Experiment set11IT010 for Agrobacterium fabrum C58

Dihydroxyacetone carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Dihydroxyacetone (10 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 9 genes in this experiment

For carbon source Dihydroxyacetone in Agrobacterium fabrum C58

For carbon source Dihydroxyacetone across organisms

SEED Subsystems

Subsystem	#Specific
Glycolate, glyoxylate interconversions	3
Photorespiration (oxidative C2 cycle)	3
Glycerol and Glycerol-3-phosphate Uptake and Utilization	2
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Entner-Doudoroff Pathway	1
Heat shock dnaK gene cluster extended	1
Homogentisate pathway of aromatic compound degradation	1
MLST	1
Methylglyoxal Metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Tryptophan metabolism
• Glycerolipid metabolism
• Glyoxylate and dicarboxylate metabolism
• Limonene and pinene degradation
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Histidine metabolism
• beta-Alanine metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycolate and glyoxylate degradation II	2	2	1
putrescine degradation V	2	2	1
ethylene glycol degradation	2	1	1
putrescine degradation I	2	1	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
putrescine degradation IV	3	2	1
glycerol degradation I	3	2	1
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
glycolate and glyoxylate degradation III	3	1	1
histamine degradation	3	1	1
superpathway of glycol metabolism and degradation	7	4	2
glycerol and glycerophosphodiester degradation	4	3	1
phytol degradation	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
glycolate and glyoxylate degradation I	4	2	1
D-arabinose degradation II	4	1	1
putrescine degradation III	4	1	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
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	4	2
serotonin degradation	7	3	1
ceramide degradation by α-oxidation	7	2	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
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
aromatic biogenic amine degradation (bacteria)	8	1	1
photorespiration I	9	6	1
photorespiration III	9	6	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
photorespiration II	10	6	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 pentose and pentitol degradation	42	16	1