Experiment set3H18 for Shewanella amazonensis SB2B

D-Glucosamine Hydrochloride nitrogen source

Group: nitrogen source
Media: ShewMM_noNitrogen + D-Glucosamine Hydrochloride (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: 510 D7, D8

Specific Phenotypes

For 6 genes in this experiment

For nitrogen source D-Glucosamine Hydrochloride in Shewanella amazonensis SB2B

For nitrogen source D-Glucosamine Hydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
Chitin and N-acetylglucosamine utilization	4
UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis	2
Ammonia assimilation	1
Beta-Glucoside Metabolism	1
Sialic Acid Metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Nucleotide sugars metabolism
• Aminosugars metabolism
• Galactose metabolism
• Starch and sucrose metabolism
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Glutamate metabolism
• Streptomycin biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
N-acetylglucosamine degradation II	3	3	3
N-acetylglucosamine degradation I	2	2	2
sucrose degradation III (sucrose invertase)	4	3	2
trehalose degradation II (cytosolic)	2	1	1
D-mannose degradation II	2	1	1
trehalose degradation I (low osmolarity)	2	1	1
chitin derivatives degradation	8	3	3
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	2
D-sorbitol degradation I	3	2	1
trehalose degradation V	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation	6	2	2
sucrose degradation I (sucrose phosphotransferase)	3	1	1
trehalose degradation IV	3	1	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	2
sucrose degradation IV (sucrose phosphorylase)	4	3	1
D-galactosamine and N-acetyl-D-galactosamine degradation	4	2	1
mannitol degradation II	4	2	1
CMP-2-keto-3-deoxy-D-glycero-D-galacto-nononate biosynthesis	4	1	1
sucrose degradation VII (sucrose 3-dehydrogenase)	4	1	1
chitin biosynthesis	9	5	2
UDP-N-acetyl-D-glucosamine biosynthesis I	5	5	1
sucrose degradation II (sucrose synthase)	5	4	1
mannitol cycle	5	3	1
glucose and glucose-1-phosphate degradation	5	3	1
1,5-anhydrofructose degradation	5	2	1
N-acetyl-D-galactosamine degradation	5	2	1
glycogen degradation II	6	5	1
UDP-N-acetyl-D-galactosamine biosynthesis III	6	2	1
chitin degradation I (archaea)	7	1	1
glycogen degradation I	8	7	1
sucrose biosynthesis II	8	6	1
heterolactic fermentation	18	15	2
1,3-propanediol biosynthesis (engineered)	9	4	1
CMP-legionaminate biosynthesis I	10	4	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
glycolysis III (from glucose)	11	9	1
superpathway of N-acetylneuraminate degradation	22	16	2
homolactic fermentation	12	9	1
peptidoglycan recycling I	14	11	1
Bifidobacterium shunt	15	13	1
superpathway of CMP-sialic acids biosynthesis	15	4	1
superpathway of anaerobic sucrose degradation	19	15	1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	10	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1