Experiment set8IT003 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 A5

Specific Phenotypes

For 12 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	4
Purine conversions	2
Allantoin Utilization	1
Molybdenum cofactor biosynthesis	1
Photorespiration (oxidative C2 cycle)	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Glyoxylate and dicarboxylate metabolism
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Caffeine metabolism
• Tyrosine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Pyruvate metabolism
• Biphenyl degradation
• 1- and 2-Methylnaphthalene degradation
• Fluorene degradation
• 3-Chloroacrylic acid degradation
• Phenylpropanoid biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
adenosine nucleotides degradation II	5	5	3
guanosine nucleotides degradation III	4	4	2
guanosine nucleotides degradation II	4	4	2
purine nucleotides degradation II (aerobic)	11	11	4
purine deoxyribonucleosides degradation II	3	3	1
superpathway of guanosine nucleotides degradation (plants)	6	5	2
adenine and adenosine salvage V	3	2	1
urate conversion to allantoin I	3	2	1
ureide biosynthesis	7	6	2
inosine 5'-phosphate degradation	4	4	1
purine deoxyribonucleosides degradation I	4	4	1
adenine and adenosine salvage III	4	4	1
adenosine nucleotides degradation I	8	7	2
purine nucleotides degradation I (plants)	12	10	3
guanosine nucleotides degradation I	4	3	1
glycolate and glyoxylate degradation I	4	3	1
superpathway of purines degradation in plants	18	14	4
purine nucleobases degradation II (anaerobic)	24	16	5
purine ribonucleosides degradation	6	5	1
superpathway of purine deoxyribonucleosides degradation	7	5	1
superpathway of glycol metabolism and degradation	7	5	1
drosopterin and aurodrosopterin biosynthesis	7	5	1
caffeine degradation III (bacteria, via demethylation)	7	1	1
theophylline degradation	9	1	1
caffeine degradation IV (bacteria, via demethylation and oxidation)	10	1	1
purine nucleobases degradation I (anaerobic)	15	6	1