Experiment set11IT003 for Agrobacterium fabrum C58

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Ethyl benzoate carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Ethyl benzoate (2.5 mM), pH=7
Culturing: Agro_ML11, 24-well plate, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 1/6/22
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 15 genes in this experiment

For carbon source Ethyl benzoate in Agrobacterium fabrum C58

For carbon source Ethyl benzoate across organisms

SEED Subsystems

Subsystem #Specific
Multidrug Resistance Efflux Pumps 3
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 2
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) 2
Bacterial RNA-metabolizing Zn-dependent hydrolases 1
Biotin biosynthesis 1
Entner-Doudoroff Pathway 1
Fermentations: Mixed acid 1
Glycolate, glyoxylate interconversions 1
Methylglyoxal Metabolism 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
n-Phenylalkanoic acid degradation 1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
long-chain fatty acid activation 1 1 1
acetaldehyde biosynthesis I 1 1 1
phytol degradation 4 3 3
ethanol degradation II 3 3 2
putrescine degradation V 2 2 1
3-methyl-branched fatty acid α-oxidation 6 3 3
γ-linolenate biosynthesis II (animals) 2 1 1
putrescine degradation I 2 1 1
ethylene glycol degradation 2 1 1
ethanol degradation I 2 1 1
linoleate biosynthesis II (animals) 2 1 1
pyruvate fermentation to ethanol II 2 1 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 4
octane oxidation 5 2 2
ethanol degradation IV 3 3 1
L-leucine degradation III 3 2 1
putrescine degradation IV 3 2 1
L-isoleucine degradation II 3 2 1
ethanol degradation III 3 2 1
hypotaurine degradation 3 2 1
L-valine degradation II 3 2 1
oleate biosynthesis I (plants) 3 1 1
alkane biosynthesis II 3 1 1
pyruvate fermentation to ethanol III 3 1 1
histamine degradation 3 1 1
L-methionine degradation III 3 1 1
starch degradation I 3 1 1
pyruvate fermentation to ethanol I 3 1 1
noradrenaline and adrenaline degradation 13 4 4
serotonin degradation 7 3 2
ceramide degradation by α-oxidation 7 2 2
fatty acid α-oxidation I (plants) 4 2 1
L-phenylalanine degradation III 4 2 1
L-tyrosine degradation III 4 2 1
L-tryptophan degradation X (mammalian, via tryptamine) 4 2 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 4
phosphatidylcholine acyl editing 4 1 1
wax esters biosynthesis II 4 1 1
salidroside biosynthesis 4 1 1
cytidine-5'-diphosphate-glycerol biosynthesis 4 1 1
putrescine degradation III 4 1 1
D-arabinose degradation II 4 1 1
long chain fatty acid ester synthesis (engineered) 4 1 1
sporopollenin precursors biosynthesis 18 4 4
pyruvate fermentation to isobutanol (engineered) 5 4 1
mitochondrial NADPH production (yeast) 5 3 1
dopamine degradation 5 1 1
(S)-propane-1,2-diol degradation 5 1 1
phenylethanol biosynthesis 5 1 1
ethanolamine utilization 5 1 1
acetylene degradation (anaerobic) 5 1 1
fatty acid salvage 6 5 1
stearate biosynthesis II (bacteria and plants) 6 5 1
stearate biosynthesis IV 6 4 1
6-gingerol analog biosynthesis (engineered) 6 2 1
alkane oxidation 6 1 1
stearate biosynthesis I (animals) 6 1 1
3-methylbutanol biosynthesis (engineered) 7 6 1
superpathway of glycol metabolism and degradation 7 4 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
capsaicin biosynthesis 7 1 1
limonene degradation IV (anaerobic) 7 1 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 6 1
glycogen degradation I 8 6 1
superpathway of ornithine degradation 8 4 1
butanol and isobutanol biosynthesis (engineered) 8 3 1
2-deoxy-D-ribose degradation II 8 2 1
aromatic biogenic amine degradation (bacteria) 8 1 1
Entner-Doudoroff pathway II (non-phosphorylative) 9 5 1
superpathway of fermentation (Chlamydomonas reinhardtii) 9 3 1
suberin monomers biosynthesis 20 3 2
superpathway of fatty acid biosynthesis II (plant) 43 38 4
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 6 1
superpathway of L-arginine and L-ornithine degradation 13 8 1
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 5 1
L-tryptophan degradation V (side chain pathway) 13 1 1
palmitate biosynthesis II (type II fatty acid synthase) 31 29 2
mixed acid fermentation 16 9 1
cutin biosynthesis 16 1 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 5 1
heterolactic fermentation 18 12 1
superpathway of anaerobic sucrose degradation 19 13 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 10 1
superpathway of N-acetylneuraminate degradation 22 12 1
superpathway of fatty acids biosynthesis (E. coli) 53 49 2
palmitate biosynthesis III 29 28 1
oleate β-oxidation 35 27 1
superpathway of pentose and pentitol degradation 42 16 1