Strain Fitness in Pseudomonas putida KT2440 around PP_0409

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_0408 and PP_0409 are separated by 95 nucleotidesPP_0409 and PP_0410 are separated by 10 nucleotidesPP_0410 and PP_0411 are separated by 295 nucleotides PP_0408: PP_0408 - conserved exported protein of unknown function, at 495,035 to 496,033 _0408 PP_0409: PP_0409 - Sensory box histidine kinase, at 496,129 to 498,516 _0409 PP_0410: PP_0410 - DNA-binding response regulator UhpA, at 498,527 to 499,156 _0410 PP_0411: PP_0411 - Polyamine ABC transporter, ATP-binding protein, at 499,452 to 500,576 _0411 Position (kb) 496 497 498 499Strain fitness (log2 ratio) -3 -2 -1 0 1 2at 495.139 kb on + strand, within PP_0408at 495.139 kb on + strand, within PP_0408at 495.207 kb on + strand, within PP_0408at 495.208 kb on - strand, within PP_0408at 495.208 kb on - strand, within PP_0408at 495.208 kb on - strand, within PP_0408at 495.208 kb on - strand, within PP_0408at 495.210 kb on + strand, within PP_0408at 495.210 kb on + strand, within PP_0408at 495.210 kb on + strand, within PP_0408at 495.210 kb on + strand, within PP_0408at 495.210 kb on + strand, within PP_0408at 495.210 kb on + strand, within PP_0408at 495.210 kb on + strand, within PP_0408at 495.210 kb on + strand, within PP_0408at 495.211 kb on - strand, within PP_0408at 495.211 kb on - strand, within PP_0408at 495.211 kb on - strand, within PP_0408at 495.211 kb on - strand, within PP_0408at 495.211 kb on - strand, within PP_0408at 495.214 kb on + strand, within PP_0408at 495.214 kb on + strand, within PP_0408at 495.308 kb on + strand, within PP_0408at 495.336 kb on + strand, within PP_0408at 495.337 kb on - strand, within PP_0408at 495.351 kb on + strand, within PP_0408at 495.361 kb on + strand, within PP_0408at 495.362 kb on - strand, within PP_0408at 495.378 kb on - strand, within PP_0408at 496.068 kb on + strandat 496.069 kb on - strandat 496.074 kb on + strandat 496.075 kb on - strandat 496.075 kb on - strandat 496.126 kb on + strandat 496.126 kb on + strandat 496.126 kb on + strandat 496.127 kb on - strandat 496.127 kb on - strandat 496.291 kb on + strandat 496.324 kb on + strandat 496.351 kb on - strandat 496.351 kb on - strandat 496.389 kb on + strand, within PP_0409at 496.389 kb on + strand, within PP_0409at 496.390 kb on - strand, within PP_0409at 496.390 kb on - strand, within PP_0409at 496.390 kb on - strand, within PP_0409at 496.490 kb on + strandat 496.637 kb on - strand, within PP_0409at 496.694 kb on + strand, within PP_0409at 496.694 kb on + strand, within PP_0409at 496.694 kb on + strand, within PP_0409at 496.694 kb on + strand, within PP_0409at 496.694 kb on + strand, within PP_0409at 496.695 kb on - strand, within PP_0409at 496.695 kb on - strand, within PP_0409at 496.695 kb on - strand, within PP_0409at 496.850 kb on + strand, within PP_0409at 496.924 kb on + strand, within PP_0409at 497.142 kb on + strand, within PP_0409at 497.280 kb on - strand, within PP_0409at 497.422 kb on + strand, within PP_0409at 497.423 kb on - strand, within PP_0409at 497.507 kb on + strand, within PP_0409at 497.507 kb on + strand, within PP_0409at 497.566 kb on + strand, within PP_0409at 497.567 kb on - strand, within PP_0409at 497.567 kb on - strand, within PP_0409at 497.568 kb on + strand, within PP_0409at 497.569 kb on - strand, within PP_0409at 497.569 kb on - strand, within PP_0409at 497.580 kb on + strand, within PP_0409at 497.672 kb on - strand, within PP_0409at 497.804 kb on + strand, within PP_0409at 497.805 kb on - strand, within PP_0409at 497.805 kb on - strand, within PP_0409at 497.819 kb on + strand, within PP_0409at 497.820 kb on - strand, within PP_0409at 498.090 kb on - strand, within PP_0409at 498.180 kb on + strand, within PP_0409at 498.181 kb on - strand, within PP_0409at 498.258 kb on + strand, within PP_0409at 498.312 kb on - strandat 498.326 kb on + strandat 498.326 kb on + strandat 498.327 kb on - strandat 498.327 kb on - strandat 498.515 kb on - strandat 498.515 kb on - strandat 498.538 kb on - strandat 498.538 kb on - strandat 498.678 kb on + strand, within PP_0410at 498.678 kb on + strand, within PP_0410at 498.896 kb on + strand, within PP_0410at 498.897 kb on - strand, within PP_0410at 498.898 kb on + strand, within PP_0410at 498.898 kb on + strand, within PP_0410at 498.898 kb on + strand, within PP_0410at 498.899 kb on - strand, within PP_0410at 498.899 kb on - strand, within PP_0410at 498.936 kb on + strand, within PP_0410at 498.937 kb on - strand, within PP_0410at 498.937 kb on - strand, within PP_0410at 499.130 kb on + strandat 499.131 kb on - strandat 499.131 kb on - strandat 499.131 kb on - strandat 499.131 kb on - strandat 499.131 kb on - strandat 499.131 kb on - strandat 499.165 kb on + strandat 499.166 kb on - strandat 499.166 kb on - strandat 499.166 kb on - strandat 499.166 kb on - strandat 499.166 kb on - strandat 499.192 kb on + strandat 499.193 kb on - strandat 499.193 kb on - strandat 499.239 kb on + strandat 499.240 kb on - strandat 499.240 kb on - strandat 499.340 kb on - strandat 499.340 kb on - strandat 499.340 kb on - strandat 499.378 kb on + strandat 499.410 kb on + strandat 499.411 kb on - strandat 499.422 kb on + strand

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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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495,139 + PP_0408 0.10 -0.5
495,139 + PP_0408 0.10 +0.5
495,207 + PP_0408 0.17 +0.6
495,208 - PP_0408 0.17 +0.1
495,208 - PP_0408 0.17 +2.2
495,208 - PP_0408 0.17 +0.6
495,208 - PP_0408 0.17 +1.4
495,210 + PP_0408 0.18 -1.3
495,210 + PP_0408 0.18 -2.5
495,210 + PP_0408 0.18 -0.8
495,210 + PP_0408 0.18 +0.5
495,210 + PP_0408 0.18 -1.7
495,210 + PP_0408 0.18 +1.2
495,210 + PP_0408 0.18 -0.4
495,210 + PP_0408 0.18 -0.2
495,211 - PP_0408 0.18 -0.9
495,211 - PP_0408 0.18 +1.0
495,211 - PP_0408 0.18 +0.4
495,211 - PP_0408 0.18 -0.7
495,211 - PP_0408 0.18 -0.0
495,214 + PP_0408 0.18 -1.2
495,214 + PP_0408 0.18 -0.4
495,308 + PP_0408 0.27 -1.2
495,336 + PP_0408 0.30 +0.4
495,337 - PP_0408 0.30 -0.1
495,351 + PP_0408 0.32 +0.5
495,361 + PP_0408 0.33 +0.2
495,362 - PP_0408 0.33 -0.5
495,378 - PP_0408 0.34 +2.4
496,068 + +0.2
496,069 - -0.6
496,074 + +0.0
496,075 - -0.2
496,075 - +0.5
496,126 + +0.2
496,126 + -1.5
496,126 + -1.5
496,127 - -0.3
496,127 - +0.1
496,291 + -2.5
496,324 + -1.8
496,351 - -0.6
496,351 - -0.7
496,389 + PP_0409 0.11 -1.8
496,389 + PP_0409 0.11 +0.6
496,390 - PP_0409 0.11 -0.9
496,390 - PP_0409 0.11 -0.4
496,390 - PP_0409 0.11 +0.6
496,490 + +2.4
496,637 - PP_0409 0.21 -0.3
496,694 + PP_0409 0.24 -1.6
496,694 + PP_0409 0.24 -1.0
496,694 + PP_0409 0.24 +0.6
496,694 + PP_0409 0.24 -2.3
496,694 + PP_0409 0.24 -1.0
496,695 - PP_0409 0.24 -1.0
496,695 - PP_0409 0.24 -1.7
496,695 - PP_0409 0.24 -1.0
496,850 + PP_0409 0.30 -2.3
496,924 + PP_0409 0.33 -2.2
497,142 + PP_0409 0.42 -1.3
497,280 - PP_0409 0.48 -0.5
497,422 + PP_0409 0.54 -1.9
497,423 - PP_0409 0.54 +1.4
497,507 + PP_0409 0.58 +0.2
497,507 + PP_0409 0.58 -1.5
497,566 + PP_0409 0.60 -1.5
497,567 - PP_0409 0.60 +0.9
497,567 - PP_0409 0.60 -2.7
497,568 + PP_0409 0.60 -2.4
497,569 - PP_0409 0.60 +0.0
497,569 - PP_0409 0.60 +0.0
497,580 + PP_0409 0.61 -2.3
497,672 - PP_0409 0.65 -1.0
497,804 + PP_0409 0.70 -2.2
497,805 - PP_0409 0.70 -0.2
497,805 - PP_0409 0.70 -1.5
497,819 + PP_0409 0.71 -2.9
497,820 - PP_0409 0.71 -0.2
498,090 - PP_0409 0.82 +0.4
498,180 + PP_0409 0.86 -1.3
498,181 - PP_0409 0.86 -0.1
498,258 + PP_0409 0.89 -1.4
498,312 - -1.6
498,326 + -2.6
498,326 + -1.2
498,327 - +0.1
498,327 - -0.2
498,515 - -0.0
498,515 - -0.8
498,538 - +1.7
498,538 - -0.3
498,678 + PP_0410 0.24 +0.3
498,678 + PP_0410 0.24 -0.1
498,896 + PP_0410 0.59 +0.1
498,897 - PP_0410 0.59 +0.4
498,898 + PP_0410 0.59 -1.3
498,898 + PP_0410 0.59 -0.1
498,898 + PP_0410 0.59 -0.2
498,899 - PP_0410 0.59 +0.3
498,899 - PP_0410 0.59 -0.6
498,936 + PP_0410 0.65 -1.5
498,937 - PP_0410 0.65 -1.7
498,937 - PP_0410 0.65 +0.9
499,130 + +1.0
499,131 - +0.2
499,131 - +0.0
499,131 - +0.0
499,131 - -0.5
499,131 - -1.2
499,131 - +0.1
499,165 + +0.4
499,166 - +0.8
499,166 - +1.1
499,166 - +0.6
499,166 - -0.6
499,166 - -0.1
499,192 + -0.1
499,193 - +0.1
499,193 - +0.4
499,239 + -0.6
499,240 - +1.2
499,240 - -1.2
499,340 - -0.3
499,340 - +0.4
499,340 - +1.6
499,378 + +0.2
499,410 + +0.3
499,411 - +0.3
499,422 + -0.3

Or see this region's nucleotide sequence