Strain Fitness in Pseudomonas putida KT2440 around PP_3908

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_3905 and PP_3906 are separated by 19 nucleotidesPP_3906 and PP_3907 overlap by 4 nucleotidesPP_3907 and PP_3908 are separated by 81 nucleotidesPP_3908 and PP_3909 are separated by 13 nucleotidesPP_3909 and PP_3910 are separated by 106 nucleotidesPP_3910 and PP_3911 are separated by 14 nucleotides PP_3905: PP_3905 - Transcriptional regulator, LuxR family, at 4,417,108 to 4,417,659 _3905 PP_3906: PP_3906 - conserved protein of unknown function, at 4,417,679 to 4,417,948 _3906 PP_3907: PP_3907 - conserved protein of unknown function, at 4,417,945 to 4,418,403 _3907 PP_3908: PP_3908 - conserved protein of unknown function, at 4,418,485 to 4,418,835 _3908 PP_3909: PP_3909 - conserved protein of unknown function, at 4,418,849 to 4,419,127 _3909 PP_3910: PP_3910 - conserved protein of unknown function, at 4,419,234 to 4,419,785 _3910 PP_3911: PP_3911 - conserved protein of unknown function, at 4,419,800 to 4,420,183 _3911 Position (kb) 4418 4419Strain fitness (log2 ratio) -2 -1 0 1 2at 4417.648 kb on + strandat 4417.649 kb on - strandat 4417.877 kb on + strand, within PP_3906at 4417.878 kb on - strand, within PP_3906at 4417.878 kb on - strand, within PP_3906at 4417.878 kb on - strand, within PP_3906at 4418.093 kb on + strand, within PP_3907at 4418.093 kb on + strand, within PP_3907at 4418.093 kb on + strand, within PP_3907at 4418.094 kb on - strand, within PP_3907at 4418.094 kb on - strand, within PP_3907at 4418.143 kb on + strand, within PP_3907at 4418.143 kb on + strand, within PP_3907at 4418.143 kb on + strand, within PP_3907at 4418.143 kb on + strand, within PP_3907at 4418.144 kb on - strand, within PP_3907at 4418.183 kb on - strand, within PP_3907at 4418.219 kb on - strand, within PP_3907at 4418.219 kb on - strand, within PP_3907at 4418.219 kb on - strand, within PP_3907at 4418.257 kb on + strand, within PP_3907at 4418.257 kb on + strand, within PP_3907at 4418.257 kb on + strand, within PP_3907at 4418.258 kb on - strand, within PP_3907at 4418.259 kb on + strand, within PP_3907at 4418.322 kb on + strand, within PP_3907at 4418.477 kb on + strandat 4418.718 kb on + strand, within PP_3908at 4418.719 kb on - strand, within PP_3908at 4418.743 kb on + strand, within PP_3908at 4418.797 kb on - strand, within PP_3908at 4418.797 kb on - strand, within PP_3908at 4418.819 kb on + strandat 4418.851 kb on - strandat 4418.903 kb on + strand, within PP_3909at 4418.903 kb on + strand, within PP_3909at 4418.904 kb on - strand, within PP_3909at 4418.904 kb on - strand, within PP_3909at 4418.904 kb on - strand, within PP_3909at 4419.015 kb on + strand, within PP_3909at 4419.015 kb on + strand, within PP_3909at 4419.016 kb on - strand, within PP_3909at 4419.069 kb on + strand, within PP_3909at 4419.070 kb on - strand, within PP_3909at 4419.085 kb on - strand, within PP_3909at 4419.185 kb on - strandat 4419.240 kb on + strandat 4419.240 kb on + strandat 4419.241 kb on - strandat 4419.247 kb on - strandat 4419.366 kb on + strand, within PP_3910at 4419.366 kb on + strand, within PP_3910at 4419.366 kb on + strand, within PP_3910at 4419.366 kb on + strand, within PP_3910at 4419.367 kb on - strand, within PP_3910at 4419.367 kb on - strand, within PP_3910at 4419.384 kb on + strand, within PP_3910at 4419.385 kb on - strand, within PP_3910at 4419.385 kb on - strand, within PP_3910at 4419.641 kb on + strand, within PP_3910at 4419.642 kb on - strand, within PP_3910at 4419.642 kb on - strand, within PP_3910at 4419.642 kb on - strand, within PP_3910at 4419.667 kb on + strand, within PP_3910at 4419.667 kb on + strand, within PP_3910at 4419.667 kb on + strand, within PP_3910at 4419.667 kb on + strand, within PP_3910at 4419.668 kb on - strand, within PP_3910at 4419.668 kb on - strand, within PP_3910at 4419.669 kb on + strand, within PP_3910at 4419.670 kb on - strand, within PP_3910at 4419.787 kb on + strandat 4419.809 kb on + strandat 4419.810 kb on - strandat 4419.810 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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4,417,648 + +2.0
4,417,649 - -0.4
4,417,877 + PP_3906 0.73 -0.7
4,417,878 - PP_3906 0.74 -2.1
4,417,878 - PP_3906 0.74 -0.1
4,417,878 - PP_3906 0.74 -0.3
4,418,093 + PP_3907 0.32 +0.3
4,418,093 + PP_3907 0.32 -1.0
4,418,093 + PP_3907 0.32 +0.2
4,418,094 - PP_3907 0.32 +0.7
4,418,094 - PP_3907 0.32 +0.3
4,418,143 + PP_3907 0.43 -0.5
4,418,143 + PP_3907 0.43 -1.5
4,418,143 + PP_3907 0.43 +0.2
4,418,143 + PP_3907 0.43 +0.6
4,418,144 - PP_3907 0.43 -0.3
4,418,183 - PP_3907 0.52 -0.3
4,418,219 - PP_3907 0.60 +0.3
4,418,219 - PP_3907 0.60 -0.1
4,418,219 - PP_3907 0.60 +0.9
4,418,257 + PP_3907 0.68 -1.0
4,418,257 + PP_3907 0.68 +0.7
4,418,257 + PP_3907 0.68 +0.6
4,418,258 - PP_3907 0.68 -0.3
4,418,259 + PP_3907 0.68 -0.7
4,418,322 + PP_3907 0.82 -0.9
4,418,477 + -0.4
4,418,718 + PP_3908 0.66 -0.5
4,418,719 - PP_3908 0.67 -0.3
4,418,743 + PP_3908 0.74 -1.4
4,418,797 - PP_3908 0.89 -1.0
4,418,797 - PP_3908 0.89 -0.6
4,418,819 + +1.6
4,418,851 - +0.0
4,418,903 + PP_3909 0.19 +1.2
4,418,903 + PP_3909 0.19 +0.3
4,418,904 - PP_3909 0.20 -1.3
4,418,904 - PP_3909 0.20 +0.0
4,418,904 - PP_3909 0.20 +0.0
4,419,015 + PP_3909 0.59 -0.6
4,419,015 + PP_3909 0.59 +0.2
4,419,016 - PP_3909 0.60 +2.0
4,419,069 + PP_3909 0.79 +1.0
4,419,070 - PP_3909 0.79 +0.2
4,419,085 - PP_3909 0.85 -0.4
4,419,185 - +0.9
4,419,240 + +0.5
4,419,240 + -0.9
4,419,241 - -0.9
4,419,247 - -0.4
4,419,366 + PP_3910 0.24 +0.3
4,419,366 + PP_3910 0.24 +0.3
4,419,366 + PP_3910 0.24 -0.3
4,419,366 + PP_3910 0.24 -0.6
4,419,367 - PP_3910 0.24 +1.5
4,419,367 - PP_3910 0.24 +0.3
4,419,384 + PP_3910 0.27 +0.3
4,419,385 - PP_3910 0.27 -0.9
4,419,385 - PP_3910 0.27 -0.6
4,419,641 + PP_3910 0.74 +0.6
4,419,642 - PP_3910 0.74 +0.3
4,419,642 - PP_3910 0.74 +0.5
4,419,642 - PP_3910 0.74 -0.6
4,419,667 + PP_3910 0.78 -1.0
4,419,667 + PP_3910 0.78 -0.7
4,419,667 + PP_3910 0.78 -0.1
4,419,667 + PP_3910 0.78 -0.2
4,419,668 - PP_3910 0.79 +0.2
4,419,668 - PP_3910 0.79 -0.4
4,419,669 + PP_3910 0.79 +1.0
4,419,670 - PP_3910 0.79 +0.6
4,419,787 + +0.3
4,419,809 + -0.6
4,419,810 - -1.3
4,419,810 - -0.6

Or see this region's nucleotide sequence