Strain Fitness in Pseudomonas putida KT2440 around PP_0012

Experiment: 72hr 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_0011 and PP_0012 are separated by 15 nucleotidesPP_0012 and PP_0013 are separated by 4 nucleotides PP_0011: PP_0011 - DNA polymerase III subunit beta, at 11,103 to 12,206 _0011 PP_0012: PP_0012 - DNA replication and repair protein, at 12,222 to 13,325 _0012 PP_0013: PP_0013 - DNA gyrase subunit B, at 13,330 to 15,750 _0013 Position (kb) 12 13 14Strain fitness (log2 ratio) -2 -1 0 1 2 3 4at 12.211 kb on + strandat 12.211 kb on + strandat 12.236 kb on + strandat 12.236 kb on + strandat 12.236 kb on + strandat 12.280 kb on + strandat 12.280 kb on + strandat 12.280 kb on + strandat 12.281 kb on - strandat 12.307 kb on - strandat 12.401 kb on + strand, within PP_0012at 12.408 kb on + strand, within PP_0012at 12.425 kb on + strand, within PP_0012at 12.425 kb on + strand, within PP_0012at 12.425 kb on + strand, within PP_0012at 12.425 kb on + strand, within PP_0012at 12.425 kb on + strand, within PP_0012at 12.426 kb on - strand, within PP_0012at 12.426 kb on - strand, within PP_0012at 12.426 kb on - strand, within PP_0012at 12.426 kb on - strand, within PP_0012at 12.462 kb on - strand, within PP_0012at 12.503 kb on + strandat 12.503 kb on + strand, within PP_0012at 12.503 kb on + strand, within PP_0012at 12.504 kb on - strand, within PP_0012at 12.504 kb on - strand, within PP_0012at 12.504 kb on - strand, within PP_0012at 12.504 kb on - strand, within PP_0012at 12.504 kb on - strand, within PP_0012at 12.504 kb on - strand, within PP_0012at 12.504 kb on - strand, within PP_0012at 12.504 kb on - strand, within PP_0012at 12.504 kb on - strand, within PP_0012at 12.504 kb on - strand, within PP_0012at 12.556 kb on + strand, within PP_0012at 12.556 kb on + strand, within PP_0012at 12.556 kb on + strand, within PP_0012at 12.728 kb on + strand, within PP_0012at 12.885 kb on + strand, within PP_0012at 12.965 kb on + strand, within PP_0012at 13.118 kb on + strand, within PP_0012at 13.118 kb on + strand, within PP_0012at 13.118 kb on + strand, within PP_0012at 13.118 kb on + strand, within PP_0012at 13.118 kb on + strand, within PP_0012at 13.118 kb on + strand, within PP_0012at 13.118 kb on + strand, within PP_0012at 13.122 kb on + strand, within PP_0012at 13.122 kb on + strand, within PP_0012at 13.122 kb on + strand, within PP_0012at 13.122 kb on + strand, within PP_0012at 13.222 kb on + strandat 13.222 kb on + strand

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Per-strain Table

Position Strand Gene LocusTag Fraction 72hr timepoint from 1L M9/1% dextrose BATCH fermentation in 2L Sartorius Biostat reactor kept at 10% DO.
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12,211 + +3.9
12,211 + +2.3
12,236 + -0.1
12,236 + -1.9
12,236 + +0.4
12,280 + +0.1
12,280 + +0.6
12,280 + +0.4
12,281 - +2.3
12,307 - -0.0
12,401 + PP_0012 0.16 -1.0
12,408 + PP_0012 0.17 -0.6
12,425 + PP_0012 0.18 -0.5
12,425 + PP_0012 0.18 +1.4
12,425 + PP_0012 0.18 +0.1
12,425 + PP_0012 0.18 +2.3
12,425 + PP_0012 0.18 +1.4
12,426 - PP_0012 0.18 -1.1
12,426 - PP_0012 0.18 +1.2
12,426 - PP_0012 0.18 +2.9
12,426 - PP_0012 0.18 -0.9
12,462 - PP_0012 0.22 -0.6
12,503 + +1.3
12,503 + PP_0012 0.25 +0.6
12,503 + PP_0012 0.25 +1.3
12,504 - PP_0012 0.26 +1.4
12,504 - PP_0012 0.26 -0.2
12,504 - PP_0012 0.26 +0.4
12,504 - PP_0012 0.26 -0.5
12,504 - PP_0012 0.26 -0.3
12,504 - PP_0012 0.26 -0.2
12,504 - PP_0012 0.26 -2.7
12,504 - PP_0012 0.26 +0.2
12,504 - PP_0012 0.26 -0.7
12,504 - PP_0012 0.26 +1.6
12,556 + PP_0012 0.30 -0.8
12,556 + PP_0012 0.30 -0.4
12,556 + PP_0012 0.30 -0.5
12,728 + PP_0012 0.46 +0.1
12,885 + PP_0012 0.60 -0.7
12,965 + PP_0012 0.67 +0.1
13,118 + PP_0012 0.81 +2.3
13,118 + PP_0012 0.81 -0.6
13,118 + PP_0012 0.81 +0.6
13,118 + PP_0012 0.81 +0.7
13,118 + PP_0012 0.81 +1.4
13,118 + PP_0012 0.81 +1.1
13,118 + PP_0012 0.81 -0.2
13,122 + PP_0012 0.82 +2.3
13,122 + PP_0012 0.82 +0.3
13,122 + PP_0012 0.82 +3.9
13,122 + PP_0012 0.82 -1.4
13,222 + -0.9
13,222 + +0.9

Or see this region's nucleotide sequence