Experiment set2H43 for Shewanella amazonensis SB2B

Minimal media with D-Glucose as carbon source

Group: carbon source
Media: ShewMM_noCarbon + D-Glucose (20 mM), pH=7
Culturing: SB2B_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Jake on 4/15/2013
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)
Growth plate: 505 A1,A2

Specific Phenotypes

For 11 genes in this experiment

For carbon source D-Glucose in Shewanella amazonensis SB2B

For carbon source D-Glucose across organisms

SEED Subsystems

Subsystem	#Specific
Maltose and Maltodextrin Utilization	3
Mannose Metabolism	3
N-Acetyl-Galactosamine and Galactosamine Utilization	3
Beta-Glucoside Metabolism	1
Chitin and N-acetylglucosamine utilization	1
Fructooligosaccharides(FOS) and Raffinose Utilization	1
Lactose and Galactose Uptake and Utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose and glucuronate interconversions
• Galactose metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Glycolysis / Gluconeogenesis
• Biosynthesis of steroids
• Cyanoamino acid metabolism
• Starch and sucrose metabolism
• Other glycan degradation
• Lipopolysaccharide biosynthesis
• Inositol phosphate metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Biosynthesis of ansamycins

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
N-acetylglucosamine degradation II	3	3	2
neolinustatin bioactivation	3	2	2
N-acetylglucosamine degradation I	2	2	1
linustatin bioactivation	4	2	2
linamarin degradation	2	1	1
trehalose degradation VI (periplasmic)	2	1	1
lotaustralin degradation	2	1	1
cellulose degradation II (fungi)	3	1	1
D-galactosamine and N-acetyl-D-galactosamine degradation	4	2	1
chitin derivatives degradation	8	3	2
D-galactose degradation I (Leloir pathway)	5	4	1
N-acetyl-D-galactosamine degradation	5	2	1
coumarin biosynthesis (via 2-coumarate)	5	2	1
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation	6	2	1
α-tomatine degradation	6	1	1
peptidoglycan recycling I	14	11	1
firefly bioluminescence	14	2	1
superpathway of N-acetylneuraminate degradation	22	16	1