Strain Fitness in Pseudomonas putida KT2440 around PP_5080

Experiment: Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=72_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_5078 and PP_5079 are separated by 96 nucleotidesPP_5079 and PP_5080 are separated by 4 nucleotidesPP_5080 and PP_5081 overlap by 53 nucleotidesPP_5081 and PP_5082 overlap by 4 nucleotides PP_5078: PP_5078 - 3-dehydroquinate synthase, at 5,799,878 to 5,800,975 _5078 PP_5079: PP_5079 - Shikimate kinase, at 5,801,072 to 5,801,590 _5079 PP_5080: PP_5080 - type 4 pili biogenesis protein, at 5,801,595 to 5,802,833 _5080 PP_5081: PP_5081 - Type IV pili biogenesis protein, at 5,802,781 to 5,803,797 _5081 PP_5082: PP_5082 - Type IV pili biogenesis protein PilN, at 5,803,794 to 5,804,330 _5082 Position (kb) 5801 5802 5803Strain fitness (log2 ratio) -2 -1 0 1 2 3at 5800.965 kb on - strandat 5800.978 kb on - strandat 5801.062 kb on + strandat 5801.062 kb on + strandat 5801.674 kb on - strandat 5801.704 kb on + strandat 5801.704 kb on + strandat 5801.705 kb on - strandat 5801.705 kb on - strandat 5801.838 kb on + strand, within PP_5080at 5801.839 kb on - strand, within PP_5080at 5801.928 kb on + strand, within PP_5080at 5801.929 kb on - strand, within PP_5080at 5801.995 kb on + strand, within PP_5080at 5802.215 kb on - strand, within PP_5080at 5802.254 kb on - strand, within PP_5080at 5802.275 kb on + strand, within PP_5080at 5802.685 kb on - strand, within PP_5080at 5802.685 kb on - strand, within PP_5080at 5802.685 kb on - strand, within PP_5080at 5802.718 kb on + strandat 5802.719 kb on - strandat 5802.838 kb on + strandat 5802.839 kb on - strandat 5802.839 kb on - strandat 5802.839 kb on - strandat 5802.970 kb on + strand, within PP_5081at 5802.970 kb on + strand, within PP_5081at 5802.970 kb on + strand, within PP_5081at 5802.970 kb on + strand, within PP_5081at 5802.970 kb on + strand, within PP_5081at 5802.971 kb on - strand, within PP_5081at 5802.971 kb on - strand, within PP_5081at 5802.971 kb on - strand, within PP_5081at 5802.971 kb on - strand, within PP_5081at 5802.971 kb on - strand, within PP_5081at 5802.971 kb on - strand, within PP_5081at 5802.971 kb on - strand, within PP_5081at 5802.971 kb on - strand, within PP_5081at 5802.971 kb on - strand, within PP_5081at 5802.971 kb on - strand, within PP_5081at 5802.971 kb on - strand, within PP_5081at 5802.972 kb on + strand, within PP_5081at 5802.972 kb on + strand, within PP_5081at 5802.972 kb on + strand, within PP_5081at 5802.972 kb on + strand, within PP_5081at 5802.972 kb on + strand, within PP_5081at 5802.973 kb on - strand, within PP_5081at 5802.973 kb on - strand, within PP_5081at 5802.973 kb on - strand, within PP_5081at 5802.973 kb on - strand, within PP_5081at 5802.973 kb on - strand, within PP_5081at 5803.230 kb on + strand, within PP_5081at 5803.231 kb on - strand, within PP_5081at 5803.399 kb on + strand, within PP_5081at 5803.435 kb on + strand, within PP_5081at 5803.435 kb on + strand, within PP_5081at 5803.436 kb on - strand, within PP_5081at 5803.436 kb on - strand, within PP_5081at 5803.526 kb on + strand, within PP_5081at 5803.526 kb on + strand, within PP_5081at 5803.567 kb on + strand, within PP_5081at 5803.568 kb on - strand, within PP_5081at 5803.568 kb on - strand, within PP_5081at 5803.666 kb on + strand, within PP_5081at 5803.666 kb on + strand, within PP_5081at 5803.667 kb on - strand, within PP_5081

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Per-strain Table

Position Strand Gene LocusTag Fraction Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=72_hrs
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5,800,965 - +2.4
5,800,978 - -2.2
5,801,062 + +0.1
5,801,062 + +1.4
5,801,674 - +0.1
5,801,704 + +0.2
5,801,704 + -0.2
5,801,705 - -0.8
5,801,705 - +1.1
5,801,838 + PP_5080 0.20 +0.7
5,801,839 - PP_5080 0.20 -0.9
5,801,928 + PP_5080 0.27 +0.5
5,801,929 - PP_5080 0.27 +0.2
5,801,995 + PP_5080 0.32 +0.9
5,802,215 - PP_5080 0.50 -0.2
5,802,254 - PP_5080 0.53 +2.3
5,802,275 + PP_5080 0.55 +0.6
5,802,685 - PP_5080 0.88 +0.7
5,802,685 - PP_5080 0.88 -1.3
5,802,685 - PP_5080 0.88 +0.8
5,802,718 + +0.4
5,802,719 - -0.2
5,802,838 + +0.8
5,802,839 - -0.1
5,802,839 - -0.7
5,802,839 - -0.8
5,802,970 + PP_5081 0.19 +0.6
5,802,970 + PP_5081 0.19 +0.8
5,802,970 + PP_5081 0.19 +1.2
5,802,970 + PP_5081 0.19 +0.1
5,802,970 + PP_5081 0.19 -0.5
5,802,971 - PP_5081 0.19 +0.5
5,802,971 - PP_5081 0.19 -0.5
5,802,971 - PP_5081 0.19 +0.4
5,802,971 - PP_5081 0.19 -1.3
5,802,971 - PP_5081 0.19 +0.9
5,802,971 - PP_5081 0.19 -0.5
5,802,971 - PP_5081 0.19 +0.3
5,802,971 - PP_5081 0.19 +0.2
5,802,971 - PP_5081 0.19 -0.6
5,802,971 - PP_5081 0.19 +1.4
5,802,971 - PP_5081 0.19 -0.0
5,802,972 + PP_5081 0.19 -1.1
5,802,972 + PP_5081 0.19 +1.0
5,802,972 + PP_5081 0.19 -0.3
5,802,972 + PP_5081 0.19 +0.3
5,802,972 + PP_5081 0.19 +0.5
5,802,973 - PP_5081 0.19 +0.6
5,802,973 - PP_5081 0.19 -0.7
5,802,973 - PP_5081 0.19 -0.6
5,802,973 - PP_5081 0.19 -0.0
5,802,973 - PP_5081 0.19 -0.5
5,803,230 + PP_5081 0.44 +2.8
5,803,231 - PP_5081 0.44 -0.5
5,803,399 + PP_5081 0.61 -0.1
5,803,435 + PP_5081 0.64 +0.5
5,803,435 + PP_5081 0.64 -0.9
5,803,436 - PP_5081 0.64 -0.4
5,803,436 - PP_5081 0.64 +0.5
5,803,526 + PP_5081 0.73 -0.4
5,803,526 + PP_5081 0.73 -1.1
5,803,567 + PP_5081 0.77 +0.2
5,803,568 - PP_5081 0.77 -0.3
5,803,568 - PP_5081 0.77 +0.4
5,803,666 + PP_5081 0.87 +1.2
5,803,666 + PP_5081 0.87 +0.1
5,803,667 - PP_5081 0.87 -0.1

Or see this region's nucleotide sequence