Experiment set11IT007 for Paraburkholderia graminis OAS925

Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_liquid; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=21_days

Group: in planta
Media: + Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_liquid; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=21_days
Culturing: Burkholderia_OAS925_ML2, pot, at 26 (C), (Solid)
By: Marta Torres on 26-Aug-21

Specific Phenotypes

For 13 genes in this experiment

For in planta Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_liquid; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=21_days in Paraburkholderia graminis OAS925

For in planta Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_liquid; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=21_days across organisms

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	4
Aromatic amino acid degradation	1
Bacterial Chemotaxis	1
Fructose utilization	1
NAD and NADP cofactor biosynthesis global	1
Peptidoglycan Biosynthesis	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Type IV pilus	1
Xylose utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Peptidoglycan biosynthesis
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Lysine degradation
• Tryptophan metabolism
• 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
• Glyoxylate and dicarboxylate 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
xylitol degradation I	2	2	1
D-xylose degradation I	2	2	1
D-arabinitol degradation I	2	2	1
L-tryptophan degradation I (via anthranilate)	3	3	1
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde	5	3	1
3-hydroxy-4-methyl-anthranilate biosynthesis II	5	3	1
3-hydroxy-4-methyl-anthranilate biosynthesis I	6	2	1
3-hydroxyquinaldate biosynthesis	8	2	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
NAD de novo biosynthesis II (from tryptophan)	9	7	1
quinoxaline-2-carboxylate biosynthesis	10	4	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	12	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	1
L-tryptophan degradation IX	12	4	1
L-tryptophan degradation XII (Geobacillus)	12	4	1
superpathway of NAD biosynthesis in eukaryotes	14	8	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
L-tryptophan degradation III (eukaryotic)	15	6	1
superpathway of glucose and xylose degradation	17	16	1
L-tryptophan degradation XI (mammalian, via kynurenine)	23	7	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	19	1
superpathway of pentose and pentitol degradation	42	21	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	13	1