Experiment set4IT042 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 13 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
Bacterial Chemotaxis	1
Benzoate transport and degradation cluster	1
CO Dehydrogenase	1
Carbon monoxide dehydrogenase maturation factors	1
Multidrug Resistance Efflux Pumps	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Oxidative stress	1
Photorespiration (oxidative C2 cycle)	1
Purine conversions	1
Queuosine-Archaeosine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Nicotinate and nicotinamide metabolism
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Glutamate metabolism
• Lysine degradation
• Penicillin and cephalosporin biosynthesis
• beta-Lactam resistance
• Arginine and proline metabolism
• Tryptophan metabolism
• Peptidoglycan biosynthesis
• Methane metabolism
• Biotin 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
adenosine nucleotides degradation III	1	1	1
superoxide radicals degradation	2	2	1
methanol oxidation to formaldehyde IV	2	1	1
NAD salvage pathway II (PNC IV cycle)	5	4	2
NAD de novo biosynthesis I	6	6	2
ethanol degradation IV	3	3	1
NAD de novo biosynthesis IV (anaerobic)	6	5	2
NAD de novo biosynthesis III	6	5	2
NAD salvage pathway I (PNC VI cycle)	7	6	2
reactive oxygen species degradation	4	4	1
NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde	4	4	1
L-ornithine biosynthesis I	5	5	1
NAD salvage pathway V (PNC V cycle)	5	4	1
benzoyl-CoA degradation I (aerobic)	7	6	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
NAD de novo biosynthesis II (from tryptophan)	9	7	1
NAD salvage (plants)	11	6	1
aspartate superpathway	25	24	2
superpathway of NAD biosynthesis in eukaryotes	14	9	1
superpathway of arginine and polyamine biosynthesis	17	16	1