Experiment set6S35 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 7 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	2
Ethanolamine utilization	1
Fermentations: Lactate	1
Fermentations: Mixed acid	1
Formate hydrogenase	1
Glycine and Serine Utilization	1
MLST	1
Molybdenum cofactor biosynthesis	1
Propanediol utilization	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Threonine anaerobic catabolism gene cluster	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
• Taurine and hypotaurine metabolism
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Propanoate metabolism
• Methane metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
bis(guanylyl molybdenum cofactor) biosynthesis	2	2	2
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	2
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	2
choline degradation I	2	2	2
formate oxidation to CO2	1	1	1
guanylyl molybdenum cofactor biosynthesis	1	1	1
bis(guanylyl tungstenpterin) cofactor biosynthesis	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
acetate and ATP formation from acetyl-CoA I	2	2	1
β-alanine biosynthesis IV	2	1	1
sulfoacetaldehyde degradation I	2	1	1
β-alanine biosynthesis I	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
pyruvate fermentation to acetate II	3	3	1
glycine degradation	3	3	1
superpathway of acetate utilization and formation	3	3	1
L-methionine biosynthesis II	6	5	2
pyruvate fermentation to acetate I	3	2	1
pyruvate fermentation to acetate VII	3	2	1
glycine betaine biosynthesis III (plants)	3	2	1
pyruvate fermentation to acetate IV	3	2	1
dimethylsulfoniopropanoate biosynthesis I (Wollastonia)	3	1	1
pyruvate fermentation to acetate and (S)-lactate I	4	4	1
pyruvate fermentation to acetate and lactate II	4	3	1
L-mimosine degradation	8	4	2
choline degradation IV	4	2	1
glutathione-mediated detoxification I	8	3	2
sulfolactate degradation II	4	1	1
dimethylsulfoniopropanoate biosynthesis II (Spartina)	4	1	1
oxalate degradation VI	4	1	1
purine nucleobases degradation II (anaerobic)	24	16	5
ethanolamine utilization	5	5	1
acetylene degradation (anaerobic)	5	4	1
(S)-propane-1,2-diol degradation	5	2	1
oxalate degradation III	5	1	1
L-threonine degradation I	6	4	1
superpathway of sulfolactate degradation	6	3	1
methanogenesis from acetate	6	2	1
superpathway of taurine degradation	6	2	1
acetyl-CoA fermentation to butanoate	7	3	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	3	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
superpathway of L-alanine fermentation (Stickland reaction)	9	4	1
L-lysine fermentation to acetate and butanoate	10	3	1
gallate degradation III (anaerobic)	11	3	1
superpathway of C1 compounds oxidation to CO2	12	5	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	5	1
purine nucleobases degradation I (anaerobic)	15	6	1
mixed acid fermentation	16	12	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
heterolactic fermentation	18	16	1
superpathway of L-threonine metabolism	18	13	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of methanogenesis	21	2	1
superpathway of N-acetylneuraminate degradation	22	15	1
superpathway of L-lysine degradation	43	18	1