Experiment set13IT041 for Pseudomonas fluorescens SBW25-INTG

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

Group: stress
Media: MME_noNitrogen_noCarbon + Betaine (10 mM) + Betaine (10 mM) + Sodium Chloride (400 mM), pH=7
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 3-(N-morpholino)propanesulfonic acid, 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 25 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
Formate hydrogenase	2
Oxidative stress	2
Phosphate metabolism	2
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Aromatic amino acid degradation	1
Bacterial Chemotaxis	1
Butanol Biosynthesis	1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
DNA-binding regulatory proteins, strays	1
Flagellar motility	1
Folate Biosynthesis	1
Glycine and Serine Utilization	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Isoleucine degradation	1
Orphan regulatory proteins	1
Polyamine Metabolism	1
Proline, 4-hydroxyproline uptake and utilization	1
Pyruvate Alanine Serine Interconversions	1
Thioredoxin-disulfide reductase	1
Threonine degradation	1
Two-component regulatory systems in Campylobacter	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Methane metabolism
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Geraniol degradation
• Arginine and proline metabolism
• Tyrosine metabolism
• Benzoate degradation via hydroxylation
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Nicotinate and nicotinamide metabolism
• Folate biosynthesis
• Brassinosteroid biosynthesis
• Caprolactam degradation
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
L-glutamine degradation I	1	1	1
formaldehyde oxidation IV (thiol-independent)	1	1	1
formate oxidation to CO2	1	1	1
D-serine degradation	3	3	2
L-cysteine degradation II	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
4-aminobenzoate biosynthesis I	2	2	1
L-glutamate biosynthesis I	2	2	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
ammonia assimilation cycle III	3	3	1
glycine degradation	3	3	1
L-methionine biosynthesis II	6	5	2
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
L-mimosine degradation	8	4	2
glutathione-mediated detoxification I	8	3	2
oxalate degradation VI	4	1	1
putrescine degradation II	4	1	1
oxalate degradation III	5	1	1
fatty acid salvage	6	6	1
purine nucleobases degradation II (anaerobic)	24	16	4
pyruvate fermentation to butanol II (engineered)	6	4	1
NAD(P)/NADPH interconversion	6	3	1
methanol oxidation to carbon dioxide	6	3	1
superpathway of C1 compounds oxidation to CO2	12	5	2
L-glutamate and L-glutamine biosynthesis	7	6	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
L-citrulline biosynthesis	8	8	1
4-hydroxyphenylacetate degradation	8	6	1
superpathway of ornithine degradation	8	4	1
chloramphenicol biosynthesis	9	1	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
pyruvate fermentation to hexanol (engineered)	11	7	1
superpathway of candicidin biosynthesis	11	4	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
superpathway of L-citrulline metabolism	12	10	1
superpathway of L-arginine and L-ornithine degradation	13	9	1
purine nucleobases degradation I (anaerobic)	15	6	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
oleate β-oxidation	35	33	1
superpathway of chorismate metabolism	59	42	1