Experiment set5IT039 for Pseudomonas fluorescens SBW25-INTG

N-Acetyl-D-Glucosamine carbon source; with MOPS

Group: carbon source
Media: soilextract_PNNL_Prosser_PlotA_B_20191220 + N-Acetyl-D-Glucosamine (10 mM) + Ammonium chloride (10 mM) + 3-(N-morpholino)propanesulfonic acid (40 mM), pH=7
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 17 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
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis	2
Calvin-Benson cycle	1
Folate Biosynthesis	1
Fructose and Mannose Inducible PTS	1
Fructose utilization	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Mannitol Utilization	1
Pentose phosphate pathway	1
Sialic Acid Metabolism	1
Threonine and Homoserine Biosynthesis	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
• Biosynthesis of phenylpropanoids
• Glycolysis / Gluconeogenesis
• Galactose metabolism
• Glutamate metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of plant hormones
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Alanine and aspartate metabolism
• Cysteine metabolism
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Starch and sucrose metabolism
• One carbon pool by folate
• Methane metabolism
• Folate biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of ansamycins
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• T cell receptor signaling pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
N-acetylglucosamine degradation I	2	2	2
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
pentose phosphate pathway (partial)	3	3	2
N-acetylglucosamine degradation II	3	2	2
L-glutamate degradation II	2	2	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
pentose phosphate pathway (non-oxidative branch) I	5	5	2
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
pentose phosphate pathway (non-oxidative branch) II	6	5	2
D-apiose degradation I	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation	6	2	2
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
oxalate degradation II	3	1	1
(R)-cysteate degradation	3	1	1
sulfolactate degradation III	3	1	1
pentose phosphate pathway	8	8	2
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-phenylalanine degradation III	4	2	1
D-galactosamine and N-acetyl-D-galactosamine degradation	4	2	1
L-tyrosine degradation III	4	2	1
chitin derivatives degradation	8	2	2
L-tryptophan degradation VIII (to tryptophol)	4	1	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	6	2
UDP-N-acetyl-D-glucosamine biosynthesis I	5	5	1
L-tyrosine degradation I	5	5	1
Rubisco shunt	10	8	2
trans-4-hydroxy-L-proline degradation I	5	3	1
N-acetyl-D-galactosamine degradation	5	2	1
superpathway of plastoquinol biosynthesis	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	2
superpathway of L-threonine biosynthesis	6	6	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	2
TCA cycle VIII (Chlamydia)	6	5	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
superpathway of sulfolactate degradation	6	2	1
UDP-N-acetyl-D-galactosamine biosynthesis III	6	2	1
coenzyme M biosynthesis II	6	1	1
Calvin-Benson-Bassham cycle	13	10	2
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
chitin degradation I (archaea)	7	1	1
superpathway of glucose and xylose degradation	17	16	2
oxygenic photosynthesis	17	11	2
superpathway of aromatic amino acid biosynthesis	18	18	2
folate transformations III (E. coli)	9	9	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
chitin biosynthesis	9	5	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
CMP-legionaminate biosynthesis I	10	2	1
rosmarinic acid biosynthesis I	10	1	1
folate transformations II (plants)	11	10	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
superpathway of N-acetylneuraminate degradation	22	14	2
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
indole-3-acetate biosynthesis II	12	5	1
ethene biosynthesis V (engineered)	25	18	2
superpathway of L-isoleucine biosynthesis I	13	13	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
1-butanol autotrophic biosynthesis (engineered)	27	19	2
peptidoglycan recycling I	14	11	1
superpathway of rosmarinic acid biosynthesis	14	1	1
Bifidobacterium shunt	15	12	1
superpathway of anaerobic energy metabolism (invertebrates)	17	8	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
superpathway of chorismate metabolism	59	42	3
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	9	1
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1