Experiment set15IT024 for Pseudomonas fluorescens SBW25-INTG

D,L-Malic Acid (C) and Ammonium chloride (N); with TAPS; with Sodium chloride

Group: stress
Media: MTM_noNitrogen_noCarbon + D,L-Malic Acid (20 mM) + Ammonium chloride (10 mM) + Sodium Chloride (400 mM), pH=8.5
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 33 (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 31 genes in this experiment

For stress D,L-Malic Acid in Pseudomonas fluorescens SBW25-INTG

For stress D,L-Malic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	2
Trehalose Uptake and Utilization	2
Acetyl-CoA fermentation to Butyrate	1
Alanine biosynthesis	1
Anaerobic respiratory reductases	1
Arginine and Ornithine Degradation	1
Butanol Biosynthesis	1
Cobalt-zinc-cadmium resistance	1
Cysteine Biosynthesis	1
D-gluconate and ketogluconates metabolism	1
DNA-binding regulatory proteins, strays	1
DNA repair, bacterial	1
Entner-Doudoroff Pathway	1
Fructose and Mannose Inducible PTS	1
Fructose utilization	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine and Serine Utilization	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Isoleucine degradation	1
Mannitol Utilization	1
Methylglyoxal Metabolism	1
Proline Synthesis	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Queuosine-Archaeosine Biosynthesis	1
TCA Cycle	1
Threonine anaerobic catabolism gene cluster	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
• Tryptophan metabolism
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Arginine and proline metabolism
• Histidine metabolism
• Pyruvate metabolism
• Butanoate metabolism
• Fructose and mannose metabolism
• Galactose metabolism
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Glutamate metabolism
• Geraniol degradation
• Lysine degradation
• Tyrosine metabolism
• Benzoxazinone biosynthesis
• beta-Alanine metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Glycerolipid metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Thiamine metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Caprolactam degradation
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-alanine biosynthesis III	1	1	1
L-cysteine degradation IV	1	1	1
L-glutamate biosynthesis III	1	1	1
phenylethylamine degradation I	2	2	1
putrescine degradation V	2	2	1
cytidylyl molybdenum cofactor sulfurylation	2	1	1
ethylene glycol degradation	2	1	1
putrescine degradation I	2	1	1
phenylethanol degradation	2	1	1
phenylethylamine degradation II	2	1	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
sucrose degradation I (sucrose phosphotransferase)	3	2	1
putrescine degradation IV	3	2	1
hypotaurine degradation	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
ethanol degradation III	3	2	1
styrene degradation	3	1	1
bis(guanylyl molybdopterin) cofactor sulfurylation	3	1	1
histamine degradation	3	1	1
thiazole component of thiamine diphosphate biosynthesis II	7	5	2
superpathway of L-alanine biosynthesis	4	4	1
putrescine degradation III	4	3	1
phytol degradation	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
D-arabinose degradation II	4	2	1
tRNA-uridine 2-thiolation (mammalian mitochondria)	4	1	1
tRNA-uridine 2-thiolation (yeast mitochondria)	4	1	1
mitochondrial NADPH production (yeast)	5	4	1
octane oxidation	5	4	1
[2Fe-2S] iron-sulfur cluster biosynthesis	10	4	2
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	2	1
tRNA-uridine 2-thiolation (thermophilic bacteria)	5	1	1
superpathway of thiamine diphosphate biosynthesis II	11	9	2
fatty acid salvage	6	6	1
molybdopterin biosynthesis	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
thiazole component of thiamine diphosphate biosynthesis I	6	4	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
L-glutamate and L-glutamine biosynthesis	7	6	1
superpathway of glycol metabolism and degradation	7	5	1
serotonin degradation	7	4	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
partial TCA cycle (obligate autotrophs)	8	8	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
superpathway of ornithine degradation	8	4	1
aromatic biogenic amine degradation (bacteria)	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
tRNA-uridine 2-thiolation (cytoplasmic)	8	1	1
TCA cycle VII (acetate-producers)	9	7	1
TCA cycle VI (Helicobacter)	9	7	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
TCA cycle I (prokaryotic)	10	9	1
superpathway of thiamine diphosphate biosynthesis I	10	8	1
pyruvate fermentation to hexanol (engineered)	11	7	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
superpathway of phenylethylamine degradation	11	6	1
tRNA-uridine 2-thiolation and selenation (bacteria)	11	4	1
superpathway of glyoxylate bypass and TCA	12	11	1
superpathway of L-arginine and L-ornithine degradation	13	9	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
oleate β-oxidation	35	33	1
superpathway of pentose and pentitol degradation	42	16	1