Experiment set4IT062 for Paraburkholderia graminis OAS925

Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=soil; 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=soil; 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 on 20-May-21

Specific Phenotypes

For 13 genes in this experiment

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

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	5
Formate hydrogenase	2
Calvin-Benson cycle	1
Cobalt-zinc-cadmium resistance	1
Pentose phosphate pathway	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 phosphate pathway
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Lysine degradation
• 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
• Methane metabolism
• Carbon fixation in photosynthetic organisms
• Biotin metabolism
• Carotenoid biosynthesis - General
• Zeatin biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis
• Biosynthesis of ansamycins
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pentose phosphate pathway (partial)	3	3	2
D-arabinitol degradation I	2	2	1
xylitol degradation I	2	2	1
D-xylose degradation I	2	2	1
pentose phosphate pathway (non-oxidative branch) I	5	5	2
pentose phosphate pathway (non-oxidative branch) II	6	5	2
sulfoquinovose degradation V	7	2	2
pentose phosphate pathway	8	8	2
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	6	2
Rubisco shunt	10	10	2
superpathway of glucose and xylose degradation	17	16	3
formaldehyde assimilation III (dihydroxyacetone cycle)	12	11	2
Calvin-Benson-Bassham cycle	13	11	2
peptidoglycan biosynthesis II (staphylococci)	17	12	2
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	2
oxygenic photosynthesis	17	12	2
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	12	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	1
ethene biosynthesis V (engineered)	25	19	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
1-butanol autotrophic biosynthesis (engineered)	27	20	2
Bifidobacterium shunt	15	14	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
superpathway of pentose and pentitol degradation	42	21	1