Experiment set10IT029 for Paraburkholderia graminis OAS925

Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=quartz_sand; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=19_days

Group: in planta
Media: + Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=quartz_sand; 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 30 genes in this experiment

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

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

SEED Subsystems

Subsystem	#Specific
Alkanesulfonate assimilation	2
Bacterial Chemotaxis	2
High affinity phosphate transporter and control of PHO regulon	2
Phosphate metabolism	2
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	1
Benzoate transport and degradation cluster	1
Colanic acid biosynthesis	1
Cysteine Biosynthesis	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycogen metabolism	1
Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway	1
Lactose and Galactose Uptake and Utilization	1
Multidrug Resistance Efflux Pumps	1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	1
N-linked Glycosylation in Bacteria	1
Peptidoglycan Biosynthesis	1
Protein chaperones	1
Proteolysis in bacteria, ATP-dependent	1
Rhamnose containing glycans	1
Type IV pilus	1
linker unit-arabinogalactan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Peptidoglycan biosynthesis
• Nucleotide sugars metabolism
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Fructose and mannose metabolism
• Galactose metabolism
• Purine metabolism
• Lysine degradation
• Selenoamino acid metabolism
• Starch and sucrose metabolism
• N-Glycan biosynthesis
• Other glycan degradation
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Biotin metabolism
• Carotenoid biosynthesis - General
• Zeatin biosynthesis
• Sulfur metabolism
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis
• T cell receptor signaling pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-N-acetyl-D-galactosamine biosynthesis I	1	1	1
UDP-α-D-galactose biosynthesis	1	1	1
di-trans,poly-cis-undecaprenyl phosphate biosynthesis	2	2	1
sulfate activation for sulfonation	2	2	1
UDP-α-D-galactofuranose biosynthesis	2	1	1
assimilatory sulfate reduction III	3	3	1
sulfite oxidation III	3	2	1
assimilatory sulfate reduction II	3	2	1
chitin degradation II (Vibrio)	6	2	2
D-galactose detoxification	3	1	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	4	1
assimilatory sulfate reduction I	4	4	1
assimilatory sulfate reduction IV	4	3	1
arsenic detoxification (bacteria)	4	2	1
polyisoprenoid biosynthesis (E. coli)	5	5	1
D-galactose degradation I (Leloir pathway)	5	3	1
dissimilatory sulfate reduction I (to hydrogen sufide))	5	2	1
selenate reduction	5	2	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
arsenate detoxification I	6	3	1
superpathway of sulfur metabolism (Desulfocapsa sulfoexigens)	6	3	1
superpathway of thiosulfate metabolism (Desulfovibrio sulfodismutans)	6	2	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
chitin degradation III (Serratia)	7	2	1
stachyose degradation	7	2	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	2
peptidoglycan biosynthesis II (staphylococci)	17	12	2
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
UDP-sugars interconversion	9	3	1
teichuronic acid biosynthesis (B. subtilis 168)	9	2	1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	7	1
starch biosynthesis	10	6	1
peptidoglycan recycling II	10	5	1
colanic acid building blocks biosynthesis	11	11	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	12	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	11	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	1
superpathway of sulfide oxidation (phototrophic sulfur bacteria)	12	4	1
peptidoglycan recycling I	14	10	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	18	1	1
superpathway of seleno-compound metabolism	19	5	1
phosphinothricin tripeptide biosynthesis	25	6	1
phosalacine biosynthesis	25	6	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1