Experiment set6IT045 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 12 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
Two cell division clusters relating to chromosome partitioning	2
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
Methionine Biosynthesis	1
Proline, 4-hydroxyproline uptake and utilization	1
Respiratory dehydrogenases 1	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
• Biosynthesis of plant hormones
• Methionine metabolism
• Cysteine metabolism
• Biosynthesis of phenylpropanoids
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Biosynthesis of steroids
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Glutamate metabolism
• Valine, leucine and isoleucine biosynthesis
• gamma-Hexachlorocyclohexane degradation
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Benzoxazinone biosynthesis
• Selenoamino acid metabolism
• Sphingolipid metabolism
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Pantothenate and CoA biosynthesis
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Sulfur metabolism
• Phenylpropanoid biosynthesis
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
mannosylfructose biosynthesis	2	2	2
L-proline degradation I	3	3	2
L-homocysteine biosynthesis	2	2	1
proline to cytochrome bo oxidase electron transfer	2	2	1
urea degradation I	3	3	1
L-arginine degradation I (arginase pathway)	3	2	1
superpathway of L-cysteine biosynthesis (fungi)	6	3	2
biotin-carboxyl carrier protein assembly	4	4	1
L-valine biosynthesis	4	4	1
L-methionine biosynthesis III	4	4	1
homocysteine and cysteine interconversion	4	1	1
ethene biosynthesis II (microbes)	4	1	1
chorismate biosynthesis from 3-dehydroquinate	5	5	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
L-methionine biosynthesis I	5	4	1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	7	2
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III	5	1	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II	5	1	1
L-methionine biosynthesis II	6	5	1
superpathway of allantoin degradation in yeast	6	3	1
L-isoleucine biosynthesis IV	6	3	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
superpathway of L-homoserine and L-methionine biosynthesis	8	7	1
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-methionine biosynthesis (transsulfuration)	9	8	1
superpathway of S-adenosyl-L-methionine biosynthesis	9	8	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	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
3-hydroxypropanoate cycle	13	8	1
glyoxylate assimilation	13	5	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	17	1
superpathway of L-threonine metabolism	18	11	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
superpathway of the 3-hydroxypropanoate cycle	18	8	1
aspartate superpathway	25	24	1
superpathway of chorismate metabolism	59	38	1