Experiment set8IT004 for Pseudomonas simiae WCS417

Deoxyribonucleic acid from herring sperm 5 mg/mL carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Deoxyribonucleic acid from herring sperm (5 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 A6

Specific Phenotypes

For 9 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	2
Allantoin Utilization	1
Coenzyme PQQ synthesis	1
Molybdenum cofactor biosynthesis	1
Photorespiration (oxidative C2 cycle)	1
Purine conversions	1
Pyrroloquinoline Quinone biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine 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
• Glyoxylate and dicarboxylate metabolism
• 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
purine deoxyribonucleosides degradation II	3	3	1
adenine and adenosine salvage V	3	2	1
urate conversion to allantoin I	3	2	1
ureide biosynthesis	7	6	2
pyrroloquinoline quinone biosynthesis	7	4	2
purine nucleotides degradation II (aerobic)	11	11	3
purine deoxyribonucleosides degradation I	4	4	1
guanosine nucleotides degradation III	4	4	1
guanosine nucleotides degradation II	4	4	1
adenine and adenosine salvage 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
purine nucleotides degradation I (plants)	12	10	2
superpathway of guanosine nucleotides degradation (plants)	6	5	1
purine ribonucleosides degradation	6	5	1
superpathway of purines degradation in plants	18	14	3
purine nucleobases degradation II (anaerobic)	24	16	4
superpathway of glycol metabolism and degradation	7	5	1
superpathway of purine deoxyribonucleosides degradation	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