Experiment set1IT063 for Pantoea sp. MT58

copper (II) chloride dihydrate 5 uM, aerobic

Group: stress
Media: DefinedMedia_AdamsLab_Glucose + copper (II) chloride dihydrate (5 uM), pH=7
Culturing: MT058_ML2, hungate, Aerobic, at 24 (C), shaken=150 rpm
Growth: about 5.6 generations
By: Mike Thorgersen on 19-Feb-19
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 5 mM Sodium phosphate monobasic monohydrate, 2.5 g/L Sodium bicarbonate, 20 mM D-Glucose, 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 9 genes in this experiment

For stress copper (II) chloride dihydrate in Pantoea sp. MT58

For stress copper (II) chloride dihydrate across organisms

SEED Subsystems

Subsystem	#Specific
NAD and NADP cofactor biosynthesis global	2
NAD regulation	2
Coenzyme A Biosynthesis	1
Copper homeostasis	1
Copper homeostasis: copper tolerance	1
Peptidoglycan Biosynthesis	1
Phosphate metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Nicotinate and nicotinamide metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Alanine and aspartate metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Peptidoglycan biosynthesis
• Pantothenate and CoA biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
NAD de novo biosynthesis IV (anaerobic)	6	5	2
NAD de novo biosynthesis I	6	5	2
phosphopantothenate biosynthesis I	4	4	1
NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde	4	3	1
phosphopantothenate biosynthesis III (archaea)	4	2	1
nicotine biosynthesis	9	3	2
NAD de novo biosynthesis III	6	4	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	2
superpathway of nicotine biosynthesis	12	4	2
superpathway of coenzyme A biosynthesis I (bacteria)	9	9	1
NAD de novo biosynthesis II (from tryptophan)	9	3	1
peptidoglycan recycling II	10	7	1
superpathway of coenzyme A biosynthesis II (plants)	10	5	1
aspartate superpathway	25	24	2
peptidoglycan recycling I	14	14	1
superpathway of NAD biosynthesis in eukaryotes	14	7	1
peptidoglycan biosynthesis II (staphylococci)	17	12	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	1