Experiment set10IT015 for Paraburkholderia graminis OAS925

Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=19_days

Group: in planta
Media: + Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; 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=0.5X_MS_agar; 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=0.5X_MS_agar; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=19_days across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	1
ATP-dependent RNA helicases, bacterial	1
Acetyl-CoA fermentation to Butyrate	1
Alkanesulfonate assimilation	1
Aromatic amino acid degradation	1
Bacterial Chemotaxis	1
Benzoate transport and degradation cluster	1
Cobalt-zinc-cadmium resistance	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
HMG CoA Synthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Methanogenesis	1
Methylcitrate cycle	1
NAD and NADP cofactor biosynthesis global	1
Peptidoglycan Biosynthesis	1
Propionate-CoA to Succinate Module	1
Serine-glyoxylate cycle	1
Type IV pilus	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Peptidoglycan biosynthesis
• Carotenoid biosynthesis - General
• Fructose and mannose metabolism
• Synthesis and degradation of ketone bodies
• Puromycin biosynthesis
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Tryptophan metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Nucleotide sugars metabolism
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• alpha-Linolenic acid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Glyoxylate and dicarboxylate metabolism
• Trinitrotoluene degradation
• Propanoate metabolism
• Butanoate metabolism
• Biotin metabolism
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Zeatin biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-tryptophan degradation I (via anthranilate)	3	3	1
ketolysis	3	3	1
D-threitol degradation	3	1	1
2-methylcitrate cycle I	5	5	1
ketogenesis	5	4	1
3-hydroxy-4-methyl-anthranilate biosynthesis II	5	3	1
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde	5	3	1
L-leucine degradation I	6	5	1
2-methylcitrate cycle II	6	5	1
methyl-coenzyme M oxidation to CO2 II	6	4	1
methanogenesis from H2 and CO2	6	3	1
reductive acetyl coenzyme A pathway II (autotrophic methanogens)	6	3	1
methyl-coenzyme M oxidation to CO2 I	6	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
phenylacetate degradation I (aerobic)	9	7	1
NAD de novo biosynthesis II (from tryptophan)	9	7	1
methoxylated aromatic compound degradation II	9	5	1
nicotinate degradation III	9	3	1
quinoxaline-2-carboxylate biosynthesis	10	4	1
superpathway of phenylethylamine degradation	11	7	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	12	1
L-tryptophan degradation XII (Geobacillus)	12	4	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	1
L-tryptophan degradation IX	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
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	11	1
superpathway of nicotinate degradation	18	4	1
superpathway of methanogenesis	21	5	1
L-tryptophan degradation XI (mammalian, via kynurenine)	23	7	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	19	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	13	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	23	1