Experiment set34S667 for Pseudomonas simiae WCS417

Plant=Zea_mays-B73; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days

Group: in planta
Media: + Plant=Zea_mays-B73; 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 26 genes in this experiment

For in planta Plant=Zea_mays-B73; 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-B73; 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
Peptidoglycan Biosynthesis	2
Acetyl-CoA fermentation to Butyrate	1
Bacterial Cell Division	1
Bacterial Cytoskeleton	1
Flagellum in Campylobacter	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Lipid A modifications	1
Lysine Biosynthesis DAP Pathway	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Photorespiration (oxidative C2 cycle)	1
Pyrroloquinoline Quinone biosynthesis	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:

• Inositol phosphate metabolism
• Ascorbate and aldarate metabolism
• Propanoate metabolism
• Biotin metabolism
• Pentose and glucuronate interconversions
• Galactose metabolism
• Ubiquinone and menaquinone biosynthesis
• 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
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Peptidoglycan 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
myo-, chiro- and scyllo-inositol degradation	10	7	7
β-alanine degradation II	2	2	1
β-alanine degradation I	2	1	1
8-amino-7-oxononanoate biosynthesis III	2	1	1
8-amino-7-oxononanoate biosynthesis II	2	1	1
glycine biosynthesis II	3	3	1
glycine degradation	3	3	1
glycine cleavage	3	3	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
peptido-conjugates in tissue regeneration biosynthesis	17	6	3
biotin biosynthesis II	6	4	1
leukotriene biosynthesis	6	2	1
2,4-dinitrotoluene degradation	7	3	1
biotin biosynthesis I	15	14	2
L-valine degradation I	8	6	1
peptidoglycan biosynthesis II (staphylococci)	17	12	2
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	2
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
L-lysine biosynthesis I	9	9	1
folate transformations III (E. coli)	9	9	1
photorespiration I	9	5	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
photorespiration III	9	5	1
gliotoxin biosynthesis	9	2	1
photorespiration II	10	6	1
8-amino-7-oxononanoate biosynthesis I	11	10	1
folate transformations II (plants)	11	10	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	12	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	1
folate transformations I	13	9	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	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
arachidonate metabolites biosynthesis	74	3	1