Experiment set34S672 for Pseudomonas simiae WCS417

Plant=Zea_mays-bx1; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days

Group: in planta
Media: + Plant=Zea_mays-bx1; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days
Culturing: fluoroDangl_ML3b, pot, at 24 (C), (Solid)
By: Marta Torres on 2-Jul-24

Specific Phenotypes

For 29 genes in this experiment

For in planta Plant=Zea_mays-bx1; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days in Pseudomonas simiae WCS417

For in planta Plant=Zea_mays-bx1; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days across organisms

SEED Subsystems

Subsystem	#Specific
Inositol catabolism	8
Biotin biosynthesis	2
Acetyl-CoA fermentation to Butyrate	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
De Novo Pyrimidine Synthesis	1
LMPTP YwlE cluster	1
Lipid A modifications	1
Lysine Biosynthesis DAP Pathway	1
Maltose and Maltodextrin Utilization	1
Molybdenum cofactor biosynthesis	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Trehalose Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Inositol phosphate metabolism
• Propanoate metabolism
• Biotin metabolism
• Pentose and glucuronate interconversions
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Lysine biosynthesis
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• beta-Alanine metabolism
• Starch and sucrose metabolism
• Streptomycin biosynthesis
• Biphenyl degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Nicotinate and nicotinamide metabolism
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of ansamycins

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
myo-inositol degradation I	7	7	7
bis(guanylyl molybdenum cofactor) biosynthesis	2	2	2
guanylyl molybdenum cofactor biosynthesis	1	1	1
pyrimidine nucleobases salvage I	1	1	1
sulfoacetaldehyde degradation III	1	1	1
bis(guanylyl tungstenpterin) cofactor biosynthesis	1	1	1
myo-, chiro- and scyllo-inositol degradation	10	7	7
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
β-alanine degradation II	2	2	1
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
pyrimidine nucleobases salvage II	2	2	1
choline degradation I	2	2	1
8-amino-7-oxononanoate biosynthesis III	2	1	1
8-amino-7-oxononanoate biosynthesis II	2	1	1
β-alanine degradation I	2	1	1
choline-O-sulfate degradation	3	3	1
superpathway of pyrimidine nucleobases salvage	4	4	1
biotin biosynthesis from 8-amino-7-oxononanoate I	4	4	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
acrylate degradation I	5	3	1
propanoyl-CoA degradation II	5	3	1
myo-inositol degradation II	5	1	1
biotin biosynthesis II	6	4	1
2,4-dinitrotoluene degradation	7	3	1
biotin biosynthesis I	15	14	2
L-valine degradation I	8	6	1
L-lysine biosynthesis I	9	9	1
superpathway of pyrimidine ribonucleosides salvage	10	6	1
8-amino-7-oxononanoate biosynthesis I	11	10	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
streptomycin biosynthesis	18	3	1
aspartate superpathway	25	22	1