Experiment set19IT061 for Pseudomonas fluorescens SBW25-INTG

Glycine betaine (C)(N); with TAPS

Group: no stress control
Media: MTM_noNitrogen_noCarbon + Betaine (20 mM), pH=8.5
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 8 (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 8 genes in this experiment

For no stress control Betaine in Pseudomonas fluorescens SBW25-INTG

For no stress control Betaine across organisms

SEED Subsystems

Subsystem	#Specific
Phosphate metabolism	2
Choline and Betaine Uptake and Betaine Biosynthesis	1
Molybdenum cofactor biosynthesis	1
Purine conversions	1
Riboflavin, FMN and FAD metabolism	1
Threonine degradation	1
Ubiquinone Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Riboflavin metabolism
• Purine metabolism
• Glycine, serine and threonine metabolism
• Nucleotide sugars metabolism
• Methane metabolism
• Nicotinate and nicotinamide metabolism
• Porphyrin and chlorophyll metabolism
• Drug metabolism - other enzymes
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
formaldehyde oxidation IV (thiol-independent)	1	1	1
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
choline degradation I	2	2	1
β-alanine biosynthesis IV	2	1	1
β-alanine biosynthesis I	2	1	1
choline-O-sulfate degradation	3	3	1
glycine betaine biosynthesis III (plants)	3	2	1
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis	3	1	1
dimethylsulfoniopropanoate biosynthesis I (Wollastonia)	3	1	1
guanosine ribonucleotides de novo biosynthesis	4	4	1
inosine 5'-phosphate degradation	4	4	1
choline degradation IV	4	2	1
dimethylsulfoniopropanoate biosynthesis II (Spartina)	4	1	1
flavin biosynthesis I (bacteria and plants)	9	8	2
flavin biosynthesis III (fungi)	9	7	2
6-hydroxymethyl-dihydropterin diphosphate biosynthesis III (Chlamydia)	5	3	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
methanol oxidation to carbon dioxide	6	3	1
NAD(P)/NADPH interconversion	6	3	1
ureide biosynthesis	7	6	1
toxoflavin biosynthesis	7	3	1
superpathway of guanosine nucleotides de novo biosynthesis II	8	7	1
adenosine nucleotides degradation I	8	7	1
superpathway of CDP-glucose-derived O-antigen building blocks biosynthesis	8	1	1
flavin biosynthesis II (archaea)	10	5	1
purine nucleotides degradation II (aerobic)	11	11	1
purine nucleotides degradation I (plants)	12	10	1
superpathway of C1 compounds oxidation to CO2	12	5	1
superpathway of purine nucleotide salvage	14	13	1
superpathway of purines degradation in plants	18	14	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	1
superpathway of purine nucleotides de novo biosynthesis II	26	24	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	44	1