Fitness for 5 genes in Escherichia coli BW25113

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500 ntnadB and yfiC overlap by 16 nucleotidesyfiC and srmB are separated by 131 nucleotidessrmB and yfiE are separated by 208 nucleotidesyfiE and yfiK are separated by 102 nucleotides b2574: nadB - L-aspartate oxidase (NCBI), at 2,708,442 to 2,710,064 nadB b2575: yfiC - putative enzyme (VIMSS), at 2,710,049 to 2,710,786 yfiC b2576: srmB - ATP-dependent RNA helicase (NCBI), at 2,710,918 to 2,712,252 srmB b2577: yfiE - putative transcriptional regulator LYSR-type (VIMSS), at 2,712,461 to 2,713,342 yfiE b2578: yfiK - neutral amino-acid efflux system (NCBI), at 2,713,445 to 2,714,032 yfiK
Group Condition b2574 b2575 b2576 b2577 b2578
nadB yfiC srmB yfiE yfiK
phage Phage_N4_cage_3_mouse_3_Cecum_40 hr +0.4 -0.4 -6.3 -0.4 -0.5
stress octanol 0.08 vol% -0.8 -0.3 -4.6 -0.4 -0.4
stress 2,4-Dinitrophenol 2 mM -0.1 -0.1 -5.0 -0.7 +0.0
carbon source carbon source D-Mannose 5mM -0.3 -0.7 -4.2 -0.3 +0.5
micoeukaryotes Tetrahymena sp., Mixed culture-1 -0.2 -0.1 -4.8 +0.1 -0.0
predation 6 hr rep1_HD100_10fold_dilution_grewON +0.3 -0.2 -4.2 -0.9 +0.1
TN_18CS_warm37C_5dbl_rep3 +0.1 -0.1 -5.0 +0.2 -0.0
control PBS_cage_2_mouse_1_Cecum_40 hr +0.3 -0.1 -4.7 +0.1 -0.3
predation 6 hr rep2_HD100_10fold_dilution_grewON -0.2 -0.1 -4.1 +0.0 -0.2
carbon source Ying_all64 rep A; time point 3 +0.1 -0.0 -4.6 +0.2 -0.2
carbon source Ying_all64 rep B; time point 3 -0.1 -0.1 -4.1 +0.2 -0.2
TN_15CS_15C_10dbl_rep3 -0.2 +0.0 -3.9 -0.1 -0.2
nophagecontrol R1_N4_T1_phage0 -0.5 -0.5 -2.5 -0.5 -0.3
attachment_assay_attached_sample Time0_Wash=PBS; Attachment_time=2hrs; Attachment_surface=PDMS; Sample_type=attached; Outgrowth=LB -0.1 -0.5 -2.7 -0.5 -0.3
carbon source carbon source D-Mannose 0.5mM -0.1 -0.1 -3.8 -0.3 +0.2
stress 2,4-Dinitrophenol 2 mM -0.0 -0.2 -3.9 +0.2 -0.1
carbon source Ying_all64 rep B; time point 2 +0.0 -0.1 -3.6 +0.1 -0.4
phage TP4 -0.3 +0.1 -3.8 +0.0 -0.1
motility outer cut, LB soft agar motility assay +0.2 +0.0 -3.5 +0.0 -0.7
TN_18CS_18C_10dbl_rep2 +0.1 +0.1 -3.9 +0.1 -0.2
carbon source Ying_all64 rep C; time point 2 +0.1 +0.1 -3.9 +0.2 -0.3
control PBS_cage_1_mice _Feces_40 hr +0.4 +0.0 -3.3 -0.2 -0.3
carbon source acetate (C) -1.0 +0.3 +2.9 -0.8 -0.2
carbon source a-Ketoglutaric (C) -1.0 +0.2 +2.9 -0.3 -0.1
carbon source a-Ketoglutaric (C) -1.1 +0.1 +2.9 -0.0 -0.0
plasmid transformation mariner vector transformation; agar assay +0.2 +0.4 +2.8 +0.2 +0.5
plasmid transformation vcDART vector transformation; agar assay +0.2 +0.3 +3.6 +0.1 +0.4
plasmid transformation mariner vector transformation; agar assay +0.2 +0.2 +3.7 +0.3 +0.3
plasmid transformation vcDART vector transformation; agar assay +0.4 +0.3 +3.4 +0.4 +0.4
plasmid transformation vcDART vector transformation; liquid outgrowth assay +0.4 +0.1 +3.9 +0.2 +0.4
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