Strain Fitness in Pseudomonas putida KT2440 around PP_5628

Experiment: Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; 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_3788 and PP_5628 overlap by 4 nucleotidesPP_5628 and PP_3789 overlap by 1 nucleotides PP_3788: PP_3788 - putative Non-ribosomal peptide synthetase, at 4,315,918 to 4,317,471 _3788 PP_5628: PP_5628 - conserved protein of unknown function, at 4,317,468 to 4,317,740 _5628 PP_3789: PP_3789 - putative Efflux transporter, at 4,317,740 to 4,318,960 _3789 Position (kb) 4317 4318Strain fitness (log2 ratio) -2 -1 0 1at 4316.491 kb on + strand, within PP_3788at 4316.491 kb on + strand, within PP_3788at 4316.494 kb on + strand, within PP_3788at 4316.494 kb on + strandat 4316.495 kb on - strand, within PP_3788at 4316.495 kb on - strand, within PP_3788at 4316.495 kb on - strand, within PP_3788at 4316.632 kb on + strand, within PP_3788at 4316.633 kb on - strandat 4316.745 kb on + strand, within PP_3788at 4316.746 kb on - strand, within PP_3788at 4316.746 kb on - strand, within PP_3788at 4316.818 kb on - strand, within PP_3788at 4316.818 kb on - strand, within PP_3788at 4316.818 kb on - strand, within PP_3788at 4316.821 kb on + strand, within PP_3788at 4316.822 kb on - strand, within PP_3788at 4316.907 kb on - strand, within PP_3788at 4317.000 kb on + strand, within PP_3788at 4317.000 kb on + strand, within PP_3788at 4317.001 kb on - strand, within PP_3788at 4317.001 kb on - strand, within PP_3788at 4317.001 kb on - strand, within PP_3788at 4317.001 kb on - strand, within PP_3788at 4317.002 kb on + strand, within PP_3788at 4317.002 kb on + strand, within PP_3788at 4317.002 kb on + strand, within PP_3788at 4317.002 kb on + strand, within PP_3788at 4317.002 kb on + strand, within PP_3788at 4317.002 kb on + strand, within PP_3788at 4317.003 kb on - strand, within PP_3788at 4317.003 kb on - strand, within PP_3788at 4317.003 kb on - strand, within PP_3788at 4317.003 kb on - strand, within PP_3788at 4317.003 kb on - strand, within PP_3788at 4317.003 kb on - strand, within PP_3788at 4317.020 kb on - strand, within PP_3788at 4317.094 kb on + strand, within PP_3788at 4317.095 kb on - strand, within PP_3788at 4317.159 kb on + strand, within PP_3788at 4317.264 kb on + strand, within PP_3788at 4317.265 kb on - strand, within PP_3788at 4317.303 kb on + strand, within PP_3788at 4317.303 kb on + strand, within PP_3788at 4317.303 kb on + strand, within PP_3788at 4317.303 kb on + strand, within PP_3788at 4317.303 kb on + strand, within PP_3788at 4317.303 kb on + strand, within PP_3788at 4317.303 kb on + strand, within PP_3788at 4317.304 kb on - strand, within PP_3788at 4317.304 kb on - strand, within PP_3788at 4317.304 kb on - strand, within PP_3788at 4317.304 kb on - strand, within PP_3788at 4317.328 kb on - strandat 4317.328 kb on - strandat 4317.328 kb on - strandat 4317.328 kb on - strandat 4317.328 kb on - strandat 4317.328 kb on - strandat 4317.414 kb on + strandat 4317.415 kb on - strandat 4317.415 kb on - strandat 4317.500 kb on + strand, within PP_5628at 4317.501 kb on - strand, within PP_5628at 4317.605 kb on + strand, within PP_5628at 4317.606 kb on - strand, within PP_5628at 4317.957 kb on + strand, within PP_3789at 4317.958 kb on - strand, within PP_3789at 4317.992 kb on - strand, within PP_3789at 4318.020 kb on + strand, within PP_3789at 4318.020 kb on + strand, within PP_3789at 4318.021 kb on - strand, within PP_3789at 4318.065 kb on + strand, within PP_3789at 4318.065 kb on + strand, within PP_3789at 4318.066 kb on - strand, within PP_3789at 4318.111 kb on + strand, within PP_3789at 4318.112 kb on - strand, within PP_3789at 4318.112 kb on - strand, within PP_3789at 4318.166 kb on + strand, within PP_3789at 4318.172 kb on + strand, within PP_3789at 4318.173 kb on - strand, within PP_3789at 4318.173 kb on - strand, within PP_3789at 4318.173 kb on - strand, within PP_3789at 4318.173 kb on - strand, within PP_3789at 4318.240 kb on + strand, within PP_3789at 4318.241 kb on - strand, within PP_3789at 4318.241 kb on - strand, within PP_3789at 4318.241 kb on - strand, within PP_3789at 4318.403 kb on + strand, within PP_3789at 4318.403 kb on + strand, within PP_3789at 4318.403 kb on + strand, within PP_3789at 4318.404 kb on - strand, within PP_3789at 4318.405 kb on + strand, within PP_3789at 4318.405 kb on + strand, within PP_3789at 4318.406 kb on - strand, within PP_3789at 4318.406 kb on - strand, within PP_3789at 4318.406 kb on - strand, within PP_3789at 4318.424 kb on - strand, within PP_3789at 4318.475 kb on + strand, within PP_3789at 4318.475 kb on + strand, within PP_3789at 4318.476 kb on - strand, within PP_3789at 4318.499 kb on - strand, within PP_3789at 4318.499 kb on - strand, within PP_3789at 4318.499 kb on - strand, within PP_3789at 4318.571 kb on + strand, within PP_3789at 4318.572 kb on - strand, within PP_3789at 4318.663 kb on + strand, within PP_3789at 4318.663 kb on + strand, within PP_3789at 4318.727 kb on + strand, within PP_3789at 4318.733 kb on + strand, within PP_3789at 4318.733 kb on + strand, within PP_3789at 4318.733 kb on + strand, within PP_3789at 4318.733 kb on + strand, within PP_3789at 4318.733 kb on + strand, within PP_3789at 4318.734 kb on - strand, within PP_3789at 4318.734 kb on - strand, within PP_3789

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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=coldshock; SoilTreatmentTime=144_hrs
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4,316,491 + PP_3788 0.37 -1.0
4,316,491 + PP_3788 0.37 -0.3
4,316,494 + PP_3788 0.37 +0.4
4,316,494 + -1.6
4,316,495 - PP_3788 0.37 -0.9
4,316,495 - PP_3788 0.37 -0.6
4,316,495 - PP_3788 0.37 +0.6
4,316,632 + PP_3788 0.46 -0.5
4,316,633 - +0.3
4,316,745 + PP_3788 0.53 +0.6
4,316,746 - PP_3788 0.53 -1.0
4,316,746 - PP_3788 0.53 +0.9
4,316,818 - PP_3788 0.58 +0.3
4,316,818 - PP_3788 0.58 -0.2
4,316,818 - PP_3788 0.58 +0.5
4,316,821 + PP_3788 0.58 +0.3
4,316,822 - PP_3788 0.58 -0.1
4,316,907 - PP_3788 0.64 -0.1
4,317,000 + PP_3788 0.70 +0.8
4,317,000 + PP_3788 0.70 -0.2
4,317,001 - PP_3788 0.70 -0.0
4,317,001 - PP_3788 0.70 -0.3
4,317,001 - PP_3788 0.70 -0.6
4,317,001 - PP_3788 0.70 +0.6
4,317,002 + PP_3788 0.70 -0.3
4,317,002 + PP_3788 0.70 -0.8
4,317,002 + PP_3788 0.70 -0.3
4,317,002 + PP_3788 0.70 +0.2
4,317,002 + PP_3788 0.70 -0.4
4,317,002 + PP_3788 0.70 +0.5
4,317,003 - PP_3788 0.70 +1.7
4,317,003 - PP_3788 0.70 -0.6
4,317,003 - PP_3788 0.70 +1.0
4,317,003 - PP_3788 0.70 -0.4
4,317,003 - PP_3788 0.70 -0.2
4,317,003 - PP_3788 0.70 +0.3
4,317,020 - PP_3788 0.71 -0.6
4,317,094 + PP_3788 0.76 -0.7
4,317,095 - PP_3788 0.76 -1.1
4,317,159 + PP_3788 0.80 -0.1
4,317,264 + PP_3788 0.87 +1.3
4,317,265 - PP_3788 0.87 -0.6
4,317,303 + PP_3788 0.89 +0.0
4,317,303 + PP_3788 0.89 -1.2
4,317,303 + PP_3788 0.89 +0.6
4,317,303 + PP_3788 0.89 -0.9
4,317,303 + PP_3788 0.89 -0.8
4,317,303 + PP_3788 0.89 -0.8
4,317,303 + PP_3788 0.89 +0.4
4,317,304 - PP_3788 0.89 -0.5
4,317,304 - PP_3788 0.89 -0.3
4,317,304 - PP_3788 0.89 -0.1
4,317,304 - PP_3788 0.89 -0.9
4,317,328 - -1.0
4,317,328 - +0.8
4,317,328 - +0.7
4,317,328 - -1.1
4,317,328 - -0.5
4,317,328 - -0.2
4,317,414 + +1.3
4,317,415 - +0.6
4,317,415 - -0.2
4,317,500 + PP_5628 0.12 +0.7
4,317,501 - PP_5628 0.12 +0.0
4,317,605 + PP_5628 0.50 +0.4
4,317,606 - PP_5628 0.51 +0.5
4,317,957 + PP_3789 0.18 +0.2
4,317,958 - PP_3789 0.18 +1.1
4,317,992 - PP_3789 0.21 -0.2
4,318,020 + PP_3789 0.23 -0.0
4,318,020 + PP_3789 0.23 +0.5
4,318,021 - PP_3789 0.23 -1.8
4,318,065 + PP_3789 0.27 +0.1
4,318,065 + PP_3789 0.27 -0.1
4,318,066 - PP_3789 0.27 -0.1
4,318,111 + PP_3789 0.30 +0.5
4,318,112 - PP_3789 0.30 -1.1
4,318,112 - PP_3789 0.30 -0.7
4,318,166 + PP_3789 0.35 +0.8
4,318,172 + PP_3789 0.35 -0.2
4,318,173 - PP_3789 0.35 +0.3
4,318,173 - PP_3789 0.35 +0.3
4,318,173 - PP_3789 0.35 -0.7
4,318,173 - PP_3789 0.35 -0.9
4,318,240 + PP_3789 0.41 -0.7
4,318,241 - PP_3789 0.41 -0.6
4,318,241 - PP_3789 0.41 +1.0
4,318,241 - PP_3789 0.41 +0.4
4,318,403 + PP_3789 0.54 -0.1
4,318,403 + PP_3789 0.54 +0.4
4,318,403 + PP_3789 0.54 +0.3
4,318,404 - PP_3789 0.54 -2.4
4,318,405 + PP_3789 0.54 -0.1
4,318,405 + PP_3789 0.54 -0.7
4,318,406 - PP_3789 0.55 -0.4
4,318,406 - PP_3789 0.55 +1.6
4,318,406 - PP_3789 0.55 +0.1
4,318,424 - PP_3789 0.56 -0.0
4,318,475 + PP_3789 0.60 -0.9
4,318,475 + PP_3789 0.60 +1.3
4,318,476 - PP_3789 0.60 -0.3
4,318,499 - PP_3789 0.62 +0.1
4,318,499 - PP_3789 0.62 -1.1
4,318,499 - PP_3789 0.62 +0.3
4,318,571 + PP_3789 0.68 +0.3
4,318,572 - PP_3789 0.68 +0.5
4,318,663 + PP_3789 0.76 +0.9
4,318,663 + PP_3789 0.76 -0.0
4,318,727 + PP_3789 0.81 +0.7
4,318,733 + PP_3789 0.81 +0.4
4,318,733 + PP_3789 0.81 +0.3
4,318,733 + PP_3789 0.81 +1.4
4,318,733 + PP_3789 0.81 +0.5
4,318,733 + PP_3789 0.81 -0.2
4,318,734 - PP_3789 0.81 +1.1
4,318,734 - PP_3789 0.81 +0.5

Or see this region's nucleotide sequence