Experiment set4IT065 for Pseudomonas simiae WCS417

LB with L-Lysine 60 mM

Group: stress
Media: LB + L-Lysine (60 mM)
Culturing: fluoroDangl_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Mark on 3/2/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 1167 F5,F6

Specific Phenotypes

For 10 genes in this experiment

For stress L-Lysine in Pseudomonas simiae WCS417

For stress L-Lysine across organisms

SEED Subsystems

Subsystem	#Specific
Sodium Hydrogen Antiporter	2
Bacterial Cell Division	1
Carboxysome	1
Cyanate hydrolysis	1
DNA-replication	1
DNA Repair Base Excision	1
Lysine degradation	1
Oxidative stress	1
Peptidoglycan Biosynthesis	1
Photorespiration (oxidative C2 cycle)	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tryptophan metabolism
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Pyrimidine metabolism
• Lysine degradation
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Methane metabolism
• Nitrogen metabolism
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
superoxide radicals degradation	2	2	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
indole-3-acetate biosynthesis III (bacteria)	2	2	1
methanol oxidation to formaldehyde IV	2	1	1
ethanol degradation IV	3	3	1
cyanate degradation	3	3	1
reactive oxygen species degradation	4	4	1
L-lysine degradation IV	5	5	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	1
3-hydroxypropanoate cycle	13	6	1
glyoxylate assimilation	13	4	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	9	1
superpathway of the 3-hydroxypropanoate cycle	18	6	1
superpathway of L-lysine degradation	43	17	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1