Experiment set6IT048 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
Bacterial hemoglobins	1
Branched-Chain Amino Acid Biosynthesis	1
DNA-replication	1
DNA repair, bacterial RecFOR pathway	1
Di-Inositol-Phosphate biosynthesis	1
Proline, 4-hydroxyproline uptake and utilization	1
Respiratory dehydrogenases 1	1
Two cell division clusters relating to chromosome partitioning	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
• Fatty acid biosynthesis
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Glutamate metabolism
• Valine, leucine and isoleucine biosynthesis
• Streptomycin biosynthesis
• Lipopolysaccharide biosynthesis
• Inositol phosphate metabolism
• Pantothenate and CoA biosynthesis
• Folate biosynthesis
• Biosynthesis of alkaloids derived from histidine and purine
• Phosphatidylinositol signaling system

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-proline degradation I	3	3	2
proline to cytochrome bo oxidase electron transfer	2	2	1
two-component alkanesulfonate monooxygenase	2	2	1
sulfoquinovose degradation IV	2	2	1
myo-inositol biosynthesis	2	1	1
urea degradation I	3	3	1
L-arginine degradation I (arginase pathway)	3	2	1
D-myo-inositol (1,4,5)-trisphosphate degradation	3	1	1
L-valine biosynthesis	4	4	1
biotin-carboxyl carrier protein assembly	4	4	1
ethene biosynthesis II (microbes)	4	1	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
superpathway of allantoin degradation in yeast	6	3	1
L-isoleucine biosynthesis IV	6	3	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism	6	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-Nδ-acetylornithine biosynthesis	7	5	1
L-isoleucine biosynthesis III	7	4	1
phytate degradation I	14	2	2
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-citrulline metabolism	12	9	1
superpathway of L-isoleucine biosynthesis I	13	13	1
3-hydroxypropanoate cycle	13	8	1
glyoxylate assimilation	13	5	1
succinoglycan biosynthesis	14	10	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
superpathway of L-threonine metabolism	18	11	1
superpathway of the 3-hydroxypropanoate cycle	18	8	1