Experiment set1IT059 for Pseudomonas fluorescens FW300-N2E3

Potassium acetate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Potassium acetate (20 mM), pH=7
Culturing: pseudo3_N2E3_ML2, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.4 generations
By: Jayashree on 4/28/2014
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)

Specific Phenotypes

For 29 genes in this experiment

For carbon source Potassium acetate in Pseudomonas fluorescens FW300-N2E3

For carbon source Potassium acetate across organisms

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	2
Biotin biosynthesis	1
Carboxysome	1
Cyanate hydrolysis	1
Fermentations: Mixed acid	1
Fructose utilization	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Hemin transport system	1
Isoleucine degradation	1
Lactate utilization	1
Leucine Degradation and HMG-CoA Metabolism	1
Peptidyl-prolyl cis-trans isomerase	1
Potassium homeostasis	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
TCA Cycle	1
Valine degradation	1
ZZ gjo need homes	1
n-Phenylalkanoic acid degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Urea cycle and metabolism of amino groups
• Lysine biosynthesis
• Pyruvate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Citrate cycle (TCA cycle)
• Fatty acid metabolism
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Tryptophan metabolism
• Glutathione metabolism
• 1- and 2-Methylnaphthalene degradation
• Carbon fixation in photosynthetic organisms
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
CO2 fixation into oxaloacetate (anaplerotic)	2	2	2
L-glutamine biosynthesis I	1	1	1
long-chain fatty acid activation	1	1	1
ammonia assimilation cycle I	2	2	1
γ-linolenate biosynthesis II (animals)	2	2	1
ammonia assimilation cycle II	2	2	1
linoleate biosynthesis II (animals)	2	1	1
L-proline biosynthesis III (from L-ornithine)	3	3	1
ammonia assimilation cycle III	3	3	1
cyanate degradation	3	3	1
superpathway of ammonia assimilation (plants)	3	3	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
L-ornithine biosynthesis II	3	3	1
L-aspartate degradation III (anaerobic)	3	2	1
L-arginine degradation I (arginase pathway)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
alkane biosynthesis II	3	1	1
oleate biosynthesis I (plants)	3	1	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	2
partial TCA cycle (obligate autotrophs)	8	8	2
queuosine biosynthesis I (de novo)	4	4	1
nitrogen remobilization from senescing leaves	8	6	2
L-arginine degradation VI (arginase 2 pathway)	4	3	1
putrescine degradation II	4	3	1
phytol degradation	4	3	1
long chain fatty acid ester synthesis (engineered)	4	1	1
wax esters biosynthesis II	4	1	1
phosphatidylcholine acyl editing	4	1	1
sporopollenin precursors biosynthesis	18	4	4
L-arginine biosynthesis II (acetyl cycle)	10	10	2
L-ornithine biosynthesis I	5	5	1
L-arginine degradation XIII (reductive Stickland reaction)	5	5	1
octane oxidation	5	4	1
cytosolic NADPH production (yeast)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	2
fatty acid salvage	6	6	1
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
6-gingerol analog biosynthesis (engineered)	6	2	1
stearate biosynthesis I (animals)	6	1	1
L-glutamate and L-glutamine biosynthesis	7	6	1
L-Nδ-acetylornithine biosynthesis	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
ceramide degradation by α-oxidation	7	2	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	2	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	2	1
capsaicin biosynthesis	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
superpathway of ornithine degradation	8	7	1
L-citrulline biosynthesis	8	7	1
mixed acid fermentation	16	12	2
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
2-deoxy-D-ribose degradation II	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	1
TCA cycle V (2-oxoglutarate synthase)	9	7	1
TCA cycle VI (Helicobacter)	9	7	1
TCA cycle VII (acetate-producers)	9	7	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	2
TCA cycle I (prokaryotic)	10	9	1
peptidoglycan recycling II	10	8	1
suberin monomers biosynthesis	20	2	2
NiFe(CO)(CN)2 cofactor biosynthesis	10	1	1
superpathway of fatty acid biosynthesis II (plant)	43	38	4
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
reductive TCA cycle I	11	6	1
superpathway of glyoxylate bypass and TCA	12	11	1
superpathway of L-citrulline metabolism	12	9	1
ethene biosynthesis V (engineered)	25	19	2
superpathway of L-arginine and L-ornithine degradation	13	11	1
formaldehyde assimilation I (serine pathway)	13	6	1
3-hydroxypropanoate cycle	13	5	1
glyoxylate assimilation	13	4	1
peptidoglycan recycling I	14	11	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
superpathway of arginine and polyamine biosynthesis	17	16	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	8	1
superpathway of the 3-hydroxypropanoate cycle	18	5	1
methylaspartate cycle	19	9	1
aspartate superpathway	25	22	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
superpathway of fatty acids biosynthesis (E. coli)	53	49	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	2
palmitate biosynthesis III	29	21	1
oleate β-oxidation	35	30	1