Experiment set9IT030 for Pseudomonas fluorescens SBW25-INTG

Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs

Group: soil
Media: + Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs
Culturing: PseudoSBW25_INTG_ML3, at 21 (C)
By: Joshua Elmore on 13-Feb-20

Specific Phenotypes

For 19 genes in this experiment

For soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs in Pseudomonas fluorescens SBW25-INTG

For soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs across organisms

SEED Subsystems

Subsystem	#Specific
Isoleucine degradation	2
Leucine Degradation and HMG-CoA Metabolism	2
Valine degradation	2
Bacterial Chemotaxis	1
Flagellar motility	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Lysine degradation	1
Methylcitrate cycle	1
Potassium homeostasis	1
Propionate-CoA to Succinate Module	1
Ribosome activity modulation	1
Ribosome biogenesis bacterial	1
Two-component regulatory systems in Campylobacter	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• Propanoate metabolism
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Arginine and proline metabolism
• beta-Alanine metabolism
• Butanoate metabolism
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate degradation I	1	1	1
4-aminobutanoate degradation II	2	2	1
4-aminobutanoate degradation I	2	2	1
4-aminobutanoate degradation III	2	2	1
pseudouridine degradation	2	1	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
superpathway of 4-aminobutanoate degradation	3	3	1
ethene biosynthesis IV (engineered)	3	1	1
4-aminobutanoate degradation V	7	3	2
queuosine biosynthesis I (de novo)	4	4	1
GABA shunt II	4	3	1
GABA shunt I	4	2	1
2-methylcitrate cycle I	5	5	1
L-lysine degradation IV	5	5	1
2-methylcitrate cycle II	6	5	1
L-lysine degradation X	6	5	1
L-lysine degradation III	6	2	1
L-lysine degradation I	7	4	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
superpathway of L-arginine and L-ornithine degradation	13	9	1
nicotine degradation I (pyridine pathway)	17	5	1
methylaspartate cycle	19	9	1
superpathway of L-lysine degradation	43	17	1