Experiment set1IT062 for Variovorax sp. OAS795

2-Deoxy-D-Ribose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 2-Deoxy-D-Ribose (20 mM)
Culturing: Variovorax_OAS795_ML2, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Marta on 10-Apr-21
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 11 genes in this experiment

For carbon source 2-Deoxy-D-Ribose in Variovorax sp. OAS795

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

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	2
Bacterial Cell Division	1
DNA-binding regulatory proteins, strays	1
HMG CoA Synthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Maltose and Maltodextrin Utilization	1
Oxidative stress	1
Polyhydroxybutyrate metabolism	1
Thioredoxin-disulfide reductase	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Galactose metabolism
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Tyrosine metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Ethylbenzene degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Caprolactam degradation
• Alkaloid biosynthesis II
• 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

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
choline degradation I	2	2	1
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
trehalose degradation I (low osmolarity)	2	1	1
trehalose degradation II (cytosolic)	2	1	1
choline-O-sulfate degradation	3	3	1
oxalate degradation II	3	2	1
trehalose degradation IV	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
trehalose degradation V	3	2	1
2-deoxy-D-ribose degradation II	8	6	2
sucrose degradation III (sucrose invertase)	4	3	1
acrylate degradation I	5	5	1
propanoyl-CoA degradation II	5	4	1
glucose and glucose-1-phosphate degradation	5	4	1
octane oxidation	5	4	1
glycogen degradation II	6	5	1
β-alanine biosynthesis II	6	5	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
6-gingerol analog biosynthesis (engineered)	6	3	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	4	1
glycogen degradation I	8	7	1
sucrose biosynthesis II	8	6	1
1,3-propanediol biosynthesis (engineered)	9	5	1
chitin biosynthesis	9	5	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
glycolysis III (from glucose)	11	11	1
homolactic fermentation	12	11	1
Bifidobacterium shunt	15	14	1
heterolactic fermentation	18	15	1