Strain Fitness in Pseudomonas putida KT2440 around PP_3948

Experiment: Growth at pH6 and (C) D-Glucose

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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_3946 and PP_3947 are separated by 441 nucleotidesPP_3947 and PP_3948 overlap by 4 nucleotidesPP_3948 and PP_3949 are separated by 3 nucleotidesPP_3949 and PP_3950 are separated by 204 nucleotides PP_3946: PP_3946 - HTH-type transcriptional repressor NicR, at 4,449,009 to 4,449,485 _3946 PP_3947: PP_3947 - nicotinate dehydrogenase subunit A, at 4,449,927 to 4,450,400 _3947 PP_3948: PP_3948 - nicotinate dehydrogenase subunit B (EC 1.17.2.1) (from data), at 4,450,397 to 4,453,960 _3948 PP_3949: PP_3949 - HTH-type transcriptional repressor NicS, at 4,453,964 to 4,454,602 _3949 PP_3950: PP_3950 - Methyl-accepting chemotaxis transducer, at 4,454,807 to 4,456,984 _3950 Position (kb) 4450 4451 4452 4453 4454Strain fitness (log2 ratio) -4 -3 -2 -1 0 1 2 3 4at 4449.441 kb on + strandat 4449.680 kb on - strandat 4449.680 kb on - strandat 4449.689 kb on + strandat 4449.690 kb on - strandat 4449.701 kb on + strandat 4449.800 kb on + strandat 4449.800 kb on + strandat 4449.801 kb on - strandat 4449.801 kb on - strandat 4449.801 kb on - strandat 4449.801 kb on - strandat 4449.801 kb on - strandat 4449.801 kb on - strandat 4449.801 kb on - strandat 4449.801 kb on - strandat 4449.801 kb on - strandat 4449.851 kb on + strandat 4449.858 kb on + strandat 4449.858 kb on + strandat 4449.858 kb on + strandat 4449.858 kb on + strandat 4449.859 kb on - strandat 4449.859 kb on - strandat 4449.925 kb on + strandat 4449.926 kb on - strandat 4449.926 kb on - strandat 4449.926 kb on - strandat 4449.926 kb on - strandat 4450.073 kb on + strand, within PP_3947at 4450.073 kb on + strand, within PP_3947at 4450.074 kb on - strand, within PP_3947at 4450.074 kb on - strand, within PP_3947at 4450.142 kb on + strand, within PP_3947at 4450.142 kb on + strand, within PP_3947at 4450.143 kb on - strand, within PP_3947at 4450.231 kb on - strand, within PP_3947at 4450.231 kb on - strand, within PP_3947at 4450.231 kb on - strand, within PP_3947at 4450.513 kb on + strandat 4450.513 kb on + strandat 4450.513 kb on + strandat 4450.513 kb on + strandat 4450.514 kb on - strandat 4450.571 kb on + strandat 4450.572 kb on - strandat 4450.613 kb on - strandat 4450.613 kb on - strandat 4450.782 kb on - strand, within PP_3948at 4450.782 kb on - strand, within PP_3948at 4450.782 kb on - strand, within PP_3948at 4450.956 kb on - strand, within PP_3948at 4450.986 kb on + strand, within PP_3948at 4450.986 kb on + strand, within PP_3948at 4450.986 kb on + strand, within PP_3948at 4451.021 kb on + strand, within PP_3948at 4451.021 kb on + strand, within PP_3948at 4451.022 kb on - strand, within PP_3948at 4451.022 kb on - strand, within PP_3948at 4451.079 kb on - strand, within PP_3948at 4451.284 kb on + strand, within PP_3948at 4451.285 kb on - strand, within PP_3948at 4451.396 kb on + strand, within PP_3948at 4451.397 kb on - strand, within PP_3948at 4451.408 kb on + strand, within PP_3948at 4451.486 kb on - strand, within PP_3948at 4451.582 kb on + strand, within PP_3948at 4451.583 kb on - strand, within PP_3948at 4451.778 kb on - strand, within PP_3948at 4451.885 kb on + strand, within PP_3948at 4451.886 kb on - strand, within PP_3948at 4451.987 kb on + strand, within PP_3948at 4451.988 kb on - strand, within PP_3948at 4451.988 kb on - strand, within PP_3948at 4451.988 kb on - strand, within PP_3948at 4452.171 kb on - strand, within PP_3948at 4452.181 kb on + strand, within PP_3948at 4452.181 kb on + strand, within PP_3948at 4452.182 kb on - strand, within PP_3948at 4452.182 kb on - strand, within PP_3948at 4452.862 kb on + strand, within PP_3948at 4452.907 kb on + strand, within PP_3948at 4452.907 kb on + strand, within PP_3948at 4452.907 kb on + strand, within PP_3948at 4452.926 kb on + strand, within PP_3948at 4452.926 kb on + strand, within PP_3948at 4452.926 kb on + strand, within PP_3948at 4452.926 kb on + strand, within PP_3948at 4452.927 kb on - strand, within PP_3948at 4452.927 kb on - strand, within PP_3948at 4452.938 kb on - strand, within PP_3948at 4452.938 kb on - strand, within PP_3948at 4453.009 kb on + strand, within PP_3948at 4453.010 kb on - strand, within PP_3948at 4453.010 kb on - strand, within PP_3948at 4453.010 kb on - strand, within PP_3948at 4453.049 kb on + strand, within PP_3948at 4453.049 kb on + strand, within PP_3948at 4453.094 kb on + strand, within PP_3948at 4453.094 kb on + strand, within PP_3948at 4453.094 kb on + strand, within PP_3948at 4453.094 kb on + strand, within PP_3948at 4453.095 kb on - strand, within PP_3948at 4453.095 kb on - strand, within PP_3948at 4453.100 kb on + strand, within PP_3948at 4453.262 kb on + strand, within PP_3948at 4453.263 kb on - strand, within PP_3948at 4453.343 kb on + strand, within PP_3948at 4453.343 kb on + strand, within PP_3948at 4453.343 kb on + strand, within PP_3948at 4453.344 kb on - strand, within PP_3948at 4453.439 kb on + strand, within PP_3948at 4453.439 kb on + strand, within PP_3948at 4453.440 kb on - strand, within PP_3948at 4453.811 kb on + strandat 4453.811 kb on + strandat 4453.868 kb on + strandat 4454.081 kb on - strand, within PP_3949at 4454.082 kb on + strand, within PP_3949at 4454.082 kb on + strand, within PP_3949at 4454.082 kb on + strand, within PP_3949at 4454.083 kb on - strand, within PP_3949at 4454.083 kb on - strand, within PP_3949at 4454.083 kb on - strand, within PP_3949at 4454.083 kb on - strand, within PP_3949at 4454.088 kb on + strand, within PP_3949at 4454.112 kb on + strand, within PP_3949at 4454.131 kb on + strand, within PP_3949at 4454.131 kb on + strandat 4454.132 kb on - strand, within PP_3949at 4454.132 kb on - strand, within PP_3949at 4454.295 kb on + strand, within PP_3949at 4454.295 kb on + strand, within PP_3949at 4454.295 kb on + strand, within PP_3949at 4454.295 kb on + strand, within PP_3949at 4454.295 kb on + strand, within PP_3949at 4454.295 kb on + strand, within PP_3949at 4454.298 kb on + strand, within PP_3949at 4454.298 kb on + strand, within PP_3949at 4454.298 kb on + strand, within PP_3949at 4454.298 kb on + strand, within PP_3949at 4454.299 kb on - strand, within PP_3949at 4454.299 kb on - strand, within PP_3949at 4454.299 kb on - strand, within PP_3949at 4454.391 kb on + strand, within PP_3949at 4454.391 kb on + strand, within PP_3949at 4454.391 kb on + strand, within PP_3949at 4454.392 kb on - strand, within PP_3949at 4454.392 kb on - strand, within PP_3949at 4454.392 kb on - strand, within PP_3949at 4454.392 kb on - strand, within PP_3949at 4454.392 kb on - strand, within PP_3949at 4454.392 kb on - strand, within PP_3949at 4454.392 kb on - strand, within PP_3949at 4454.392 kb on - strand, within PP_3949at 4454.392 kb on - strand, within PP_3949at 4454.392 kb on - strand, within PP_3949at 4454.392 kb on - strand, within PP_3949at 4454.442 kb on + strand, within PP_3949at 4454.443 kb on - strand, within PP_3949at 4454.443 kb on - strand, within PP_3949at 4454.445 kb on + strand, within PP_3949at 4454.445 kb on + strand, within PP_3949at 4454.445 kb on + strand, within PP_3949at 4454.445 kb on + strand, within PP_3949at 4454.445 kb on + strand, within PP_3949at 4454.445 kb on + strand, within PP_3949at 4454.445 kb on + strand, within PP_3949at 4454.445 kb on + strand, within PP_3949at 4454.446 kb on - strand, within PP_3949at 4454.446 kb on - strand, within PP_3949at 4454.446 kb on - strand, within PP_3949at 4454.446 kb on - strand, within PP_3949at 4454.446 kb on - strand, within PP_3949at 4454.446 kb on - strand, within PP_3949at 4454.446 kb on - strand, within PP_3949at 4454.446 kb on - strand, within PP_3949at 4454.545 kb on + strandat 4454.545 kb on + strandat 4454.546 kb on - strandat 4454.546 kb on - strandat 4454.546 kb on - strandat 4454.755 kb on + strandat 4454.756 kb on - strand

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Per-strain Table

Position Strand Gene LocusTag Fraction Growth at pH6 and (C) D-Glucose
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4,449,441 + +1.6
4,449,680 - -1.0
4,449,680 - -0.2
4,449,689 + +1.0
4,449,690 - +1.0
4,449,701 + +0.7
4,449,800 + -1.2
4,449,800 + -1.3
4,449,801 - -0.7
4,449,801 - +0.2
4,449,801 - +2.3
4,449,801 - -2.3
4,449,801 - -0.5
4,449,801 - -1.6
4,449,801 - +0.2
4,449,801 - -1.5
4,449,801 - -3.4
4,449,851 + -3.0
4,449,858 + -0.2
4,449,858 + -2.6
4,449,858 + +0.9
4,449,858 + -2.9
4,449,859 - +2.5
4,449,859 - -0.3
4,449,925 + -0.4
4,449,926 - -2.0
4,449,926 - +0.4
4,449,926 - -1.4
4,449,926 - -0.2
4,450,073 + PP_3947 0.31 -0.2
4,450,073 + PP_3947 0.31 -3.5
4,450,074 - PP_3947 0.31 -3.2
4,450,074 - PP_3947 0.31 +1.3
4,450,142 + PP_3947 0.45 -1.6
4,450,142 + PP_3947 0.45 -3.2
4,450,143 - PP_3947 0.46 +0.6
4,450,231 - PP_3947 0.64 -0.3
4,450,231 - PP_3947 0.64 +1.5
4,450,231 - PP_3947 0.64 -1.2
4,450,513 + +1.1
4,450,513 + -0.6
4,450,513 + -3.3
4,450,513 + +1.8
4,450,514 - +0.1
4,450,571 + +1.3
4,450,572 - +0.1
4,450,613 - +1.6
4,450,613 - -2.4
4,450,782 - PP_3948 0.11 +1.0
4,450,782 - PP_3948 0.11 +0.4
4,450,782 - PP_3948 0.11 -2.4
4,450,956 - PP_3948 0.16 +0.7
4,450,986 + PP_3948 0.17 +0.2
4,450,986 + PP_3948 0.17 -4.5
4,450,986 + PP_3948 0.17 -3.4
4,451,021 + PP_3948 0.18 +1.8
4,451,021 + PP_3948 0.18 -1.9
4,451,022 - PP_3948 0.18 -3.4
4,451,022 - PP_3948 0.18 -4.1
4,451,079 - PP_3948 0.19 -0.0
4,451,284 + PP_3948 0.25 +1.0
4,451,285 - PP_3948 0.25 -3.1
4,451,396 + PP_3948 0.28 -3.5
4,451,397 - PP_3948 0.28 -0.2
4,451,408 + PP_3948 0.28 +1.7
4,451,486 - PP_3948 0.31 +0.1
4,451,582 + PP_3948 0.33 -2.8
4,451,583 - PP_3948 0.33 -3.6
4,451,778 - PP_3948 0.39 -3.6
4,451,885 + PP_3948 0.42 -3.6
4,451,886 - PP_3948 0.42 -2.0
4,451,987 + PP_3948 0.45 +1.3
4,451,988 - PP_3948 0.45 +0.6
4,451,988 - PP_3948 0.45 -4.3
4,451,988 - PP_3948 0.45 +0.1
4,452,171 - PP_3948 0.50 -0.5
4,452,181 + PP_3948 0.50 +0.1
4,452,181 + PP_3948 0.50 +2.0
4,452,182 - PP_3948 0.50 -3.5
4,452,182 - PP_3948 0.50 -4.0
4,452,862 + PP_3948 0.69 +0.9
4,452,907 + PP_3948 0.70 -2.9
4,452,907 + PP_3948 0.70 -1.7
4,452,907 + PP_3948 0.70 -3.4
4,452,926 + PP_3948 0.71 -4.6
4,452,926 + PP_3948 0.71 -0.1
4,452,926 + PP_3948 0.71 +0.2
4,452,926 + PP_3948 0.71 -2.3
4,452,927 - PP_3948 0.71 +0.9
4,452,927 - PP_3948 0.71 -3.4
4,452,938 - PP_3948 0.71 -0.4
4,452,938 - PP_3948 0.71 +0.5
4,453,009 + PP_3948 0.73 +2.0
4,453,010 - PP_3948 0.73 -2.9
4,453,010 - PP_3948 0.73 +1.1
4,453,010 - PP_3948 0.73 +1.2
4,453,049 + PP_3948 0.74 -3.8
4,453,049 + PP_3948 0.74 -1.3
4,453,094 + PP_3948 0.76 -0.2
4,453,094 + PP_3948 0.76 +0.8
4,453,094 + PP_3948 0.76 +0.3
4,453,094 + PP_3948 0.76 -3.8
4,453,095 - PP_3948 0.76 -2.6
4,453,095 - PP_3948 0.76 +1.2
4,453,100 + PP_3948 0.76 -3.0
4,453,262 + PP_3948 0.80 +1.3
4,453,263 - PP_3948 0.80 -4.0
4,453,343 + PP_3948 0.83 -3.5
4,453,343 + PP_3948 0.83 -3.8
4,453,343 + PP_3948 0.83 -3.3
4,453,344 - PP_3948 0.83 +0.8
4,453,439 + PP_3948 0.85 +0.3
4,453,439 + PP_3948 0.85 -2.2
4,453,440 - PP_3948 0.85 -2.5
4,453,811 + -2.6
4,453,811 + +1.6
4,453,868 + -0.6
4,454,081 - PP_3949 0.18 +0.3
4,454,082 + PP_3949 0.18 -3.6
4,454,082 + PP_3949 0.18 -2.6
4,454,082 + PP_3949 0.18 -2.0
4,454,083 - PP_3949 0.19 -0.9
4,454,083 - PP_3949 0.19 -4.0
4,454,083 - PP_3949 0.19 +0.6
4,454,083 - PP_3949 0.19 -0.3
4,454,088 + PP_3949 0.19 -0.8
4,454,112 + PP_3949 0.23 -0.1
4,454,131 + PP_3949 0.26 +0.9
4,454,131 + +4.2
4,454,132 - PP_3949 0.26 -1.0
4,454,132 - PP_3949 0.26 -2.3
4,454,295 + PP_3949 0.52 -2.8
4,454,295 + PP_3949 0.52 -1.1
4,454,295 + PP_3949 0.52 +0.8
4,454,295 + PP_3949 0.52 -3.8
4,454,295 + PP_3949 0.52 -1.1
4,454,295 + PP_3949 0.52 +0.2
4,454,298 + PP_3949 0.52 -0.4
4,454,298 + PP_3949 0.52 +1.0
4,454,298 + PP_3949 0.52 +0.0
4,454,298 + PP_3949 0.52 -2.7
4,454,299 - PP_3949 0.52 -3.5
4,454,299 - PP_3949 0.52 +2.2
4,454,299 - PP_3949 0.52 +1.8
4,454,391 + PP_3949 0.67 -0.1
4,454,391 + PP_3949 0.67 -2.7
4,454,391 + PP_3949 0.67 +0.0
4,454,392 - PP_3949 0.67 +1.0
4,454,392 - PP_3949 0.67 +0.9
4,454,392 - PP_3949 0.67 +0.1
4,454,392 - PP_3949 0.67 +0.2
4,454,392 - PP_3949 0.67 +0.2
4,454,392 - PP_3949 0.67 -2.4
4,454,392 - PP_3949 0.67 +2.0
4,454,392 - PP_3949 0.67 -0.2
4,454,392 - PP_3949 0.67 -3.5
4,454,392 - PP_3949 0.67 +0.1
4,454,392 - PP_3949 0.67 -3.7
4,454,442 + PP_3949 0.75 -4.1
4,454,443 - PP_3949 0.75 +2.0
4,454,443 - PP_3949 0.75 +0.5
4,454,445 + PP_3949 0.75 -1.1
4,454,445 + PP_3949 0.75 -3.4
4,454,445 + PP_3949 0.75 +1.7
4,454,445 + PP_3949 0.75 -3.9
4,454,445 + PP_3949 0.75 -4.2
4,454,445 + PP_3949 0.75 -1.1
4,454,445 + PP_3949 0.75 +0.1
4,454,445 + PP_3949 0.75 +0.1
4,454,446 - PP_3949 0.75 +0.3
4,454,446 - PP_3949 0.75 +0.3
4,454,446 - PP_3949 0.75 +1.2
4,454,446 - PP_3949 0.75 -2.8
4,454,446 - PP_3949 0.75 +2.0
4,454,446 - PP_3949 0.75 +2.0
4,454,446 - PP_3949 0.75 -3.2
4,454,446 - PP_3949 0.75 +1.5
4,454,545 + +1.2
4,454,545 + -3.8
4,454,546 - +0.3
4,454,546 - -3.1
4,454,546 - -0.5
4,454,755 + +2.2
4,454,756 - -1.8

Or see this region's nucleotide sequence