Experiment set22IT081 for Pseudomonas fluorescens SBW25-INTG

Sodium propionate 20 mM carbon source

Group: carbon source
Media: MME_noNitrogen_noCarbon + Sodium propionate (20 mM) + Ammonium chloride (10 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on 8-Mar-22
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 28 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
Methylcitrate cycle	2
Propionate-CoA to Succinate Module	2
Biotin biosynthesis	1
Glutathione: Redox cycle	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine cleavage system	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1
Orphan regulatory proteins	1
Periplasmic disulfide interchange	1
Phosphate metabolism	1
Queuosine-Archaeosine Biosynthesis	1
Ribosomal protein S12p Asp methylthiotransferase	1
Serine-glyoxylate cycle	1
Ubiquinone Biosynthesis	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Propanoate metabolism
• Tryptophan metabolism
• Porphyrin and chlorophyll metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Puromycin biosynthesis
• Geraniol degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Benzoxazinone biosynthesis
• Cyanoamino acid metabolism
• Glutathione metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Styrene degradation
• Reductive carboxylate cycle (CO2 fixation)
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
2-methylcitrate cycle I	5	5	3
acrylonitrile degradation I	2	2	1
indole-3-acetate biosynthesis IV (bacteria)	2	2	1
indole-3-acetate biosynthesis III (bacteria)	2	2	1
2-methylcitrate cycle II	6	5	3
glyoxylate cycle	6	5	2
superpathway of acrylonitrile degradation	3	2	1
L-arginine degradation X (arginine monooxygenase pathway)	3	2	1
glutathione-peroxide redox reactions	3	2	1
oleate biosynthesis III (cyanobacteria)	3	2	1
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis	3	1	1
partial TCA cycle (obligate autotrophs)	8	8	2
CDP-diacylglycerol biosynthesis I	4	4	1
CDP-diacylglycerol biosynthesis II	4	4	1
nitrogen remobilization from senescing leaves	8	6	2
TCA cycle VI (Helicobacter)	9	7	2
TCA cycle II (plants and fungi)	9	7	2
TCA cycle V (2-oxoglutarate synthase)	9	7	2
TCA cycle VII (acetate-producers)	9	7	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	2
adipate degradation	5	5	1
TCA cycle I (prokaryotic)	10	9	2
TCA cycle III (animals)	10	7	2
phosphatidate biosynthesis (yeast)	5	3	1
reductive TCA cycle I	11	6	2
fatty acid salvage	6	6	1
superpathway of glyoxylate bypass and TCA	12	11	2
superpathway of phospholipid biosynthesis III (E. coli)	12	10	2
phosphatidylglycerol biosynthesis I	6	5	1
phosphatidylglycerol biosynthesis II	6	5	1
reductive TCA cycle II	12	5	2
superpathway of stearidonate biosynthesis (cyanobacteria)	6	2	1
palmitoyl ethanolamide biosynthesis	6	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	12	2
diacylglycerol and triacylglycerol biosynthesis	7	3	1
stigma estolide biosynthesis	7	2	1
mixed acid fermentation	16	11	2
anandamide biosynthesis II	8	2	1
superpathway of CDP-glucose-derived O-antigen building blocks biosynthesis	8	1	1
methylaspartate cycle	19	9	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
oleate β-oxidation	35	33	3
indole-3-acetate biosynthesis II	12	5	1
anandamide biosynthesis I	12	3	1
ethene biosynthesis V (engineered)	25	18	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	2
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
2-methyl-branched fatty acid β-oxidation	14	11	1
superpathway of phospholipid biosynthesis II (plants)	28	9	2