Experiment set7IT078 for Pseudomonas fluorescens SBW25-INTG

Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs

Group: soil
Media: + Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs
Culturing: PseudoSBW25_INTG_ML3, at 21 (C)
By: Joshua Elmore on 13-Feb-20

Specific Phenotypes

For 4 genes in this experiment

For soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs in Pseudomonas fluorescens SBW25-INTG

For soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs across organisms

SEED Subsystems

Subsystem	#Specific
HMG CoA Synthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Phenylalanine and Tyrosine Branches from Chorismate	1
Terminal cytochrome C oxidases	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Synthesis and degradation of ketone bodies
• Oxidative phosphorylation
• Methionine metabolism
• Valine, leucine and isoleucine degradation
• Lysine biosynthesis
• Histidine metabolism
• Butanoate metabolism
• Alkaloid biosynthesis I
• Biosynthesis of alkaloids derived from shikimate pathway
• 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
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
mevalonate degradation	2	1	1
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	2	1	1
arsenite to oxygen electron transfer	2	1	1
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine degradation II (anaerobic)	3	2	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
queuosine biosynthesis I (de novo)	4	4	1
aerobic respiration I (cytochrome c)	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
L-phenylalanine biosynthesis II	4	3	1
L-tyrosine biosynthesis III	4	3	1
L-tyrosine biosynthesis II	4	2	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
L-tyrosine degradation I	5	5	1
superpathway of L-phenylalanine and L-tyrosine biosynthesis	5	3	1
ketogenesis	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-leucine degradation I	6	5	1
Fe(II) oxidation	6	3	1
superpathway of aromatic amino acid biosynthesis	18	18	2
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
cis-geranyl-CoA degradation	9	4	1
L-histidine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	1	1
tropane alkaloids biosynthesis	11	1	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of rosmarinic acid biosynthesis	14	1	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	4	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of chorismate metabolism	59	42	2
superpathway of histidine, purine, and pyrimidine biosynthesis	46	44	1