Experiment set27S417 for Pseudomonas fluorescens SBW25-INTG

sn-glycero-3-phosphocholine carbon source

Group: carbon source
Media: MME_noCarbon + sn-glycero-3-phosphocholine (10 mM)
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C)
By: Andrew Frank on 1/31/23
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium 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 10 genes in this experiment

For carbon source sn-glycero-3-phosphocholine in Pseudomonas fluorescens SBW25-INTG

For carbon source sn-glycero-3-phosphocholine across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	2
Glycerol and Glycerol-3-phosphate Uptake and Utilization	2
Iron acquisition in Vibrio	2
Formate hydrogenase	1
High affinity phosphate transporter and control of PHO regulon	1
Phosphate metabolism	1
Threonine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Methane metabolism
• Glycerophospholipid metabolism
• Glyoxylate and dicarboxylate metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	2
choline degradation I	2	2	2
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	2
formate oxidation to CO2	1	1	1
formaldehyde oxidation IV (thiol-independent)	1	1	1
choline-O-sulfate degradation	3	3	2
glycerophosphodiester degradation	2	2	1
phosphatidylcholine resynthesis via glycerophosphocholine	2	1	1
β-alanine biosynthesis I	2	1	1
β-alanine biosynthesis IV	2	1	1
glycine betaine biosynthesis III (plants)	3	2	1
dimethylsulfoniopropanoate biosynthesis I (Wollastonia)	3	1	1
glycerol and glycerophosphodiester degradation	4	4	1
choline degradation IV	4	2	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
oxalate degradation VI	4	1	1
dimethylsulfoniopropanoate biosynthesis II (Spartina)	4	1	1
oxalate degradation III	5	1	1
methanol oxidation to carbon dioxide	6	3	1
superpathway of C1 compounds oxidation to CO2	12	5	2
anandamide biosynthesis I	12	3	1
purine nucleobases degradation I (anaerobic)	15	6	1
purine nucleobases degradation II (anaerobic)	24	16	1