Experiment set4IT020 for Agrobacterium fabrum C58

R2A with Calcium Chloride Dihydrate 87.5 mM

Group: stress
Media: R2A + Calcium chloride dihydrate (87.5 mM)
Culturing: Agro_ML11, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 28 (C), shaken=700 rpm
By: Hans Carlson and Mitchell Thompson on 22-Jun-21
Media components: 0.5 g/L Bacto Peptone, 0.5 g/L casamino acids, 0.5 g/L Yeast Extract, 0.5 g/L D-Glucose, 0.5 g/L Starch, 0.3 g/L Potassium phosphate dibasic, 0.05 g/L Magnesium Sulfate Heptahydrate, 0.3 g/L Sodium pyruvate
Growth plate: 2 D3

Specific Phenotypes

For 17 genes in this experiment

For stress Calcium chloride dihydrate in Agrobacterium fabrum C58

For stress Calcium chloride dihydrate across organisms

SEED Subsystems

Subsystem	#Specific
Transport of Manganese	4
Arginine Biosynthesis extended	1
Campylobacter Iron Metabolism	1
Copper homeostasis: copper tolerance	1
Peptidyl-prolyl cis-trans isomerase	1
Phosphate metabolism	1
Potassium homeostasis	1
Protein chaperones	1
Proteolysis in bacteria, ATP-dependent	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Fatty acid biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-arginine biosynthesis II (acetyl cycle)	10	10	2
tRNA processing	10	10	2
L-ornithine biosynthesis I	5	5	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
superpathway of arginine and polyamine biosynthesis	17	14	1