Experiment set6IT030 for Pseudomonas fluorescens SBW25-INTG

Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=0_hrs

Group: soil
Media: + Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=0_hrs
Culturing: PseudoSBW25_INTG_ML3, at 21 (C)
By: Joshua Elmore on 13-Feb-20

Specific Phenotypes

For 8 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=coldshock; SoilTreatmentTime=0_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=coldshock; SoilTreatmentTime=0_hrs across organisms

SEED Subsystems

Subsystem	#Specific
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Phenylalanine and Tyrosine Branches from Chorismate	1
Queuosine-Archaeosine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tyrosine metabolism
• Histidine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Ubiquinone and menaquinone biosynthesis
• Methionine metabolism
• Lysine biosynthesis
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Starch and sucrose metabolism
• Naphthalene and anthracene degradation
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• mTOR signaling pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
cellulose biosynthesis	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	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
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
L-tyrosine biosynthesis III	4	3	1
L-phenylalanine biosynthesis II	4	3	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
L-tyrosine biosynthesis II	4	2	1
L-tyrosine degradation I	5	5	1
superpathway of L-phenylalanine and L-tyrosine biosynthesis	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
superpathway of aromatic amino acid biosynthesis	18	18	2
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
L-histidine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	1	1
(S)-reticuline biosynthesis I	11	1	1
tropane alkaloids biosynthesis	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