _5374 PP_5375: PP_5375 - Transcriptional regulator, LysR family, at 6,126,976 to 6,127,884 _5375 Position (kb) 6125 6126 6127Strain fitness (log2 ratio) -3 -2 -1 0 1 2 3at 6124.450 kb on + strand, within PP_5373at 6124.451 kb on - strand, within PP_5373at 6124.451 kb on - strand, within PP_5373at 6124.466 kb on - strand, within PP_5373at 6124.615 kb on + strand, within PP_5373at 6124.615 kb on + strand, within PP_5373at 6124.615 kb on + strand, within PP_5373at 6124.616 kb on - strand, within PP_5373at 6124.648 kb on - strand, within PP_5373at 6124.648 kb on - strand, within PP_5373at 6124.649 kb on + strand, within PP_5373at 6124.649 kb on + strand, within PP_5373at 6124.649 kb on + strand, within PP_5373at 6124.649 kb on + strand, within PP_5373at 6124.650 kb on - strand, within PP_5373at 6124.650 kb on - strand, within PP_5373at 6124.661 kb on + strand, within PP_5373at 6124.662 kb on - strand, within PP_5373at 6124.662 kb on - strand, within PP_5373at 6124.697 kb on - strandat 6124.745 kb on + strandat 6124.781 kb on + strandat 6124.800 kb on + strandat 6124.825 kb on + strandat 6124.825 kb on + strandat 6124.899 kb on - strandat 6124.899 kb on - strandat 6124.909 kb on + strandat 6124.910 kb on - strandat 6124.953 kb on + strandat 6124.954 kb on - strandat 6124.954 kb on - strandat 6124.959 kb on + strandat 6124.960 kb on - strandat 6124.963 kb on + strandat 6124.964 kb on - strandat 6125.030 kb on + strandat 6125.055 kb on + strandat 6125.056 kb on - strandat 6125.090 kb on - strandat 6125.090 kb on - strandat 6125.090 kb on - strandat 6125.090 kb on - strandat 6125.194 kb on - strandat 6125.273 kb on + strandat 6125.273 kb on + strandat 6125.274 kb on - strandat 6125.274 kb on - strandat 6125.274 kb on - strandat 6125.277 kb on - strandat 6125.410 kb on + strand, within PP_5374at 6125.410 kb on + strand, within PP_5374at 6125.411 kb on - strand, within PP_5374at 6125.411 kb on - strand, within PP_5374at 6125.411 kb on - strand, within PP_5374at 6125.436 kb on + strand, within PP_5374at 6125.436 kb on + strand, within PP_5374at 6125.436 kb on + strand, within PP_5374at 6125.437 kb on - strand, within PP_5374at 6125.437 kb on - strandat 6125.560 kb on + strand, within PP_5374at 6125.560 kb on + strand, within PP_5374at 6125.561 kb on - strand, within PP_5374at 6125.613 kb on + strand, within PP_5374at 6125.613 kb on + strand, within PP_5374at 6125.614 kb on - strand, within PP_5374at 6125.622 kb on + strand, within PP_5374at 6125.623 kb on - strand, within PP_5374at 6125.623 kb on - strand, within PP_5374at 6125.627 kb on + strand, within PP_5374at 6125.628 kb on - strand, within PP_5374at 6125.655 kb on + strand, within PP_5374at 6125.655 kb on + strand, within PP_5374at 6125.686 kb on + strand, within PP_5374at 6125.687 kb on - strand, within PP_5374at 6125.758 kb on + strand, within PP_5374at 6125.758 kb on + strand, within PP_5374at 6125.758 kb on + strand, within PP_5374at 6125.758 kb on + strand, within PP_5374at 6125.758 kb on + strandat 6125.758 kb on + strand, within PP_5374at 6125.759 kb on - strand, within PP_5374at 6125.759 kb on - strand, within PP_5374at 6125.759 kb on - strand, within PP_5374at 6125.922 kb on + strand, within PP_5374at 6125.931 kb on + strand, within PP_5374at 6125.932 kb on - strand, within PP_5374at 6125.932 kb on - strand, within PP_5374at 6125.935 kb on - strand, within PP_5374at 6125.935 kb on - strand, within PP_5374at 6125.991 kb on + strand, within PP_5374at 6125.991 kb on + strand, within PP_5374at 6125.991 kb on + strand, within PP_5374at 6125.991 kb on + strand, within PP_5374at 6125.991 kb on + strand, within PP_5374at 6125.992 kb on - strand, within PP_5374at 6125.992 kb on - strand, within PP_5374at 6125.992 kb on - strand, within PP_5374at 6125.992 kb on - strand, within PP_5374at 6125.992 kb on - strand, within PP_5374at 6126.046 kb on + strand, within PP_5374at 6126.046 kb on + strand, within PP_5374at 6126.046 kb on + strand, within PP_5374at 6126.082 kb on + strand, within PP_5374at 6126.082 kb on + strand, within PP_5374at 6126.083 kb on - strand, within PP_5374at 6126.083 kb on - strand, within PP_5374at 6126.095 kb on + strand, within PP_5374at 6126.095 kb on + strand, within PP_5374at 6126.096 kb on - strand, within PP_5374at 6126.096 kb on - strandat 6126.096 kb on - strand, within PP_5374at 6126.163 kb on + strand, within PP_5374at 6126.163 kb on + strand, within PP_5374at 6126.164 kb on - strand, within PP_5374at 6126.164 kb on - strand, within PP_5374at 6126.394 kb on + strand, within PP_5374at 6126.394 kb on + strand, within PP_5374at 6126.394 kb on + strand, within PP_5374at 6126.394 kb on + strand, within PP_5374at 6126.395 kb on - strand, within PP_5374at 6126.395 kb on - strand, within PP_5374at 6126.395 kb on - strand, within PP_5374at 6126.411 kb on - strand, within PP_5374at 6126.411 kb on - strand, within PP_5374at 6126.411 kb on - strand, within PP_5374at 6126.411 kb on - strand, within PP_5374at 6126.510 kb on + strand, within PP_5374at 6126.510 kb on + strand, within PP_5374at 6126.510 kb on + strand, within PP_5374at 6126.526 kb on + strand, within PP_5374at 6126.526 kb on + strand, within PP_5374at 6126.526 kb on + strand, within PP_5374at 6126.527 kb on - strand, within PP_5374at 6126.527 kb on - strand, within PP_5374at 6126.527 kb on - strand, within PP_5374at 6126.567 kb on + strand, within PP_5374at 6126.568 kb on - strand, within PP_5374at 6126.568 kb on - strand, within PP_5374at 6126.568 kb on - strand, within PP_5374at 6126.639 kb on + strand, within PP_5374at 6126.639 kb on + strand, within PP_5374at 6126.639 kb on + strand, within PP_5374at 6126.639 kb on + strand, within PP_5374at 6126.639 kb on + strand, within PP_5374at 6126.639 kb on + strand, within PP_5374at 6126.639 kb on + strand, within PP_5374at 6126.640 kb on - strand, within PP_5374at 6126.640 kb on - strand, within PP_5374at 6126.640 kb on - strand, within PP_5374at 6126.640 kb on - strand, within PP_5374at 6126.640 kb on - strand, within PP_5374at 6126.640 kb on - strand, within PP_5374at 6126.640 kb on - strand, within PP_5374at 6126.640 kb on - strand, within PP_5374at 6126.642 kb on - strand, within PP_5374at 6126.642 kb on - strand, within PP_5374at 6126.642 kb on - strand, within PP_5374at 6126.736 kb on - strand, within PP_5374at 6126.736 kb on - strand, within PP_5374at 6126.739 kb on + strandat 6126.739 kb on + strandat 6126.739 kb on + strandat 6126.739 kb on + strandat 6126.740 kb on - strandat 6126.740 kb on - strandat 6126.740 kb on - strandat 6126.790 kb on - strandat 6126.790 kb on - strandat 6126.813 kb on + strandat 6126.813 kb on + strandat 6126.813 kb on + strandat 6126.814 kb on - strandat 6126.814 kb on - strandat 6126.814 kb on - strandat 6126.814 kb on - strandat 6126.814 kb on - strandat 6126.814 kb on - strandat 6126.814 kb on - strandat 6126.814 kb on - strandat 6126.815 kb on + strandat 6126.879 kb on + strandat 6126.880 kb on - strandat 6126.880 kb on - strandat 6126.880 kb on - strandat 6126.908 kb on - strandat 6126.913 kb on - strandat 6126.913 kb on - strandat 6126.978 kb on - strandat 6127.090 kb on + strand, within PP_5375at 6127.090 kb on + strand, within PP_5375at 6127.091 kb on - strand, within PP_5375at 6127.091 kb on - strand, within PP_5375at 6127.091 kb on - strand, within PP_5375at 6127.197 kb on + strand, within PP_5375at 6127.198 kb on - strand, within PP_5375at 6127.202 kb on + strand, within PP_5375at 6127.202 kb on + strand, within PP_5375at 6127.202 kb on + strand, within PP_5375at 6127.203 kb on - strand, within PP_5375at 6127.276 kb on + strand, within PP_5375at 6127.276 kb on + strandat 6127.277 kb on - strand, within PP_5375at 6127.314 kb on + strand, within PP_5375at 6127.314 kb on + strand, within PP_5375at 6127.314 kb on + strand, within PP_5375at 6127.315 kb on - strand, within PP_5375at 6127.315 kb on - strand, within PP_5375at 6127.446 kb on - strand, within PP_5375at 6127.446 kb on - strand, within PP_5375at 6127.446 kb on - strand, within PP_5375at 6127.446 kb on - strand, within PP_5375at 6127.475 kb on + strand, within PP_5375at 6127.621 kb on + strand, within PP_5375at 6127.621 kb on + strand, within PP_5375at 6127.621 kb on + strand, within PP_5375at 6127.621 kb on + strand, within PP_5375at 6127.621 kb on + strand, within PP_5375at 6127.621 kb on + strand, within PP_5375at 6127.622 kb on - strand, within PP_5375at 6127.622 kb on - strand, within PP_5375at 6127.622 kb on - strand, within PP_5375at 6127.674 kb on - strand, within PP_5375at 6127.674 kb on - strand, within PP_5375at 6127.677 kb on - strand, within PP_5375at 6127.707 kb on + strand, within PP_5375at 6127.717 kb on - strand, within PP_5375at 6127.727 kb on - strand, within PP_5375at 6127.742 kb on + strand, within PP_5375at 6127.742 kb on + strand, within PP_5375at 6127.770 kb on + strand, within PP_5375at 6127.770 kb on + strand, within PP_5375at 6127.770 kb on + strand, within PP_5375at 6127.907 kb on + strand

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Per-strain Table

Position Strand Gene LocusTag Fraction Parafilmed volatile agar plate with Trichoderma atroviridae IMI tmk3mutant
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6,124,450 + PP_5373 0.70 -0.4
6,124,451 - PP_5373 0.70 +0.4
6,124,451 - PP_5373 0.70 -1.3
6,124,466 - PP_5373 0.71 -0.5
6,124,615 + PP_5373 0.84 +0.7
6,124,615 + PP_5373 0.84 +1.6
6,124,615 + PP_5373 0.84 -0.4
6,124,616 - PP_5373 0.84 -2.0
6,124,648 - PP_5373 0.86 -0.3
6,124,648 - PP_5373 0.86 +0.6
6,124,649 + PP_5373 0.87 +1.5
6,124,649 + PP_5373 0.87 -1.1
6,124,649 + PP_5373 0.87 +1.2
6,124,649 + PP_5373 0.87 -0.4
6,124,650 - PP_5373 0.87 -3.3
6,124,650 - PP_5373 0.87 -1.9
6,124,661 + PP_5373 0.88 -0.6
6,124,662 - PP_5373 0.88 -0.1
6,124,662 - PP_5373 0.88 -0.5
6,124,697 - +1.1
6,124,745 + +1.0
6,124,781 + -0.6
6,124,800 + +2.9
6,124,825 + -0.6
6,124,825 + +1.0
6,124,899 - +0.9
6,124,899 - -0.4
6,124,909 + -0.9
6,124,910 - +1.6
6,124,953 + -1.4
6,124,954 - +1.4
6,124,954 - +0.4
6,124,959 + +1.1
6,124,960 - -2.5
6,124,963 + -1.6
6,124,964 - -3.1
6,125,030 + -0.2
6,125,055 + +0.9
6,125,056 - -2.5
6,125,090 - +0.6
6,125,090 - -0.0
6,125,090 - -2.2
6,125,090 - +1.2
6,125,194 - -2.4
6,125,273 + -2.0
6,125,273 + +0.3
6,125,274 - -0.2
6,125,274 - +0.5
6,125,274 - +0.6
6,125,277 - +0.7
6,125,410 + PP_5374 0.12 +1.0
6,125,410 + PP_5374 0.12 -0.4
6,125,411 - PP_5374 0.12 -3.7
6,125,411 - PP_5374 0.12 +0.5
6,125,411 - PP_5374 0.12 -1.0
6,125,436 + PP_5374 0.13 +0.5
6,125,436 + PP_5374 0.13 +0.5
6,125,436 + PP_5374 0.13 +0.2
6,125,437 - PP_5374 0.14 +0.8
6,125,437 - +1.7
6,125,560 + PP_5374 0.21 +1.0
6,125,560 + PP_5374 0.21 +1.1
6,125,561 - PP_5374 0.21 +0.5
6,125,613 + PP_5374 0.24 -0.9
6,125,613 + PP_5374 0.24 -0.1
6,125,614 - PP_5374 0.24 -1.3
6,125,622 + PP_5374 0.24 -0.0
6,125,623 - PP_5374 0.24 -0.0
6,125,623 - PP_5374 0.24 +0.5
6,125,627 + PP_5374 0.25 +1.8
6,125,628 - PP_5374 0.25 -0.6
6,125,655 + PP_5374 0.26 -0.4
6,125,655 + PP_5374 0.26 -0.8
6,125,686 + PP_5374 0.28 +0.0
6,125,687 - PP_5374 0.28 -0.3
6,125,758 + PP_5374 0.32 -1.9
6,125,758 + PP_5374 0.32 -1.3
6,125,758 + PP_5374 0.32 -0.4
6,125,758 + PP_5374 0.32 -1.9
6,125,758 + +0.7
6,125,758 + PP_5374 0.32 -0.1
6,125,759 - PP_5374 0.32 +0.9
6,125,759 - PP_5374 0.32 -0.9
6,125,759 - PP_5374 0.32 -2.2
6,125,922 + PP_5374 0.42 -3.3
6,125,931 + PP_5374 0.43 +0.2
6,125,932 - PP_5374 0.43 -1.1
6,125,932 - PP_5374 0.43 -2.7
6,125,935 - PP_5374 0.43 -1.2
6,125,935 - PP_5374 0.43 +0.8
6,125,991 + PP_5374 0.46 -1.7
6,125,991 + PP_5374 0.46 -0.1
6,125,991 + PP_5374 0.46 -2.6
6,125,991 + PP_5374 0.46 -1.3
6,125,991 + PP_5374 0.46 +0.3
6,125,992 - PP_5374 0.46 -3.3
6,125,992 - PP_5374 0.46 +0.5
6,125,992 - PP_5374 0.46 -0.2
6,125,992 - PP_5374 0.46 +1.0
6,125,992 - PP_5374 0.46 +0.1
6,126,046 + PP_5374 0.49 +0.0
6,126,046 + PP_5374 0.49 -0.7
6,126,046 + PP_5374 0.49 +1.3
6,126,082 + PP_5374 0.51 -0.6
6,126,082 + PP_5374 0.51 +0.3
6,126,083 - PP_5374 0.51 +0.4
6,126,083 - PP_5374 0.51 -2.0
6,126,095 + PP_5374 0.52 -0.9
6,126,095 + PP_5374 0.52 -1.3
6,126,096 - PP_5374 0.52 -1.9
6,126,096 - +3.7
6,126,096 - PP_5374 0.52 +1.8
6,126,163 + PP_5374 0.56 -1.7
6,126,163 + PP_5374 0.56 -1.9
6,126,164 - PP_5374 0.56 +2.4
6,126,164 - PP_5374 0.56 -0.8
6,126,394 + PP_5374 0.70 +0.2
6,126,394 + PP_5374 0.70 -1.5
6,126,394 + PP_5374 0.70 -3.6
6,126,394 + PP_5374 0.70 -0.4
6,126,395 - PP_5374 0.70 +0.0
6,126,395 - PP_5374 0.70 +0.8
6,126,395 - PP_5374 0.70 +0.4
6,126,411 - PP_5374 0.71 -1.9
6,126,411 - PP_5374 0.71 -2.9
6,126,411 - PP_5374 0.71 +1.8
6,126,411 - PP_5374 0.71 -1.8
6,126,510 + PP_5374 0.77 -2.3
6,126,510 + PP_5374 0.77 -1.3
6,126,510 + PP_5374 0.77 -1.2
6,126,526 + PP_5374 0.77 -1.7
6,126,526 + PP_5374 0.77 -0.6
6,126,526 + PP_5374 0.77 -1.0
6,126,527 - PP_5374 0.78 +0.1
6,126,527 - PP_5374 0.78 -0.6
6,126,527 - PP_5374 0.78 -0.4
6,126,567 + PP_5374 0.80 -1.9
6,126,568 - PP_5374 0.80 +0.3
6,126,568 - PP_5374 0.80 +1.2
6,126,568 - PP_5374 0.80 +0.5
6,126,639 + PP_5374 0.84 -0.5
6,126,639 + PP_5374 0.84 -0.8
6,126,639 + PP_5374 0.84 +1.3
6,126,639 + PP_5374 0.84 -1.5
6,126,639 + PP_5374 0.84 -0.0
6,126,639 + PP_5374 0.84 +1.2
6,126,639 + PP_5374 0.84 +0.9
6,126,640 - PP_5374 0.84 -0.9
6,126,640 - PP_5374 0.84 -1.0
6,126,640 - PP_5374 0.84 -0.6
6,126,640 - PP_5374 0.84 -1.8
6,126,640 - PP_5374 0.84 -1.4
6,126,640 - PP_5374 0.84 -0.5
6,126,640 - PP_5374 0.84 +0.4
6,126,640 - PP_5374 0.84 -1.6
6,126,642 - PP_5374 0.84 +0.7
6,126,642 - PP_5374 0.84 -1.8
6,126,642 - PP_5374 0.84 +0.9
6,126,736 - PP_5374 0.90 +1.9
6,126,736 - PP_5374 0.90 +0.6
6,126,739 + -1.8
6,126,739 + +1.0
6,126,739 + +0.4
6,126,739 + +0.4
6,126,740 - +0.4
6,126,740 - -1.4
6,126,740 - +2.1
6,126,790 - +1.0
6,126,790 - +0.5
6,126,813 + -2.3
6,126,813 + -0.6
6,126,813 + -1.4
6,126,814 - -0.0
6,126,814 - -2.0
6,126,814 - -0.0
6,126,814 - -1.1
6,126,814 - +1.2
6,126,814 - -1.9
6,126,814 - +0.7
6,126,814 - -2.0
6,126,815 + +0.3
6,126,879 + -2.0
6,126,880 - -0.9
6,126,880 - +0.3
6,126,880 - +1.6
6,126,908 - +1.6
6,126,913 - +0.2
6,126,913 - -0.7
6,126,978 - -0.4
6,127,090 + PP_5375 0.13 -2.1
6,127,090 + PP_5375 0.13 +0.1
6,127,091 - PP_5375 0.13 -1.3
6,127,091 - PP_5375 0.13 -0.6
6,127,091 - PP_5375 0.13 +1.1
6,127,197 + PP_5375 0.24 -0.5
6,127,198 - PP_5375 0.24 +0.3
6,127,202 + PP_5375 0.25 -1.5
6,127,202 + PP_5375 0.25 +2.8
6,127,202 + PP_5375 0.25 -1.0
6,127,203 - PP_5375 0.25 +0.3
6,127,276 + PP_5375 0.33 +0.9
6,127,276 + +0.3
6,127,277 - PP_5375 0.33 +0.3
6,127,314 + PP_5375 0.37 +0.3
6,127,314 + PP_5375 0.37 +0.8
6,127,314 + PP_5375 0.37 -0.0
6,127,315 - PP_5375 0.37 -2.3
6,127,315 - PP_5375 0.37 +0.4
6,127,446 - PP_5375 0.52 +1.4
6,127,446 - PP_5375 0.52 +0.1
6,127,446 - PP_5375 0.52 +0.5
6,127,446 - PP_5375 0.52 -2.0
6,127,475 + PP_5375 0.55 -1.2
6,127,621 + PP_5375 0.71 -2.1
6,127,621 + PP_5375 0.71 -2.0
6,127,621 + PP_5375 0.71 -1.0
6,127,621 + PP_5375 0.71 +0.6
6,127,621 + PP_5375 0.71 -0.6
6,127,621 + PP_5375 0.71 +0.4
6,127,622 - PP_5375 0.71 +2.1
6,127,622 - PP_5375 0.71 +0.5
6,127,622 - PP_5375 0.71 +1.8
6,127,674 - PP_5375 0.77 +1.7
6,127,674 - PP_5375 0.77 -1.9
6,127,677 - PP_5375 0.77 -0.6
6,127,707 + PP_5375 0.80 -1.8
6,127,717 - PP_5375 0.82 +0.7
6,127,727 - PP_5375 0.83 -0.6
6,127,742 + PP_5375 0.84 -0.5
6,127,742 + PP_5375 0.84 -1.4
6,127,770 + PP_5375 0.87 +0.2
6,127,770 + PP_5375 0.87 +1.0
6,127,770 + PP_5375 0.87 +1.3
6,127,907 + -0.4

Or see this region's nucleotide sequence