Experiment set3IT048 for Pseudomonas fluorescens SBW25-INTG

Sodium acetate carbon source

Group: carbon source
Media: soilextract_PNNL_Prosser_PlotA_B_20191220 + Sodium acetate (40 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 9 genes in this experiment

For carbon source Sodium acetate in Pseudomonas fluorescens SBW25-INTG

For carbon source Sodium acetate across organisms

SEED Subsystems

Subsystem	#Specific
Beta-Glucoside Metabolism	1
Experimental tye	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Heme and Siroheme Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lysine biosynthesis
• Arginine and proline metabolism
• Starch and sucrose metabolism
• Pentose and glucuronate interconversions
• Ascorbate and aldarate metabolism
• Urea cycle and metabolism of amino groups
• Geraniol degradation
• Cyanoamino acid metabolism
• Nucleotide sugars metabolism
• Glycerophospholipid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Porphyrin and chlorophyll metabolism
• Phenylpropanoid biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-α-D-glucuronate biosynthesis (from UDP-glucose)	1	1	1
neolinustatin bioactivation	3	2	2
glycerophosphodiester degradation	2	2	1
linustatin bioactivation	4	2	2
linamarin degradation	2	1	1
phosphatidylcholine resynthesis via glycerophosphocholine	2	1	1
UDP-α-D-xylose biosynthesis	2	1	1
lotaustralin degradation	2	1	1
L-proline biosynthesis III (from L-ornithine)	3	3	1
L-ornithine biosynthesis II	3	3	1
L-arginine degradation I (arginase pathway)	3	3	1
cellulose degradation II (fungi)	3	2	1
L-arginine degradation VI (arginase 2 pathway)	4	4	1
glycerol and glycerophosphodiester degradation	4	4	1
heme b biosynthesis II (oxygen-independent)	4	3	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
L-ornithine biosynthesis I	5	5	1
L-arginine degradation XIII (reductive Stickland reaction)	5	5	1
coumarin biosynthesis (via 2-coumarate)	5	2	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	4	1
α-tomatine degradation	6	1	1
L-Nδ-acetylornithine biosynthesis	7	6	1
L-citrulline biosynthesis	8	8	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)	9	3	1
teichuronic acid biosynthesis (B. subtilis 168)	9	2	1
UDP-sugars interconversion	9	2	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
colanic acid building blocks biosynthesis	11	11	1
superpathway of L-citrulline metabolism	12	10	1
anandamide biosynthesis I	12	3	1
firefly bioluminescence	14	2	1
superpathway of arginine and polyamine biosynthesis	17	15	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1
superpathway of bacteriochlorophyll a biosynthesis	26	5	1