Experiment set52S621 for Pseudomonas putida KT2440

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: Putida_ML5a, pot, at 24 (C), (Solid)
By: Marta Torres on 1-Jul-24

Specific Phenotypes

For 32 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 putida KT2440

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
Choline and Betaine Uptake and Betaine Biosynthesis	3
Polyamine Metabolism	2
Acetyl-CoA fermentation to Butyrate	1
Ammonia assimilation	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
One-carbon metabolism by tetrahydropterines	1
Pyrroloquinoline Quinone biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Propanoate metabolism
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• beta-Alanine metabolism
• Glyoxylate and dicarboxylate metabolism
• 1,2-Dichloroethane degradation
• Butanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation II	1	1	1
L-glutamine degradation I	1	1	1
ammonia assimilation cycle III	3	3	2
glycine betaine degradation III	7	7	2
L-glutamate and L-glutamine biosynthesis	7	6	2
formaldehyde oxidation VII (THF pathway)	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glycine betaine degradation I	8	6	2
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
creatinine degradation I	4	2	1
creatinine degradation II	5	3	1
peptido-conjugates in tissue regeneration biosynthesis	17	6	3
L-leucine degradation I	6	5	1
leukotriene biosynthesis	6	2	1
L-citrulline biosynthesis	8	7	1
gliotoxin biosynthesis	9	2	1
superpathway of L-citrulline metabolism	12	9	1
folate transformations I	13	9	1
purine nucleobases degradation I (anaerobic)	15	6	1
purine nucleobases degradation II (anaerobic)	24	16	1
arachidonate metabolites biosynthesis	74	3	1