Experiment set8IT076 for Cupriavidus basilensis FW507-4G11

Carbon source 2-Deoxy-D-Ribose 20 mM

Group: carbon source
Media: RCH2_defined_noCarbon + 2-Deoxy-D-Ribose (20 mM), pH=7
Culturing: cupriavidus_4G11_ML11, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 5/2/18
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)
Growth plate: Cup4G11_plate C6

Specific Phenotypes

For 5 genes in this experiment

For carbon source 2-Deoxy-D-Ribose in Cupriavidus basilensis FW507-4G11

For carbon source 2-Deoxy-D-Ribose across organisms

SEED Subsystems

Subsystem	#Specific
Glycine cleavage system	1
Leucine Degradation and HMG-CoA Metabolism	1
Photorespiration (oxidative C2 cycle)	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine degradation
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Fatty acid metabolism
• Glycine, serine and threonine metabolism
• beta-Alanine metabolism
• Pyruvate metabolism
• Propanoate metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycine cleavage	3	3	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
glycine biosynthesis II	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
L-leucine degradation I	6	5	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	1