Experiment set6H19 for Shewanella oneidensis MR-1

LB with 1-ethyl-3-methylimidazolium acetate 20 mM

Group: stress
Media: LB + 1-ethyl-3-methylimidazolium acetate (20 mM)
Culturing: MR1_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Adam on 10/22/2013
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 755 D3,D4

Specific Phenotypes

For 26 genes in this experiment

For stress 1-ethyl-3-methylimidazolium acetate in Shewanella oneidensis MR-1

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

SEED Subsystems

Subsystem	#Specific
Ammonia assimilation	1
Campylobacter Iron Metabolism	1
Carboxysome	1
Experimental tye	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Heme and Siroheme Biosynthesis	1
Lactose and Galactose Uptake and Utilization	1
Lipid A modifications	1
Polyamine Metabolism	1
Respiratory dehydrogenases 1	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Histidine metabolism
• beta-Alanine metabolism
• Porphyrin and chlorophyll metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Galactose metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Urea cycle and metabolism of amino groups
• Glutamate metabolism
• Alanine and aspartate metabolism
• Arginine and proline metabolism
• Tyrosine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Glutathione metabolism
• Nucleotide sugars metabolism
• Naphthalene and anthracene degradation
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation II	1	1	1
L-glutamine degradation I	1	1	1
ammonia assimilation cycle III	3	3	2
NADH to cytochrome bd oxidase electron transfer I	2	2	1
glutathione degradation (DUG pathway)	2	2	1
NADH to cytochrome bd oxidase electron transfer II	2	2	1
NADH to cytochrome aa3 oxidase electron transfer	2	1	1
NADH to cytochrome bo oxidase electron transfer I	2	1	1
nitrate reduction VIIIb (dissimilatory)	2	1	1
NADH to cytochrome bo oxidase electron transfer II	2	1	1
NADH to nitrate electron transfer	2	1	1
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	6	2
D-galactose detoxification	3	2	1
aerobic respiration III (alternative oxidase pathway)	3	2	1
L-glutamate and L-glutamine biosynthesis	7	6	2
heme b biosynthesis V (aerobic)	4	4	1
heme b biosynthesis II (oxygen-independent)	4	4	1
heme b biosynthesis I (aerobic)	4	4	1
aerobic respiration I (cytochrome c)	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
muropeptide degradation	4	1	1
L-asparagine biosynthesis III (tRNA-dependent)	4	1	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	1	1
D-galactose degradation I (Leloir pathway)	5	4	1
mitochondrial NADPH production (yeast)	5	3	1
γ-glutamyl cycle	6	4	1
NAD(P)/NADPH interconversion	6	3	1
Fe(II) oxidation	6	3	1
stachyose degradation	7	3	1
L-citrulline biosynthesis	8	7	1
superpathway of heme b biosynthesis from glycine	8	7	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	5	1
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)	9	3	1
3,8-divinyl-chlorophyllide a biosynthesis I (aerobic, light-dependent)	9	3	1
3,8-divinyl-chlorophyllide a biosynthesis III (aerobic, light independent)	9	3	1
superpathway of heme b biosynthesis from glutamate	10	10	1
superpathway of L-citrulline metabolism	12	9	1
superpathway of bacteriochlorophyll a biosynthesis	26	6	1