Experiment set11IT002 for Agrobacterium fabrum C58

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 7 genes in this experiment

For carbon source Ethyl benzoate in Agrobacterium fabrum C58

For carbon source Ethyl benzoate across organisms

SEED Subsystems

Subsystem	#Specific
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Biotin biosynthesis	1
Entner-Doudoroff Pathway	1
Fermentations: Mixed acid	1
Glycolate, glyoxylate interconversions	1
Methylglyoxal Metabolism	1
Multidrug Resistance Efflux Pumps	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:

• Fatty acid metabolism
• Glycolysis / Gluconeogenesis
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Tryptophan metabolism
• 1- and 2-Methylnaphthalene degradation
• 3-Chloroacrylic acid degradation
• Limonene and pinene degradation
• Ascorbate and aldarate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• Butanoate metabolism
• Retinol metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450

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
pyruvate fermentation to ethanol II	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
ethanol degradation I	2	1	1
ethylene glycol degradation	2	1	1
putrescine degradation I	2	1	1
linoleate biosynthesis II (animals)	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
ethanol degradation III	3	2	1
putrescine degradation IV	3	2	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
hypotaurine degradation	3	2	1
alkane biosynthesis II	3	1	1
pyruvate fermentation to ethanol III	3	1	1
L-methionine degradation III	3	1	1
histamine degradation	3	1	1
pyruvate fermentation to ethanol I	3	1	1
oleate biosynthesis I (plants)	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-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	4
wax esters biosynthesis II	4	1	1
D-arabinose degradation II	4	1	1
phosphatidylcholine acyl editing	4	1	1
putrescine degradation III	4	1	1
salidroside biosynthesis	4	1	1
cytidine-5'-diphosphate-glycerol biosynthesis	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
(S)-propane-1,2-diol degradation	5	1	1
phenylethanol biosynthesis	5	1	1
dopamine degradation	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
capsaicin biosynthesis	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
limonene degradation IV (anaerobic)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	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