Experiment set22S220 for Agrobacterium fabrum C58

Plant=Ntabacum; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Cocuture=C58C1OD0.075

Group: in planta
Media: + Plant=Ntabacum; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Cocuture=C58C1OD0.075
Culturing: Agro_ML11b, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 6/16/2023

Specific Phenotypes

For 12 genes in this experiment

For in planta Plant=Ntabacum; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Cocuture=C58C1OD0.075 in Agrobacterium fabrum C58

For in planta Plant=Ntabacum; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Cocuture=C58C1OD0.075 across organisms

SEED Subsystems

Subsystem	#Specific
Di-Inositol-Phosphate biosynthesis	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Heat shock dnaK gene cluster extended	1
L-Arabinose utilization	1
Lipid A modifications	1
Methionine Biosynthesis	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Orphan regulatory proteins	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Methionine metabolism
• Cysteine metabolism
• Biosynthesis of plant hormones
• Ascorbate and aldarate metabolism
• Biosynthesis of steroids
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• gamma-Hexachlorocyclohexane degradation
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Selenoamino acid metabolism
• Streptomycin biosynthesis
• Lipopolysaccharide biosynthesis
• Inositol phosphate metabolism
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Folate biosynthesis
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Sulfur metabolism
• Phenylpropanoid biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Phosphatidylinositol signaling system

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-homocysteine biosynthesis	2	2	1
glycerophosphodiester degradation	2	2	1
myo-inositol biosynthesis	2	1	1
phosphatidylcholine resynthesis via glycerophosphocholine	2	1	1
superpathway of L-cysteine biosynthesis (fungi)	6	3	2
D-myo-inositol (1,4,5)-trisphosphate degradation	3	1	1
L-methionine biosynthesis III	4	4	1
glycerol and glycerophosphodiester degradation	4	3	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
homocysteine and cysteine interconversion	4	1	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 II	5	1	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III	5	1	1
L-methionine biosynthesis II	6	5	1
superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism	6	1	1
phytate degradation I	14	2	2
superpathway of L-homoserine and L-methionine biosynthesis	8	7	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	8	1
superpathway of S-adenosyl-L-methionine biosynthesis	9	8	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
anandamide biosynthesis I	12	3	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	17	1
aspartate superpathway	25	24	1