Experiment set16IT035 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 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 23 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
Glycine and Serine Utilization	3
Pyruvate Alanine Serine Interconversions	3
Ammonia assimilation	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Biogenesis of c-type cytochromes	1
CBSS-262719.3.peg.410	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
DNA repair, bacterial	1
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycogen metabolism	1
Maltose and Maltodextrin Utilization	1
Methylglyoxal Metabolism	1
Orphan regulatory proteins	1
Periplasmic disulfide interchange	1
Potassium homeostasis	1
Putative TldE-TldD proteolytic complex	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Ribosome biogenesis bacterial	1
TCA Cycle	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:

• Lysine degradation
• Histidine metabolism
• Lipopolysaccharide biosynthesis
• Pyruvate metabolism
• Butanoate metabolism
• Limonene and pinene degradation
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine degradation
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Starch and sucrose metabolism
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• 1,2-Dichloroethane degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Ethylbenzene degradation
• Folate biosynthesis
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
L-cysteine degradation II	3	3	2
D-serine degradation	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
phenylethylamine degradation I	2	2	1
putrescine degradation V	2	2	1
putrescine degradation I	2	1	1
phenylethylamine degradation II	2	1	1
phenylethanol degradation	2	1	1
ethylene glycol degradation	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 II	3	3	1
ethanol degradation IV	3	3	1
glycine degradation	3	3	1
L-methionine biosynthesis II	6	5	2
L-phenylalanine degradation II (anaerobic)	3	2	1
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
putrescine degradation IV	3	2	1
styrene degradation	3	1	1
histamine degradation	3	1	1
starch degradation V	4	3	1
phytol degradation	4	3	1
putrescine degradation III	4	3	1
L-mimosine degradation	8	4	2
fatty acid α-oxidation I (plants)	4	2	1
D-arabinose degradation II	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
glutathione-mediated detoxification I	8	3	2
mitochondrial NADPH production (yeast)	5	4	1
octane oxidation	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	2	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
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
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
partial TCA cycle (obligate autotrophs)	8	8	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
glycogen degradation I	8	6	1
sucrose biosynthesis II	8	6	1
purine nucleobases degradation II (anaerobic)	24	16	3
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
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
starch degradation II	9	1	1
TCA cycle I (prokaryotic)	10	9	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
superpathway of phenylethylamine degradation	11	6	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
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of pentose and pentitol degradation	42	16	1