Experiment set6H40 for Pseudomonas stutzeri RCH2

RCH2 defined media with Sodium Chlorate 20 mM

Group: stress
Media: RCH2_defined_no_vitamin + Sodium Chlorate (20 mM), pH=7.2
Culturing: psRCH2_ML7, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Kelly on 8/12/2013
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)
Growth plate: 627 C5,C6

Specific Phenotypes

For 17 genes in this experiment

For stress Sodium Chlorate in Pseudomonas stutzeri RCH2

For stress Sodium Chlorate across organisms

SEED Subsystems

Subsystem	#Specific
N-linked Glycosylation in Bacteria	2
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
DNA repair, bacterial	1
Hemin transport system	1
Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway	1
Lactose and Galactose Uptake and Utilization	1
Molybdenum cofactor biosynthesis	1
Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes	1
Rhamnose containing glycans	1
Terminal cytochrome C oxidases	1
linker unit-arabinogalactan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Phenylalanine, tyrosine and tryptophan biosynthesis
• Nucleotide sugars metabolism
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Galactose metabolism
• Fatty acid biosynthesis
• Oxidative phosphorylation
• Purine metabolism
• Tyrosine metabolism
• Benzoate degradation via hydroxylation
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Zeatin biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-N-acetyl-α-D-quinovosamine biosynthesis	2	2	2
UDP-α-D-galactose biosynthesis	1	1	1
UDP-N-acetyl-D-galactosamine biosynthesis I	1	1	1
UDP-2-acetamido-4-amino-2,4,6-trideoxy-α-D-galactose biosynthesis	2	2	1
3-dehydroquinate biosynthesis I	2	2	1
UDP-α-D-galactofuranose biosynthesis	2	2	1
arsenite to oxygen electron transfer	2	1	1
UDP-N-acetyl-α-D-fucosamine biosynthesis	2	1	1
UDP-yelosamine biosynthesis	3	2	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
D-galactose detoxification	3	1	1
UDP-N,N'-diacetylbacillosamine biosynthesis	3	1	1
guanosine ribonucleotides de novo biosynthesis	4	4	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
UDP-N-acetyl-β-L-fucosamine biosynthesis	4	1	1
UDP-N-acetyl-β-L-quinovosamine biosynthesis	4	1	1
methylphosphonate degradation I	5	4	1
dZTP biosynthesis	5	3	1
D-galactose degradation I (Leloir pathway)	5	2	1
CMP-pseudaminate biosynthesis	6	6	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
Fe(II) oxidation	6	3	1
chorismate biosynthesis I	7	7	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	4	1
glyphosate degradation III	7	4	1
stachyose degradation	7	2	1
CMP-diacetamido-8-epilegionaminic acid biosynthesis	7	1	1
superpathway of guanosine nucleotides de novo biosynthesis II	8	7	1
(aminomethyl)phosphonate degradation	8	6	1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	9	3
UDP-sugars interconversion	9	1	1
teichuronic acid biosynthesis (B. subtilis 168)	9	1	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
colanic acid building blocks biosynthesis	11	10	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of purine nucleotide salvage	14	11	1
superpathway of aromatic amino acid biosynthesis	18	18	1
mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	18	2	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	1
superpathway of purine nucleotides de novo biosynthesis II	26	24	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	14	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	44	1
superpathway of chorismate metabolism	59	44	1