Experiment set3IT011 for Agrobacterium fabrum C58

Ethanolamine nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Succinate_noNitrogen + Ethanolamine (10 mM)
Culturing: Agro_ML11, 24-well transparent microplate; Multitron, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 11/20/20
Media components: 10 mM Sodium succinate dibasic hexahydrate, 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 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 8 genes in this experiment

For nitrogen source Ethanolamine in Agrobacterium fabrum C58

For nitrogen source Ethanolamine across organisms

SEED Subsystems

Subsystem	#Specific
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Entner-Doudoroff Pathway	1
Fermentations: Mixed acid	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Methylglyoxal Metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Tryptophan metabolism
• 1- and 2-Methylnaphthalene degradation
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Retinol metabolism
• Limonene and pinene degradation
• Fructose and mannose metabolism
• C21-Steroid hormone metabolism
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Bisphenol A degradation
• beta-Alanine metabolism
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Glycerolipid metabolism
• Linoleic acid metabolism
• Pyruvate metabolism
• Tetrachloroethene degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Nitrogen metabolism
• Sulfur metabolism
• Alkaloid biosynthesis I
• Metabolism of xenobiotics by cytochrome P450
• Insect hormone biosynthesis
• Drug metabolism - cytochrome P450
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide products
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
L-glutamine biosynthesis I	1	1	1
ethanol degradation II	3	3	2
putrescine degradation V	2	2	1
ammonia assimilation cycle I	2	2	1
phytol degradation	4	3	2
ethanol degradation I	2	1	1
putrescine degradation I	2	1	1
ethylene glycol degradation	2	1	1
ammonia assimilation cycle II	2	1	1
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation IV	3	3	1
ammonia assimilation cycle III	3	3	1
L-isoleucine degradation II	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
hypotaurine degradation	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
L-leucine degradation III	3	2	1
L-valine degradation II	3	2	1
putrescine degradation IV	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
ethanol degradation III	3	2	1
pyruvate fermentation to ethanol I	3	1	1
L-methionine degradation III	3	1	1
pyruvate fermentation to ethanol III	3	1	1
histamine degradation	3	1	1
noradrenaline and adrenaline degradation	13	4	4
serotonin degradation	7	3	2
L-tyrosine degradation III	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
L-phenylalanine degradation III	4	2	1
putrescine degradation III	4	1	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
salidroside biosynthesis	4	1	1
D-arabinose degradation II	4	1	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
mitochondrial NADPH production (yeast)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
dopamine degradation	5	1	1
ethanolamine utilization	5	1	1
phenylethanol biosynthesis	5	1	1
acetylene degradation (anaerobic)	5	1	1
(S)-propane-1,2-diol degradation	5	1	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
3-methylbutanol biosynthesis (engineered)	7	6	1
superpathway of glycol metabolism and degradation	7	4	1
L-glutamate and L-glutamine biosynthesis	7	4	1
ceramide degradation by α-oxidation	7	2	1
isopropylamine degradation	7	1	1
limonene degradation IV (anaerobic)	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
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
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
L-arginine biosynthesis II (acetyl cycle)	10	10	1
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
mixed acid fermentation	16	9	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 pentose and pentitol degradation	42	16	1