Experiment set14IT015 for Paraburkholderia graminis OAS925

Indole-3-pyruvic acid 5 mM in soil extract

Group: soil extract
Media: Soil Extract + Indole-3-pyruvic acid (5 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Burkholderia_OAS925_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Albina on 15-Mar-22

Specific Phenotypes

For 46 genes in this experiment

For soil extract Indole-3-pyruvic acid in Paraburkholderia graminis OAS925

For soil extract Indole-3-pyruvic acid across organisms

SEED Subsystems

Subsystem	#Specific
DNA-replication	3
Formate hydrogenase	3
ATP-dependent RNA helicases, bacterial	1
Ammonia assimilation	1
Branched-Chain Amino Acid Biosynthesis	1
Cobalt-zinc-cadmium resistance	1
F0F1-type ATP synthase	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methanogenesis	1
Methionine Biosynthesis	1
Methionine Degradation	1
Multidrug Resistance Efflux Pumps	1
Naphtalene and antracene degradation	1
Oxidative stress	1
Phosphonate metabolism	1
Photorespiration (oxidative C2 cycle)	1
Polyhydroxybutyrate metabolism	1
Protein chaperones	1
TCA Cycle	1
Transport of Manganese	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Aminophosphonate metabolism
• Lysine degradation
• Tryptophan metabolism
• Methane metabolism
• Citrate cycle (TCA cycle)
• Synthesis and degradation of ketone bodies
• Methionine metabolism
• Valine, leucine and isoleucine degradation
• Lysine biosynthesis
• Arginine and proline metabolism
• Nucleotide sugars metabolism
• Glycerophospholipid metabolism
• Glyoxylate and dicarboxylate metabolism
• Butanoate metabolism
• Folate biosynthesis
• Caprolactam degradation
• 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
2-aminoethylphosphonate biosynthesis	3	3	3
2-aminoethylphosphonate degradation II	2	2	1
superoxide radicals degradation	2	2	1
methylphosphonate biosynthesis	4	2	2
methanol oxidation to formaldehyde IV	2	1	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
ethanol degradation IV	3	3	1
ketolysis	3	3	1
cardiolipin biosynthesis II	3	3	1
cardiolipin biosynthesis I	3	2	1
2-aminoethylphosphonate degradation I	3	2	1
cardiolipin biosynthesis III	3	2	1
fosfomycin biosynthesis	7	2	2
reactive oxygen species degradation	4	4	1
ketogenesis	5	4	1
phosphatidylglycerol biosynthesis II	6	6	1
phosphatidylglycerol biosynthesis I	6	6	1
L-leucine degradation I	6	5	1
β-alanine biosynthesis 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
rhizocticin A and B biosynthesis	12	2	2
dehydrophos biosynthesis	13	2	2
valproate β-oxidation	9	6	1
methoxylated aromatic compound degradation II	9	5	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
FR-900098 and FR-33289 antibiotics biosynthesis	10	1	1
superpathway of phospholipid biosynthesis III (E. coli)	12	10	1
phosphinothricin tripeptide biosynthesis	25	6	2
phosalacine biosynthesis	25	6	2
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	11	1
superpathway of methanogenesis	21	5	1
superpathway of phospholipid biosynthesis II (plants)	28	10	1
oleate β-oxidation	35	29	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	23	1