Strain Fitness in Pseudomonas putida KT2440 around PP_0625

Experiment: 48hr timepoint from 1L M9/1% dextrose BATCH fermentation in 2L Sartorius Biostat reactor kept at 10% DO.

Add experiment(s):

Zoom: Pan:

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.

download SVG
500 ntPP_0623 and PP_0624 overlap by 4 nucleotidesPP_0624 and PP_0625 are separated by 249 nucleotidesPP_0625 and PP_t07 are separated by 362 nucleotidesPP_t07 and PP_t08 are separated by 4 nucleotidesPP_t08 and PP_t09 are separated by 6 nucleotidesPP_t09 and PP_t10 are separated by 46 nucleotidesPP_t10 and PP_t11 are separated by 5 nucleotidesPP_t11 and PP_0626 are separated by 190 nucleotides PP_0623: PP_0623 - 23S rRNA pseudouridine(1911,1915,1917) synthase, at 728,512 to 729,474 _0623 PP_0624: PP_0624 - Uncharacterized protein YfiH, at 729,471 to 730,211 _0624 PP_0625: PP_0625 - Chaperone protein ClpB, at 730,461 to 733,025 _0625 PP_t07: PP_t07 - tRNA-Asn, at 733,388 to 733,463 _t07 PP_t08: PP_t08 - tRNA-Pro, at 733,468 to 733,544 _t08 PP_t09: PP_t09 - tRNA-Lys, at 733,551 to 733,626 _t09 PP_t10: PP_t10 - tRNA-Pro, at 733,673 to 733,749 _t10 PP_t11: PP_t11 - tRNA-Lys, at 733,755 to 733,830 _t11 PP_0626: PP_0626 - NADH dehydrogenase, at 734,021 to 735,316 _0626 Position (kb) 730 731 732 733 734Strain fitness (log2 ratio) -2 -1 0 1 2 3at 730.056 kb on - strand, within PP_0624at 730.056 kb on - strand, within PP_0624at 730.057 kb on + strand, within PP_0624at 730.059 kb on + strand, within PP_0624at 730.059 kb on + strand, within PP_0624at 730.059 kb on + strand, within PP_0624at 730.059 kb on + strand, within PP_0624at 730.059 kb on + strand, within PP_0624at 730.060 kb on - strand, within PP_0624at 730.060 kb on - strand, within PP_0624at 730.060 kb on - strand, within PP_0624at 730.060 kb on - strand, within PP_0624at 730.060 kb on - strand, within PP_0624at 730.108 kb on - strand, within PP_0624at 730.152 kb on + strandat 730.152 kb on + strandat 730.210 kb on - strandat 730.280 kb on + strandat 730.281 kb on - strandat 730.281 kb on - strandat 730.281 kb on - strandat 730.377 kb on + strandat 730.377 kb on + strandat 730.378 kb on - strandat 730.378 kb on - strandat 730.381 kb on + strandat 730.381 kb on + strandat 730.381 kb on + strandat 730.382 kb on - strandat 730.382 kb on - strandat 730.382 kb on - strandat 730.383 kb on + strandat 730.383 kb on + strandat 730.384 kb on - strandat 730.408 kb on + strandat 730.408 kb on + strandat 730.446 kb on - strandat 730.455 kb on + strandat 730.455 kb on + strandat 730.455 kb on + strandat 730.455 kb on + strandat 730.455 kb on + strandat 730.456 kb on - strandat 730.456 kb on - strandat 730.456 kb on - strandat 730.456 kb on - strandat 730.456 kb on - strandat 730.456 kb on - strandat 730.456 kb on - strandat 730.456 kb on - strandat 730.468 kb on + strandat 730.477 kb on + strandat 730.681 kb on + strandat 730.950 kb on + strand, within PP_0625at 730.950 kb on + strand, within PP_0625at 730.951 kb on - strand, within PP_0625at 730.951 kb on - strand, within PP_0625at 731.194 kb on + strand, within PP_0625at 731.195 kb on - strand, within PP_0625at 731.195 kb on - strand, within PP_0625at 731.211 kb on + strand, within PP_0625at 731.392 kb on + strand, within PP_0625at 731.416 kb on - strand, within PP_0625at 731.530 kb on - strand, within PP_0625at 731.598 kb on + strand, within PP_0625at 731.598 kb on + strand, within PP_0625at 731.599 kb on - strand, within PP_0625at 731.599 kb on - strand, within PP_0625at 731.599 kb on - strand, within PP_0625at 731.755 kb on - strand, within PP_0625at 732.212 kb on - strand, within PP_0625at 732.212 kb on - strand, within PP_0625at 732.417 kb on + strand, within PP_0625at 732.417 kb on + strand, within PP_0625at 732.417 kb on + strand, within PP_0625at 732.417 kb on + strand, within PP_0625at 732.418 kb on - strand, within PP_0625at 732.421 kb on + strand, within PP_0625at 732.421 kb on + strand, within PP_0625at 732.421 kb on + strand, within PP_0625at 732.421 kb on + strand, within PP_0625at 732.421 kb on + strand, within PP_0625at 732.421 kb on + strand, within PP_0625at 732.422 kb on - strand, within PP_0625at 732.422 kb on - strand, within PP_0625at 732.422 kb on - strand, within PP_0625at 732.422 kb on - strand, within PP_0625at 732.442 kb on - strand, within PP_0625at 732.777 kb on - strandat 732.889 kb on - strandat 733.179 kb on + strandat 733.181 kb on + strandat 733.181 kb on + strandat 733.181 kb on + strandat 733.475 kb on + strandat 733.475 kb on + strandat 733.629 kb on + strandat 733.681 kb on - strand, within PP_t10at 733.681 kb on - strand, within PP_t10at 733.763 kb on - strand, within PP_t11at 733.763 kb on - strand, within PP_t11at 733.775 kb on - strand, within PP_t11at 733.775 kb on - strand, within PP_t11at 733.775 kb on - strand, within PP_t11at 733.912 kb on + strandat 733.913 kb on - strandat 733.913 kb on - strandat 733.930 kb on + strandat 733.931 kb on - strandat 733.931 kb on - strandat 733.934 kb on + strandat 733.934 kb on + strandat 733.934 kb on + strandat 733.935 kb on - strandat 733.935 kb on - strandat 733.935 kb on - strandat 733.935 kb on - strandat 733.935 kb on - strandat 733.935 kb on - strandat 733.935 kb on - strandat 733.935 kb on - strandat 733.989 kb on - strandat 734.022 kb on + strandat 734.023 kb on - strand

download strain data

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.
remove
730,056 - PP_0624 0.79 +0.1
730,056 - PP_0624 0.79 -0.5
730,057 + PP_0624 0.79 -0.8
730,059 + PP_0624 0.79 +1.1
730,059 + PP_0624 0.79 -2.1
730,059 + PP_0624 0.79 -0.1
730,059 + PP_0624 0.79 +0.3
730,059 + PP_0624 0.79 -0.0
730,060 - PP_0624 0.79 -0.4
730,060 - PP_0624 0.79 -0.2
730,060 - PP_0624 0.79 +0.1
730,060 - PP_0624 0.79 +3.7
730,060 - PP_0624 0.79 +0.5
730,108 - PP_0624 0.86 -0.2
730,152 + -0.1
730,152 + +1.0
730,210 - -0.6
730,280 + -1.9
730,281 - -0.7
730,281 - -0.8
730,281 - -0.7
730,377 + +1.1
730,377 + +1.1
730,378 - +1.2
730,378 - -1.3
730,381 + -0.3
730,381 + +0.9
730,381 + +0.7
730,382 - +0.2
730,382 - +0.7
730,382 - -0.4
730,383 + +0.4
730,383 + -1.5
730,384 - +0.8
730,408 + -2.0
730,408 + +0.7
730,446 - -0.4
730,455 + -0.7
730,455 + +0.4
730,455 + +0.2
730,455 + +1.6
730,455 + -0.4
730,456 - -0.3
730,456 - -1.0
730,456 - -1.8
730,456 - -0.7
730,456 - -0.5
730,456 - -0.7
730,456 - -0.8
730,456 - -0.6
730,468 + +1.5
730,477 + -0.1
730,681 + +2.2
730,950 + PP_0625 0.19 +1.6
730,950 + PP_0625 0.19 -0.9
730,951 - PP_0625 0.19 -1.1
730,951 - PP_0625 0.19 +0.9
731,194 + PP_0625 0.29 -0.4
731,195 - PP_0625 0.29 -0.4
731,195 - PP_0625 0.29 +0.1
731,211 + PP_0625 0.29 +1.2
731,392 + PP_0625 0.36 -1.2
731,416 - PP_0625 0.37 -1.0
731,530 - PP_0625 0.42 +0.3
731,598 + PP_0625 0.44 -0.2
731,598 + PP_0625 0.44 +0.8
731,599 - PP_0625 0.44 +0.3
731,599 - PP_0625 0.44 -0.1
731,599 - PP_0625 0.44 +0.2
731,755 - PP_0625 0.50 -0.6
732,212 - PP_0625 0.68 -0.0
732,212 - PP_0625 0.68 -0.4
732,417 + PP_0625 0.76 +0.0
732,417 + PP_0625 0.76 -0.4
732,417 + PP_0625 0.76 +0.6
732,417 + PP_0625 0.76 +0.8
732,418 - PP_0625 0.76 -0.3
732,421 + PP_0625 0.76 -0.7
732,421 + PP_0625 0.76 -1.2
732,421 + PP_0625 0.76 -0.0
732,421 + PP_0625 0.76 -0.9
732,421 + PP_0625 0.76 -0.8
732,421 + PP_0625 0.76 -0.4
732,422 - PP_0625 0.76 -0.1
732,422 - PP_0625 0.76 +0.8
732,422 - PP_0625 0.76 -0.4
732,422 - PP_0625 0.76 +0.6
732,442 - PP_0625 0.77 +2.7
732,777 - +0.0
732,889 - +1.7
733,179 + +0.7
733,181 + +3.7
733,181 + +1.2
733,181 + +2.7
733,475 + +2.2
733,475 + +0.7
733,629 + -0.6
733,681 - PP_t10 0.10 -1.7
733,681 - PP_t10 0.10 +0.4
733,763 - PP_t11 0.11 +0.4
733,763 - PP_t11 0.11 +0.2
733,775 - PP_t11 0.26 -0.7
733,775 - PP_t11 0.26 +1.7
733,775 - PP_t11 0.26 +1.4
733,912 + -1.0
733,913 - +1.6
733,913 - +0.4
733,930 + -1.5
733,931 - -1.1
733,931 - +0.4
733,934 + -0.2
733,934 + -0.7
733,934 + +0.6
733,935 - -0.6
733,935 - +0.3
733,935 - -1.4
733,935 - +0.0
733,935 - -1.4
733,935 - +1.7
733,935 - -0.2
733,935 - -1.8
733,989 - -1.6
734,022 + +0.8
734,023 - +0.7

Or see this region's nucleotide sequence