Experiment set8IT031 for Burkholderia phytofirmans PsJN

Deoxyribonucleic acid from herring sperm 10 mg/mL carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Deoxyribonucleic acid from herring sperm (10 mg/mL), pH=7
Culturing: BFirm_ML3a, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 5/2/18
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)
Growth plate: Bfirm_deoxyribosePlus_plate C5

Specific Phenotypes

For 20 genes in this experiment

For carbon source Deoxyribonucleic acid from herring sperm in Burkholderia phytofirmans PsJN

For carbon source Deoxyribonucleic acid from herring sperm across organisms

SEED Subsystems

Subsystem	#Specific
Purine conversions	6
Purine Utilization	2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
Ammonia assimilation	1
Folate Biosynthesis	1
Lysine degradation	1
Proteolysis in bacteria, ATP-dependent	1
TCA Cycle	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Pyruvate metabolism
• Drug metabolism - other enzymes
• 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
adenosine nucleotides degradation III	1	1	1
adenine salvage	3	3	2
adenosine nucleotides degradation II	5	4	3
guanosine nucleotides degradation II	4	4	2
guanine and guanosine salvage II	2	2	1
adenine and adenosine salvage II	2	2	1
guanosine nucleotides degradation III	4	3	2
adenine and adenosine salvage III	4	2	2
adenine and adenosine salvage I	2	1	1
guanine and guanosine salvage I	2	1	1
xanthine and xanthosine salvage	2	1	1
purine nucleotides degradation II (aerobic)	11	8	4
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
glycine cleavage	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
glycine biosynthesis II	3	3	1
superpathway of guanosine nucleotides degradation (plants)	6	5	2
adenine and adenosine salvage V	3	1	1
superpathway of guanine and guanosine salvage	3	1	1
purine deoxyribonucleosides degradation II	3	1	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	1	1
adenosine nucleotides degradation I	8	7	2
purine nucleotides degradation I (plants)	12	10	3
guanosine nucleotides degradation I	4	3	1
inosine 5'-phosphate degradation	4	3	1
purine deoxyribonucleosides degradation I	4	1	1
purine nucleobases degradation II (anaerobic)	24	16	5
NAD salvage pathway II (PNC IV cycle)	5	5	1
superpathway of purines degradation in plants	18	14	3
purine ribonucleosides degradation	6	1	1
superpathway of purine nucleotide salvage	14	12	2
ureide biosynthesis	7	5	1
drosopterin and aurodrosopterin biosynthesis	7	5	1
glyphosate degradation III	7	3	1
superpathway of purine deoxyribonucleosides degradation	7	3	1
caffeine degradation III (bacteria, via demethylation)	7	1	1
(aminomethyl)phosphonate degradation	8	5	1
theophylline degradation	9	1	1
caffeine degradation IV (bacteria, via demethylation and oxidation)	10	1	1
purine nucleobases degradation I (anaerobic)	15	6	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	17	1