Experiment set25S550 for Pseudomonas fluorescens FW300-N2E2

Ying_Others16 rep B; time point 3

Group: carbon source
Media: SDM_noCarbon + 1X Ying_Others16
Culturing: pseudo6_N2E2_ML5b, tube, Aerobic, at 28 (C), shaken=180 rpm
By: Ying and Valentine on 1-Sep-23
Media components: 1.5 g/L Ammonium chloride, 0.6 g/L Potassium phosphate monobasic, 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)

Ying_Others16 1x includes: 160 uM Gamma-Aminobutyric Acid Hydrochloride, 160 uM Ectoine, 160 uM Betaine, 160 uM N-Acetyl-L-Glutamic Acid, 160 uM Nicotinamide, 160 uM L-Ornithine, 160 uM Shikimic Acid, 160 uM spermidine, 160 uM Taurine, 160 uM Trigonelline HCl, 160 uM L-Carnitine hydrochloride, 160 uM Choline, 160 uM N-alpha-Acetyl-L-glutamate, 160 uM n-Acetyl-lysine, 160 uM n-Acetyl-muramic acid, 160 uM sn-glycero-3-phosphocholine

Specific Phenotypes

For 16 genes in this experiment

For carbon source Ying_Others16 in Pseudomonas fluorescens FW300-N2E2

For carbon source Ying_Others16 across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	5
Choline and Betaine Uptake and Betaine Biosynthesis	2
Acid resistance mechanisms	1
Folate Biosynthesis	1
Glycine Biosynthesis	1
Glycine and Serine Utilization	1
Glycogen metabolism	1
L-rhamnose utilization	1
LMPTP YwlE cluster	1
Lactate utilization	1
Maltose and Maltodextrin Utilization	1
Photorespiration (oxidative C2 cycle)	1
Polyamine Metabolism	1
Serine-glyoxylate cycle	1
Serine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Benzoate degradation via CoA ligation
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Arginine and proline metabolism
• Butanoate metabolism
• Biosynthesis of plant hormones
• Fatty acid biosynthesis
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Bile acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine degradation
• Tryptophan metabolism
• Cyanoamino acid metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• alpha-Linolenic acid metabolism
• One carbon pool by folate
• Methane metabolism
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
cadaverine biosynthesis	1	1	1
arginine dependent acid resistance	1	1	1
glycine biosynthesis I	1	1	1
L-carnitine degradation III	3	3	2
putrescine biosynthesis I	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
superpathway of putrescine biosynthesis	4	3	2
putrescine biosynthesis III	2	1	1
D-carnitine degradation II	2	1	1
glycine betaine degradation III	7	7	3
glycogen degradation I	8	6	3
glycine betaine degradation I	8	6	3
superpathway of polyamine biosynthesis I	8	5	3
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
putrescine biosynthesis II	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
benzoyl-CoA biosynthesis	3	3	1
glycine degradation	3	3	1
glycogen degradation II	6	5	2
D-carnitine degradation I	3	2	1
aminopropylcadaverine biosynthesis	3	1	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
starch degradation V	4	3	1
superpathway of polyamine biosynthesis II	8	5	2
starch degradation III	4	2	1
spermidine biosynthesis III	4	1	1
glycine betaine degradation II (mammalian)	4	1	1
creatinine degradation I	4	1	1
oleate β-oxidation	35	30	8
valproate β-oxidation	9	7	2
adipate degradation	5	5	1
folate polyglutamylation	5	4	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	1
4-hydroxybenzoate biosynthesis III (plants)	5	4	1
adipate biosynthesis	5	4	1
glutaryl-CoA degradation	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
bisucaberin biosynthesis	5	1	1
lupanine biosynthesis	5	1	1
desferrioxamine E biosynthesis	5	1	1
creatinine degradation II	5	1	1
desferrioxamine B biosynthesis	5	1	1
folate transformations II (plants)	11	10	2
pyruvate fermentation to hexanol (engineered)	11	7	2
superpathway of arginine and polyamine biosynthesis	17	14	3
fatty acid salvage	6	6	1
L-lysine degradation X	6	5	1
pyruvate fermentation to butanol II (engineered)	6	4	1
methyl ketone biosynthesis (engineered)	6	3	1
superpathway of L-arginine and L-ornithine degradation	13	11	2
2-methyl-branched fatty acid β-oxidation	14	11	2
fatty acid β-oxidation I (generic)	7	5	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
L-lysine degradation I	7	4	1
pyruvate fermentation to butanoate	7	3	1
benzoyl-CoA degradation I (aerobic)	7	3	1
superpathway of ornithine degradation	8	7	1
sucrose biosynthesis II	8	6	1
pyruvate fermentation to butanol I	8	3	1
2-methylpropene degradation	8	2	1
folate transformations III (E. coli)	9	9	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
photorespiration III	9	5	1
photorespiration I	9	5	1
phenylacetate degradation I (aerobic)	9	4	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
photorespiration II	10	6	1
3-phenylpropanoate degradation	10	5	1
methyl tert-butyl ether degradation	10	3	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
superpathway of phenylethylamine degradation	11	6	1
L-glutamate degradation VII (to butanoate)	12	3	1
androstenedione degradation I (aerobic)	25	6	2
folate transformations I	13	9	1
formaldehyde assimilation I (serine pathway)	13	6	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
androstenedione degradation II (anaerobic)	27	4	2
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
superpathway of cholesterol degradation I (cholesterol oxidase)	42	9	3
superpathway of testosterone and androsterone degradation	28	6	2
L-tryptophan degradation III (eukaryotic)	15	3	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	9	3
glycerol degradation to butanol	16	9	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	4	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	4	1
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	3	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	9	1
toluene degradation VI (anaerobic)	18	4	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	3	1
purine nucleobases degradation II (anaerobic)	24	16	1
superpathway of cholesterol degradation III (oxidase)	49	5	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	20	1
platensimycin biosynthesis	26	6	1
1-butanol autotrophic biosynthesis (engineered)	27	20	1
superpathway of L-lysine degradation	43	19	1