Experiment set5IT010 for Pseudomonas fluorescens FW300-N2E3

Carnitine Hydrochloride carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Carnitine Hydrochloride (20 mM), pH=7
Culturing: pseudo3_N2E3_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/17/2015
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 32 genes in this experiment

For carbon source Carnitine Hydrochloride in Pseudomonas fluorescens FW300-N2E3

For carbon source Carnitine Hydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	9
Serine-glyoxylate cycle	3
Catechol branch of beta-ketoadipate pathway	2
Fermentations: Mixed acid	2
Leucine Degradation and HMG-CoA Metabolism	2
Protocatechuate branch of beta-ketoadipate pathway	2
Acetyl-CoA fermentation to Butyrate	1
DNA-binding regulatory proteins, strays	1
Ethanolamine utilization	1
Fermentations: Lactate	1
Folate Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycine Biosynthesis	1
Glycine and Serine Utilization	1
L-rhamnose utilization	1
LMPTP YwlE cluster	1
Lactate utilization	1
MLST	1
Phosphate metabolism	1
Photorespiration (oxidative C2 cycle)	1
Potassium homeostasis	1
Propanediol utilization	1
Pyrroloquinoline Quinone biosynthesis	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Serine Biosynthesis	1
Threonine anaerobic catabolism gene cluster	1
Threonine and Homoserine 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
• Arginine and proline metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Carbon fixation in photosynthetic organisms
• Alkaloid biosynthesis I
• Biosynthesis of plant hormones
• Fatty acid biosynthesis
• Synthesis and degradation of ketone bodies
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• Glutamate metabolism
• Alanine and aspartate metabolism
• Methionine metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Taurine and hypotaurine metabolism
• Aminophosphonate metabolism
• Cyanoamino acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Trinitrotoluene degradation
• Propanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Nicotinate and nicotinamide metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Alkaloid biosynthesis II
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-carnitine degradation III	3	3	3
L-alanine biosynthesis II	1	1	1
L-aspartate biosynthesis	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
glycine biosynthesis I	1	1	1
L-alanine degradation III	1	1	1
D-carnitine degradation I	3	2	2
glycine betaine degradation III	7	7	4
L-glutamate degradation II	2	2	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
acetate and ATP formation from acetyl-CoA I	2	2	1
sulfoacetaldehyde degradation I	2	1	1
L-tyrosine degradation II	2	1	1
D-carnitine degradation II	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
atromentin biosynthesis	2	1	1
L-alanine degradation V (oxidative Stickland reaction)	2	1	1
glycine betaine degradation I	8	6	3
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	4
superpathway of acetate utilization and formation	3	3	1
L-phenylalanine biosynthesis I	3	3	1
pyruvate fermentation to acetate II	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
glycine degradation	3	3	1
L-tyrosine biosynthesis I	3	3	1
ketolysis	3	3	1
L-phenylalanine degradation II (anaerobic)	3	2	1
pyruvate fermentation to acetate I	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
pyruvate fermentation to acetate IV	3	2	1
pyruvate fermentation to acetate VII	3	2	1
superpathway of sulfolactate degradation	6	2	2
(R)-cysteate degradation	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
sulfolactate degradation III	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
pyruvate fermentation to acetate and alanine	3	1	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	4
anaerobic energy metabolism (invertebrates, cytosol)	7	4	2
superpathway of L-alanine biosynthesis	4	4	1
pyruvate fermentation to acetate and (S)-lactate I	4	4	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
pyruvate fermentation to acetate and lactate II	4	3	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
sulfolactate degradation II	4	1	1
glycine betaine degradation II (mammalian)	4	1	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
creatinine degradation I	4	1	1
superpathway of L-alanine fermentation (Stickland reaction)	9	4	2
ethanolamine utilization	5	5	1
L-tyrosine degradation I	5	5	1
acetylene degradation (anaerobic)	5	4	1
folate polyglutamylation	5	4	1
trans-4-hydroxy-L-proline degradation I	5	3	1
(S)-propane-1,2-diol degradation	5	2	1
superpathway of plastoquinol biosynthesis	5	2	1
creatinine degradation II	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
folate transformations II (plants)	11	10	2
peptido-conjugates in tissue regeneration biosynthesis	17	6	3
superpathway of L-threonine biosynthesis	6	6	1
TCA cycle VIII (Chlamydia)	6	5	1
L-threonine degradation I	6	4	1
NAD(P)/NADPH interconversion	6	3	1
L-alanine degradation VI (reductive Stickland reaction)	6	2	1
superpathway of taurine degradation	6	2	1
methanogenesis from acetate	6	2	1
leukotriene biosynthesis	6	2	1
coenzyme M biosynthesis II	6	1	1
formaldehyde assimilation I (serine pathway)	13	6	2
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
acetyl-CoA fermentation to butanoate	7	4	1
partial TCA cycle (obligate autotrophs)	8	8	1
mixed acid fermentation	16	12	2
nitrogen remobilization from senescing leaves	8	6	1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	3	1
superpathway of anaerobic energy metabolism (invertebrates)	17	8	2
superpathway of aromatic amino acid biosynthesis	18	18	2
folate transformations III (E. coli)	9	9	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
TCA cycle VI (Helicobacter)	9	7	1
photorespiration I	9	5	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
photorespiration III	9	5	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
gliotoxin biosynthesis	9	2	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
photorespiration II	10	6	1
L-lysine fermentation to acetate and butanoate	10	3	1
rosmarinic acid biosynthesis I	10	1	1
gallate degradation III (anaerobic)	11	3	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
purine nucleobases degradation II (anaerobic)	24	16	2
indole-3-acetate biosynthesis II	12	4	1
superpathway of L-isoleucine biosynthesis I	13	13	1
folate transformations I	13	9	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	5	1
superpathway of rosmarinic acid biosynthesis	14	1	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	8	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
heterolactic fermentation	18	16	1
superpathway of L-threonine metabolism	18	12	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	3
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of methanogenesis	21	2	1
superpathway of N-acetylneuraminate degradation	22	15	1
aspartate superpathway	25	22	1
ethene biosynthesis V (engineered)	25	19	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	2	1
superpathway of chorismate metabolism	59	43	2
superpathway of L-lysine degradation	43	18	1
arachidonate metabolites biosynthesis	74	3	1