Experiment set46IT024 for Escherichia coli BW25113

Compare to:

Mixed culture; Bdellovibrio bacteriovorus HD100 1:100 starting OD to Ecoli; 0.02X nutrient broth; outgrowth in LBwithKan

200 most important genes:

  gene name fitness t score description  
b1830 prc -5.1 -10.3 carboxy-terminal protease for penicillin-binding protein 3 (NCBI) compare
b3839 tatC -3.5 -12.9 TatABCE protein translocation system subunit (NCBI) compare
b2567 rnc -3.3 -2.3 ribonuclease III (NCBI) compare
b4402 yjjY -3.0 -2.2 hypothetical protein (NCBI) compare
b0438 clpX -2.7 -9.7 ATP-dependent protease ATP-binding subunit (NCBI) compare
b0437 clpP -2.7 -8.8 ATP-dependent Clp protease proteolytic subunit (NCBI) compare
b4552 yrhC -2.5 -1.6 no description compare
b3613 yibP -2.5 -7.9 putative membrane protein (VIMSS) compare
b1236 galU -2.5 -7.2 glucose-1-phosphate uridylyltransferase (NCBI) compare
b3290 trkA -2.4 -3.2 potassium transporter peripheral membrane component (NCBI) compare
b3052 rfaE -2.3 -9.3 fused heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase (NCBI) compare
b3621 rfaC -2.1 -9.1 ADP-heptose:LPS heptosyl transferase I (NCBI) compare
b2699 recA -2.1 -2.8 recombinase A (NCBI) compare
b2620 smpB -2.1 -2.3 SsrA-binding protein (NCBI) compare
b4593 ymgI -2.1 -1.4 hypothetical protein (RefSeq) compare
b0222 lpcA -2.1 -3.2 phosphoheptose isomerase (NCBI) compare
b3792 wzxE -2.1 -10.5 O-antigen translocase (NCBI) compare
b0738 tolR -2.0 -3.6 membrane spanning protein in TolA-TolQ-TolR complex (NCBI) compare
b3619 rfaD -2.0 -7.1 ADP-L-glycero-D-mannoheptose-6-epimerase, NAD(P)-binding (NCBI) compare
b2820 recB -1.9 -2.6 exonuclease V (RecBCD complex), beta subunit (NCBI) compare
b1192 ldcA -1.9 -5.5 L,D-carboxypeptidase A (NCBI) compare
b0114 aceE -1.8 -2.8 pyruvate dehydrogenase subunit E1 (NCBI) compare
b2297 pta -1.8 -1.7 phosphate acetyltransferase (NCBI) compare
b3838 tatB -1.8 -5.9 sec-independent translocase (NCBI) compare
b1292 sapC -1.7 -2.6 predicted antimicrobial peptide transporter subunit (NCBI) compare
b4375 prfC -1.7 -5.9 peptide chain release factor 3 (NCBI) compare
b3386 rpe -1.7 -1.1 ribulose-phosphate 3-epimerase (NCBI) compare
b3811 xerC -1.6 -2.9 site-specific tyrosine recombinase XerC (NCBI) compare
b0890 ftsK -1.6 -6.4 DNA-binding membrane protein required for chromosome resolution and partitioning (NCBI) compare
b1951 rcsA -1.6 -1.9 DNA-binding transcriptional activator, co-regulator with RcsB (NCBI) compare
b1860 ruvB -1.6 -1.8 Holliday junction DNA helicase B (NCBI) compare
b4172 hfq -1.6 -1.5 RNA-binding protein Hfq (NCBI) compare
b3631 rfaG -1.6 -12.7 glucosyltransferase I (NCBI) compare
b0739 tolA -1.6 -4.7 cell envelope integrity inner membrane protein TolA (NCBI) compare
b4239 treC -1.6 -3.1 trehalose-6-P hydrolase (NCBI) compare
b2894 xerD -1.6 -1.8 site-specific tyrosine recombinase XerD (NCBI) compare
b0741 pal -1.5 -5.3 peptidoglycan-associated outer membrane lipoprotein (NCBI) compare
b3341 rpsG -1.5 -1.9 30S ribosomal protein S7 (NCBI) compare
b2912 ygfA -1.5 -4.6 putative ligase (VIMSS) compare
b1506 yneL -1.5 -2.5 predicted transcriptional regulator (NCBI) compare
b4042 dgkA -1.4 -2.9 diacylglycerol kinase (NCBI) compare
b3620 rfaF -1.4 -6.9 ADP-heptose:LPS heptosyltransferase II (NCBI) compare
b3163 nlpI -1.4 -4.1 hypothetical protein (NCBI) compare
b2501 ppk -1.4 -7.3 polyphosphate kinase (NCBI) compare
b1677 lpp -1.3 -2.2 murein lipoprotein (NCBI) compare
b0726 sucA -1.3 -5.0 alpha-ketoglutarate decarboxylase (NCBI) compare
b4202 rpsR -1.3 -2.1 30S ribosomal protein S18 (NCBI) compare
b4676 yoaK -1.3 -0.7 expressed protein (RefSeq) compare
b1551 b1551 -1.3 -0.8 orf, hypothetical protein (VIMSS) compare
b3162 deaD -1.3 -4.8 inducible ATP-independent RNA helicase (VIMSS) compare
b0740 tolB -1.3 -4.9 translocation protein TolB precursor (NCBI) compare
b2288 nuoA -1.2 -3.1 NADH dehydrogenase I chain A (VIMSS) compare
b0049 apaH -1.2 -3.6 diadenosinetetraphosphatase (NCBI) compare
b0407 yajC -1.2 -2.6 preprotein translocase subunit YajC (NCBI) compare
b3725 pstB -1.2 -1.2 phosphate transporter subunit (NCBI) compare
b1863 ruvC -1.2 -2.3 Holliday junction resolvase (NCBI) compare
b0053 surA -1.2 -5.8 peptidyl-prolyl cis-trans isomerase (PPIase) (NCBI) compare
b1351 racC -1.2 -0.8 Rac prophage; predicted protein (NCBI) compare
b1291 sapD -1.1 -2.3 predicted antimicrobial peptide transporter subunit (NCBI) compare
b0912 ihfB -1.1 -4.1 integration host factor subunit beta (NCBI) compare
b3027 ygiZ -1.1 -0.7 conserved inner membrane protein (NCBI) compare
b3977 tyrU -1.0 -1.2 tRNA-Tyr (NCBI) compare
b2846 yqeH -1.0 -0.6 orf, hypothetical protein (VIMSS) compare
b3390 aroK -1.0 -1.8 shikimate kinase I (NCBI) compare
b0688 pgm -1.0 -4.4 phosphoglucomutase (NCBI) compare
b2276 nuoN -1.0 -4.9 NADH:ubiquinone oxidoreductase, membrane subunit N (RefSeq) compare
b1129 phoQ -1.0 -1.7 sensory histidine kinase in two-compoent regulatory system with PhoP (NCBI) compare
b4520 ymgF -1.0 -1.7 hypothetical protein (NCBI) compare
b3933 ftsN -1.0 -6.0 essential cell division protein (NCBI) compare
b2808 gcvA -1.0 -3.9 DNA-binding transcriptional dual regulator (NCBI) compare
b3261 fis -1.0 -2.7 DNA-binding protein Fis (NCBI) compare
b1429 tehA -1.0 -1.7 potassium-tellurite ethidium and proflavin transporter (NCBI) compare
b4155 yjeA -1.0 -0.7 putative lysyl-tRNA synthetase (VIMSS) compare
b3806 cyaA -1.0 -5.3 adenylate cyclase (NCBI) compare
b2285 nuoE -1.0 -2.3 NADH dehydrogenase subunit E (NCBI) compare
b3836 b3836 -1.0 -2.0 orf, hypothetical protein (VIMSS) compare
b1502 ydeQ -1.0 -2.5 predicted fimbrial-like adhesin protein (NCBI) compare
b3183 obgE -1.0 -1.0 GTPase involved in cell partioning and DNA repair (NCBI) compare
b3204 ptsN -1.0 -4.0 sugar-specific enzyme IIA component of PTS (NCBI) compare
b1182 hlyE -1.0 -0.6 hemolysin E (VIMSS) compare
b0677 nagA -0.9 -5.1 N-acetylglucosamine-6-phosphate deacetylase (NCBI) compare
b1505 ydeT -0.9 -1.2 hypothetical protein (RefSeq) compare
b3229 sspA -0.9 -3.1 stringent starvation protein A (NCBI) compare
b2329 aroC -0.9 -4.5 chorismate synthase (NCBI) compare
b1984 asnW -0.9 -1.4 tRNA-Asn (NCBI) compare
b0737 tolQ -0.9 -2.7 membrane spanning protein in TolA-TolQ-TolR complex (NCBI) compare
b1572 ydfB -0.9 -1.7 orf, hypothetical protein (VIMSS) compare
b1576 ydfD -0.9 -0.6 Qin prophage; predicted protein (NCBI) compare
b0386 proC -0.9 -5.3 pyrroline-5-carboxylate reductase (NCBI) compare
b0439 lon -0.9 -4.1 DNA-binding ATP-dependent protease La (NCBI) compare
b0200 gmhB -0.9 -1.8 hypothetical protein (NCBI) compare
b3226 yhcK -0.9 -4.6 putative FADA-type transcriptional regulator (VIMSS) compare
b2286 nuoC -0.9 -4.5 NADH:ubiquinone oxidoreductase, chain C,D (RefSeq) compare
b3790 rffC -0.9 -4.5 TDP-fucosamine acetyltransferase (RefSeq) compare
b3870 glnA -0.9 -2.9 glutamine synthetase (NCBI) compare
b1058 yceO -0.9 -0.4 hypothetical protein (NCBI) compare
b1712 ihfA -0.9 -2.0 integration host factor subunit alpha (NCBI) compare
b3405 ompR -0.9 -3.7 osmolarity response regulator (NCBI) compare
b0303 ykgI -0.9 -0.8 orf, hypothetical protein (VIMSS) compare
b1785 yeaI -0.9 -2.9 predicted diguanylate cyclase (NCBI) compare
b1961 dcm -0.9 -1.6 DNA cytosine methylase (NCBI) compare
b0721 sdhC -0.9 -4.9 succinate dehydrogenase cytochrome b556 large membrane subunit (NCBI) compare
b4435 isrC -0.8 -1.7 unknown RNA (NCBI) compare
b1304 pspA -0.8 -3.3 regulatory protein for phage-shock-protein operon (NCBI) compare
b3630 rfaP -0.8 -6.6 kinase that phosphorylates core heptose of lipopolysaccharide (NCBI) compare
b2017 yefM -0.8 -1.9 orf, hypothetical protein (VIMSS) compare
b3463 ftsE -0.8 -1.1 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI) compare
b1179 ycgL -0.8 -2.3 conserved protein (NCBI) compare
b3609 secB -0.8 -2.3 export protein SecB (NCBI) compare
b1293 sapB -0.8 -1.3 predicted antimicrobial peptide transporter subunit (NCBI) compare
b2363 yfdT -0.8 -2.3 CPS-53 (KpLE1) prophage; predicted protein (NCBI) compare
b0902 pflA -0.8 -5.7 pyruvate formate lyase activating enzyme 1 (NCBI) compare
b0658 ybeX -0.8 -0.9 predicteed ion transport (NCBI) compare
b2279 nuoK -0.8 -2.0 NADH dehydrogenase subunit K (NCBI) compare
b3414 gntY -0.8 -3.7 predicted gluconate transport associated protein (NCBI) compare
b0730 mngR -0.8 -1.5 DNA-binding transcriptional dual regulator, fatty-acyl-binding (NCBI) compare
b1257 yciE -0.8 -0.5 hypothetical protein (NCBI) compare
b1273 yciN -0.8 -1.7 hypothetical protein (NCBI) compare
b2424 cysU -0.8 -2.9 sulfate/thiosulfate transporter subunit (NCBI) compare
b2352 yfdI -0.8 -0.5 CPS-53 (KpLE1) prophage; predicted inner membrane protein (NCBI) compare
b4481 rffT -0.8 -4.1 4-alpha-L-fucosyltransferase (NCBI) compare
b1363 trkG -0.8 -0.5 Rac prophage; potassium transporter subunit (NCBI) compare
b4139 aspA -0.8 -5.4 aspartate ammonia-lyase (aspartase) (VIMSS) compare
b2168 fruK -0.8 -1.3 1-phosphofructokinase (NCBI) compare
b2282 nuoH -0.8 -3.1 NADH dehydrogenase subunit H (NCBI) compare
b2287 nuoB -0.8 -3.5 NADH dehydrogenase subunit B (NCBI) compare
b3791 rffA -0.8 -4.5 TDP-4-oxo-6-deoxy-D-glucose transaminase (NCBI) compare
b4177 purA -0.7 -1.3 adenylosuccinate synthetase (NCBI) compare
b3623 rfaK -0.7 -1.8 lipopolysaccharide core biosynthesis (NCBI) compare
b1028 ymdE -0.7 -3.7 orf, hypothetical protein (VIMSS) compare
b2277 nuoM -0.7 -4.7 NADH dehydrogenase subunit M (NCBI) compare
b3210 arcB -0.7 -4.2 hybrid sensory histidine kinase in two-component regulatory system with ArcA (NCBI) compare
b2512 yfgL -0.7 -3.9 protein assembly complex, lipoprotein component (NCBI) compare
b3916 pfkA -0.7 -2.5 6-phosphofructokinase (NCBI) compare
b4557 yidD -0.7 -2.4 hypothetical protein (NCBI) compare
b3169 nusA -0.7 -2.6 transcription elongation factor NusA (NCBI) compare
b4407 thiS -0.7 -1.6 sulfur carrier protein ThiS (NCBI) compare
b2284 nuoF -0.7 -3.3 NADH:ubiquinone oxidoreductase, chain F (NCBI) compare
b0903 pflB -0.7 -5.6 pyruvate formate lyase I (NCBI) compare
b0908 aroA -0.7 -4.2 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI) compare
b3858 yihD -0.7 -1.8 hypothetical protein (NCBI) compare
b2278 nuoL -0.7 -5.0 NADH dehydrogenase subunit L (NCBI) compare
b3624 rfaZ -0.7 -1.7 lipopolysaccharide core biosynthesis protein (NCBI) compare
b4025 pgi -0.7 -5.0 glucose-6-phosphate isomerase (NCBI) compare
b3164 pnp -0.7 -2.1 polynucleotide phosphorylase/polyadenylase (RefSeq) compare
b2281 nuoI -0.7 -2.5 NADH dehydrogenase subunit I (NCBI) compare
b2935 tktA -0.7 -1.8 transketolase 1, thiamin-binding (NCBI) compare
b2498 upp -0.7 -1.5 uracil phosphoribosyltransferase (VIMSS) compare
b1482 osmC -0.7 -1.3 osmotically inducible, stress-inducible membrane protein (NCBI) compare
b2055 wcaE -0.7 -0.4 predicted glycosyl transferase (NCBI) compare
b2569 lepA -0.7 -2.8 GTP-binding protein LepA (NCBI) compare
b1579 intQ -0.7 -2.8 Qin prophage; predicted defective integrase (RefSeq) compare
b0310 ykgH -0.7 -1.0 predicted inner membrane protein (NCBI) compare
b2141 yohJ -0.7 -2.4 hypothetical protein (NCBI) compare
b2280 nuoJ -0.7 -3.8 NADH dehydrogenase subunit J (NCBI) compare
b0471 ybaB -0.7 -2.6 hypothetical protein (NCBI) compare
b1499 ydeO -0.7 -0.3 predicted DNA-binding transcriptional acfivator (NCBI) compare
b1850 eda -0.7 -1.0 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase (NCBI) compare
b2937 speB -0.7 -3.4 agmatinase (NCBI) compare
b0720 gltA -0.7 -4.0 citrate synthase (NCBI) compare
b2830 nudH -0.7 -1.0 dinucleoside polyphosphate hydrolase (NCBI) compare
b3626 rfaJ -0.7 -3.4 UDP-D-glucose:(galactosyl)lipopolysaccharide glucosyltransferase (NCBI) compare
b1693 aroD -0.7 -3.2 3-dehydroquinate dehydratase (NCBI) compare
b3842 rfaH -0.7 -3.9 transcriptional activator RfaH (NCBI) compare
b4175 hflC -0.6 -5.2 modulator for HflB protease specific for phage lambda cII repressor (NCBI) compare
b1332 ynaJ -0.6 -0.5 predicted inner membrane protein (NCBI) compare
b0279 yagM -0.6 -0.4 CP4-6 prophage; predicted protein (NCBI) compare
b2110 yehC -0.6 -1.0 predicted periplasmic pilin chaperone (NCBI) compare
b0928 aspC -0.6 -3.2 aspartate aminotransferase, PLP-dependent (NCBI) compare
b3979 thrT -0.6 -0.4 tRNA-Thr (NCBI) compare
b3075 ebgR -0.6 -3.7 DNA-binding transcriptional repressor (NCBI) compare
b3094 exuR -0.6 -3.1 negative regulator of exu regulon, exuT, uxaAC, and uxuB (VIMSS) compare
b4640 yoeG -0.6 -2.1 no description compare
b3462 ftsX -0.6 -3.3 predicted transporter subunit: membrane component of ABC superfamily (NCBI) compare
b3794 rffM -0.6 -4.0 putative UDP-N-acetyl-D-mannosaminuronic acid transferase (NCBI) compare
b1545 pinQ -0.6 -0.2 Qin prophage; predicted site-specific recombinase (NCBI) compare
b1877 yecT -0.6 -2.0 orf, hypothetical protein (VIMSS) compare
b3728 pstS -0.6 -2.4 phosphate transporter subunit (NCBI) compare
b4171 miaA -0.6 -2.4 tRNA delta(2)-isopentenylpyrophosphate transferase (NCBI) compare
b1831 proQ -0.6 -1.4 putative solute/DNA competence effector (NCBI) compare
b0080 fruR -0.6 -3.6 DNA-binding transcriptional dual regulator (NCBI) compare
b2283 nuoG -0.6 -4.1 NADH:ubiquinone oxidoreductase, chain G (RefSeq) compare
b1048 mdoG -0.6 -3.2 glucan biosynthesis protein, periplasmic (NCBI) compare
b0705 ybfL -0.6 -0.4 putative receptor protein (VIMSS) compare
b3625 rfaY -0.6 -2.9 lipopolysaccharide core biosynthesis protein (NCBI) compare
b3198 kdsC -0.6 -2.7 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (NCBI) compare
b1176 minC -0.6 -1.2 septum formation inhibitor (NCBI) compare
b1347 ydaC -0.6 -0.3 Rac prophage; predicted protein (NCBI) compare
b4494 arpB -0.6 -1.5 no description compare
b0364 yaiS -0.6 -2.3 orf, hypothetical protein (VIMSS) compare
b4458 oxyS -0.6 -1.1 global regulatory RNA (NCBI) compare
b2951 yggS -0.6 -2.7 predicted enzyme (NCBI) compare
b3849 trkH -0.6 -4.5 potassium transporter (NCBI) compare
b3292 zntR -0.6 -2.3 zinc-responsive transcriptional regulator (NCBI) compare
b2504 yfgG -0.6 -0.8 Negative regulator of nickel and cobalt uptake (YfgG) (from data) compare
b1258 yciF -0.6 -0.7 hypothetical protein (NCBI) compare
b4508 peaD -0.6 -2.1 putative sensory transduction regulator (VIMSS) compare
b4373 rimI -0.6 -2.5 ribosomal-protein-alanine N-acetyltransferase (NCBI) compare
b3816 corA -0.6 -4.1 magnesium/nickel/cobalt transporter (NCBI) compare
b1222 narX -0.6 -2.9 sensory histidine kinase in two-component regulatory system with NarL (NCBI) compare


Specific Phenotypes

None in this experiment

For Escherichia coli BW25113 in mixed community experiments

For mixed community Mixed culture; Bdellovibrio bacteriovorus HD100 1:100 starting OD to Ecoli; outgrowth in LBwithKan across organisms