Strain Fitness in Shewanella oneidensis MR-1 around SO0379

Experiment: 5-Hydroxymethylfurfural 10 mM

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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 ntSO0378 and SO0379 are separated by 39 nucleotidesSO0379 and hsdR-1 are separated by 2 nucleotides SO0378: SO0378 - ISSod4, transposase (NCBI ptt file), at 389,568 to 390,770 SO0378 SO0379: SO0379 - conserved hypothetical protein (NCBI ptt file), at 390,810 to 391,523 SO0379 SO0380: hsdR-1 - type I restriction-modification system, R subunit (NCBI ptt file), at 391,526 to 394,627 hsdR-1 Position (kb) 390 391 392Strain fitness (log2 ratio) -2 -1 0 1 2at 390.869 kb on + strandat 390.876 kb on - strandat 390.876 kb on - strandat 390.925 kb on - strand, within SO0379at 390.951 kb on - strand, within SO0379at 391.084 kb on - strand, within SO0379at 391.089 kb on - strand, within SO0379at 391.095 kb on - strand, within SO0379at 391.124 kb on + strand, within SO0379at 391.124 kb on + strand, within SO0379at 391.134 kb on + strand, within SO0379at 391.142 kb on - strand, within SO0379at 391.167 kb on + strand, within SO0379at 391.175 kb on - strand, within SO0379at 391.219 kb on - strand, within SO0379at 391.228 kb on - strand, within SO0379at 391.235 kb on + strand, within SO0379at 391.265 kb on + strand, within SO0379at 391.323 kb on + strand, within SO0379at 391.409 kb on - strand, within SO0379at 391.447 kb on + strand, within SO0379at 391.447 kb on + strand, within SO0379at 391.486 kb on + strandat 391.486 kb on + strandat 391.486 kb on + strandat 391.486 kb on + strandat 391.494 kb on - strandat 391.494 kb on - strandat 391.494 kb on - strandat 391.494 kb on - strandat 391.517 kb on + strandat 391.571 kb on - strandat 391.576 kb on + strandat 391.581 kb on + strandat 391.584 kb on - strandat 391.682 kb on + strandat 391.690 kb on - strandat 391.711 kb on + strandat 391.712 kb on + strandat 391.712 kb on + strandat 391.791 kb on - strandat 391.791 kb on - strandat 391.853 kb on - strand, within hsdR-1at 391.883 kb on - strand, within hsdR-1at 391.889 kb on - strand, within hsdR-1at 391.907 kb on + strand, within hsdR-1at 391.942 kb on + strand, within hsdR-1at 391.942 kb on + strandat 391.942 kb on + strand, within hsdR-1at 391.942 kb on + strand, within hsdR-1at 391.942 kb on + strand, within hsdR-1at 391.942 kb on + strand, within hsdR-1at 391.942 kb on + strand, within hsdR-1at 391.942 kb on + strand, within hsdR-1at 391.942 kb on + strand, within hsdR-1at 391.942 kb on + strand, within hsdR-1at 391.942 kb on + strand, within hsdR-1at 391.942 kb on + strand, within hsdR-1at 391.942 kb on + strand, within hsdR-1at 391.942 kb on + strand, within hsdR-1at 391.942 kb on + strand, within hsdR-1at 391.942 kb on + strand, within hsdR-1at 391.944 kb on - strand, within hsdR-1at 391.950 kb on - strand, within hsdR-1at 391.950 kb on - strand, within hsdR-1at 391.950 kb on - strand, within hsdR-1at 391.950 kb on - strand, within hsdR-1at 391.950 kb on - strand, within hsdR-1at 391.950 kb on - strand, within hsdR-1at 391.950 kb on - strand, within hsdR-1at 391.950 kb on - strand, within hsdR-1at 391.950 kb on - strand, within hsdR-1at 391.950 kb on - strand, within hsdR-1at 391.975 kb on - strand, within hsdR-1at 392.000 kb on - strand, within hsdR-1at 392.010 kb on - strand, within hsdR-1at 392.028 kb on + strand, within hsdR-1at 392.121 kb on - strand, within hsdR-1at 392.152 kb on + strand, within hsdR-1at 392.160 kb on - strand, within hsdR-1at 392.160 kb on - strand, within hsdR-1at 392.174 kb on + strand, within hsdR-1at 392.174 kb on + strand, within hsdR-1at 392.181 kb on - strand, within hsdR-1at 392.208 kb on + strand, within hsdR-1at 392.210 kb on + strand, within hsdR-1at 392.216 kb on - strand, within hsdR-1at 392.218 kb on - strand, within hsdR-1at 392.248 kb on - strand, within hsdR-1at 392.267 kb on + strand, within hsdR-1at 392.320 kb on + strand, within hsdR-1at 392.320 kb on + strand, within hsdR-1at 392.358 kb on - strand, within hsdR-1at 392.367 kb on + strand, within hsdR-1at 392.437 kb on + strand, within hsdR-1at 392.520 kb on - strand, within hsdR-1at 392.520 kb on - strand, within hsdR-1

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Per-strain Table

Position Strand Gene LocusTag Fraction 5-Hydroxymethylfurfural 10 mM
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390,869 + -1.4
390,876 - -0.6
390,876 - -0.5
390,925 - SO0379 0.16 -0.7
390,951 - SO0379 0.20 -1.9
391,084 - SO0379 0.38 -0.6
391,089 - SO0379 0.39 -0.9
391,095 - SO0379 0.40 -0.0
391,124 + SO0379 0.44 -1.7
391,124 + SO0379 0.44 -0.3
391,134 + SO0379 0.45 -0.8
391,142 - SO0379 0.46 -1.2
391,167 + SO0379 0.50 +0.6
391,175 - SO0379 0.51 -1.4
391,219 - SO0379 0.57 -1.0
391,228 - SO0379 0.59 +0.2
391,235 + SO0379 0.60 +0.2
391,265 + SO0379 0.64 -1.2
391,323 + SO0379 0.72 -0.5
391,409 - SO0379 0.84 -1.0
391,447 + SO0379 0.89 +1.0
391,447 + SO0379 0.89 -0.4
391,486 + -1.4
391,486 + +0.1
391,486 + -1.2
391,486 + -1.1
391,494 - -0.3
391,494 - -0.4
391,494 - -0.4
391,494 - -0.5
391,517 + -1.2
391,571 - -0.3
391,576 + +1.0
391,581 + -0.9
391,584 - +1.3
391,682 + +0.5
391,690 - -0.8
391,711 + -0.6
391,712 + +0.0
391,712 + -0.9
391,791 - +0.5
391,791 - +0.2
391,853 - hsdR-1 SO0380 0.11 +1.3
391,883 - hsdR-1 SO0380 0.12 +0.4
391,889 - hsdR-1 SO0380 0.12 +0.2
391,907 + hsdR-1 SO0380 0.12 +0.4
391,942 + hsdR-1 SO0380 0.13 +0.5
391,942 + +1.4
391,942 + hsdR-1 SO0380 0.13 +2.0
391,942 + hsdR-1 SO0380 0.13 +0.7
391,942 + hsdR-1 SO0380 0.13 -1.1
391,942 + hsdR-1 SO0380 0.13 -0.1
391,942 + hsdR-1 SO0380 0.13 +1.3
391,942 + hsdR-1 SO0380 0.13 -0.1
391,942 + hsdR-1 SO0380 0.13 +0.1
391,942 + hsdR-1 SO0380 0.13 -0.2
391,942 + hsdR-1 SO0380 0.13 +0.1
391,942 + hsdR-1 SO0380 0.13 -0.6
391,942 + hsdR-1 SO0380 0.13 +0.1
391,942 + hsdR-1 SO0380 0.13 -0.4
391,942 + hsdR-1 SO0380 0.13 -0.4
391,942 + hsdR-1 SO0380 0.13 -0.4
391,944 - hsdR-1 SO0380 0.13 -0.6
391,950 - hsdR-1 SO0380 0.14 -0.2
391,950 - hsdR-1 SO0380 0.14 -0.0
391,950 - hsdR-1 SO0380 0.14 +0.3
391,950 - hsdR-1 SO0380 0.14 -0.7
391,950 - hsdR-1 SO0380 0.14 +0.1
391,950 - hsdR-1 SO0380 0.14 +1.4
391,950 - hsdR-1 SO0380 0.14 +0.6
391,950 - hsdR-1 SO0380 0.14 +0.4
391,950 - hsdR-1 SO0380 0.14 +0.4
391,950 - hsdR-1 SO0380 0.14 -0.3
391,975 - hsdR-1 SO0380 0.14 -0.8
392,000 - hsdR-1 SO0380 0.15 +0.4
392,010 - hsdR-1 SO0380 0.16 -0.1
392,028 + hsdR-1 SO0380 0.16 -0.9
392,121 - hsdR-1 SO0380 0.19 -2.2
392,152 + hsdR-1 SO0380 0.20 +0.2
392,160 - hsdR-1 SO0380 0.20 +0.4
392,160 - hsdR-1 SO0380 0.20 -0.5
392,174 + hsdR-1 SO0380 0.21 -0.1
392,174 + hsdR-1 SO0380 0.21 +0.4
392,181 - hsdR-1 SO0380 0.21 +0.2
392,208 + hsdR-1 SO0380 0.22 +0.7
392,210 + hsdR-1 SO0380 0.22 +0.6
392,216 - hsdR-1 SO0380 0.22 -0.0
392,218 - hsdR-1 SO0380 0.22 +0.5
392,248 - hsdR-1 SO0380 0.23 +0.7
392,267 + hsdR-1 SO0380 0.24 -1.9
392,320 + hsdR-1 SO0380 0.26 +0.4
392,320 + hsdR-1 SO0380 0.26 +0.5
392,358 - hsdR-1 SO0380 0.27 +0.1
392,367 + hsdR-1 SO0380 0.27 -1.0
392,437 + hsdR-1 SO0380 0.29 -0.4
392,520 - hsdR-1 SO0380 0.32 -0.5
392,520 - hsdR-1 SO0380 0.32 -1.9

Or see this region's nucleotide sequence