Experiment set3IT038 for Herbaspirillum seropedicae SmR1

Plant assay with Setaria viridis; 10 days of inoculation with plant; outgrowth in LB

Group: plant
Media: LB + Root Epiphytic Bacteria, pH=7
Culturing: HerbieS_ML4, flask, at 30 (C), shaken=120 rpm
By: Thalita Tuleski on 19-May-16
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 8 genes in this experiment

For plant Root Epiphytic Bacteria in Herbaspirillum seropedicae SmR1

For plant Root Epiphytic Bacteria across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	1
CO2 uptake, carboxysome	1
Homogentisate pathway of aromatic compound degradation	1
Polyamine Metabolism	1
Polyhydroxybutyrate metabolism	1
Respiratory Complex I	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ascorbate and aldarate metabolism
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Glycerophospholipid metabolism
• 2,4-Dichlorobenzoate degradation
• Butanoate metabolism
• Retinol metabolism
• Alkaloid biosynthesis II

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
putrescine biosynthesis I	2	2	1
L-arginine degradation X (arginine monooxygenase pathway)	3	2	1
superpathway of putrescine biosynthesis	4	4	1
L-arginine degradation IX (arginine:pyruvate transaminase pathway)	4	1	1
L-arginine degradation XII	4	1	1
L-arginine degradation VIII (arginine oxidase pathway)	4	1	1
superpathway of polyamine biosynthesis I	8	6	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	4	1
superpathway of L-arginine and L-ornithine degradation	13	6	1
superpathway of arginine and polyamine biosynthesis	17	15	1