Experiment set22S223 for Agrobacterium fabrum C58

Plant=Ntabacum; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Cocuture=C58C1OD2.0

Group: in planta
Media: + Plant=Ntabacum; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Cocuture=C58C1OD2.0
Culturing: Agro_ML11b, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 6/16/2023

Specific Phenotypes

For 22 genes in this experiment

For in planta Plant=Ntabacum; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Cocuture=C58C1OD2.0 in Agrobacterium fabrum C58

For in planta Plant=Ntabacum; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Cocuture=C58C1OD2.0 across organisms

SEED Subsystems

Subsystem	#Specific
Agrobacterium opine transport	4
Arginine and Ornithine Degradation	3
ABC transporter oligopeptide (TC 3.A.1.5.1)	2
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
L-Arabinose utilization	1
Lipid A modifications	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:

• Arginine and proline metabolism
• Ascorbate and aldarate metabolism
• Biosynthesis of steroids
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• gamma-Hexachlorocyclohexane degradation
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-arginine degradation VII (arginase 3 pathway)	2	2	2
L-ornithine degradation I (L-proline biosynthesis)	1	1	1
glycerophosphodiester degradation	2	2	1
putrescine biosynthesis III	2	2	1
2-oxoglutarate-derived opine biosynthesis	2	2	1
phosphatidylcholine resynthesis via glycerophosphocholine	2	1	1
L-canavanine degradation I	2	1	1
L-proline biosynthesis II (from arginine)	2	1	1
L-arginine degradation I (arginase pathway)	3	2	1
superpathway of putrescine biosynthesis	4	4	1
L-arginine degradation VI (arginase 2 pathway)	4	3	1
glycerol and glycerophosphodiester degradation	4	3	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
urea cycle	5	4	1
L-Nδ-acetylornithine biosynthesis	7	5	1
L-citrulline biosynthesis	8	7	1
superpathway of polyamine biosynthesis I	8	5	1
superpathway of polyamine biosynthesis II	8	3	1
superpathway of L-citrulline metabolism	12	9	1
anandamide biosynthesis I	12	3	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	4	1
superpathway of arginine and polyamine biosynthesis	17	14	1