Experiment set11IT071 for Pseudomonas fluorescens SBW25-INTG

Sodium malate (C) and Ammonium chloride (N); with TAPS

Group: stress
Media: MME_noNitrogen_noCarbon + Sodium malate (30 mM) + Ammonium chloride (10 mM) + TAPS sodium salt (20 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=1300 rpm
By: Rob Egbert on 11-May-21
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 27 genes in this experiment

For stress Sodium malate in Pseudomonas fluorescens SBW25-INTG

For stress Sodium malate across organisms

SEED Subsystems

Subsystem	#Specific
D-gluconate and ketogluconates metabolism	2
Entner-Doudoroff Pathway	2
Trehalose Uptake and Utilization	2
Arginine and Ornithine Degradation	1
Calvin-Benson cycle	1
Cluster-based Subsystem Grouping Hypotheticals - perhaps Proteosome Related	1
Fructose and Mannose Inducible PTS	1
Fructose utilization	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycogen metabolism	1
Lipid A modifications	1
Maltose and Maltodextrin Utilization	1
Mannitol Utilization	1
Methylglyoxal Metabolism	1
Pentose phosphate pathway	1
Polyhydroxybutyrate metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
TCA Cycle	1
Trehalose Biosynthesis	1
Twin-arginine translocation system	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Starch and sucrose metabolism
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Ascorbate and aldarate metabolism
• Arginine and proline metabolism
• Pyruvate metabolism
• Fructose and mannose metabolism
• Galactose metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Glycerolipid metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Carbon fixation in photosynthetic organisms
• Limonene and pinene degradation
• Biosynthesis of ansamycins
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
trehalose biosynthesis IV	1	1	1
pentose phosphate pathway (partial)	3	3	2
phenylethylamine degradation I	2	2	1
putrescine degradation V	2	2	1
phenylethanol degradation	2	1	1
phenylethylamine degradation II	2	1	1
ethylene glycol degradation	2	1	1
putrescine degradation I	2	1	1
pentose phosphate pathway (non-oxidative branch) I	5	5	2
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
pentose phosphate pathway (non-oxidative branch) II	6	5	2
sucrose degradation I (sucrose phosphotransferase)	3	2	1
D-apiose degradation I	3	2	1
hypotaurine degradation	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
putrescine degradation IV	3	2	1
ethanol degradation III	3	2	1
histamine degradation	3	1	1
styrene degradation	3	1	1
pentose phosphate pathway	8	8	2
putrescine degradation III	4	3	1
phytol degradation	4	3	1
starch degradation V	4	3	1
D-arabinose degradation II	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	6	2
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	2
L-arginine degradation II (AST pathway)	5	5	1
Rubisco shunt	10	8	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
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	2
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
Calvin-Benson-Bassham cycle	13	10	2
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
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
superpathway of ornithine degradation	8	4	1
aromatic biogenic amine degradation (bacteria)	8	4	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
superpathway of glucose and xylose degradation	17	16	2
oxygenic photosynthesis	17	11	2
TCA cycle VI (Helicobacter)	9	7	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	7	1
TCA cycle VII (acetate-producers)	9	7	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
peptidoglycan recycling II	10	8	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
ethene biosynthesis V (engineered)	25	18	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
superpathway of L-arginine and L-ornithine degradation	13	9	1
1-butanol autotrophic biosynthesis (engineered)	27	19	2
peptidoglycan recycling I	14	11	1
Bifidobacterium shunt	15	12	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