Experiment set10IT055 for Phaeobacter inhibens DSM 17395

DinoMM minimal media with L-Threonine

Group: nutrient
Media: DinoMM_L_lactateCarbon_HighNutrient + L-Threonine (1 mM)
Culturing: Phaeo_ML1, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 6.0 generations
By: Adam on 29-Jun-16
Media components: 20 g/L Sea salts, 0.3 g/L Ammonium Sulfate, 0.1 g/L Potassium phosphate monobasic, 20 mM Sodium L-Lactate, 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 17 genes in this experiment

For nutrient L-Threonine in Phaeobacter inhibens DSM 17395

For nutrient L-Threonine across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	2
Glycine Biosynthesis	2
Polyamine Metabolism	2
Acid resistance mechanisms	1
Adenosyl nucleosidases	1
Arginine Deiminase Pathway	1
Deoxyribose and Deoxynucleoside Catabolism	1
Glycine and Serine Utilization	1
Purine conversions	1
Pyruvate Alanine Serine Interconversions	1
Synechocystis experimental	1
Threonine degradation	1
Triacylglycerol metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Urea cycle and metabolism of amino groups
• Purine metabolism
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Arginine and proline metabolism
• Taurine and hypotaurine metabolism
• Glutathione metabolism
• Glycerophospholipid metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Nicotinate and nicotinamide metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-threonine degradation II	2	2	2
cadaverine biosynthesis	1	1	1
L-alanine degradation IV	1	1	1
arginine dependent acid resistance	1	1	1
purine deoxyribonucleosides degradation I	4	3	3
purine ribonucleosides degradation	6	5	4
L-threonine degradation III (to methylglyoxal)	3	2	2
purine deoxyribonucleosides degradation II	3	2	2
superpathway of putrescine biosynthesis	4	4	2
guanine and guanosine salvage I	2	2	1
putrescine biosynthesis I	2	2	1
xanthine and xanthosine salvage	2	2	1
adenine and adenosine salvage I	2	2	1
putrescine biosynthesis III	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
adenine and adenosine salvage III	4	3	2
aminopropanol phosphate biosynthesis II	4	2	2
superpathway of purine deoxyribonucleosides degradation	7	6	3
superpathway of polyamine biosynthesis I	8	8	3
aminopropylcadaverine biosynthesis	3	3	1
pyrimidine deoxyribonucleosides degradation	3	3	1
superpathway of guanine and guanosine salvage	3	2	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	2	1
putrescine biosynthesis II	3	2	1
adenine and adenosine salvage V	3	1	1
purine nucleotides degradation II (aerobic)	11	10	3
inosine 5'-phosphate degradation	4	4	1
guanosine nucleotides degradation III	4	4	1
superpathway of polyamine biosynthesis II	8	6	2
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
spermidine biosynthesis III	4	2	1
adenosine nucleotides degradation II	5	4	1
nucleoside and nucleotide degradation (archaea)	10	3	2
lupanine biosynthesis	5	1	1
bisucaberin biosynthesis	5	1	1
desferrioxamine E biosynthesis	5	1	1
desferrioxamine B biosynthesis	5	1	1
superpathway of arginine and polyamine biosynthesis	17	17	3
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	1
superpathway of L-threonine metabolism	18	15	3
L-lysine degradation X	6	3	1
nucleoside and nucleotide degradation (halobacteria)	6	2	1
fluoroacetate and fluorothreonine biosynthesis	6	1	1
superpathway of L-arginine and L-ornithine degradation	13	7	2
superpathway of purine nucleotide salvage	14	13	2
ureide biosynthesis	7	6	1
L-lysine degradation I	7	2	1
superpathway of ornithine degradation	8	3	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	5	1
salinosporamide A biosynthesis	15	3	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	4	1
arsenic detoxification (mammals)	17	8	1
superpathway of L-lysine degradation	43	10	1