Experiment set6IT051 for Pseudomonas fluorescens FW300-N2C3

Adenine hydrochloride hydrate nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Adenine hydrochloride hydrate (5 mM), pH=7
Culturing: pseudo5_N2-C3_1_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/17/2014
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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)

Specific Phenotypes

For 13 genes in this experiment

For nitrogen source Adenine hydrochloride hydrate in Pseudomonas fluorescens FW300-N2C3

For nitrogen source Adenine hydrochloride hydrate across organisms

SEED Subsystems

Subsystem	#Specific
Urea decomposition	4
Allantoin Utilization	1
Methionine Biosynthesis	1
Purine conversions	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
• Urea cycle and metabolism of amino groups
• Caffeine metabolism
• Methionine metabolism
• Arginine and proline 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
• One carbon pool by folate
• Atrazine degradation
• Phenylpropanoid biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
allantoin degradation to ureidoglycolate I (urea producing)	2	2	2
urea degradation II	1	1	1
allantoin degradation to glyoxylate I	3	3	2
urate conversion to allantoin I	3	2	2
superpathway of allantoin degradation in plants	8	5	3
superpathway of allantoin degradation in yeast	6	6	2
purine deoxyribonucleosides degradation II	3	3	1
L-methionine salvage from L-homocysteine	3	2	1
adenine and adenosine salvage V	3	2	1
urate conversion to allantoin III	3	1	1
urate conversion to allantoin II	3	1	1
ureide biosynthesis	7	6	2
adenine and adenosine salvage III	4	4	1
purine deoxyribonucleosides degradation I	4	4	1
L-methionine biosynthesis III	4	4	1
allantoin degradation to ureidoglycolate II (ammonia producing)	4	1	1
superpathway of purines degradation in plants	18	15	4
adenosine nucleotides degradation II	5	5	1
L-methionine biosynthesis I	5	3	1
allantoin degradation to glyoxylate III	5	2	1
allantoin degradation to glyoxylate II	5	2	1
purine ribonucleosides degradation	6	5	1
superpathway of purine deoxyribonucleosides degradation	7	5	1
superpathway of L-homoserine and L-methionine biosynthesis	8	6	1
folate transformations III (E. coli)	9	9	1
superpathway of S-adenosyl-L-methionine biosynthesis	9	7	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
allantoin degradation IV (anaerobic)	9	3	1
purine nucleotides degradation II (aerobic)	11	11	1
folate transformations II (plants)	11	10	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
folate transformations I	13	9	1
superpathway of L-methionine salvage and degradation	16	9	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1