Experiment set8IT093 for Pseudomonas fluorescens SBW25-INTG

N-Acetyl-D-Glucosamine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + N-Acetyl-D-Glucosamine (20 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 15-Mar-20
Media components: 0.25 g/L Ammonium chloride, 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 22 genes in this experiment

For carbon source N-Acetyl-D-Glucosamine in Pseudomonas fluorescens SBW25-INTG

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

SEED Subsystems

Subsystem	#Specific
Chitin and N-acetylglucosamine utilization	3
Folate Biosynthesis	2
Fructose utilization	2
UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis	2
Alginate metabolism	1
Arginine and Ornithine Degradation	1
Fructose and Mannose Inducible PTS	1
Heat shock dnaK gene cluster extended	1
Mannitol Utilization	1
Mannose Metabolism	1
Methylcitrate cycle	1
Oxidative stress	1
Pentose phosphate pathway	1
Propionate-CoA to Succinate Module	1
Ribosome biogenesis bacterial	1
Sialic Acid Metabolism	1
Transport of Manganese	1
Trehalose Uptake and Utilization	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
• Glycolysis / Gluconeogenesis
• Galactose metabolism
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Tryptophan metabolism
• Starch and sucrose metabolism
• Propanoate metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Pentose and glucuronate interconversions
• Ascorbate and aldarate metabolism
• Biosynthesis of steroids
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Arginine and proline metabolism
• Glutathione metabolism
• Streptomycin biosynthesis
• Lipopolysaccharide biosynthesis
• Glyoxylate and dicarboxylate metabolism
• One carbon pool by folate
• Methane metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-serine degradation	3	3	3
N-acetylglucosamine degradation I	2	2	2
L-serine degradation	3	3	2
L-cysteine degradation II	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
N-acetylglucosamine degradation II	3	2	2
UDP-α-D-glucose biosynthesis	2	2	1
2-methylcitrate cycle I	5	5	2
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
dTMP de novo biosynthesis (mitochondrial)	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
pentose phosphate pathway (oxidative branch) I	3	3	1
glyoxylate cycle	6	5	2
2-methylcitrate cycle II	6	5	2
L-methionine biosynthesis II	6	5	2
β-1,4-D-mannosyl-N-acetyl-D-glucosamine degradation	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
trehalose degradation V	3	2	1
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation	6	2	2
glycine betaine degradation III	7	7	2
partial TCA cycle (obligate autotrophs)	8	8	2
GDP-mannose biosynthesis	4	4	1
glycine betaine degradation I	8	6	2
nitrogen remobilization from senescing leaves	8	6	2
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
sucrose degradation IV (sucrose phosphorylase)	4	3	1
starch degradation V	4	3	1
L-mimosine degradation	8	4	2
D-galactosamine and N-acetyl-D-galactosamine degradation	4	2	1
tetrahydromonapterin biosynthesis	4	2	1
starch degradation III	4	2	1
glutathione-mediated detoxification I	8	3	2
chitin derivatives degradation	8	2	2
TCA cycle V (2-oxoglutarate synthase)	9	7	2
TCA cycle VI (Helicobacter)	9	7	2
TCA cycle VII (acetate-producers)	9	7	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	2
TCA cycle II (plants and fungi)	9	7	2
chitin biosynthesis	9	5	2
L-arginine degradation II (AST pathway)	5	5	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
UDP-N-acetyl-D-glucosamine biosynthesis I	5	5	1
TCA cycle I (prokaryotic)	10	9	2
sucrose degradation II (sucrose synthase)	5	4	1
glucose and glucose-1-phosphate degradation	5	4	1
TCA cycle III (animals)	10	7	2
D-galactose degradation I (Leloir pathway)	5	3	1
glucosylglycerol biosynthesis	5	2	1
N-acetyl-D-galactosamine degradation	5	2	1
CDP-6-deoxy-D-gulose biosynthesis	5	1	1
colanic acid building blocks biosynthesis	11	11	2
O-antigen building blocks biosynthesis (E. coli)	11	10	2
reductive TCA cycle I	11	6	2
superpathway of glyoxylate bypass and TCA	12	11	2
glycogen degradation II	6	5	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
reductive TCA cycle II	12	5	2
UDP-N-acetyl-D-galactosamine biosynthesis III	6	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	12	2
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
β-(1,4)-mannan degradation	7	2	1
chitin degradation I (archaea)	7	1	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
pentose phosphate pathway	8	8	1
glycogen degradation I	8	6	1
sucrose biosynthesis II	8	6	1
mixed acid fermentation	16	11	2
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	3	1
folate transformations III (E. coli)	9	9	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
methylaspartate cycle	19	9	2
superpathway of tetrahydrofolate biosynthesis	10	8	1
starch biosynthesis	10	5	1
CMP-legionaminate biosynthesis I	10	2	1
folate transformations II (plants)	11	10	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
superpathway of N-acetylneuraminate degradation	22	14	2
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
purine nucleobases degradation II (anaerobic)	24	16	2
ethene biosynthesis V (engineered)	25	18	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	2
peptidoglycan recycling I	14	11	1
superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis	14	9	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	2
superpathway of glucose and xylose degradation	17	16	1
streptomycin biosynthesis	18	2	1
superpathway of anaerobic sucrose degradation	19	14	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	5	1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	9	1
superpathway of chorismate metabolism	59	42	1