Experiment set5IT092 for Pseudomonas fluorescens FW300-N2C3

Carnitine Hydrochloride nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Carnitine Hydrochloride (5 mM), pH=7
Culturing: pseudo5_N2-C3_1_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/17/2014
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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 24 genes in this experiment

For nitrogen source Carnitine Hydrochloride in Pseudomonas fluorescens FW300-N2C3

For nitrogen source Carnitine Hydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	9
Glutathione-dependent pathway of formaldehyde detoxification	2
Glycine and Serine Utilization	2
Acetyl-CoA fermentation to Butyrate	1
Folate Biosynthesis	1
Glycine Biosynthesis	1
L-rhamnose utilization	1
LMPTP YwlE cluster	1
Lactate utilization	1
Photorespiration (oxidative C2 cycle)	1
Pyrroloquinoline Quinone biosynthesis	1
Pyruvate Alanine Serine Interconversions	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:

• Glycine, serine and threonine metabolism
• Benzoate degradation via CoA ligation
• Fatty acid metabolism
• Butanoate metabolism
• Methane metabolism
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Fatty acid biosynthesis
• Fatty acid elongation in mitochondria
• Bile acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Cysteine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine degradation
• Tyrosine metabolism
• Tryptophan metabolism
• Cyanoamino acid metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• 3-Chloroacrylic acid degradation
• One carbon pool by folate
• Retinol metabolism
• Limonene and pinene degradation
• Caprolactam degradation
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of unsaturated fatty acids

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
L-carnitine degradation III	3	3	3
acetaldehyde biosynthesis I	1	1	1
glycine biosynthesis I	1	1	1
glycine betaine degradation I	8	6	6
L-cysteine degradation II	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
ethanol degradation I	2	2	1
pyruvate fermentation to ethanol II	2	1	1
D-carnitine degradation II	2	1	1
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
benzoyl-CoA biosynthesis	3	3	1
ethanol degradation II	3	3	1
formaldehyde oxidation II (glutathione-dependent)	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
L-methionine biosynthesis II	6	5	2
L-valine degradation II	3	2	1
pyruvate fermentation to ethanol III	3	2	1
L-isoleucine degradation II	3	2	1
pyruvate fermentation to ethanol I	3	2	1
L-leucine degradation III	3	2	1
L-methionine degradation III	3	1	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
phytol degradation	4	3	1
L-mimosine degradation	8	4	2
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
creatinine degradation I	4	2	1
salidroside biosynthesis	4	2	1
glutathione-mediated detoxification I	8	3	2
glycine betaine degradation II (mammalian)	4	1	1
oleate β-oxidation	35	30	8
valproate β-oxidation	9	7	2
ethanolamine utilization	5	5	1
adipate degradation	5	5	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	1
acetylene degradation (anaerobic)	5	4	1
adipate biosynthesis	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
4-hydroxybenzoate biosynthesis III (plants)	5	4	1
folate polyglutamylation	5	4	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
protein S-nitrosylation and denitrosylation	5	3	1
glutaryl-CoA degradation	5	3	1
phenylethanol biosynthesis	5	2	1
(S)-propane-1,2-diol degradation	5	2	1
creatinine degradation II	5	1	1
folate transformations II (plants)	11	10	2
pyruvate fermentation to hexanol (engineered)	11	7	2
peptido-conjugates in tissue regeneration biosynthesis	17	6	3
fatty acid salvage	6	6	1
purine nucleobases degradation II (anaerobic)	24	16	4
pyruvate fermentation to butanol II (engineered)	6	4	1
methyl ketone biosynthesis (engineered)	6	3	1
leukotriene biosynthesis	6	2	1
noradrenaline and adrenaline degradation	13	8	2
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	2
3-methylbutanol biosynthesis (engineered)	7	6	1
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
serotonin degradation	7	4	1
benzoyl-CoA degradation I (aerobic)	7	3	1
pyruvate fermentation to butanoate	7	3	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
butanol and isobutanol biosynthesis (engineered)	8	3	1
pyruvate fermentation to butanol I	8	3	1
2-methylpropene degradation	8	2	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	2
folate transformations III (E. coli)	9	9	1
photorespiration III	9	5	1
photorespiration I	9	5	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	4	1
phenylacetate degradation I (aerobic)	9	3	1
gliotoxin biosynthesis	9	2	1
photorespiration II	10	6	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
3-phenylpropanoate degradation	10	5	1
methyl tert-butyl ether degradation	10	2	1
superpathway of phenylethylamine degradation	11	5	1
superpathway of C1 compounds oxidation to CO2	12	5	1
L-glutamate degradation VII (to butanoate)	12	4	1
androstenedione degradation I (aerobic)	25	6	2
folate transformations I	13	9	1
formaldehyde assimilation I (serine pathway)	13	6	1
L-tryptophan degradation V (side chain pathway)	13	1	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
mixed acid fermentation	16	12	1
glycerol degradation to butanol	16	9	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	4	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	4	1
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	3	1
heterolactic fermentation	18	16	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	8	1
toluene degradation VI (anaerobic)	18	4	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	15	1
superpathway of anaerobic sucrose degradation	19	15	1
superpathway of N-acetylneuraminate degradation	22	15	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	3	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
arachidonate metabolites biosynthesis	74	3	1