Experiment set8IT033 for Pseudomonas fluorescens FW300-N2E2

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Trisodium citrate dihydrate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Trisodium citrate dihydrate (5 mM), pH=7
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=500 rpm
Growth: about 2.6 generations
By: Mark on 1/21/2016
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 25 genes in this experiment

For carbon source Trisodium citrate dihydrate in Pseudomonas fluorescens FW300-N2E2

For carbon source Trisodium citrate dihydrate across organisms

SEED Subsystems

Subsystem #Specific
Protocatechuate branch of beta-ketoadipate pathway 3
Transport of Iron 2
p-Hydroxybenzoate degradation 2
ABC transporter dipeptide (TC 3.A.1.5.2) 1
Cinnamic Acid Degradation 1
Copper homeostasis 1
Gentisare degradation 1
Lysine Biosynthesis DAP Pathway 1
Phenylpropanoid compound degradation 1
Salicylate and gentisate catabolism 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
3-oxoadipate degradation 2 2 1
assimilatory sulfate reduction III 3 3 1
toluene degradation III (aerobic) (via p-cresol) 11 8 3
protocatechuate degradation II (ortho-cleavage pathway) 4 4 1
assimilatory sulfate reduction I 4 4 1
4-sulfocatechol degradation 4 2 1
4-methylphenol degradation to protocatechuate 4 2 1
4-chlorobenzoate degradation 4 2 1
aromatic compounds degradation via β-ketoadipate 9 7 2
bisphenol A degradation 5 2 1
4-coumarate degradation (aerobic) 5 2 1
catechol degradation III (ortho-cleavage pathway) 6 4 1
4-hydroxymandelate degradation 6 2 1
superpathway of salicylate degradation 7 4 1
L-glutamate degradation XI (reductive Stickland reaction) 7 3 1
4-methylcatechol degradation (ortho cleavage) 7 3 1
spongiadioxin C biosynthesis 7 2 1
polybrominated dihydroxylated diphenyl ethers biosynthesis 8 2 1
L-lysine biosynthesis I 9 9 1
superpathway of sulfate assimilation and cysteine biosynthesis 9 9 1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) 10 8 1
L-glutamate degradation V (via hydroxyglutarate) 10 6 1
superpathway of aerobic toluene degradation 30 14 3
superpathway of aromatic compound degradation via 3-oxoadipate 35 15 3
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 12 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 1
mandelate degradation to acetyl-CoA 18 9 1
aspartate superpathway 25 22 1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate 42 10 1