Strain Fitness in Pseudomonas putida KT2440 around PP_1062

Experiment: Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs

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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_1061 and PP_1062 are separated by 136 nucleotidesPP_1062 and PP_1063 overlap by 17 nucleotidesPP_1063 and PP_1064 are separated by 54 nucleotides PP_1061: PP_1061 - putative ATP-dependent DNA helicase lhr, at 1,212,654 to 1,216,958 _1061 PP_1062: PP_1062 - MutT/nudix family protein, at 1,217,095 to 1,217,508 _1062 PP_1063: PP_1063 - DNA-binding transcriptional regulator, homocysteine-binding, at 1,217,492 to 1,218,409 _1063 PP_1064: PP_1064 - Hydrolase, alpha/beta fold family, at 1,218,464 to 1,219,600 _1064 Position (kb) 1217 1218Strain fitness (log2 ratio) -2 -1 0 1at 1216.113 kb on + strand, within PP_1061at 1216.114 kb on - strand, within PP_1061at 1216.159 kb on + strand, within PP_1061at 1216.159 kb on + strand, within PP_1061at 1216.159 kb on + strand, within PP_1061at 1216.160 kb on - strand, within PP_1061at 1216.160 kb on - strand, within PP_1061at 1216.160 kb on - strand, within PP_1061at 1216.699 kb on + strandat 1216.699 kb on + strandat 1216.700 kb on - strandat 1216.968 kb on - strandat 1217.007 kb on + strandat 1217.225 kb on + strand, within PP_1062at 1217.225 kb on + strand, within PP_1062at 1217.226 kb on - strand, within PP_1062at 1217.287 kb on - strand, within PP_1062at 1217.565 kb on + strandat 1217.565 kb on + strandat 1217.566 kb on - strandat 1217.566 kb on - strandat 1217.566 kb on - strandat 1217.566 kb on - strandat 1217.601 kb on + strand, within PP_1063at 1217.602 kb on - strand, within PP_1063at 1217.602 kb on - strand, within PP_1063at 1217.602 kb on - strand, within PP_1063at 1217.649 kb on + strand, within PP_1063at 1217.649 kb on + strand, within PP_1063at 1217.649 kb on + strand, within PP_1063at 1217.650 kb on - strand, within PP_1063at 1217.664 kb on + strand, within PP_1063at 1217.749 kb on + strand, within PP_1063at 1217.750 kb on - strand, within PP_1063at 1217.827 kb on - strand, within PP_1063at 1217.868 kb on + strand, within PP_1063at 1217.868 kb on + strand, within PP_1063at 1217.868 kb on + strand, within PP_1063at 1217.868 kb on + strand, within PP_1063at 1217.868 kb on + strand, within PP_1063at 1217.868 kb on + strand, within PP_1063at 1217.868 kb on + strand, within PP_1063at 1217.868 kb on + strand, within PP_1063at 1217.869 kb on - strand, within PP_1063at 1217.869 kb on - strand, within PP_1063at 1217.919 kb on + strand, within PP_1063at 1217.937 kb on + strand, within PP_1063at 1217.937 kb on + strand, within PP_1063at 1217.937 kb on + strand, within PP_1063at 1217.937 kb on + strandat 1217.937 kb on + strand, within PP_1063at 1217.938 kb on - strand, within PP_1063at 1217.938 kb on - strand, within PP_1063

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Per-strain Table

Position Strand Gene LocusTag Fraction Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs
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1,216,113 + PP_1061 0.80 +0.2
1,216,114 - PP_1061 0.80 -0.5
1,216,159 + PP_1061 0.81 -0.4
1,216,159 + PP_1061 0.81 -0.8
1,216,159 + PP_1061 0.81 -0.8
1,216,160 - PP_1061 0.81 -0.4
1,216,160 - PP_1061 0.81 +0.7
1,216,160 - PP_1061 0.81 +0.8
1,216,699 + +0.8
1,216,699 + +0.5
1,216,700 - +0.5
1,216,968 - -0.8
1,217,007 + -0.2
1,217,225 + PP_1062 0.31 -0.6
1,217,225 + PP_1062 0.31 -1.1
1,217,226 - PP_1062 0.32 -0.4
1,217,287 - PP_1062 0.46 -1.8
1,217,565 + -0.6
1,217,565 + -1.8
1,217,566 - +0.4
1,217,566 - +0.3
1,217,566 - -0.4
1,217,566 - -0.1
1,217,601 + PP_1063 0.12 +0.5
1,217,602 - PP_1063 0.12 +0.9
1,217,602 - PP_1063 0.12 +0.4
1,217,602 - PP_1063 0.12 -0.4
1,217,649 + PP_1063 0.17 +0.9
1,217,649 + PP_1063 0.17 -0.4
1,217,649 + PP_1063 0.17 +0.4
1,217,650 - PP_1063 0.17 +1.3
1,217,664 + PP_1063 0.19 +0.6
1,217,749 + PP_1063 0.28 -1.0
1,217,750 - PP_1063 0.28 +0.9
1,217,827 - PP_1063 0.36 -0.8
1,217,868 + PP_1063 0.41 +0.1
1,217,868 + PP_1063 0.41 -0.2
1,217,868 + PP_1063 0.41 -0.8
1,217,868 + PP_1063 0.41 +0.0
1,217,868 + PP_1063 0.41 -0.5
1,217,868 + PP_1063 0.41 -1.1
1,217,868 + PP_1063 0.41 -1.8
1,217,868 + PP_1063 0.41 +0.4
1,217,869 - PP_1063 0.41 -1.2
1,217,869 - PP_1063 0.41 +0.2
1,217,919 + PP_1063 0.47 +1.2
1,217,937 + PP_1063 0.48 +0.0
1,217,937 + PP_1063 0.48 -0.1
1,217,937 + PP_1063 0.48 +0.2
1,217,937 + +1.2
1,217,937 + PP_1063 0.48 +1.0
1,217,938 - PP_1063 0.49 +0.1
1,217,938 - PP_1063 0.49 +0.8

Or see this region's nucleotide sequence