Experiment set4H26 for Shewanella oneidensis MR-1

Gly-Glu carbon source replicate 2

Group: carbon source
Media: ShewMM_noCarbon + Gly-Glu (10 mM), pH=7
Culturing: MR1_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.0 generations
By: Adam on 8/18/2013
Media components: 1.5 g/L Ammonium chloride, 1.75 g/L Sodium Chloride, 0.61 g/L Magnesium chloride hexahydrate, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 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), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 17 genes in this experiment

For carbon source Gly-Glu in Shewanella oneidensis MR-1

For carbon source Gly-Glu across organisms

SEED Subsystems

Subsystem	#Specific
Cysteine Biosynthesis	4
Arginine and Ornithine Degradation	1
Bacterial Cell Division	1
Bacterial Cytoskeleton	1
Heat shock dnaK gene cluster extended	1
Polyamine Metabolism	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
• Urea cycle and metabolism of amino groups
• Cysteine metabolism
• Arginine and proline metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Selenoamino acid metabolism
• Glutathione metabolism
• Naphthalene and anthracene degradation
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Sulfur metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-cysteine biosynthesis I	2	2	1
putrescine biosynthesis III	2	1	1
molybdenum cofactor biosynthesis	3	2	1
L-cysteine biosynthesis VII (from S-sulfo-L-cysteine)	4	3	1
superpathway of putrescine biosynthesis	4	2	1
seleno-amino acid biosynthesis (plants)	5	3	1
hydrogen sulfide biosynthesis II (mammalian)	6	1	1
superpathway of polyamine biosynthesis II	8	6	1
superpathway of ornithine degradation	8	6	1
superpathway of polyamine biosynthesis I	8	4	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
superpathway of L-arginine and L-ornithine degradation	13	8	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
superpathway of arginine and polyamine biosynthesis	17	13	1
superpathway of seleno-compound metabolism	19	8	1