Experiment set34S671 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 19 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	7
Biotin biosynthesis	2
Bacterial Cell Division	1
Bacterial Cytoskeleton	1
De Novo Pyrimidine Synthesis	1
Flagellum in Campylobacter	1
LMPTP YwlE cluster	1
Lipid A modifications	1
Lysine Biosynthesis DAP Pathway	1
Peptidoglycan 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
• Ubiquinone and menaquinone biosynthesis
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine degradation
• Lysine biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• beta-Alanine metabolism
• Peptidoglycan biosynthesis
• Biphenyl degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Nicotinate and nicotinamide metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of ansamycins
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyrimidine nucleobases salvage I	1	1	1
myo-inositol degradation I	7	7	6
myo-, chiro- and scyllo-inositol degradation	10	7	6
β-alanine degradation II	2	2	1
pyrimidine nucleobases salvage II	2	2	1
8-amino-7-oxononanoate biosynthesis II	2	1	1
8-amino-7-oxononanoate biosynthesis III	2	1	1
β-alanine degradation I	2	1	1
biotin biosynthesis from 8-amino-7-oxononanoate I	4	4	1
superpathway of pyrimidine nucleobases salvage	4	4	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
propanoyl-CoA degradation II	5	3	1
acrylate degradation I	5	3	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
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	2
peptidoglycan biosynthesis II (staphylococci)	17	12	2
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
L-lysine biosynthesis I	9	9	1
superpathway of pyrimidine ribonucleosides salvage	10	6	1
8-amino-7-oxononanoate biosynthesis I	11	10	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	12	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1