Experiment set2IT013 for Shewanella loihica PV-4

N-Acetyl-D-Glucosamine carbon source

Group: carbon source
Media: ShewMM_noCarbon + N-Acetyl-D-Glucosamine (20 mM), pH=7
Culturing: PV4_ML1, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 6.1 generations
By: Adam on 12/11/2013
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 9 genes in this experiment

For carbon source N-Acetyl-D-Glucosamine in Shewanella loihica PV-4

For carbon source N-Acetyl-D-Glucosamine across organisms

SEED Subsystems

Subsystem	#Specific
Chitin and N-acetylglucosamine utilization	3
Sialic Acid Metabolism	2
UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis	2
Lactose and Galactose Uptake and Utilization	1
Lysine Biosynthesis DAP Pathway	1
Maltose and Maltodextrin Utilization	1
Methionine Biosynthesis	1
N-Acetyl-Galactosamine and Galactosamine Utilization	1
Pentose phosphate pathway	1
Threonine and Homoserine Biosynthesis	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
• Biosynthesis of plant hormones
• Glycine, serine and threonine metabolism
• Lysine biosynthesis
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Galactose metabolism
• Glutathione metabolism
• Other glycan degradation
• Glycosaminoglycan degradation
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
N-acetylglucosamine degradation I	2	2	2
L-homoserine biosynthesis	3	3	2
N-acetylglucosamine degradation II	3	3	2
trehalose degradation VI (periplasmic)	2	1	1
superpathway of L-threonine biosynthesis	6	6	2
pentose phosphate pathway (oxidative branch) I	3	3	1
chitin degradation II (Vibrio)	6	3	2
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation	6	2	2
superpathway of L-homoserine and L-methionine biosynthesis	8	8	2
dipicolinate biosynthesis	4	3	1
L-methionine biosynthesis IV	4	2	1
spermidine biosynthesis II	4	2	1
chitin derivatives degradation	8	3	2
D-galactosamine and N-acetyl-D-galactosamine degradation	4	1	1
superpathway of S-adenosyl-L-methionine biosynthesis	9	9	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	9	2
D-galactose degradation I (Leloir pathway)	5	5	1
ectoine biosynthesis	5	2	1
N-acetyl-D-galactosamine degradation	5	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	11	2
norspermidine biosynthesis	6	2	1
superpathway of L-isoleucine biosynthesis I	13	13	2
L-lysine biosynthesis VI	7	6	1
L-lysine biosynthesis III	7	6	1
peptidoglycan recycling I	14	10	2
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
3-dehydroquinate biosynthesis II (archaea)	7	3	1
chitin degradation III (Serratia)	7	3	1
chitin degradation I (archaea)	7	2	1
cremeomycin biosynthesis	7	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
pentose phosphate pathway	8	8	1
grixazone biosynthesis	8	2	1
superpathway of polyamine biosynthesis III	8	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	2
L-lysine biosynthesis I	9	9	1
L-lysine biosynthesis II	9	7	1
peptidoglycan recycling II	10	4	1
superpathway of N-acetylneuraminate degradation	22	16	2
chorismate biosynthesis II (archaea)	12	8	1
aspartate superpathway	25	24	2
superpathway of glucose and xylose degradation	17	14	1
platensimycin biosynthesis	26	6	1