Experiment set3H24 for Shewanella oneidensis MR-1

Compare to:

Gly-DL-Asp carbon source replicate 2

Group: carbon source
Media: ShewMM_noCarbon + Gly-DL-Asp (10 mM), pH=7
Culturing: MR1_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.1 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 11 genes in this experiment

For carbon source Gly-DL-Asp in Shewanella oneidensis MR-1

For carbon source Gly-DL-Asp across organisms

SEED Subsystems

Subsystem #Specific
Arginine and Ornithine Degradation 1
Glycine Biosynthesis 1
Methionine Biosynthesis 1
Polyamine Metabolism 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Redox-dependent regulation of nucleus processes 1
Threonine degradation 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-threonine degradation III (to methylglyoxal) 3 2 2
glutathione degradation (DUG pathway) 2 2 1
L-threonine degradation II 2 2 1
aminopropanol phosphate biosynthesis II 4 2 2
L-homocysteine biosynthesis 2 1 1
putrescine biosynthesis III 2 1 1
superpathway of L-cysteine biosynthesis (fungi) 6 2 2
superpathway of ornithine degradation 8 6 2
L-methionine biosynthesis III 4 3 1
putrescine degradation II 4 3 1
superpathway of putrescine biosynthesis 4 2 1
muropeptide degradation 4 1 1
homocysteine and cysteine interconversion 4 1 1
L-methionine biosynthesis I 5 4 1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) 10 6 2
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II 5 1 1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III 5 1 1
L-methionine biosynthesis II 6 5 1
γ-glutamyl cycle 6 4 1
superpathway of L-arginine and L-ornithine degradation 13 8 2
superpathway of L-homoserine and L-methionine biosynthesis 8 7 1
superpathway of polyamine biosynthesis II 8 6 1
superpathway of polyamine biosynthesis I 8 4 1
superpathway of L-methionine biosynthesis (transsulfuration) 9 8 1
superpathway of S-adenosyl-L-methionine biosynthesis 9 8 1
superpathway of L-threonine metabolism 18 15 2
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 6 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 11 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis 16 3 1
superpathway of arginine and polyamine biosynthesis 17 13 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 17 1
aspartate superpathway 25 23 1