Experiment set8H37 for Pseudomonas stutzeri RCH2

RCH2 defined media with Carbenicillin disodium salt 0.008 mg/ml

Group: stress
Media: RCH2_defined_no_vitamin + Carbenicillin disodium salt (0.008 mg/ml), pH=7.2
Culturing: psRCH2_ML7c, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Adam on 9/23/2013
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: extra_min6 B5,B6

Specific Phenotypes

For 64 genes in this experiment

For stress Carbenicillin disodium salt in Pseudomonas stutzeri RCH2

For stress Carbenicillin disodium salt across organisms

SEED Subsystems

Subsystem	#Specific
Cobalt-zinc-cadmium resistance	2
Beta-lactamase	1
Coenzyme A Biosynthesis	1
DNA Repair Base Excision	1
Di-Inositol-Phosphate biosynthesis	1
Gentisare degradation	1
Glutathione: Non-redox reactions	1
Iron acquisition in Vibrio	1
Peptidoglycan Biosynthesis	1
Polyamine Metabolism	1
Protocatechuate branch of beta-ketoadipate pathway	1
Restriction-Modification System	1
Sodium Hydrogen Antiporter	1
Tn552	1
Urea decomposition	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ubiquinone and menaquinone biosynthesis
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Alanine and aspartate metabolism
• Penicillin and cephalosporin biosynthesis
• beta-Lactam resistance
• Benzoate degradation via hydroxylation
• beta-Alanine metabolism
• Glutathione metabolism
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Glycosaminoglycan degradation
• Inositol phosphate metabolism
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Pantothenate and CoA biosynthesis
• Limonene and pinene degradation
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones
• Phosphatidylinositol signaling system

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
β-alanine biosynthesis III	1	1	1
myo-inositol biosynthesis	2	1	1
NAD salvage pathway III (to nicotinamide riboside)	3	2	1
D-myo-inositol (1,4,5)-trisphosphate degradation	3	1	1
protocatechuate degradation II (ortho-cleavage pathway)	4	2	1
4-hydroxy-2-nonenal detoxification	4	1	1
NAD salvage pathway II (PNC IV cycle)	5	4	1
pentachlorophenol degradation	10	3	2
superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism	6	1	1
NAD salvage pathway I (PNC VI cycle)	7	4	1
phytate degradation I	14	3	2
glutathione-mediated detoxification I	8	3	1
superpathway of coenzyme A biosynthesis I (bacteria)	9	9	1
aromatic compounds degradation via β-ketoadipate	9	7	1
gliotoxin biosynthesis	9	1	1
glutathione-mediated detoxification II	9	1	1
toluene degradation III (aerobic) (via p-cresol)	11	4	1
NAD salvage (plants)	11	4	1
indole glucosinolate activation (intact plant cell)	12	3	1
camalexin biosynthesis	12	2	1
superpathway of aerobic toluene degradation	30	7	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	11	1