Experiment set11IT019 for Pseudomonas fluorescens FW300-N2E2

RCH2 defined with Cobalt chloride hexahydrate 0.04 mM

Group: stress
Media: RCH2_defined + Cobalt chloride hexahydrate (0.04 mM)
Culturing: pseudo6_N2E2_ML5b, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 21-Jun-16
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 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: plate3 D5

Specific Phenotypes

For 41 genes in this experiment

For stress Cobalt chloride hexahydrate in Pseudomonas fluorescens FW300-N2E2

For stress Cobalt chloride hexahydrate across organisms

SEED Subsystems

Subsystem	#Specific
Iron acquisition in Vibrio	4
Transport of Iron	4
Arginine and Ornithine Degradation	2
Campylobacter Iron Metabolism	2
Phosphate metabolism	2
Polyamine Metabolism	2
Acid resistance mechanisms	1
Alanine biosynthesis	1
Carboxysome	1
Conserved gene cluster possibly involved in RNA metabolism	1
Copper homeostasis: copper tolerance	1
Cysteine Biosynthesis	1
Folate Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Heat shock dnaK gene cluster extended	1
Methionine Biosynthesis	1
Protein degradation	1
Respiratory dehydrogenases 1	1
Ribosome biogenesis bacterial	1
Triacylglycerol metabolism	1
YcfH	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Alkaloid biosynthesis I
• Cysteine metabolism
• Arginine and proline metabolism
• Tryptophan metabolism
• Glycerophospholipid metabolism
• Carotenoid biosynthesis - General
• Insect hormone biosynthesis
• Urea cycle and metabolism of amino groups
• Histidine metabolism
• Tyrosine metabolism
• Nucleotide sugars metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Porphyrin and chlorophyll metabolism
• Anthocyanin biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from shikimate pathway
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• C21-Steroid hormone metabolism
• Oxidative phosphorylation
• Puromycin biosynthesis
• Glycine, serine and threonine metabolism
• Lysine degradation
• Phenylalanine metabolism
• Bisphenol A degradation
• Benzoxazinone biosynthesis
• Glutathione metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Ether lipid metabolism
• Linoleic acid metabolism
• alpha-Linolenic acid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Tetrachloroethene degradation
• Naphthalene and anthracene degradation
• Trinitrotoluene degradation
• Ethylbenzene degradation
• One carbon pool by folate
• Methane metabolism
• Thiamine metabolism
• Folate biosynthesis
• Retinol metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Sulfur metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Alkaloid biosynthesis II
• Biosynthesis of type II polyketide backbone
• Biosynthesis of type II polyketide products
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-ornithine degradation I (L-proline biosynthesis)	1	1	1
L-alanine biosynthesis III	1	1	1
thiosulfate disproportionation IV (rhodanese)	1	1	1
L-cysteine degradation IV	1	1	1
arginine dependent acid resistance	1	1	1
cadaverine biosynthesis	1	1	1
L-cysteine degradation II	3	3	2
L-serine degradation	3	3	2
D-serine degradation	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
L-cysteine biosynthesis I	2	2	1
NADH to cytochrome bo oxidase electron transfer I	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
putrescine biosynthesis I	2	2	1
NADH to cytochrome bo oxidase electron transfer II	2	2	1
superpathway of putrescine biosynthesis	4	3	2
nitrate reduction VIIIb (dissimilatory)	2	1	1
L-proline biosynthesis II (from arginine)	2	1	1
L-cysteine degradation III	2	1	1
NADH to cytochrome bd oxidase electron transfer I	2	1	1
NADH to cytochrome bd oxidase electron transfer II	2	1	1
NADH to cytochrome aa3 oxidase electron transfer	2	1	1
L-arginine degradation VII (arginase 3 pathway)	2	1	1
putrescine biosynthesis III	2	1	1
NADH to nitrate electron transfer	2	1	1
cytidylyl molybdenum cofactor sulfurylation	2	1	1
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
superpathway of polyamine biosynthesis I	8	5	3
dTMP de novo biosynthesis (mitochondrial)	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
putrescine biosynthesis II	3	3	1
aerobic respiration III (alternative oxidase pathway)	3	3	1
L-methionine biosynthesis II	6	5	2
oleate biosynthesis III (cyanobacteria)	3	2	1
bis(guanylyl molybdopterin) cofactor sulfurylation	3	1	1
aminopropylcadaverine biosynthesis	3	1	1
glycine betaine degradation III	7	7	2
thiazole component of thiamine diphosphate biosynthesis II	7	4	2
CDP-diacylglycerol biosynthesis II	4	4	1
CDP-diacylglycerol biosynthesis I	4	4	1
superpathway of L-alanine biosynthesis	4	4	1
glycine betaine degradation I	8	6	2
aerobic respiration I (cytochrome c)	4	3	1
tetrahydromonapterin biosynthesis	4	3	1
L-cysteine biosynthesis VII (from S-sulfo-L-cysteine)	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
superpathway of polyamine biosynthesis II	8	5	2
L-mimosine degradation	8	4	2
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
glutathione-mediated detoxification I	8	3	2
tRNA-uridine 2-thiolation (yeast mitochondria)	4	1	1
N-3-oxalyl-L-2,3-diaminopropanoate biosynthesis	4	1	1
tRNA-uridine 2-thiolation (mammalian mitochondria)	4	1	1
spermidine biosynthesis III	4	1	1
mitochondrial NADPH production (yeast)	5	4	1
seleno-amino acid biosynthesis (plants)	5	3	1
phosphatidate biosynthesis (yeast)	5	3	1
[2Fe-2S] iron-sulfur cluster biosynthesis	10	4	2
sulfide oxidation IV (mitochondria)	5	2	1
bisucaberin biosynthesis	5	1	1
tRNA-uridine 2-thiolation (thermophilic bacteria)	5	1	1
desferrioxamine E biosynthesis	5	1	1
desferrioxamine B biosynthesis	5	1	1
lupanine biosynthesis	5	1	1
superpathway of thiamine diphosphate biosynthesis II	11	8	2
superpathway of arginine and polyamine biosynthesis	17	14	3
phosphatidylglycerol biosynthesis II	6	6	1
phosphatidylglycerol biosynthesis I	6	6	1
superpathway of phospholipid biosynthesis III (E. coli)	12	11	2
L-lysine degradation X	6	5	1
molybdopterin biosynthesis	6	4	1
Fe(II) oxidation	6	3	1
NAD(P)/NADPH interconversion	6	3	1
thiazole component of thiamine diphosphate biosynthesis I	6	3	1
palmitoyl ethanolamide biosynthesis	6	2	1
superpathway of stearidonate biosynthesis (cyanobacteria)	6	2	1
D-cycloserine biosynthesis	6	1	1
superpathway of L-arginine and L-ornithine degradation	13	11	2
L-lysine degradation I	7	4	1
diacylglycerol and triacylglycerol biosynthesis	7	3	1
L-cysteine biosynthesis VI (reverse transsulfuration)	7	3	1
stigma estolide biosynthesis	7	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
superpathway of ornithine degradation	8	7	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
anandamide biosynthesis II	8	2	1
tRNA-uridine 2-thiolation (cytoplasmic)	8	1	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
superpathway of thiamine diphosphate biosynthesis I	10	7	1
folate transformations II (plants)	11	10	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
tRNA-uridine 2-thiolation and selenation (bacteria)	11	4	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 phospholipid biosynthesis II (plants)	28	10	2
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
superpathway of seleno-compound metabolism	19	6	1
superpathway of L-lysine degradation	43	19	1
superpathway of chorismate metabolism	59	43	1