Experiment set4S66 for Pseudomonas segetis P6

Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=20h_outgrowth_LB; Time=7_days

Group: in planta
Media: + Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=20h_outgrowth_LB; Time=7_days
Culturing: Pseudo_segetis_P6_ML4b, pot, at 26 (C)
By: Marta Torres on 6-Nov-23

Specific Phenotypes

For 39 genes in this experiment

For in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=20h_outgrowth_LB; Time=7_days in Pseudomonas segetis P6

For in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=20h_outgrowth_LB; Time=7_days across organisms

SEED Subsystems

Subsystem	#Specific
Glycine and Serine Utilization	2
Glycine cleavage system	2
Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes	2
Orphan regulatory proteins	2
Photorespiration (oxidative C2 cycle)	2
Choline and Betaine Uptake and Betaine Biosynthesis	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Lipid A modifications	1
Peptidoglycan Biosynthesis	1
Phage capsid proteins	1
Protein degradation	1
Sodium Hydrogen Antiporter	1
ZZ gjo need homes	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Ubiquinone and menaquinone biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Aminophosphonate metabolism
• High-mannose type N-glycan biosynthesis
• Nucleotide sugars metabolism
• Peptidoglycan biosynthesis
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• Naphthalene and anthracene degradation
• One carbon pool by folate
• Biotin metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
cis-cyclopropane fatty acid (CFA) biosynthesis	1	1	1
glycine cleavage	3	3	2
glycine biosynthesis II	3	3	2
sterculate biosynthesis	2	1	1
cardiolipin biosynthesis II	3	3	1
glycine degradation	3	3	1
2-chloroacrylate degradation I	3	2	1
glycine betaine degradation I	8	6	2
cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas)	4	3	1
creatinine degradation I	4	1	1
creatinine degradation II	5	1	1
folate transformations III (E. coli)	9	9	1
photorespiration III	9	5	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
photorespiration I	9	5	1
photorespiration II	10	6	1
folate transformations II (plants)	11	10	1
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
folate transformations I	13	9	1
mycolate biosynthesis	205	20	3
superpathway of mycolate biosynthesis	239	21	3