Experiment set6H44 for Pseudomonas stutzeri RCH2

RCH2 defined media with Sodium Chloride 400 mM

Group: stress
Media: RCH2_defined_no_vitamin + Sodium Chloride (400 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 F5,F6

Specific Phenotypes

For 19 genes in this experiment

For stress Sodium Chloride in Pseudomonas stutzeri RCH2

For stress Sodium Chloride across organisms

SEED Subsystems

Subsystem	#Specific
Ectoine biosynthesis and regulation	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Pyruvate metabolism I: anaplerotic reactions, PEP	2
DNA-replication	1
Fermentations: Mixed acid	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Lactate utilization	1
Na+ translocating decarboxylases and related biotin-dependent enzymes	1
Pyruvate Alanine Serine Interconversions	1
Ribosomal protein S12p Asp methylthiotransferase	1
Sodium Hydrogen Antiporter	1
ZZ gjo need homes	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Nucleotide sugars metabolism
• Purine metabolism
• Glycine, serine and threonine metabolism
• Aminophosphonate metabolism
• Pyruvate metabolism
• Pentose phosphate pathway
• Fatty acid biosynthesis
• Urea cycle and metabolism of amino groups
• Puromycin biosynthesis
• Pyrimidine metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Methionine metabolism
• Valine, leucine and isoleucine degradation
• Lysine biosynthesis
• Lysine degradation
• Tyrosine metabolism
• Benzoate degradation via hydroxylation
• Phenylalanine, tyrosine and tryptophan biosynthesis
• beta-Alanine metabolism
• High-mannose type N-glycan biosynthesis
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Butanoate metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Nitrogen metabolism
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine biosynthesis I	1	1	1
putrescine degradation V	2	2	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
β-alanine degradation II	2	2	1
ammonia assimilation cycle I	2	2	1
ammonia assimilation cycle II	2	1	1
ectoine biosynthesis	5	5	2
ammonia assimilation cycle III	3	3	1
cardiolipin biosynthesis II	3	3	1
L-aspartate degradation III (anaerobic)	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
guanosine ribonucleotides de novo biosynthesis	4	4	1
cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas)	4	3	1
putrescine degradation II	4	3	1
ectoine degradation	4	1	1
methylphosphonate degradation I	5	4	1
dZTP biosynthesis	5	3	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
β-alanine biosynthesis II	6	5	1
norspermidine biosynthesis	6	4	1
methylgallate degradation	6	2	1
L-glutamate and L-glutamine biosynthesis	7	5	1
glyphosate degradation III	7	4	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
rhizobactin 1021 biosynthesis	7	1	1
partial TCA cycle (obligate autotrophs)	8	8	1
superpathway of guanosine nucleotides de novo biosynthesis II	8	7	1
(aminomethyl)phosphonate degradation	8	6	1
superpathway of ornithine degradation	8	6	1
superpathway of polyamine biosynthesis III	8	5	1
nitrogen remobilization from senescing leaves	8	5	1
protocatechuate degradation I (meta-cleavage pathway)	8	3	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
superpathway of vanillin and vanillate degradation	10	3	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	1
pyoverdine I biosynthesis	11	2	1
baumannoferrin biosynthesis	11	1	1
syringate degradation	12	3	1
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
superpathway of L-arginine and L-ornithine degradation	13	8	1
formaldehyde assimilation I (serine pathway)	13	5	1
superpathway of purine nucleotide salvage	14	11	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1
mixed acid fermentation	16	12	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	1
ethene biosynthesis V (engineered)	25	18	1
superpathway of purine nucleotides de novo biosynthesis II	26	24	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	44	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1