Experiment set11IT069 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 16 genes in this experiment

For stress Sodium malate in Pseudomonas fluorescens SBW25-INTG

For stress Sodium malate across organisms

SEED Subsystems

Subsystem	#Specific
Anaerobic respiratory reductases	1
Calvin-Benson cycle	1
Glycogen metabolism	1
Lipid A modifications	1
Maltose and Maltodextrin Utilization	1
Methionine Biosynthesis	1
Methionine Degradation	1
Pentose phosphate pathway	1
Polyhydroxybutyrate metabolism	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Puromycin biosynthesis
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Trinitrotoluene degradation
• Carbon fixation in photosynthetic organisms
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• 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
pentose phosphate pathway (partial)	3	3	2
pentose phosphate pathway (non-oxidative branch) I	5	5	2
pentose phosphate pathway (non-oxidative branch) II	6	5	2
D-apiose degradation I	3	2	1
pentose phosphate pathway	8	8	2
starch degradation V	4	3	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	6	2
Rubisco shunt	10	8	2
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	2
Calvin-Benson-Bassham cycle	13	10	2
partial TCA cycle (obligate autotrophs)	8	8	1
sucrose biosynthesis II	8	6	1
glycogen degradation I	8	6	1
superpathway of glucose and xylose degradation	17	16	2
oxygenic photosynthesis	17	11	2
TCA cycle VI (Helicobacter)	9	7	1
TCA cycle VII (acetate-producers)	9	7	1
starch degradation II	9	1	1
TCA cycle I (prokaryotic)	10	9	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
1-butanol autotrophic biosynthesis (engineered)	27	19	2
Bifidobacterium shunt	15	12	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1