Experiment set6IT052 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 14 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
Two cell division clusters relating to chromosome partitioning	2
Branched-Chain Amino Acid Biosynthesis	1
D-Galacturonate and D-Glucuronate Utilization	1
D-galactarate, D-glucarate and D-glycerate catabolism	1
DNA repair, bacterial RecFOR pathway	1
Homogentisate pathway of aromatic compound degradation	1
Proline, 4-hydroxyproline uptake and utilization	1
Respiratory dehydrogenases 1	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	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
• Pentose and glucuronate interconversions
• Ascorbate and aldarate metabolism
• Glutamate metabolism
• Valine, leucine and isoleucine biosynthesis
• Pantothenate and CoA biosynthesis
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-proline degradation I	3	3	2
mannosylfructose biosynthesis	2	2	1
proline to cytochrome bo oxidase electron transfer	2	2	1
ribitol degradation I	2	2	1
D-galactarate degradation II	3	3	1
D-glucarate degradation II	3	3	1
L-arginine degradation I (arginase pathway)	3	2	1
L-valine biosynthesis	4	4	1
ethene biosynthesis II (microbes)	4	1	1
D-galacturonate degradation II	5	5	1
D-glucuronate degradation II	5	5	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
L-isoleucine biosynthesis IV	6	3	1
(5R)-carbapenem carboxylate biosynthesis	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
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
superpathway of L-threonine metabolism	18	11	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	22	1
superpathway of pentose and pentitol degradation	42	16	1