Experiment set29S128 for Pseudomonas simiae WCS417

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

Group: in planta
Media: + Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=20h_outgrowth_LB; Time=7_days
Culturing: WCS417_ML3b, pot, at 26 (C), (Solid)
By: Marta Torres on 18-Dec-23

Specific Phenotypes

For 10 genes in this experiment

For in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=20h_outgrowth_LB; Time=7_days in Pseudomonas simiae WCS417

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

SEED Subsystems

Subsystem	#Specific
Widespread colonization island	2
Adenosyl nucleosidases	1
Bacterial Chemotaxis	1
Deoxyribose and Deoxynucleoside Catabolism	1
Heat shock dnaK gene cluster extended	1
Purine conversions	1
Type IV pilus	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Pyrimidine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Naphthalene and anthracene degradation
• Nicotinate and nicotinamide metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
purine deoxyribonucleosides degradation I	4	4	3
purine deoxyribonucleosides degradation II	3	3	2
purine ribonucleosides degradation	6	5	4
adenine and adenosine salvage III	4	4	2
adenine and adenosine salvage I	2	2	1
guanine and guanosine salvage I	2	2	1
xanthine and xanthosine salvage	2	2	1
superpathway of purine deoxyribonucleosides degradation	7	5	3
pyrimidine deoxyribonucleosides degradation	3	2	1
superpathway of guanine and guanosine salvage	3	2	1
adenine and adenosine salvage V	3	2	1
purine nucleotides degradation II (aerobic)	11	11	3
guanosine nucleotides degradation III	4	4	1
inosine 5'-phosphate degradation	4	4	1
adenosine nucleotides degradation II	5	5	1
tRNA processing	10	8	2
nucleoside and nucleotide degradation (archaea)	10	3	2
superpathway of pyrimidine deoxyribonucleosides degradation	6	3	1
nucleoside and nucleotide degradation (halobacteria)	6	2	1
fluoroacetate and fluorothreonine biosynthesis	6	1	1
superpathway of purine nucleotide salvage	14	13	2
ureide biosynthesis	7	6	1
salinosporamide A biosynthesis	15	4	1
arsenic detoxification (mammals)	17	8	1