Experiment set25S85 for Pseudomonas fluorescens SBW25-INTG

Sodium propionate carbon source

Group: carbon source
Media: MME_noCarbon + Sodium propionate (20 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Andrew Frank on 1/31/23
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium 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 21 genes in this experiment

For carbon source Sodium propionate in Pseudomonas fluorescens SBW25-INTG

For carbon source Sodium propionate across organisms

SEED Subsystems

Subsystem	#Specific
Terminal cytochrome C oxidases	3
Methylcitrate cycle	2
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	2
Propionate-CoA to Succinate Module	2
Biogenesis of c-type cytochromes	1
Copper homeostasis	1
De Novo Pyrimidine Synthesis	1
HMG CoA Synthesis	1
LMPTP YwlE cluster	1
Ubiquinone Biosynthesis	1
Universal stress protein family	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Propanoate metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Citrate cycle (TCA cycle)
• Oxidative phosphorylation
• Urea cycle and metabolism of amino groups
• Pyrimidine metabolism
• Geraniol degradation
• Nucleotide sugars metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Porphyrin and chlorophyll metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyrimidine nucleobases salvage I	1	1	1
2-methylcitrate cycle I	5	5	3
pyrimidine nucleobases salvage II	2	2	1
2-methylcitrate cycle II	6	5	3
arsenite to oxygen electron transfer	2	1	1
L-ornithine biosynthesis II	3	3	1
L-proline biosynthesis III (from L-ornithine)	3	3	1
L-arginine degradation I (arginase pathway)	3	3	1
glyoxylate cycle	6	5	2
arsenite to oxygen electron transfer (via azurin)	3	1	1
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis	3	1	1
partial TCA cycle (obligate autotrophs)	8	8	2
superpathway of pyrimidine nucleobases salvage	4	4	1
L-arginine degradation VI (arginase 2 pathway)	4	4	1
nitrogen remobilization from senescing leaves	8	6	2
aerobic respiration II (cytochrome c) (yeast)	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
TCA cycle V (2-oxoglutarate synthase)	9	7	2
TCA cycle VI (Helicobacter)	9	7	2
TCA cycle II (plants and fungi)	9	7	2
TCA cycle VII (acetate-producers)	9	7	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	2
L-arginine degradation XIII (reductive Stickland reaction)	5	5	1
L-ornithine biosynthesis I	5	5	1
TCA cycle I (prokaryotic)	10	9	2
TCA cycle III (animals)	10	7	2
reductive TCA cycle I	11	6	2
superpathway of glyoxylate bypass and TCA	12	11	2
Fe(II) oxidation	6	3	1
reductive TCA cycle II	12	5	2
methylgallate degradation	6	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	12	2
L-Nδ-acetylornithine biosynthesis	7	6	1
L-citrulline biosynthesis	8	8	1
mixed acid fermentation	16	11	2
protocatechuate degradation I (meta-cleavage pathway)	8	3	1
superpathway of CDP-glucose-derived O-antigen building blocks biosynthesis	8	1	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
methylaspartate cycle	19	9	2
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of pyrimidine ribonucleosides salvage	10	6	1
superpathway of vanillin and vanillate degradation	10	4	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
superpathway of L-citrulline metabolism	12	10	1
syringate degradation	12	3	1
ethene biosynthesis V (engineered)	25	18	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	2
superpathway of arginine and polyamine biosynthesis	17	15	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1