Experiment set4IT078 for Pseudomonas fluorescens FW300-N1B4

Carnitine Hydrochloride carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Carnitine Hydrochloride (20 mM), pH=7
Culturing: pseudo1_N1B4_ML1, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/16/2014
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)
Growth plate: Cplate2 A2

Specific Phenotypes

For 23 genes in this experiment

For carbon source Carnitine Hydrochloride in Pseudomonas fluorescens FW300-N1B4

For carbon source Carnitine Hydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	7
Glycine and Serine Utilization	2
Folate Biosynthesis	1
Formate hydrogenase	1
Glycine Biosynthesis	1
Ketoisovalerate oxidoreductase	1
L-rhamnose utilization	1
LMPTP YwlE cluster	1
Lactate utilization	1
Phosphate metabolism	1
Photorespiration (oxidative C2 cycle)	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Serine-glyoxylate cycle	1
Serine Biosynthesis	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• alpha-Linolenic acid metabolism
• Methane metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• Cysteine metabolism
• Cyanoamino acid metabolism
• Glutathione metabolism
• Nucleotide sugars metabolism
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Trinitrotoluene degradation
• Propanoate metabolism
• One carbon pool by folate
• Nicotinate and nicotinamide metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• 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
glycine betaine degradation III	7	7	7
L-serine degradation	3	3	3
formate oxidation to CO2	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
acetate conversion to acetyl-CoA	1	1	1
glycine biosynthesis I	1	1	1
glycine betaine degradation I	8	6	6
L-cysteine degradation II	3	3	2
L-carnitine degradation III	3	3	2
glycine degradation	3	3	2
D-serine degradation	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
D-carnitine degradation I	3	2	2
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
superpathway of acetate utilization and formation	3	3	1
L-methionine biosynthesis II	6	4	2
ethanol degradation III	3	2	1
L-isoleucine biosynthesis V	3	2	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
L-mimosine degradation	8	4	2
chitin deacetylation	4	2	1
glutathione-mediated detoxification I	8	3	2
oxalate degradation VI	4	1	1
creatinine degradation I	4	1	1
glycine betaine degradation II (mammalian)	4	1	1
purine nucleobases degradation II (anaerobic)	24	16	5
2-methylcitrate cycle I	5	5	1
cytosolic NADPH production (yeast)	5	4	1
folate polyglutamylation	5	4	1
oxalate degradation III	5	1	1
creatinine degradation II	5	1	1
folate transformations II (plants)	11	10	2
2-methylcitrate cycle II	6	5	1
β-alanine biosynthesis II	6	5	1
L-isoleucine biosynthesis IV	6	4	1
NAD(P)/NADPH interconversion	6	3	1
superpathway of bitter acids biosynthesis	18	3	3
adlupulone and adhumulone biosynthesis	6	1	1
lupulone and humulone biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	12	2
partial TCA cycle (obligate autotrophs)	8	8	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
nitrogen remobilization from senescing leaves	8	5	1
folate transformations III (E. coli)	9	9	1
TCA cycle VII (acetate-producers)	9	7	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	1
TCA cycle VI (Helicobacter)	9	7	1
TCA cycle V (2-oxoglutarate synthase)	9	7	1
photorespiration III	9	6	1
photorespiration I	9	6	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
cis-geranyl-CoA degradation	9	4	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
TCA cycle I (prokaryotic)	10	8	1
photorespiration II	10	7	1
reductive TCA cycle I	11	6	1
superpathway of glyoxylate bypass and TCA	12	10	1
superpathway of C1 compounds oxidation to CO2	12	5	1
folate transformations I	13	9	1
formaldehyde assimilation I (serine pathway)	13	6	1
purine nucleobases degradation I (anaerobic)	15	6	1
mixed acid fermentation	16	12	1
methylaspartate cycle	19	9	1
ethene biosynthesis V (engineered)	25	19	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	21	1