Experiment set18S347 for Agrobacterium fabrum C58

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

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

Specific Phenotypes

For 16 genes in this experiment

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

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

SEED Subsystems

Subsystem	#Specific
Molybdenum cofactor biosynthesis	3
Anaerobic respiratory reductases	1
Isobutyryl-CoA to Propionyl-CoA Module	1
NAD regulation	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine degradation
• beta-Alanine metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Puromycin biosynthesis
• Geraniol degradation
• Lysine degradation
• Benzoate degradation via hydroxylation
• Fluorobenzoate degradation
• Tryptophan metabolism
• Lipopolysaccharide biosynthesis
• alpha-Linolenic acid metabolism
• Butanoate metabolism
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
benzoate degradation I (aerobic)	2	1	1
benzoyl-CoA biosynthesis	3	3	1
proline betaine degradation I	3	2	1
2-methyl-branched fatty acid β-oxidation	14	9	3
adipate degradation	5	5	1
adipate biosynthesis	5	4	1
acrylate degradation I	5	3	1
propanoyl-CoA degradation II	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
fatty acid β-oxidation IV (unsaturated, even number)	5	2	1
tRNA-uridine 2-thiolation (thermophilic bacteria)	5	2	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	1	1
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
β-alanine biosynthesis II	6	3	1
methyl ketone biosynthesis (engineered)	6	3	1
fatty acid β-oxidation I (generic)	7	4	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	1
benzoyl-CoA degradation I (aerobic)	7	3	1
L-valine degradation I	8	5	1
valproate β-oxidation	9	5	1
phenylacetate degradation I (aerobic)	9	3	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
superpathway of coenzyme A biosynthesis II (plants)	10	7	1
meta cleavage pathway of aromatic compounds	10	4	1
3-phenylpropanoate degradation	10	4	1
superpathway of phenylethylamine degradation	11	3	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
oleate β-oxidation	35	27	3
toluene degradation IV (aerobic) (via catechol)	13	5	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	12	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
mandelate degradation to acetyl-CoA	18	8	1
platensimycin biosynthesis	26	6	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