Experiment set4IT061 for Pseudomonas simiae WCS417

LB with 1-ethyl-3-methylimidazolium acetate 35 mM

Group: stress
Media: LB + 1-ethyl-3-methylimidazolium acetate (35 mM)
Culturing: fluoroDangl_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Mark on 3/2/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 1167 D5,D6

Specific Phenotypes

For 8 genes in this experiment

For stress 1-ethyl-3-methylimidazolium acetate in Pseudomonas simiae WCS417

For stress 1-ethyl-3-methylimidazolium acetate across organisms

SEED Subsystems

Subsystem	#Specific
Carboxysome	2
Respiratory dehydrogenases 1	2
Cyanate hydrolysis	1
D-gluconate and ketogluconates metabolism	1
DNA-binding regulatory proteins, strays	1
Entner-Doudoroff Pathway	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Oxidative phosphorylation
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Retinol metabolism
• Limonene and pinene degradation
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
NADH to cytochrome bo oxidase electron transfer II	2	2	1
NADH to cytochrome bo oxidase electron transfer I	2	2	1
NADH to nitrate electron transfer	2	2	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
nitrate reduction VIIIb (dissimilatory)	2	1	1
NADH to cytochrome bd oxidase electron transfer II	2	1	1
NADH to cytochrome aa3 oxidase electron transfer	2	1	1
NADH to cytochrome bd oxidase electron transfer I	2	1	1
cyanate degradation	3	3	1
aerobic respiration III (alternative oxidase pathway)	3	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
glucose degradation (oxidative)	5	5	1
mitochondrial NADPH production (yeast)	5	4	1
glucose and glucose-1-phosphate degradation	5	4	1
Fe(II) oxidation	6	3	1
NAD(P)/NADPH interconversion	6	3	1
L-ascorbate biosynthesis VIII (engineered pathway)	7	5	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	1
3-hydroxypropanoate cycle	13	6	1
glyoxylate assimilation	13	4	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	9	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
superpathway of the 3-hydroxypropanoate cycle	18	6	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1