Experiment set19IT041 for Pseudomonas fluorescens SBW25-INTG

Glycine betaine (C)(N); with MOPS

Group: no stress control
Media: MME_noNitrogen_noCarbon + Betaine (20 mM), pH=7
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 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 15 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
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Phosphate metabolism	2
Ammonia assimilation	1
Arginine and Ornithine Degradation	1
Entner-Doudoroff Pathway	1
Fermentations: Mixed acid	1
Glutathione: Redox cycle	1
Glycine and Serine Utilization	1
Isoleucine degradation	1
Leucine Degradation and HMG-CoA Metabolism	1
Methylglyoxal Metabolism	1
Molybdenum cofactor biosynthesis	1
One-carbon metabolism by tetrahydropterines	1
Polyamine Metabolism	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Riboflavin, FMN and FAD metabolism	1
Threonine degradation	1
Ubiquinone Biosynthesis	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Arginine and proline metabolism
• 3-Chloroacrylic acid degradation
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism
• Ascorbate and aldarate metabolism
• Pyrimidine metabolism
• Cysteine metabolism
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glutathione metabolism
• Nucleotide sugars metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• Butanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
acetaldehyde biosynthesis I	1	1	1
formaldehyde oxidation IV (thiol-independent)	1	1	1
L-cysteine degradation II	3	3	2
D-serine degradation	3	3	2
ethanol degradation II	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
putrescine degradation V	2	2	1
phenylethylamine degradation I	2	2	1
polyphosphate metabolism	2	2	1
phytol degradation	4	3	2
putrescine degradation I	2	1	1
pyruvate fermentation to ethanol II	2	1	1
phenylethanol degradation	2	1	1
ethylene glycol degradation	2	1	1
phenylethylamine degradation II	2	1	1
ethanol degradation 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
ethanol degradation IV	3	3	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
putrescine biosynthesis II	3	3	1
glycine degradation	3	3	1
L-methionine biosynthesis II	6	5	2
L-valine degradation II	3	2	1
glutathione-peroxide redox reactions	3	2	1
ethanol degradation III	3	2	1
L-isoleucine degradation II	3	2	1
L-leucine degradation III	3	2	1
hypotaurine degradation	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
NAD salvage pathway III (to nicotinamide riboside)	3	2	1
putrescine degradation IV	3	2	1
pyruvate fermentation to ethanol I	3	1	1
L-methionine degradation III	3	1	1
pyruvate fermentation to ethanol III	3	1	1
styrene degradation	3	1	1
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis	3	1	1
histamine degradation	3	1	1
noradrenaline and adrenaline degradation	13	8	4
UTP and CTP dephosphorylation I	7	5	2
serotonin degradation	7	4	2
purine nucleotides degradation II (aerobic)	11	11	3
guanosine nucleotides degradation II	4	4	1
formaldehyde oxidation VII (THF pathway)	4	4	1
inosine 5'-phosphate degradation	4	4	1
guanosine nucleotides degradation III	4	4	1
adenosine nucleotides degradation I	8	7	2
purine nucleotides degradation I (plants)	12	10	3
putrescine degradation III	4	3	1
guanosine nucleotides degradation I	4	3	1
L-mimosine degradation	8	4	2
fatty acid α-oxidation I (plants)	4	2	1
salidroside biosynthesis	4	2	1
D-arabinose degradation II	4	2	1
L-phenylalanine degradation III	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
L-tyrosine degradation III	4	2	1
glutathione-mediated detoxification I	8	3	2
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
flavin biosynthesis I (bacteria and plants)	9	8	2
flavin biosynthesis III (fungi)	9	7	2
adenosine nucleotides degradation II	5	5	1
ethanolamine utilization	5	4	1
mitochondrial NADPH production (yeast)	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
octane oxidation	5	4	1
acetylene degradation (anaerobic)	5	3	1
6-hydroxymethyl-dihydropterin diphosphate biosynthesis III (Chlamydia)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
(S)-propane-1,2-diol degradation	5	2	1
dopamine degradation	5	2	1
phenylethanol biosynthesis	5	2	1
superpathway of guanosine nucleotides degradation (plants)	6	5	1
superpathway of purines degradation in plants	18	14	3
purine nucleobases degradation II (anaerobic)	24	16	4
NAD(P)/NADPH interconversion	6	3	1
methanol oxidation to carbon dioxide	6	3	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
3-methylbutanol biosynthesis (engineered)	7	6	1
ureide biosynthesis	7	6	1
superpathway of glycol metabolism and degradation	7	5	1
toxoflavin biosynthesis	7	3	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
superpathway of polyamine biosynthesis II	8	6	1
aromatic biogenic amine degradation (bacteria)	8	4	1
superpathway of ornithine degradation	8	4	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
superpathway of CDP-glucose-derived O-antigen building blocks biosynthesis	8	1	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	4	1
tunicamycin biosynthesis	9	2	1
flavin biosynthesis II (archaea)	10	5	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
superpathway of phenylethylamine degradation	11	6	1
NAD salvage (plants)	11	5	1
superpathway of C1 compounds oxidation to CO2	12	5	1
folate transformations I	13	9	1
superpathway of L-arginine and L-ornithine degradation	13	9	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
L-tryptophan degradation V (side chain pathway)	13	1	1
purine nucleobases degradation I (anaerobic)	15	6	1
mixed acid fermentation	16	11	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
heterolactic fermentation	18	13	1
superpathway of anaerobic sucrose degradation	19	14	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	13	1
superpathway of N-acetylneuraminate degradation	22	14	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of pentose and pentitol degradation	42	16	1