Experiment set5IT053 for Dinoroseobacter shibae DFL-12

Inosine nitrogen source

Group: nitrogen source
Media: DinoMM_noNitrogen_HighNutrient + Inosine (1.25 mM), pH=7.2
Culturing: Dino_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.4 generations
By: Adam on 5/14/2014
Media components: 20 g/L Sea salts, 0.1 g/L Potassium phosphate monobasic, 1.37 g/L Sodium acetate, 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 7 genes in this experiment

For nitrogen source Inosine in Dinoroseobacter shibae DFL-12

For nitrogen source Inosine across organisms

SEED Subsystems

Subsystem	#Specific
Urea decomposition	5

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
• 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
• Atrazine degradation
• Phenylpropanoid biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
urea degradation II	1	1	1
urate conversion to allantoin III	3	3	2
allantoin degradation to ureidoglycolate I (urea producing)	2	1	1
urate conversion to allantoin I	3	2	1
urate conversion to allantoin II	3	2	1
allantoin degradation to glyoxylate I	3	1	1
superpathway of allantoin degradation in plants	8	3	2
allantoin degradation to ureidoglycolate II (ammonia producing)	4	1	1
allantoin degradation to glyoxylate II	5	2	1
allantoin degradation to glyoxylate III	5	1	1
superpathway of allantoin degradation in yeast	6	3	1
ureide biosynthesis	7	6	1
superpathway of purines degradation in plants	18	13	2
allantoin degradation IV (anaerobic)	9	5	1