Experiment set10IT008 for Paraburkholderia graminis OAS925

Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=root; GrowthSubstrate=liquid_soil_extract; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=19_days

Group: in planta
Media: + Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=root; GrowthSubstrate=liquid_soil_extract; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=19_days
Culturing: Burkholderia_OAS925_ML2, pot, at 26 (C), (Solid)
By: Marta Torres on 2-Aug-21

Specific Phenotypes

For 10 genes in this experiment

For in planta Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=root; GrowthSubstrate=liquid_soil_extract; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=19_days in Paraburkholderia graminis OAS925

For in planta Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=root; GrowthSubstrate=liquid_soil_extract; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=19_days across organisms

SEED Subsystems

Subsystem	#Specific
Acetoin, butanediol metabolism	1
Biotin biosynthesis	1
Branched-Chain Amino Acid Biosynthesis	1
Calvin-Benson cycle	1
Colanic acid biosynthesis	1
Iron acquisition in Vibrio	1
Pentose phosphate pathway	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Valine, leucine and isoleucine biosynthesis
• Butanoate metabolism
• C5-Branched dibasic acid metabolism
• Carbon fixation in photosynthetic organisms
• Pantothenate and CoA biosynthesis
• Biotin metabolism
• Biosynthesis of ansamycins
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pentose phosphate pathway (partial)	3	3	2
pyruvate fermentation to (R)-acetoin II	2	1	1
pentose phosphate pathway (non-oxidative branch) I	5	5	2
pyruvate fermentation to (R)-acetoin I	3	3	1
pentose phosphate pathway (non-oxidative branch) II	6	5	2
pyruvate fermentation to (S)-acetoin	3	2	1
sulfoquinovose degradation V	7	2	2
pentose phosphate pathway	8	8	2
biotin biosynthesis from 8-amino-7-oxononanoate I	4	4	1
L-valine biosynthesis	4	4	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	6	2
Rubisco shunt	10	10	2
superpathway of (R,R)-butanediol biosynthesis	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	11	2
L-isoleucine biosynthesis IV	6	4	1
superpathway of 2,3-butanediol biosynthesis	6	3	1
Calvin-Benson-Bassham cycle	13	11	2
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
L-isoleucine biosynthesis II	8	5	1
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of glucose and xylose degradation	17	16	2
oxygenic photosynthesis	17	12	2
ethene biosynthesis V (engineered)	25	19	2
superpathway of L-isoleucine biosynthesis I	13	13	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
1-butanol autotrophic biosynthesis (engineered)	27	20	2
Bifidobacterium shunt	15	14	1
biotin biosynthesis I	15	13	1
superpathway of L-threonine metabolism	18	14	1