Experiment setAH37 for Shewanella amazonensis SB2B

LB with L-Lysine 200 mM

Group: stress
Media: LB + L-Lysine (200 mM)
Culturing: SB2B_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Adam on 10/14/2013
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 728 F3,F4

Specific Phenotypes

For 29 genes in this experiment

For stress L-Lysine in Shewanella amazonensis SB2B

For stress L-Lysine across organisms

SEED Subsystems

Subsystem	#Specific
Molybdenum cofactor biosynthesis	8
Formate hydrogenase	5
ABC transporter tungstate (TC 3.A.1.6.2)	3
Anaerobic respiratory reductases	1
Oxidative stress	1
Photorespiration (oxidative C2 cycle)	1
Ubiquinone Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Methane metabolism
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Puromycin biosynthesis
• Pyrimidine metabolism
• Tryptophan metabolism
• Lipopolysaccharide biosynthesis
• Glyoxylate and dicarboxylate metabolism
• Nicotinate and nicotinamide metabolism
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
bis(guanylyl molybdenum cofactor) biosynthesis	2	2	2
bis(guanylyl tungstenpterin) cofactor biosynthesis	1	1	1
formate oxidation to CO2	1	1	1
guanylyl molybdenum cofactor biosynthesis	1	1	1
4-hydroxybenzoate biosynthesis II (bacteria)	1	1	1
molybdopterin biosynthesis	6	5	4
superoxide radicals degradation	2	2	1
methanol oxidation to formaldehyde IV	2	1	1
molybdenum cofactor biosynthesis	3	3	1
ethanol degradation IV	3	3	1
NAD salvage pathway III (to nicotinamide riboside)	3	2	1
UTP and CTP dephosphorylation I	7	5	2
purine nucleotides degradation II (aerobic)	11	8	3
reactive oxygen species degradation	4	4	1
inosine 5'-phosphate degradation	4	3	1
guanosine nucleotides degradation III	4	2	1
adenosine nucleotides degradation I	8	3	2
purine nucleotides degradation I (plants)	12	4	3
polybrominated phenols biosynthesis	4	1	1
oxalate degradation VI	4	1	1
guanosine nucleotides degradation I	4	1	1
guanosine nucleotides degradation II	4	1	1
adenosine nucleotides degradation II	5	3	1
oxalate degradation III	5	1	1
superpathway of purines degradation in plants	18	4	3
superpathway of guanosine nucleotides degradation (plants)	6	1	1
ureide biosynthesis	7	3	1
spongiadioxin C biosynthesis	7	1	1
polybrominated dihydroxylated diphenyl ethers biosynthesis	8	1	1
ubiquinol-8 biosynthesis (late decarboxylation)	9	5	1
tunicamycin biosynthesis	9	1	1
p-HBAD biosynthesis	9	1	1
NAD salvage (plants)	11	3	1
superpathway of ubiquinol-8 biosynthesis (early decarboxylation)	12	11	1
superpathway of C1 compounds oxidation to CO2	12	4	1
tetrahydromethanopterin biosynthesis	14	3	1
purine nucleobases degradation I (anaerobic)	15	5	1
superpathway of polybrominated aromatic compound biosynthesis	20	2	1
phenolphthiocerol biosynthesis	23	1	1
purine nucleobases degradation II (anaerobic)	24	11	1
superpathway of chorismate metabolism	59	50	1