Experiment set8IT028 for Paraburkholderia graminis OAS925

Plant=Brachypodium_distachyon; PreTreatment=None; PlantTreatment=low_phosphate; Sample=rhizosphere; GrowthSubstrate=Agar_0.5%; Collection=R2A_with_kan10; Time=21days

Group: in planta
Media: MS_Basal_Salts_Robin_LowPhosphate_0.5x + Plant=Brachypodium_distachyon; PreTreatment=None; PlantTreatment=low_phosphate; Sample=rhizosphere; GrowthSubstrate=Agar_0.5%; Collection=R2A_with_kan10; Time=21days
Culturing: Burkholderia_OAS925_ML2, pot
By: Robin on 7/2/21
Media components: 825 mg/L Ammonium Nitrate, 3.1 mg/L Boric Acid, 166.1 mg/L Calcium chloride, 0.0125 mg/L Cobalt chloride hexahydrate, 0.0125 mg/L Copper (II) sulfate pentahydrate, 18.63 mg/L EDTA (disodium salt), 13.9 mg/L Iron (II) sulfate heptahydrate, 90.35 mg/L Magnesium sulfate, 8.45 mg/L Manganese sulfate, 0.415 mg/L Potassium iodide, 950 mg/L Potassium nitrate, 30 uM Potassium phosphate monobasic, 4.3 mg/L Zinc sulfate heptahydrate

Specific Phenotypes

For 40 genes in this experiment

For in planta Plant=Brachypodium_distachyon; PreTreatment=None; PlantTreatment=low_phosphate; Sample=rhizosphere; GrowthSubstrate=Agar_0.5%; Collection=R2A_with_kan10; Time=21days in Paraburkholderia graminis OAS925

For in planta Plant=Brachypodium_distachyon; PreTreatment=None; PlantTreatment=low_phosphate; Sample=rhizosphere; GrowthSubstrate=Agar_0.5%; Collection=R2A_with_kan10; Time=21days across organisms

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	6
Bacterial Chemotaxis	2
DNA repair, bacterial RecFOR pathway	2
Bacterial hemoglobins	1
DNA-replication	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
High affinity phosphate transporter and control of PHO regulon	1
Oxidative stress	1
Oxygen and light sensor PpaA-PpsR	1
Phosphate metabolism	1
Photorespiration (oxidative C2 cycle)	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Ribosome biogenesis bacterial	1
Threonine and Homoserine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• Alanine and aspartate metabolism
• Carbon fixation in photosynthetic organisms
• Thiamine metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Pyrimidine metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine biosynthesis
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
hydroxymethylpyrimidine salvage	2	2	2
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-alanine degradation III	1	1	1
L-alanine biosynthesis II	1	1	1
superpathway of L-alanine biosynthesis	4	4	2
malate/L-aspartate shuttle pathway	2	2	1
glycolate and glyoxylate degradation II	2	2	1
L-alanine biosynthesis I	2	2	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis I	2	2	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
pseudouridine degradation	2	1	1
atromentin biosynthesis	2	1	1
L-alanine degradation V (oxidative Stickland reaction)	2	1	1
L-tyrosine degradation II	2	1	1
L-glutamate degradation II	2	1	1
thiamine diphosphate salvage II	5	4	2
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	4
L-phenylalanine biosynthesis I	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-asparagine degradation III (mammalian)	3	2	1
pyruvate fermentation to acetate and alanine	3	2	1
sulfolactate degradation III	3	2	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
L-phenylalanine degradation II (anaerobic)	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
(R)-cysteate degradation	3	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	7	2
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	4
thiamine diphosphate salvage IV (yeast)	7	3	2
arsenic detoxification (bacteria)	4	2	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	2	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
chitin deacetylation	4	2	1
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	3	2
L-tryptophan degradation VIII (to tryptophol)	4	1	1
L-tyrosine degradation I	5	5	1
trans-4-hydroxy-L-proline degradation I	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
glyoxylate cycle	6	6	1
superpathway of L-threonine biosynthesis	6	6	1
TCA cycle VIII (Chlamydia)	6	5	1
superpathway of sulfolactate degradation	6	3	1
arsenate detoxification I	6	3	1
L-alanine degradation VI (reductive Stickland reaction)	6	2	1
coenzyme M biosynthesis II	6	1	1
superpathway of glycol metabolism and degradation	7	5	1
D-xylose degradation IV	7	4	1
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	3	1
L-arabinose degradation IV	8	6	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II	8	4	1
Salmonella enterica serotype O:8 O antigen biosynthesis	8	2	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	2
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	6	1
superpathway of L-alanine fermentation (Stickland reaction)	9	4	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of thiamine diphosphate biosynthesis I	10	8	1
rosmarinic acid biosynthesis I	10	2	1
superpathway of thiamine diphosphate biosynthesis II	11	10	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	11	1
superpathway of glyoxylate bypass and TCA	12	10	1
indole-3-acetate biosynthesis II	12	4	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	2	1
superpathway of rosmarinic acid biosynthesis	14	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	15	1
aspartate superpathway	25	22	1
phosalacine biosynthesis	25	6	1
phosphinothricin tripeptide biosynthesis	25	6	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	5	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	23	2
superpathway of chorismate metabolism	59	42	2
superpathway of pentose and pentitol degradation	42	21	1