Experiment set4IT090 for Acidovorax sp. GW101-3H11

Uridine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Uridine (20 mM), pH=7
Culturing: acidovorax_3H11_ML3a, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 5.7 generations
By: Mark on 6/10/2015
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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: Nplate2 B6

Specific Phenotypes

For 28 genes in this experiment

For nitrogen source Uridine in Acidovorax sp. GW101-3H11

For nitrogen source Uridine across organisms

SEED Subsystems

Subsystem	#Specific
Flagellum	5
Flagellar motility	4
Pyrimidine utilization	3
Hydantoin metabolism	2
Pyruvate Alanine Serine Interconversions	2
Isobutyryl-CoA to Propionyl-CoA Module	1
Oxidative stress	1
Oxygen and light sensor PpaA-PpsR	1
Polyamine Metabolism	1
Purine Utilization	1
Respiratory dehydrogenases 1	1
Sialic Acid Metabolism	1
TCA Cycle	1
Transcription initiation, bacterial sigma factors	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• beta-Alanine metabolism
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Pyrimidine metabolism
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Propanoate metabolism
• Pantothenate and CoA biosynthesis
• Drug metabolism - other enzymes
• Biosynthesis of alkaloids derived from shikimate pathway
• Citrate cycle (TCA cycle)
• Alanine and aspartate metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Phenylalanine metabolism
• Glutathione metabolism
• Inositol phosphate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Limonene and pinene degradation
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• 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
β-alanine degradation II	2	2	2
L-glutamate biosynthesis I	2	2	2
L-glutamate biosynthesis IV	1	1	1
L-glutamine degradation II	1	1	1
L-glutamine degradation I	1	1	1
ammonia assimilation cycle III	3	3	2
thymine degradation	3	2	2
uracil degradation I (reductive)	3	2	2
ammonia assimilation cycle I	2	2	1
β-alanine degradation I	2	1	1
L-glutamate and L-glutamine biosynthesis	7	7	3
superpathway of pyrimidine ribonucleosides degradation	5	2	2
superpathway of ammonia assimilation (plants)	3	3	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
acrylate degradation I	5	3	1
propanoyl-CoA degradation II	5	3	1
cytosolic NADPH production (yeast)	5	3	1
β-alanine biosynthesis II	6	5	1
2,4-dinitrotoluene degradation	7	2	1
myo-inositol degradation I	7	1	1
partial TCA cycle (obligate autotrophs)	8	7	1
L-citrulline biosynthesis	8	7	1
nitrogen remobilization from senescing leaves	8	6	1
L-valine degradation I	8	6	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	4	1
TCA cycle V (2-oxoglutarate synthase)	9	8	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	8	1
TCA cycle VII (acetate-producers)	9	7	1
TCA cycle VI (Helicobacter)	9	6	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
TCA cycle I (prokaryotic)	10	8	1
myo-, chiro- and scyllo-inositol degradation	10	1	1
reductive TCA cycle I	11	6	1
superpathway of glyoxylate bypass and TCA	12	10	1
superpathway of L-citrulline metabolism	12	9	1
mixed acid fermentation	16	10	1
methylaspartate cycle	19	12	1
ethene biosynthesis V (engineered)	25	17	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	1