Experiment set4IT089 for Variovorax sp. OAS795

Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=soil; GrowthSubstrate=quartz_sand; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=21_days

Group: in planta
Media: + Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=soil; GrowthSubstrate=quartz_sand; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=21_days
Culturing: Variovorax_OAS795_ML2, pot, at 26 (C), (Solid)
By: Marta on 3-Jun-21

Specific Phenotypes

For 11 genes in this experiment

For in planta Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=soil; GrowthSubstrate=quartz_sand; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=21_days in Variovorax sp. OAS795

For in planta Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=soil; GrowthSubstrate=quartz_sand; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=21_days across organisms

SEED Subsystems

Subsystem	#Specific
Arginine Biosynthesis extended	1
Benzoate transport and degradation cluster	1
DNA repair, UvrABC system	1
Folate Biosynthesis	1
Phosphate metabolism	1
Purine conversions	1
Queuosine-Archaeosine Biosynthesis	1
Widespread colonization island	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Oxidative phosphorylation
• Urea cycle and metabolism of amino groups
• Pyrimidine metabolism
• Lysine degradation
• Arginine and proline metabolism
• Peptidoglycan biosynthesis
• Nicotinate and nicotinamide metabolism
• Biotin metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
adenosine nucleotides degradation III	1	1	1
oxalate degradation II	3	2	1
NAD salvage pathway III (to nicotinamide riboside)	3	2	1
UTP and CTP dephosphorylation I	7	5	2
purine nucleotides degradation II (aerobic)	11	8	3
guanosine nucleotides degradation II	4	4	1
adenosine nucleotides degradation I	8	7	2
purine nucleotides degradation I (plants)	12	10	3
guanosine nucleotides degradation III	4	3	1
guanosine nucleotides degradation I	4	3	1
inosine 5'-phosphate degradation	4	3	1
L-ornithine biosynthesis I	5	5	1
adenosine nucleotides degradation II	5	4	1
superpathway of guanosine nucleotides degradation (plants)	6	5	1
superpathway of purines degradation in plants	18	12	3
benzoyl-CoA degradation I (aerobic)	7	6	1
ureide biosynthesis	7	5	1
glyphosate degradation III	7	1	1
(aminomethyl)phosphonate degradation	8	1	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
tunicamycin biosynthesis	9	1	1
NAD salvage (plants)	11	6	1
superpathway of arginine and polyamine biosynthesis	17	16	1