Experiment set4IT085 for Pseudomonas fluorescens FW300-N1B4

Compare to:

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:

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
putrescine biosynthesis II 3 3 1
assimilatory sulfate reduction III 3 3 1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway) 3 3 1
L-alanine degradation II (to D-lactate) 3 3 1
fatty acid biosynthesis initiation (type II) 3 3 1
CMP-N-acetylneuraminate biosynthesis II (bacteria) 3 2 1
L-methionine salvage from L-homocysteine 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
putrescine degradation II 4 3 1
superpathway of putrescine biosynthesis 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 I 6 5 1
CMP-pseudaminate biosynthesis 6 5 1
NAD de novo biosynthesis IV (anaerobic) 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 II 8 5 1
superpathway of polyamine biosynthesis I 8 5 1
superpathway of L-homoserine and L-methionine biosynthesis 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