Experiment set22IT030 for Pseudomonas fluorescens FW300-N2E2

nitrogen source Sodium nitrite 5mM

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Sodium nitrite (5 mM), pH=7
Culturing: pseudo6_N2E2_ML5b, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 11-Aug-20
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 12 genes in this experiment

For nitrogen source Sodium nitrite in Pseudomonas fluorescens FW300-N2E2

For nitrogen source Sodium nitrite across organisms

SEED Subsystems

Subsystem	#Specific
Maltose and Maltodextrin Utilization	2
Polyamine Metabolism	2
Trehalose Biosynthesis	2
Acid resistance mechanisms	1
Arginine and Ornithine Degradation	1
DNA Repair Base Excision	1
Glycogen metabolism	1
Methionine Biosynthesis	1
Queuosine-Archaeosine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Starch and sucrose metabolism
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Glutathione metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
cadaverine biosynthesis	1	1	1
arginine dependent acid resistance	1	1	1
trehalose biosynthesis IV	1	1	1
putrescine biosynthesis I	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
superpathway of putrescine biosynthesis	4	3	2
putrescine biosynthesis III	2	1	1
superpathway of polyamine biosynthesis I	8	5	3
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
putrescine biosynthesis II	3	3	1
aminopropylcadaverine biosynthesis	3	1	1
starch degradation V	4	3	1
superpathway of polyamine biosynthesis II	8	5	2
spermidine biosynthesis III	4	1	1
bisucaberin biosynthesis	5	1	1
desferrioxamine E biosynthesis	5	1	1
desferrioxamine B biosynthesis	5	1	1
lupanine biosynthesis	5	1	1
superpathway of arginine and polyamine biosynthesis	17	14	3
L-lysine degradation X	6	5	1
superpathway of L-arginine and L-ornithine degradation	13	11	2
L-lysine degradation I	7	4	1
superpathway of ornithine degradation	8	7	1
sucrose biosynthesis II	8	6	1
glycogen degradation I	8	6	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	3	1
starch degradation II	9	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
superpathway of L-lysine degradation	43	19	1