Experiment set4IT015 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 37 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
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	2
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	2
ATP-dependent RNA helicases, bacterial	1
Aromatic amino acid degradation	1
Bacterial Chemotaxis	1
Benzoate transport and degradation cluster	1
Cobalt-zinc-cadmium resistance	1
D-ribose utilization	1
De Novo Pyrimidine Synthesis	1
Formate hydrogenase	1
Heat shock dnaK gene cluster extended	1
Heme and Siroheme Biosynthesis	1
Mannose Metabolism	1
NAD and NADP cofactor biosynthesis global	1
Peptidoglycan Biosynthesis	1
Queuosine-Archaeosine Biosynthesis	1
TCA Cycle	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
• Glyoxylate and dicarboxylate metabolism
• Thiamine metabolism
• Citrate cycle (TCA cycle)
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Lysine degradation
• Tryptophan metabolism
• Glutathione 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
• Methane metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Biotin metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Zeatin biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
xylitol degradation I	2	2	2
hydroxymethylpyrimidine salvage	2	2	2
D-xylose degradation I	2	2	1
superoxide radicals degradation	2	2	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis I	2	2	1
D-arabinitol degradation I	2	2	1
ribitol degradation I	2	1	1
thiamine diphosphate salvage II	5	4	2
L-tryptophan degradation I (via anthranilate)	3	3	1
L-arabinose degradation II	3	2	1
erythritol degradation II	3	1	1
thiamine diphosphate salvage IV (yeast)	7	3	2
reactive oxygen species degradation	4	4	1
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	3	2
L-threitol degradation	4	1	1
cytosolic NADPH production (yeast)	5	4	1
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde	5	3	1
3-hydroxy-4-methyl-anthranilate biosynthesis II	5	3	1
UMP biosynthesis II	6	6	1
UMP biosynthesis I	6	6	1
UMP biosynthesis III	6	5	1
3-hydroxy-4-methyl-anthranilate biosynthesis I	6	2	1
ethene biosynthesis III (microbes)	7	6	1
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	3	1
partial TCA cycle (obligate autotrophs)	8	7	1
nitrogen remobilization from senescing leaves	8	6	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II	8	4	1
3-hydroxyquinaldate biosynthesis	8	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 pyrimidine ribonucleotides de novo biosynthesis	9	9	1
TCA cycle V (2-oxoglutarate synthase)	9	8	1
NAD de novo biosynthesis II (from tryptophan)	9	7	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	1
TCA cycle VI (Helicobacter)	9	6	1
TCA cycle VII (acetate-producers)	9	6	1
TCA cycle I (prokaryotic)	10	8	1
superpathway of thiamine diphosphate biosynthesis I	10	8	1
quinoxaline-2-carboxylate biosynthesis	10	4	1
superpathway of pentose and pentitol degradation	42	21	4
superpathway of thiamine diphosphate biosynthesis II	11	10	1
reductive TCA cycle I	11	6	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	12	1
superpathway of glyoxylate bypass and TCA	12	10	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
mixed acid fermentation	16	12	1
superpathway of glucose and xylose degradation	17	16	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	18	1
methylaspartate cycle	19	11	1
L-tryptophan degradation XI (mammalian, via kynurenine)	23	7	1
ethene biosynthesis V (engineered)	25	19	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	19	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	13	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	44	1