Experiment set5IT089 for Pseudomonas fluorescens FW300-N2E2

LB with Nickel (II) chloride hexahydrate 0.0025 M

Group: stress
Media: LB + Nickel (II) chloride hexahydrate (0.0025 M), pH=7
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=500 rpm
By: Hans_Hualan on 2/2/2016
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 16 genes in this experiment

For stress Nickel (II) chloride hexahydrate in Pseudomonas fluorescens FW300-N2E2

For stress Nickel (II) chloride hexahydrate across organisms

SEED Subsystems

Subsystem	#Specific
Alginate metabolism	1
Arginine and Ornithine Degradation	1
Cobalt-zinc-cadmium resistance	1
Copper homeostasis: copper tolerance	1
Cysteine Biosynthesis	1
Folate Biosynthesis	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine and Serine Utilization	1
Lysine degradation	1
Mannose Metabolism	1
Methionine Biosynthesis	1
Phosphate metabolism	1
Pyruvate Alanine Serine Interconversions	1
Queuosine-Archaeosine Biosynthesis	1
Threonine anaerobic catabolism gene cluster	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ubiquinone and menaquinone biosynthesis
• Cysteine metabolism
• Arginine and proline metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Nucleotide sugars metabolism
• Glycerophospholipid metabolism
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Glutamate metabolism
• Lysine degradation
• Phenylalanine metabolism
• Benzoxazinone biosynthesis
• Selenoamino acid metabolism
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Nitrogen metabolism
• Sulfur metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Alkaloid biosynthesis II
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate degradation I	1	1	1
L-ornithine degradation I (L-proline biosynthesis)	1	1	1
D-serine degradation	3	3	2
L-cysteine degradation II	3	3	2
L-serine degradation	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
L-cysteine biosynthesis I	2	2	1
L-proline biosynthesis II (from arginine)	2	1	1
D-mannose degradation I	2	1	1
D-mannose degradation II	2	1	1
L-arginine degradation VII (arginase 3 pathway)	2	1	1
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
tetrahydrofolate biosynthesis I	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
L-methionine biosynthesis II	6	5	2
oleate biosynthesis III (cyanobacteria)	3	2	1
β-1,4-D-mannosyl-N-acetyl-D-glucosamine degradation	3	2	1
ethene biosynthesis IV (engineered)	3	1	1
mannitol biosynthesis	3	1	1
glycine betaine degradation III	7	7	2
GDP-mannose biosynthesis	4	4	1
CDP-diacylglycerol biosynthesis I	4	4	1
CDP-diacylglycerol biosynthesis II	4	4	1
glycine betaine degradation I	8	6	2
tetrahydromonapterin biosynthesis	4	3	1
L-mimosine degradation	8	4	2
mannitol degradation II	4	2	1
glutathione-mediated detoxification I	8	3	2
phosphatidate biosynthesis (yeast)	5	3	1
seleno-amino acid biosynthesis (plants)	5	3	1
1,5-anhydrofructose degradation	5	2	1
phosphatidylglycerol biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis II	6	6	1
superpathway of phospholipid biosynthesis III (E. coli)	12	11	2
superpathway of stearidonate biosynthesis (cyanobacteria)	6	2	1
palmitoyl ethanolamide biosynthesis	6	2	1
diacylglycerol and triacylglycerol biosynthesis	7	3	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
4-aminobutanoate degradation V	7	2	1
β-(1,4)-mannan degradation	7	2	1
stigma estolide biosynthesis	7	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
anandamide biosynthesis II	8	2	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
folate transformations III (E. coli)	9	9	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
folate transformations II (plants)	11	10	1
colanic acid building blocks biosynthesis	11	9	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
purine nucleobases degradation II (anaerobic)	24	16	2
anandamide biosynthesis I	12	3	1
superpathway of cardiolipin biosynthesis (bacteria)	13	10	1
superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis	14	7	1
superpathway of phospholipid biosynthesis II (plants)	28	10	2
methylaspartate cycle	19	9	1
superpathway of seleno-compound metabolism	19	6	1
superpathway of chorismate metabolism	59	43	1