Experiment set14IT004 for Pseudomonas fluorescens SBW25-INTG

Betaine (C)(N); with TAPS; with Sodium chloride

Group: stress
Media: MTM_noNitrogen_noCarbon + Betaine (10 mM) + Betaine (10 mM) + Sodium Chloride (400 mM), pH=8.5
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on September 1, 2021
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM TAPS sodium salt, 4.3 mM Sodium Chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 20 genes in this experiment

For stress Betaine in Pseudomonas fluorescens SBW25-INTG

For stress Betaine across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	4
Phosphate metabolism	2
Polyamine Metabolism	2
Arginine and Ornithine Degradation	1
Formate hydrogenase	1
Oxidative stress	1
Proline, 4-hydroxyproline uptake and utilization	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
• Arginine and proline metabolism
• Glyoxylate and dicarboxylate metabolism
• Methane metabolism
• Nicotinate and nicotinamide metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
formate oxidation to CO2	1	1	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
putrescine biosynthesis II	3	3	1
putrescine degradation II	4	1	1
oxalate degradation VI	4	1	1
oxalate degradation III	5	1	1
NAD(P)/NADPH interconversion	6	3	1
superpathway of polyamine biosynthesis II	8	6	1
superpathway of ornithine degradation	8	4	1
peptidoglycan recycling II	10	8	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
superpathway of C1 compounds oxidation to CO2	12	5	1
superpathway of L-arginine and L-ornithine degradation	13	9	1
peptidoglycan recycling I	14	11	1
purine nucleobases degradation I (anaerobic)	15	6	1
purine nucleobases degradation II (anaerobic)	24	16	1