Experiment set8IT068 for Cupriavidus basilensis FW507-4G11

Carbon source Deoxyribonucleic acid from herring sperm 10 mg/mL

Group: carbon source
Media: RCH2_defined_noCarbon + Deoxyribonucleic acid from herring sperm (10 mg/mL), 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 A3

Specific Phenotypes

For 30 genes in this experiment

For carbon source Deoxyribonucleic acid from herring sperm in Cupriavidus basilensis FW507-4G11

For carbon source Deoxyribonucleic acid from herring sperm across organisms

SEED Subsystems

Subsystem	#Specific
Glycerol and Glycerol-3-phosphate Uptake and Utilization	2
Photorespiration (oxidative C2 cycle)	2
Purine Utilization	2
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	1
Allantoin Utilization	1
Arginine Biosynthesis extended	1
Bacterial Cell Division	1
Cysteine Biosynthesis	1
DNA-binding regulatory proteins, strays	1
Histidine Biosynthesis	1
Lysine Biosynthesis DAP Pathway	1
Molybdenum cofactor biosynthesis	1
Oxidative stress	1
Phosphate metabolism	1
Proline, 4-hydroxyproline uptake and utilization	1
TCA Cycle	1
Ton and Tol transport systems	1
YeiH	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Tryptophan metabolism
• Glyoxylate and dicarboxylate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Caffeine metabolism
• Lysine biosynthesis
• Tyrosine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Pyruvate metabolism
• Biphenyl degradation
• 1- and 2-Methylnaphthalene degradation
• Fluorene degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Methane metabolism
• Phenylpropanoid biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
urate conversion to allantoin I	3	2	2
superoxide radicals degradation	2	2	1
methanol oxidation to formaldehyde IV	2	1	1
ureide biosynthesis	7	5	3
adenosine nucleotides degradation II	5	4	2
partial TCA cycle (obligate autotrophs)	8	7	3
TCA cycle II (plants and fungi)	9	9	3
glyoxylate cycle	6	6	2
ethanol degradation IV	3	3	1
TCA cycle V (2-oxoglutarate synthase)	9	8	3
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	3
TCA cycle VII (acetate-producers)	9	6	3
TCA cycle VI (Helicobacter)	9	6	3
urate conversion to allantoin III	3	1	1
urate conversion to allantoin II	3	1	1
TCA cycle III (animals)	10	10	3
TCA cycle I (prokaryotic)	10	9	3
reductive TCA cycle I	11	7	3
reactive oxygen species degradation	4	4	1
superpathway of glyoxylate bypass and TCA	12	11	3
nitrogen remobilization from senescing leaves	8	7	2
inosine 5'-phosphate degradation	4	3	1
glycolate and glyoxylate degradation I	4	3	1
guanosine nucleotides degradation II	4	3	1
guanosine nucleotides degradation III	4	3	1
adenosine nucleotides degradation I	8	5	2
reductive TCA cycle II	12	6	3
guanosine nucleotides degradation I	4	2	1
superpathway of purines degradation in plants	18	11	4
superpathway of glyoxylate cycle and fatty acid degradation	14	11	3
2-methylcitrate cycle I	5	5	1
mixed acid fermentation	16	12	3
purine nucleotides degradation II (aerobic)	11	8	2
TCA cycle VIII (Chlamydia)	6	6	1
2-methylcitrate cycle II	6	5	1
purine nucleobases degradation II (anaerobic)	24	16	4
molybdopterin biosynthesis	6	4	1
purine nucleotides degradation I (plants)	12	7	2
superpathway of guanosine nucleotides degradation (plants)	6	3	1
methylaspartate cycle	19	14	3
superpathway of glycol metabolism and degradation	7	5	1
incomplete reductive TCA cycle	7	4	1
pyruvate fermentation to propanoate I	7	3	1
caffeine degradation III (bacteria, via demethylation)	7	1	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	3
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	3
L-lysine biosynthesis I	9	9	1
theophylline degradation	9	1	1
L-histidine biosynthesis	10	10	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	5	1
caffeine degradation IV (bacteria, via demethylation and oxidation)	10	1	1
L-glutamate degradation VIII (to propanoate)	11	3	1
ethene biosynthesis V (engineered)	25	17	2
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	7	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	23	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	44	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1