Experiment set6IT051 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 11 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
Di-Inositol-Phosphate biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Heat shock dnaK gene cluster extended	1
Proline, 4-hydroxyproline uptake and utilization	1
Respiratory dehydrogenases 1	1
Terminal cytochrome C oxidases	1
Two cell division clusters relating to chromosome partitioning	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Oxidative phosphorylation
• Glutamate metabolism
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine biosynthesis
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Cyanoamino acid metabolism
• Streptomycin biosynthesis
• Inositol phosphate metabolism
• Pantothenate and CoA biosynthesis
• Nitrogen metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones
• Phosphatidylinositol signaling system

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
mannosylfructose biosynthesis	2	2	2
L-asparagine degradation I	1	1	1
L-proline degradation I	3	3	2
proline to cytochrome bo oxidase electron transfer	2	2	1
arsenite to oxygen electron transfer	2	1	1
myo-inositol biosynthesis	2	1	1
L-arginine degradation I (arginase pathway)	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
D-myo-inositol (1,4,5)-trisphosphate degradation	3	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
L-valine biosynthesis	4	4	1
aerobic respiration I (cytochrome c)	4	3	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	2	1
ethene biosynthesis II (microbes)	4	1	1
chorismate biosynthesis from 3-dehydroquinate	5	5	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
Fe(II) oxidation	6	2	1
superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism	6	1	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
chorismate biosynthesis I	7	7	1
L-Nδ-acetylornithine biosynthesis	7	5	1
L-isoleucine biosynthesis III	7	4	1
phytate degradation I	14	2	2
L-citrulline biosynthesis	8	7	1
L-isoleucine biosynthesis II	8	5	1
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-citrulline metabolism	12	9	1
chorismate biosynthesis II (archaea)	12	8	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of L-threonine metabolism	18	11	1
superpathway of chorismate metabolism	59	38	1