Experiment set1IT014 for Pseudomonas fluorescens FW300-N2E2

Sodium propionate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Sodium propionate (20 mM), pH=7
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 3/9/2015
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 25 genes in this experiment

For carbon source Sodium propionate in Pseudomonas fluorescens FW300-N2E2

For carbon source Sodium propionate across organisms

SEED Subsystems

Subsystem	#Specific
Fermentations: Mixed acid	2
Methylcitrate cycle	2
Propionate-CoA to Succinate Module	2
Flavodoxin	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Proteasome bacterial	1
Proteolysis in bacteria, ATP-dependent	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Rubrerythrin	1
Ton and Tol transport systems	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Glycolysis / Gluconeogenesis
• Fatty acid biosynthesis
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Arginine and proline metabolism
• Tyrosine metabolism
• alpha-Linolenic acid metabolism
• 2,4-Dichlorobenzoate degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Retinol metabolism
• Limonene and pinene degradation
• Nitrogen metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
adenosine nucleotides degradation III	1	1	1
L-glutamate degradation I	1	1	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
ethanol degradation I	2	2	1
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation II	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
L-valine degradation II	3	2	1
L-leucine degradation III	3	2	1
pyruvate fermentation to ethanol III	3	2	1
pyruvate fermentation to ethanol I	3	2	1
acrylate degradation II	3	2	1
L-isoleucine degradation II	3	2	1
ethene biosynthesis IV (engineered)	3	1	1
L-methionine degradation III	3	1	1
phytol degradation	4	3	1
salidroside biosynthesis	4	2	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
4-chlorobenzoate degradation	4	2	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
4-oxopentanoate degradation	9	4	2
2-methylcitrate cycle I	5	5	1
ethanolamine utilization	5	5	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
4-hydroxybenzoate biosynthesis III (plants)	5	4	1
acetylene degradation (anaerobic)	5	4	1
octane oxidation	5	4	1
(S)-propane-1,2-diol degradation	5	2	1
phenylethanol biosynthesis	5	2	1
2-methylcitrate cycle II	6	5	1
noradrenaline and adrenaline degradation	13	8	2
3-methylbutanol biosynthesis (engineered)	7	6	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
serotonin degradation	7	4	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
4-aminobutanoate degradation V	7	2	1
partial TCA cycle (obligate autotrophs)	8	8	1
mixed acid fermentation	16	12	2
nitrogen remobilization from senescing leaves	8	6	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	1
3-hydroxypropanoate cycle	13	6	1
glyoxylate assimilation	13	6	1
formaldehyde assimilation I (serine pathway)	13	6	1
cannabinoid biosynthesis	13	6	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
L-tryptophan degradation V (side chain pathway)	13	1	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
heterolactic fermentation	18	15	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	9	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
superpathway of the 3-hydroxypropanoate cycle	18	7	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of anaerobic sucrose degradation	19	14	1
methylaspartate cycle	19	9	1
superpathway of N-acetylneuraminate degradation	22	13	1
ethene biosynthesis V (engineered)	25	19	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1