Experiment set4IT085 for Pseudomonas fluorescens FW300-N1B4

Sodium octanoate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Sodium octanoate (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 B5

Specific Phenotypes

For 29 genes in this experiment

For carbon source Sodium octanoate in Pseudomonas fluorescens FW300-N1B4

For carbon source Sodium octanoate across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	2
Acid resistance mechanisms	1
Arginine and Ornithine Degradation	1
CMP-N-acetylneuraminate Biosynthesis	1
Campylobacter Iron Metabolism	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Lipid A modifications	1
Methionine Biosynthesis	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Polyamine Metabolism	1
Sialic Acid Metabolism	1
Ton and Tol transport systems	1
ZZ gjo need homes	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
• Nucleotide sugars metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Puromycin biosynthesis
• Glutamate metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Methionine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Benzoxazinone biosynthesis
• Aminosugars metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Trinitrotoluene degradation
• One carbon pool by folate
• Nicotinate and nicotinamide metabolism
• Porphyrin and chlorophyll metabolism
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Sulfur metabolism
• Caprolactam degradation
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
arginine dependent acid resistance	1	1	1
L-glutamate degradation I	1	1	1
putrescine biosynthesis I	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
fatty acid salvage	6	6	2
assimilatory sulfate reduction III	3	3	1
fatty acid biosynthesis initiation (type II)	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
putrescine biosynthesis II	3	3	1
L-methionine salvage from L-homocysteine	3	2	1
CMP-N-acetylneuraminate biosynthesis II (bacteria)	3	2	1
ethene biosynthesis IV (engineered)	3	2	1
L-methionine biosynthesis III	4	4	1
assimilatory sulfate reduction I	4	4	1
queuosine biosynthesis I (de novo)	4	4	1
superpathway of putrescine biosynthesis	4	3	1
putrescine degradation II	4	3	1
spermidine biosynthesis III	4	1	1
adipate degradation	5	5	1
superpathway of fatty acid biosynthesis initiation	5	4	1
queuosine biosynthesis III (queuosine salvage)	5	3	1
L-methionine biosynthesis I	5	2	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	2
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	2
NAD de novo biosynthesis IV (anaerobic)	6	5	1
CMP-pseudaminate biosynthesis	6	5	1
NAD de novo biosynthesis I	6	5	1
superpathway of L-arginine and L-ornithine degradation	13	11	2
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
4-aminobutanoate degradation V	7	2	1
superpathway of ornithine degradation	8	6	1
superpathway of polyamine biosynthesis I	8	5	1
superpathway of L-homoserine and L-methionine biosynthesis	8	5	1
superpathway of polyamine biosynthesis II	8	5	1
folate transformations III (E. coli)	9	9	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	6	1
superpathway of S-adenosyl-L-methionine biosynthesis	9	6	1
nicotine biosynthesis	9	3	1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	8	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
folate transformations II (plants)	11	10	1
oleate β-oxidation	35	30	3
superpathway of nicotine biosynthesis	12	4	1
aspartate superpathway	25	21	2
folate transformations I	13	9	1
2-methyl-branched fatty acid β-oxidation	14	11	1
superpathway of CMP-sialic acids biosynthesis	15	2	1
superpathway of fatty acid biosynthesis I (E. coli)	16	15	1
superpathway of L-methionine salvage and degradation	16	8	1
superpathway of arginine and polyamine biosynthesis	17	14	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	15	1
methylaspartate cycle	19	9	1
streptorubin B biosynthesis	34	20	1
superpathway of fatty acid biosynthesis II (plant)	43	38	1
superpathway of fatty acids biosynthesis (E. coli)	53	49	1