Experiment set18S343 for Agrobacterium fabrum C58

Plant=Arabidopsis_col0; PlantTreatment=None; Sample=root; GrowthSubstrate=agar; Collection=Direct

Group: in planta
Media: + Plant=Arabidopsis_col0; PlantTreatment=None; Sample=root; GrowthSubstrate=agar; Collection=Direct
Culturing: Agro_ML11b
By: Mitchell Thompson on 6/16/23

Specific Phenotypes

For 13 genes in this experiment

For in planta Plant=Arabidopsis_col0; PlantTreatment=None; Sample=root; GrowthSubstrate=agar; Collection=Direct in Agrobacterium fabrum C58

For in planta Plant=Arabidopsis_col0; PlantTreatment=None; Sample=root; GrowthSubstrate=agar; Collection=Direct across organisms

SEED Subsystems

Subsystem	#Specific
Lipid A modifications	2
Orphan regulatory proteins	2
Peptidoglycan Biosynthesis	1
Propionyl-CoA to Succinyl-CoA Module	1
Serine-glyoxylate cycle	1
Type IV pilus	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Peptidoglycan biosynthesis
• Fructose and mannose metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Benzoate degradation via hydroxylation
• Fluorobenzoate degradation
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Biotin metabolism
• Carotenoid biosynthesis - General
• Zeatin biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
benzoate degradation I (aerobic)	2	1	1
propanoyl CoA degradation I	3	3	1
proline betaine degradation I	3	2	1
conversion of succinate to propanoate	3	1	1
2-oxobutanoate degradation I	4	3	1
pyruvate fermentation to propanoate I	7	4	1
peptidoglycan biosynthesis II (staphylococci)	17	12	2
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	2
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
anaerobic energy metabolism (invertebrates, mitochondrial)	10	8	1
meta cleavage pathway of aromatic compounds	10	4	1
L-glutamate degradation VIII (to propanoate)	11	4	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	11	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	3	1
3-hydroxypropanoate cycle	13	8	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	5	1
toluene degradation IV (aerobic) (via catechol)	13	5	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	3	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
superpathway of L-methionine salvage and degradation	16	8	1
superpathway of anaerobic energy metabolism (invertebrates)	17	13	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
mandelate degradation to acetyl-CoA	18	8	1
superpathway of the 3-hydroxypropanoate cycle	18	8	1
methylaspartate cycle	19	12	1
superpathway of aerobic toluene degradation	30	12	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	15	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	11	1