Experiment set8IT009 for Pseudomonas simiae WCS417

Deoxyribonucleic acid from herring sperm 10 mg/mL carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Deoxyribonucleic acid from herring sperm (10 mg/mL), pH=7
Culturing: fluoroDangl_ML3, 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: WCS417_deoxyribosePlus_plate C5

Specific Phenotypes

For 14 genes in this experiment

For carbon source Deoxyribonucleic acid from herring sperm in Pseudomonas simiae WCS417

For carbon source Deoxyribonucleic acid from herring sperm across organisms

SEED Subsystems

Subsystem	#Specific
Purine Utilization	3
Molybdenum cofactor biosynthesis	2
Allantoin Utilization	1
Aromatic amino acid degradation	1
Homogentisate pathway of aromatic compound degradation	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Photorespiration (oxidative C2 cycle)	1
Plastoquinone Biosynthesis	1
Purine conversions	1
Queuosine-Archaeosine Biosynthesis	1
Redox-dependent regulation of nucleus processes	1
Tocopherol Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Ubiquinone and menaquinone biosynthesis
• Tyrosine metabolism
• Phenylalanine metabolism
• Lipopolysaccharide biosynthesis
• Glyoxylate and dicarboxylate metabolism
• Nicotinate and nicotinamide metabolism
• Pentose and glucuronate interconversions
• Ascorbate and aldarate metabolism
• Biosynthesis of steroids
• Lysine biosynthesis
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Glutathione metabolism
• Nucleotide sugars metabolism
• Sphingolipid metabolism
• Pyruvate metabolism
• Biphenyl degradation
• 1- and 2-Methylnaphthalene degradation
• 1,4-Dichlorobenzene degradation
• Fluorene degradation
• 3-Chloroacrylic acid degradation
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Phenylpropanoid biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
adenosine nucleotides degradation II	5	5	3
aldoxime degradation	3	3	1
purine deoxyribonucleosides degradation II	3	3	1
adenine and adenosine salvage V	3	2	1
plastoquinol-9 biosynthesis I	3	1	1
purine nucleotides degradation II (aerobic)	11	11	3
guanosine nucleotides degradation II	4	4	1
adenine and adenosine salvage III	4	4	1
queuosine biosynthesis I (de novo)	4	4	1
purine deoxyribonucleosides degradation I	4	4	1
guanosine nucleotides degradation III	4	4	1
inosine 5'-phosphate degradation	4	4	1
adenosine nucleotides degradation I	8	7	2
glycolate and glyoxylate degradation I	4	3	1
guanosine nucleotides degradation I	4	3	1
L-tyrosine degradation I	5	5	1
queuosine biosynthesis III (queuosine salvage)	5	3	1
NAD salvage pathway V (PNC V cycle)	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
purine nucleotides degradation I (plants)	12	10	2
superpathway of guanosine nucleotides degradation (plants)	6	5	1
purine ribonucleosides degradation	6	5	1
purine nucleobases degradation II (anaerobic)	24	16	4
ureide biosynthesis	7	6	1
superpathway of glycol metabolism and degradation	7	5	1
superpathway of purine deoxyribonucleosides degradation	7	5	1
NAD salvage pathway I (PNC VI cycle)	7	5	1
caffeine degradation III (bacteria, via demethylation)	7	1	1
vitamin E biosynthesis (tocopherols)	7	1	1
superpathway of purines degradation in plants	18	14	2
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
theophylline degradation	9	1	1
caffeine degradation IV (bacteria, via demethylation and oxidation)	10	1	1
NAD salvage (plants)	11	5	1
superpathway of NAD biosynthesis in eukaryotes	14	9	1