Experiment set6IT043 for Agrobacterium fabrum C58

Plant=Tobacco; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Time=3days

Group: in planta
Media: + Plant=Tobacco; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Time=3days
Culturing: Agro_ML11, at 30 (C)
By: Mitchell Thompson on 12/1/21

Specific Phenotypes

For 6 genes in this experiment

For in planta Plant=Tobacco; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Time=3days in Agrobacterium fabrum C58

For in planta Plant=Tobacco; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Time=3days across organisms

SEED Subsystems

Subsystem	#Specific
Branched-Chain Amino Acid Biosynthesis	1
DNA repair, bacterial RecFOR pathway	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fatty acid biosynthesis
• Urea cycle and metabolism of amino groups
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine biosynthesis
• Arginine and proline metabolism
• Cyanoamino acid metabolism
• Pantothenate and CoA biosynthesis
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-asparagine degradation I	1	1	1
urea degradation I	3	3	1
L-asparagine degradation III (mammalian)	3	2	1
L-valine biosynthesis	4	4	1
biotin-carboxyl carrier protein assembly	4	4	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
N-(1-deoxy-D-fructos-1-yl)-L-asparagine degradation	5	2	1
L-isoleucine biosynthesis IV	6	3	1
superpathway of allantoin degradation in yeast	6	3	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
L-isoleucine biosynthesis II	8	5	1
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of L-isoleucine biosynthesis I	13	13	1
3-hydroxypropanoate cycle	13	8	1
glyoxylate assimilation	13	5	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
superpathway of L-threonine metabolism	18	11	1
superpathway of the 3-hydroxypropanoate cycle	18	8	1