Experiment set5H10 for Pseudomonas stutzeri RCH2

LB with Vanillin 2 mM

Group: stress
Media: LB + Vanillin (2 mM) + Dimethyl Sulfoxide (0.2 vol%)
Culturing: psRCH2_ML7, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Adam on 6/28/2013
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 563 C3,C4

Specific Phenotypes

For 8 genes in this experiment

For stress Vanillin in Pseudomonas stutzeri RCH2

For stress Vanillin across organisms

SEED Subsystems

Subsystem	#Specific
ATP-dependent RNA helicases, bacterial	1
Gentisare degradation	1
Purine conversions	1
Ribosome biogenesis bacterial	1
Salicylate and gentisate catabolism	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Citrate cycle (TCA cycle)
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Pyrimidine metabolism
• Arginine and proline metabolism
• Tyrosine metabolism
• Styrene degradation
• Reductive carboxylate cycle (CO2 fixation)
• Atrazine degradation
• Drug metabolism - other enzymes
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
adenosine nucleotides degradation III	1	1	1
urea degradation I	3	3	2
pseudouridine degradation	2	1	1
guanine and guanosine salvage II	2	1	1
guanine and guanosine salvage I	2	1	1
xanthine and xanthosine salvage	2	1	1
cyanuric acid degradation II	5	4	2
cyanuric acid degradation I	5	2	2
L-citrulline degradation	3	3	1
cyanate degradation	3	3	1
superpathway of allantoin degradation in yeast	6	5	2
adenine salvage	3	2	1
superpathway of guanine and guanosine salvage	3	1	1
L-arginine degradation V (arginine deiminase pathway)	4	4	1
superpathway of atrazine degradation	8	4	2
adenine and adenosine salvage III	4	2	1
L-tyrosine degradation I	5	5	1
uracil degradation III	5	2	1
TCA cycle VIII (Chlamydia)	6	5	1
incomplete reductive TCA cycle	7	3	1
pyruvate fermentation to propanoate I	7	1	1
partial TCA cycle (obligate autotrophs)	8	8	1
TCA cycle VII (acetate-producers)	9	8	1
TCA cycle VI (Helicobacter)	9	7	1
TCA cycle V (2-oxoglutarate synthase)	9	7	1
TCA cycle II (plants and fungi)	9	7	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	6	1
allantoin degradation IV (anaerobic)	9	2	1
TCA cycle I (prokaryotic)	10	9	1
TCA cycle III (animals)	10	7	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	5	1
reductive TCA cycle I	11	6	1
L-glutamate degradation VIII (to propanoate)	11	1	1
superpathway of glyoxylate bypass and TCA	12	11	1
reductive TCA cycle II	12	5	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	5	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
superpathway of purine nucleotide salvage	14	11	1
mixed acid fermentation	16	12	1
superpathway of anaerobic energy metabolism (invertebrates)	17	9	1
methylaspartate cycle	19	9	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1