Strain Fitness in Pseudomonas putida KT2440 around PP_4607

Experiment: Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=0_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_4606 and PP_4607 are separated by 175 nucleotidesPP_4607 and PP_4608 overlap by 4 nucleotidesPP_4608 and PP_4609 are separated by 5 nucleotidesPP_4609 and PP_4610 overlap by 1 nucleotides PP_4606: PP_4606 - putative Outer membrane ferric siderophore receptor, at 5,226,668 to 5,229,058 _4606 PP_4607: PP_4607 - putative Transmembrane sensor, at 5,229,234 to 5,230,214 _4607 PP_4608: PP_4608 - RNA polymerase sigma-70 factor, ECF subfamily, at 5,230,211 to 5,230,786 _4608 PP_4609: PP_4609 - conserved membrane protein of unknown function, at 5,230,792 to 5,231,118 _4609 PP_4610: PP_4610 - conserved protein of unknown function containing PepSY-associated TM helix domain, at 5,231,118 to 5,232,695 _4610 Position (kb) 5229 5230 5231Strain fitness (log2 ratio) -2 -1 0 1 2at 5228.265 kb on + strand, within PP_4606at 5228.266 kb on - strand, within PP_4606at 5228.266 kb on - strand, within PP_4606at 5228.295 kb on + strand, within PP_4606at 5228.295 kb on + strand, within PP_4606at 5228.295 kb on + strand, within PP_4606at 5228.295 kb on + strand, within PP_4606at 5228.295 kb on + strand, within PP_4606at 5228.296 kb on - strand, within PP_4606at 5228.296 kb on - strand, within PP_4606at 5228.296 kb on - strand, within PP_4606at 5228.296 kb on - strand, within PP_4606at 5228.359 kb on - strand, within PP_4606at 5228.673 kb on + strand, within PP_4606at 5228.674 kb on - strand, within PP_4606at 5228.680 kb on - strand, within PP_4606at 5228.680 kb on - strand, within PP_4606at 5228.680 kb on - strand, within PP_4606at 5228.758 kb on + strand, within PP_4606at 5228.759 kb on - strand, within PP_4606at 5228.877 kb on + strandat 5228.878 kb on - strandat 5228.899 kb on + strandat 5228.955 kb on + strandat 5228.955 kb on + strandat 5228.956 kb on - strandat 5229.114 kb on - strandat 5229.135 kb on - strandat 5229.196 kb on + strandat 5229.207 kb on + strandat 5229.235 kb on + strandat 5229.381 kb on - strand, within PP_4607at 5229.395 kb on - strand, within PP_4607at 5229.437 kb on - strand, within PP_4607at 5229.439 kb on + strand, within PP_4607at 5229.439 kb on + strand, within PP_4607at 5229.439 kb on + strand, within PP_4607at 5229.439 kb on + strand, within PP_4607at 5229.440 kb on - strand, within PP_4607at 5229.506 kb on + strand, within PP_4607at 5229.518 kb on - strand, within PP_4607at 5229.518 kb on - strand, within PP_4607at 5229.518 kb on - strand, within PP_4607at 5229.844 kb on + strand, within PP_4607at 5229.845 kb on - strand, within PP_4607at 5229.845 kb on - strand, within PP_4607at 5230.072 kb on + strand, within PP_4607at 5230.294 kb on + strand, within PP_4608at 5230.295 kb on - strand, within PP_4608at 5230.295 kb on - strand, within PP_4608at 5230.295 kb on - strand, within PP_4608at 5230.295 kb on - strand, within PP_4608at 5230.295 kb on - strand, within PP_4608at 5230.347 kb on + strand, within PP_4608at 5230.348 kb on - strandat 5230.423 kb on + strand, within PP_4608at 5230.522 kb on + strand, within PP_4608at 5230.544 kb on + strand, within PP_4608at 5230.544 kb on + strand, within PP_4608at 5230.544 kb on + strand, within PP_4608at 5230.545 kb on - strand, within PP_4608at 5230.545 kb on - strand, within PP_4608at 5230.575 kb on + strand, within PP_4608at 5230.575 kb on + strand, within PP_4608at 5230.575 kb on + strand, within PP_4608at 5230.576 kb on - strandat 5230.679 kb on + strand, within PP_4608at 5230.680 kb on - strand, within PP_4608at 5230.976 kb on - strand, within PP_4609at 5231.083 kb on + strand, within PP_4609at 5231.083 kb on + strand, within PP_4609at 5231.083 kb on + strandat 5231.083 kb on + strand, within PP_4609at 5231.083 kb on + strand, within PP_4609at 5231.084 kb on - strand, within PP_4609at 5231.084 kb on - strand, within PP_4609at 5231.084 kb on - strand, within PP_4609at 5231.084 kb on - strand, within PP_4609at 5231.179 kb on - strand

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Per-strain Table

Position Strand Gene LocusTag Fraction Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=0_hrs
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5,228,265 + PP_4606 0.67 +0.0
5,228,266 - PP_4606 0.67 +1.5
5,228,266 - PP_4606 0.67 -0.3
5,228,295 + PP_4606 0.68 +0.1
5,228,295 + PP_4606 0.68 +1.1
5,228,295 + PP_4606 0.68 +0.6
5,228,295 + PP_4606 0.68 +0.6
5,228,295 + PP_4606 0.68 +0.3
5,228,296 - PP_4606 0.68 +0.6
5,228,296 - PP_4606 0.68 -0.6
5,228,296 - PP_4606 0.68 -0.0
5,228,296 - PP_4606 0.68 -0.2
5,228,359 - PP_4606 0.71 +0.4
5,228,673 + PP_4606 0.84 -0.1
5,228,674 - PP_4606 0.84 +0.4
5,228,680 - PP_4606 0.84 +0.8
5,228,680 - PP_4606 0.84 -0.2
5,228,680 - PP_4606 0.84 +0.1
5,228,758 + PP_4606 0.87 +0.1
5,228,759 - PP_4606 0.87 -1.2
5,228,877 + +0.1
5,228,878 - +0.5
5,228,899 + +0.2
5,228,955 + -0.0
5,228,955 + -0.6
5,228,956 - -1.5
5,229,114 - +1.1
5,229,135 - +0.5
5,229,196 + -0.6
5,229,207 + -1.0
5,229,235 + +1.0
5,229,381 - PP_4607 0.15 +0.8
5,229,395 - PP_4607 0.16 +0.1
5,229,437 - PP_4607 0.21 +1.0
5,229,439 + PP_4607 0.21 +0.2
5,229,439 + PP_4607 0.21 +0.6
5,229,439 + PP_4607 0.21 +0.9
5,229,439 + PP_4607 0.21 +0.3
5,229,440 - PP_4607 0.21 +1.3
5,229,506 + PP_4607 0.28 -0.1
5,229,518 - PP_4607 0.29 +1.7
5,229,518 - PP_4607 0.29 +0.5
5,229,518 - PP_4607 0.29 +0.3
5,229,844 + PP_4607 0.62 +0.3
5,229,845 - PP_4607 0.62 +1.3
5,229,845 - PP_4607 0.62 +0.0
5,230,072 + PP_4607 0.85 +2.0
5,230,294 + PP_4608 0.14 +0.8
5,230,295 - PP_4608 0.15 +0.6
5,230,295 - PP_4608 0.15 +1.1
5,230,295 - PP_4608 0.15 -0.3
5,230,295 - PP_4608 0.15 -1.5
5,230,295 - PP_4608 0.15 -1.0
5,230,347 + PP_4608 0.24 +0.7
5,230,348 - +1.8
5,230,423 + PP_4608 0.37 -0.1
5,230,522 + PP_4608 0.54 -0.1
5,230,544 + PP_4608 0.58 +1.1
5,230,544 + PP_4608 0.58 -0.4
5,230,544 + PP_4608 0.58 -1.0
5,230,545 - PP_4608 0.58 +1.3
5,230,545 - PP_4608 0.58 +0.5
5,230,575 + PP_4608 0.63 -1.4
5,230,575 + PP_4608 0.63 -0.4
5,230,575 + PP_4608 0.63 -2.3
5,230,576 - -0.4
5,230,679 + PP_4608 0.81 +0.2
5,230,680 - PP_4608 0.81 +0.7
5,230,976 - PP_4609 0.56 +0.6
5,231,083 + PP_4609 0.89 +0.5
5,231,083 + PP_4609 0.89 -0.6
5,231,083 + -0.6
5,231,083 + PP_4609 0.89 -0.5
5,231,083 + PP_4609 0.89 +1.3
5,231,084 - PP_4609 0.89 +1.1
5,231,084 - PP_4609 0.89 -1.2
5,231,084 - PP_4609 0.89 -1.1
5,231,084 - PP_4609 0.89 +0.4
5,231,179 - +0.0

Or see this region's nucleotide sequence