Experiment set8IT067 for Cupriavidus basilensis FW507-4G11

Carbon source 2-Deoxyadenosine 5-monophosphate 5 mM

Group: carbon source
Media: RCH2_defined_noCarbon + 2-Deoxyadenosine 5-monophosphate (5 mM), pH=7
Culturing: cupriavidus_4G11_ML11, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 05/02/2018
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 A1

Specific Phenotypes

For 30 genes in this experiment

For carbon source 2-Deoxyadenosine 5-monophosphate in Cupriavidus basilensis FW507-4G11

For carbon source 2-Deoxyadenosine 5-monophosphate across organisms

SEED Subsystems

Subsystem	#Specific
Molybdenum cofactor biosynthesis	3
Photorespiration (oxidative C2 cycle)	2
Purine Utilization	2
Purine conversions	2
Queuosine-Archaeosine Biosynthesis	2
Transport of Molybdenum	2
Allantoin Utilization	1
Arginine Biosynthesis extended	1
Arginine and Ornithine Degradation	1
Branched-Chain Amino Acid Biosynthesis	1
Coenzyme B12 biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
High affinity phosphate transporter and control of PHO regulon	1
Lysine Biosynthesis DAP Pathway	1
Oxidative stress	1
Phosphate metabolism	1
Proline, 4-hydroxyproline uptake and utilization	1
Pyruvate Alanine Serine Interconversions	1
Respiratory dehydrogenases 1	1
Ribosome activity modulation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Arginine and proline metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Glyoxylate and dicarboxylate metabolism
• Citrate cycle (TCA cycle)
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Caffeine metabolism
• Glutamate metabolism
• Lysine biosynthesis
• Lysine degradation
• Tyrosine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Benzoate degradation via hydroxylation
• D-Arginine and D-ornithine metabolism
• D-Alanine metabolism
• Pyruvate metabolism
• Biphenyl degradation
• 1- and 2-Methylnaphthalene degradation
• Fluorene degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Methane metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Phenylpropanoid biosynthesis
• 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
D-alanine degradation	1	1	1
L-proline degradation I	3	3	2
urate conversion to allantoin I	3	2	2
adenosine nucleotides degradation II	5	4	3
polyphosphate metabolism	2	2	1
superoxide radicals degradation	2	2	1
proline to cytochrome bo oxidase electron transfer	2	2	1
methanol oxidation to formaldehyde IV	2	1	1
ureide biosynthesis	7	5	3
glyoxylate cycle	6	6	2
molybdenum cofactor biosynthesis	3	3	1
ethanol degradation IV	3	3	1
purine deoxyribonucleosides degradation II	3	1	1
urate conversion to allantoin III	3	1	1
urate conversion to allantoin II	3	1	1
adenine and adenosine salvage V	3	1	1
L-arginine degradation I (arginase pathway)	3	1	1
purine nucleotides degradation II (aerobic)	11	8	3
reactive oxygen species degradation	4	4	1
nitrogen remobilization from senescing leaves	8	7	2
partial TCA cycle (obligate autotrophs)	8	7	2
guanosine nucleotides degradation II	4	3	1
inosine 5'-phosphate degradation	4	3	1
glycolate and glyoxylate degradation I	4	3	1
guanosine nucleotides degradation III	4	3	1
adenosine nucleotides degradation I	8	5	2
adenine and adenosine salvage III	4	2	1
guanosine nucleotides degradation I	4	2	1
ethene biosynthesis II (microbes)	4	1	1
purine deoxyribonucleosides degradation I	4	1	1
TCA cycle II (plants and fungi)	9	9	2
TCA cycle V (2-oxoglutarate synthase)	9	8	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	2
TCA cycle VI (Helicobacter)	9	6	2
TCA cycle VII (acetate-producers)	9	6	2
superpathway of purines degradation in plants	18	11	4
TCA cycle III (animals)	10	10	2
2-methylcitrate cycle I	5	5	1
TCA cycle I (prokaryotic)	10	9	2
reductive TCA cycle I	11	7	2
superpathway of glyoxylate bypass and TCA	12	11	2
2-methylcitrate cycle II	6	5	1
purine nucleobases degradation II (anaerobic)	24	16	4
purine nucleotides degradation I (plants)	12	7	2
reductive TCA cycle II	12	6	2
superpathway of guanosine nucleotides degradation (plants)	6	3	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
purine ribonucleosides degradation	6	1	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
superpathway of glycol metabolism and degradation	7	5	1
L-Nδ-acetylornithine biosynthesis	7	4	1
superpathway of purine deoxyribonucleosides degradation	7	2	1
caffeine degradation III (bacteria, via demethylation)	7	1	1
mixed acid fermentation	16	12	2
L-citrulline biosynthesis	8	6	1
L-lysine biosynthesis I	9	9	1
theophylline degradation	9	1	1
methylaspartate cycle	19	14	2
caffeine degradation IV (bacteria, via demethylation and oxidation)	10	1	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	2
superpathway of L-citrulline metabolism	12	8	1
ethene biosynthesis V (engineered)	25	17	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	2
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	23	1