Strain Fitness in Shewanella oneidensis MR-1 around SO0167

Experiment: Fumarate electron acceptor; ground control

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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 ntgspD and gspE overlap by 4 nucleotidesgspE and gspF are separated by 3 nucleotides SO0166: gspD - general secretion pathway protein D (NCBI ptt file), at 172,301 to 174,415 gspD SO0167: gspE - general secretion pathway protein E (NCBI ptt file), at 174,412 to 175,977 gspE SO0168: gspF - general secretion pathway protein F (NCBI ptt file), at 175,981 to 177,204 gspF Position (kb) 174 175 176Strain fitness (log2 ratio) -4 -3 -2 -1 0 1 2at 173.416 kb on - strand, within gspDat 173.434 kb on - strand, within gspDat 173.500 kb on + strand, within gspDat 173.500 kb on + strand, within gspDat 173.588 kb on + strand, within gspDat 173.606 kb on + strand, within gspDat 173.679 kb on + strand, within gspDat 173.705 kb on - strand, within gspDat 173.781 kb on + strand, within gspDat 173.808 kb on + strand, within gspDat 173.836 kb on + strand, within gspDat 173.871 kb on + strand, within gspDat 174.092 kb on + strand, within gspDat 174.220 kb on + strandat 174.271 kb on + strandat 174.271 kb on + strandat 174.275 kb on - strandat 174.335 kb on + strandat 174.335 kb on + strandat 174.335 kb on + strandat 174.335 kb on + strandat 174.352 kb on + strandat 174.360 kb on - strandat 174.588 kb on + strand, within gspEat 174.646 kb on - strand, within gspEat 174.654 kb on + strand, within gspEat 174.669 kb on - strand, within gspEat 174.702 kb on + strand, within gspEat 174.733 kb on - strand, within gspEat 174.797 kb on + strand, within gspEat 174.807 kb on + strand, within gspEat 174.815 kb on - strand, within gspEat 174.833 kb on + strand, within gspEat 174.843 kb on + strand, within gspEat 174.866 kb on - strand, within gspEat 174.953 kb on - strand, within gspEat 174.976 kb on + strand, within gspEat 174.999 kb on + strand, within gspEat 174.999 kb on + strand, within gspEat 174.999 kb on + strand, within gspEat 175.007 kb on - strand, within gspEat 175.013 kb on - strand, within gspEat 175.269 kb on + strand, within gspEat 175.285 kb on - strand, within gspEat 175.407 kb on - strand, within gspEat 175.451 kb on - strand, within gspEat 175.484 kb on - strand, within gspEat 175.484 kb on - strand, within gspEat 175.550 kb on - strand, within gspEat 175.570 kb on + strand, within gspEat 175.578 kb on + strand, within gspEat 175.710 kb on + strand, within gspEat 175.817 kb on + strand, within gspEat 175.951 kb on + strandat 175.959 kb on - strandat 175.972 kb on + strandat 175.979 kb on - strandat 175.980 kb on - strandat 175.980 kb on - strandat 176.005 kb on - strandat 176.010 kb on + strandat 176.025 kb on + strandat 176.033 kb on - strandat 176.033 kb on - strandat 176.134 kb on + strand, within gspFat 176.229 kb on - strand, within gspFat 176.247 kb on + strand, within gspFat 176.247 kb on + strand, within gspFat 176.255 kb on - strand, within gspFat 176.255 kb on - strand, within gspFat 176.255 kb on - strand, within gspFat 176.255 kb on - strand, within gspFat 176.255 kb on - strand, within gspFat 176.260 kb on + strand, within gspFat 176.289 kb on - strand, within gspFat 176.327 kb on + strand, within gspFat 176.327 kb on + strand, within gspFat 176.335 kb on - strand, within gspFat 176.382 kb on - strand, within gspFat 176.382 kb on - strand, within gspFat 176.524 kb on - strand, within gspFat 176.555 kb on - strand, within gspFat 176.597 kb on - strand, within gspFat 176.640 kb on - strand, within gspFat 176.795 kb on - strand, within gspFat 176.834 kb on + strand, within gspFat 176.834 kb on + strand, within gspFat 176.936 kb on + strand, within gspFat 176.941 kb on + strand, within gspFat 176.941 kb on + strand, within gspFat 176.941 kb on + strand, within gspFat 176.953 kb on + strand, within gspFat 176.958 kb on + strand, within gspFat 176.958 kb on + strand, within gspFat 176.966 kb on - strand, within gspFat 176.966 kb on - strand, within gspF

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Per-strain Table

Position Strand Gene LocusTag Fraction Fumarate electron acceptor; ground control
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173,416 - gspD SO0166 0.53 -2.7
173,434 - gspD SO0166 0.54 -2.3
173,500 + gspD SO0166 0.57 +1.7
173,500 + gspD SO0166 0.57 -0.6
173,588 + gspD SO0166 0.61 +0.1
173,606 + gspD SO0166 0.62 +0.7
173,679 + gspD SO0166 0.65 +0.1
173,705 - gspD SO0166 0.66 -1.4
173,781 + gspD SO0166 0.70 -0.6
173,808 + gspD SO0166 0.71 -2.1
173,836 + gspD SO0166 0.73 -0.3
173,871 + gspD SO0166 0.74 -1.3
174,092 + gspD SO0166 0.85 -0.6
174,220 + +0.1
174,271 + -2.4
174,271 + +0.7
174,275 - -0.3
174,335 + -0.3
174,335 + -0.3
174,335 + +0.9
174,335 + +0.1
174,352 + +2.1
174,360 - -0.9
174,588 + gspE SO0167 0.11 -1.0
174,646 - gspE SO0167 0.15 -1.6
174,654 + gspE SO0167 0.15 +1.7
174,669 - gspE SO0167 0.16 +0.1
174,702 + gspE SO0167 0.19 +1.7
174,733 - gspE SO0167 0.20 -1.6
174,797 + gspE SO0167 0.25 -0.3
174,807 + gspE SO0167 0.25 -2.4
174,815 - gspE SO0167 0.26 +0.1
174,833 + gspE SO0167 0.27 -0.6
174,843 + gspE SO0167 0.28 -2.1
174,866 - gspE SO0167 0.29 -1.3
174,953 - gspE SO0167 0.35 +0.1
174,976 + gspE SO0167 0.36 -3.1
174,999 + gspE SO0167 0.37 +0.7
174,999 + gspE SO0167 0.37 -2.2
174,999 + gspE SO0167 0.37 -0.6
175,007 - gspE SO0167 0.38 +0.7
175,013 - gspE SO0167 0.38 -0.9
175,269 + gspE SO0167 0.55 -2.4
175,285 - gspE SO0167 0.56 -2.1
175,407 - gspE SO0167 0.64 +1.7
175,451 - gspE SO0167 0.66 -2.9
175,484 - gspE SO0167 0.68 -2.7
175,484 - gspE SO0167 0.68 -3.3
175,550 - gspE SO0167 0.73 -1.3
175,570 + gspE SO0167 0.74 -2.4
175,578 + gspE SO0167 0.74 -2.6
175,710 + gspE SO0167 0.83 -0.6
175,817 + gspE SO0167 0.90 +0.1
175,951 + +0.1
175,959 - -3.8
175,972 + -0.5
175,979 - +1.7
175,980 - -1.1
175,980 - -0.9
176,005 - -2.0
176,010 + +0.7
176,025 + -0.6
176,033 - -1.3
176,033 - +1.7
176,134 + gspF SO0168 0.12 +1.7
176,229 - gspF SO0168 0.20 +1.1
176,247 + gspF SO0168 0.22 -1.1
176,247 + gspF SO0168 0.22 +0.1
176,255 - gspF SO0168 0.22 -1.4
176,255 - gspF SO0168 0.22 -0.6
176,255 - gspF SO0168 0.22 -2.5
176,255 - gspF SO0168 0.22 +0.7
176,255 - gspF SO0168 0.22 -1.6
176,260 + gspF SO0168 0.23 +0.1
176,289 - gspF SO0168 0.25 -2.6
176,327 + gspF SO0168 0.28 -1.1
176,327 + gspF SO0168 0.28 -3.1
176,335 - gspF SO0168 0.29 -2.7
176,382 - gspF SO0168 0.33 -0.3
176,382 - gspF SO0168 0.33 +0.1
176,524 - gspF SO0168 0.44 -1.3
176,555 - gspF SO0168 0.47 -0.3
176,597 - gspF SO0168 0.50 +0.7
176,640 - gspF SO0168 0.54 -0.3
176,795 - gspF SO0168 0.67 -1.6
176,834 + gspF SO0168 0.70 +0.1
176,834 + gspF SO0168 0.70 +0.1
176,936 + gspF SO0168 0.78 -0.3
176,941 + gspF SO0168 0.78 +1.7
176,941 + gspF SO0168 0.78 +0.7
176,941 + gspF SO0168 0.78 +0.1
176,953 + gspF SO0168 0.79 -2.2
176,958 + gspF SO0168 0.80 +0.1
176,958 + gspF SO0168 0.80 -1.3
176,966 - gspF SO0168 0.80 -2.1
176,966 - gspF SO0168 0.80 -2.0

Or see this region's nucleotide sequence