Experiment set6S36 for Pseudomonas sp. RS175

Choline chloride carbon source

Group: carbon source
Media: MME_noCarbon + Choline chloride (10 mM)
Culturing: Pseudomonas_RS175_ML2, 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 5 genes in this experiment

For carbon source Choline chloride in Pseudomonas sp. RS175

For carbon source Choline chloride across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	3
Formate hydrogenase	1
Glycine and Serine Utilization	1
Pyruvate Alanine Serine Interconversions	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
• Cysteine metabolism
• Glyoxylate and dicarboxylate metabolism
• Methane metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
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
D-serine degradation	3	3	2
choline-O-sulfate degradation	3	3	2
L-cysteine degradation II	3	2	2
L-tryptophan degradation II (via pyruvate)	3	2	2
β-alanine biosynthesis I	2	1	1
β-alanine biosynthesis IV	2	1	1
glycine betaine degradation III	7	7	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	6	3
glycine degradation	3	3	1
L-methionine biosynthesis II	6	5	2
glycine betaine biosynthesis III (plants)	3	2	1
dimethylsulfoniopropanoate biosynthesis I (Wollastonia)	3	1	1
L-mimosine degradation	8	4	2
choline degradation IV	4	2	1
glutathione-mediated detoxification I	8	3	2
oxalate degradation VI	4	1	1
dimethylsulfoniopropanoate biosynthesis II (Spartina)	4	1	1
oxalate degradation III	5	1	1
purine nucleobases degradation II (anaerobic)	24	16	4
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
superpathway of C1 compounds oxidation to CO2	12	5	1
purine nucleobases degradation I (anaerobic)	15	6	1