Experiment set8IT058 for Phaeobacter inhibens DSM 17395

L-Citrulline nitrogen source

Group: nitrogen source
Media: DinoMM_noNitrogen_HighNutrient_SucroseC + L-Citrulline (5 mM), pH=7.2
Culturing: Phaeo_ML1, tube, Aerobic, at 25 (C), shaken=200 rpm
Growth: about 6.6 generations
By: Mark on 1/20/2015
Media components: 20 g/L Sea salts, 0.1 g/L Potassium phosphate monobasic, 20 mM Sucrose, 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 4 genes in this experiment

For nitrogen source L-Citrulline in Phaeobacter inhibens DSM 17395

For nitrogen source L-Citrulline across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Naphthalene and anthracene degradation
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-arginine degradation VII (arginase 3 pathway)	2	2	1
putrescine biosynthesis III	2	2	1
L-canavanine degradation I	2	1	1
L-arginine degradation I (arginase pathway)	3	3	1
superpathway of putrescine biosynthesis	4	4	1
L-arginine degradation VI (arginase 2 pathway)	4	4	1
urea cycle	5	4	1
L-Nδ-acetylornithine biosynthesis	7	6	1
superpathway of polyamine biosynthesis I	8	8	1
L-citrulline biosynthesis	8	8	1
superpathway of polyamine biosynthesis II	8	6	1
superpathway of L-citrulline metabolism	12	10	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	4	1
superpathway of arginine and polyamine biosynthesis	17	17	1