Experiment set1IT040 for Rhizobium sp. OAE497

Glycolic Acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Glycolic Acid (20 mM)
Culturing: Rhizobium_OAE497_ML5, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Dennis/Robin on 4/4/22
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 6 genes in this experiment

For carbon source Glycolic Acid in Rhizobium sp. OAE497

For carbon source Glycolic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Glycolate, glyoxylate interconversions	2
Aromatic Amin Catabolism	1
Photorespiration (oxidative C2 cycle)	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

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

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

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