Experiment set3H41 for Shewanella amazonensis SB2B

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Glycine nitrogen source

Group: nitrogen source
Media: ShewMM_noNitrogen + Glycine (20 mM), pH=7
Culturing: SB2B_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Jake on 4/24/2013
Media components: 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, 20 mM Sodium D,L-Lactate, 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)
Growth plate: 511 E7, E8

Specific Phenotypes

For 6 genes in this experiment

For nitrogen source Glycine in Shewanella amazonensis SB2B

For nitrogen source Glycine across organisms

SEED Subsystems

Subsystem #Specific
ATP-dependent RNA helicases, bacterial 1
Glycine and Serine Utilization 1
Pyridoxin (Vitamin B6) Biosynthesis 1
Serine Biosynthesis 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
4-aminobutanoate degradation III 2 2 1
4-aminobutanoate degradation I 2 1 1
4-aminobutanoate degradation II 2 1 1
L-serine biosynthesis I 3 3 1
L-cysteine biosynthesis IX (Trichomonas vaginalis) 3 2 1
superpathway of 4-aminobutanoate degradation 3 1 1
superpathway of L-serine and glycine biosynthesis I 4 4 1
GABA shunt II 4 3 1
GABA shunt I 4 2 1
L-lysine degradation IV 5 2 1
L-lysine degradation X 6 2 1
L-lysine degradation III 6 1 1
4-aminobutanoate degradation V 7 3 1
L-lysine degradation I 7 1 1
L-valine degradation I 8 6 1
superpathway of sulfate assimilation and cysteine biosynthesis 9 9 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 6 1
superpathway of L-arginine and L-ornithine degradation 13 8 1
nicotine degradation I (pyridine pathway) 17 4 1
superpathway of L-lysine degradation 43 8 1