Experiment set6IT049 for Agrobacterium fabrum C58

Plant=Tobacco; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Time=7days

Group: in planta
Media: + Plant=Tobacco; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Time=7days
Culturing: Agro_ML11, at 30 (C)
By: Mitchell Thompson on 12/1/21

Specific Phenotypes

For 10 genes in this experiment

For in planta Plant=Tobacco; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Time=7days in Agrobacterium fabrum C58

For in planta Plant=Tobacco; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Time=7days across organisms

SEED Subsystems

Subsystem	#Specific
Branched-Chain Amino Acid Biosynthesis	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
DNA repair, bacterial RecFOR pathway	1
Homogentisate pathway of aromatic compound degradation	1
Oxidative stress	1
Transport of Zinc	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Fatty acid biosynthesis
• Valine, leucine and isoleucine biosynthesis
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Pantothenate and CoA biosynthesis
• Atrazine degradation
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
urea degradation I	3	3	3
two-component alkanesulfonate monooxygenase	2	2	1
mannosylfructose biosynthesis	2	2	1
sulfoquinovose degradation IV	2	2	1
superpathway of allantoin degradation in yeast	6	3	3
cyanuric acid degradation II	5	3	2
cyanuric acid degradation I	5	2	2
L-citrulline degradation	3	3	1
cyanate degradation	3	2	1
L-valine biosynthesis	4	4	1
biotin-carboxyl carrier protein assembly	4	4	1
L-arginine degradation V (arginine deiminase pathway)	4	3	1
superpathway of atrazine degradation	8	3	2
chorismate biosynthesis from 3-dehydroquinate	5	5	1
uracil degradation III	5	5	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
L-isoleucine biosynthesis IV	6	3	1
chorismate biosynthesis I	7	7	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
allantoin degradation IV (anaerobic)	9	4	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
chorismate biosynthesis II (archaea)	12	8	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of L-isoleucine biosynthesis I	13	13	1
3-hydroxypropanoate cycle	13	8	1
glyoxylate assimilation	13	5	1
superpathway of aromatic amino acid biosynthesis	18	18	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
superpathway of chorismate metabolism	59	38	1