Experiment set5IT019 for Pseudomonas fluorescens SBW25-INTG

N-Acetyl-D-Glucosamine carbon source

Group: carbon source
Media: soilextract_PNNL_Prosser_PlotA_B_20191220 + N-Acetyl-D-Glucosamine (10 mM) + Ammonium chloride (10 mM)
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1 mL volume, Aerobic, at 30 (C)
By: Joshua Elmore on 1/6/20

Specific Phenotypes

For 32 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	2
Glycerol and Glycerol-3-phosphate Uptake and Utilization	2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
Bacterial Cell Division	1
Beta-Glucoside Metabolism	1
Calvin-Benson cycle	1
Folate Biosynthesis	1
Fructose and Mannose Inducible PTS	1
Fructose utilization	1
Glutathione-regulated potassium-efflux system and associated functions	1
Glycerol fermenation to 1,3-propanediol	1
Mannitol Utilization	1
Methylcitrate cycle	1
Pentose phosphate pathway	1
Proline, 4-hydroxyproline uptake and utilization	1
Propionate-CoA to Succinate Module	1
Pyruvate Alanine Serine Interconversions	1
Ribosome biogenesis bacterial	1
Sialic Acid Metabolism	1
Trehalose Uptake and Utilization	1
UDP-N-acetylmuramate from Fructose-6-phosphate 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
• Propanoate metabolism
• Starch and sucrose metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Aminosugars metabolism
• Caprolactam degradation
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Citrate cycle (TCA cycle)
• Pentose phosphate pathway
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Puromycin biosynthesis
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Methionine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Arginine and proline metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Aminophosphonate metabolism
• Cyanoamino acid metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• alpha-Linolenic acid metabolism
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• One carbon pool by folate
• Methane metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Folate biosynthesis
• Limonene and pinene degradation
• Phenylpropanoid biosynthesis
• Alkaloid biosynthesis II
• Biosynthesis of ansamycins
• Biosynthesis of terpenoids and steroids
• 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
UDP-α-D-glucuronate biosynthesis (from UDP-glucose)	1	1	1
pentose phosphate pathway (partial)	3	3	2
neolinustatin bioactivation	3	2	2
glycerol and glycerophosphodiester degradation	4	4	2
N-acetylglucosamine degradation I	2	2	1
putrescine degradation V	2	2	1
arsenate detoxification III	2	2	1
β-alanine degradation II	2	2	1
glycerophosphodiester degradation	2	2	1
linustatin bioactivation	4	2	2
lotaustralin degradation	2	1	1
pseudouridine degradation	2	1	1
UDP-α-D-xylose biosynthesis	2	1	1
linamarin degradation	2	1	1
phosphatidylcholine resynthesis via glycerophosphocholine	2	1	1
pentose phosphate pathway (non-oxidative branch) I	5	5	2
2-methylcitrate cycle I	5	5	2
dTMP de novo biosynthesis (mitochondrial)	3	3	1
glycerol degradation I	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
pentose phosphate pathway (non-oxidative branch) II	6	5	2
2-methylcitrate cycle II	6	5	2
glyoxylate cycle	6	5	2
cellulose degradation II (fungi)	3	2	1
N-acetylglucosamine degradation II	3	2	1
D-apiose degradation I	3	2	1
polymyxin resistance	6	3	2
oxalate degradation II	3	1	1
pentose phosphate pathway	8	8	2
partial TCA cycle (obligate autotrophs)	8	8	2
guanosine nucleotides degradation II	4	4	1
guanosine nucleotides degradation III	4	4	1
nitrogen remobilization from senescing leaves	8	6	2
guanosine nucleotides degradation I	4	3	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
D-galactosamine and N-acetyl-D-galactosamine degradation	4	2	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	2
TCA cycle VII (acetate-producers)	9	7	2
TCA cycle V (2-oxoglutarate synthase)	9	7	2
TCA cycle VI (Helicobacter)	9	7	2
TCA cycle II (plants and fungi)	9	7	2
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	6	2
adipate degradation	5	5	1
TCA cycle I (prokaryotic)	10	9	2
Rubisco shunt	10	8	2
TCA cycle III (animals)	10	7	2
N-acetyl-D-galactosamine degradation	5	2	1
coumarin biosynthesis (via 2-coumarate)	5	2	1
reductive TCA cycle I	11	6	2
fatty acid salvage	6	6	1
superpathway of glyoxylate bypass and TCA	12	11	2
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	2
purine nucleotides degradation I (plants)	12	10	2
superpathway of guanosine nucleotides degradation (plants)	6	5	1
β-alanine biosynthesis II	6	5	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
arsenic detoxification (plants)	6	4	1
reductive TCA cycle II	12	5	2
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation	6	2	1
α-tomatine degradation	6	1	1
ethene biosynthesis V (engineered)	25	18	4
Calvin-Benson-Bassham cycle	13	10	2
superpathway of glyoxylate cycle and fatty acid degradation	14	12	2
adenosine nucleotides degradation I	8	7	1
mixed acid fermentation	16	11	2
chitin derivatives degradation	8	2	1
superpathway of glucose and xylose degradation	17	16	2
oxygenic photosynthesis	17	11	2
folate transformations III (E. coli)	9	9	1
superpathway of purines degradation in plants	18	14	2
teichuronic acid biosynthesis (B. subtilis 168)	9	2	1
UDP-sugars interconversion	9	2	1
methylaspartate cycle	19	9	2
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
purine nucleotides degradation II (aerobic)	11	11	1
colanic acid building blocks biosynthesis	11	11	1
folate transformations II (plants)	11	10	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
oleate β-oxidation	35	33	3
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
arsenic detoxification (yeast)	12	4	1
anandamide biosynthesis I	12	3	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
1-butanol autotrophic biosynthesis (engineered)	27	19	2
peptidoglycan recycling I	14	11	1
2-methyl-branched fatty acid β-oxidation	14	11	1
firefly bioluminescence	14	2	1
Bifidobacterium shunt	15	12	1
arsenic detoxification (mammals)	17	8	1
superpathway of N-acetylneuraminate degradation	22	14	1
superpathway of chorismate metabolism	59	42	1