Experiment set8IT022 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 A5

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	5
Purine Utilization	3
Allantoin Utilization	1
Ammonia assimilation	1
Folate Biosynthesis	1
Luciferases	1
Lysine degradation	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Redox-dependent regulation of nucleus processes	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
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Cyanoamino acid metabolism
• Nucleotide sugars metabolism
• Benzoate degradation via CoA ligation
• Styrene degradation
• Nicotinate and nicotinamide metabolism
• Drug metabolism - other enzymes
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• 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
acrylonitrile degradation I	2	2	1
adenine and adenosine salvage II	2	2	1
indole-3-acetate biosynthesis IV (bacteria)	2	2	1
guanine and guanosine salvage II	2	2	1
guanosine nucleotides degradation III	4	3	2
adenine and adenosine salvage III	4	2	2
xanthine and xanthosine salvage	2	1	1
adenine and adenosine salvage I	2	1	1
allantoin degradation to ureidoglycolate I (urea producing)	2	1	1
guanine and guanosine salvage I	2	1	1
indole-3-acetate biosynthesis III (bacteria)	2	1	1
purine nucleotides degradation II (aerobic)	11	8	4
superpathway of acrylonitrile degradation	3	3	1
superpathway of guanosine nucleotides degradation (plants)	6	5	2
allantoin degradation to glyoxylate I	3	2	1
L-arginine degradation X (arginine monooxygenase pathway)	3	2	1
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis	3	1	1
purine deoxyribonucleosides degradation II	3	1	1
adenine and adenosine salvage V	3	1	1
superpathway of guanine and guanosine salvage	3	1	1
adenosine nucleotides degradation I	8	7	2
purine nucleotides degradation I (plants)	12	10	3
inosine 5'-phosphate degradation	4	3	1
guanosine nucleotides degradation I	4	3	1
purine deoxyribonucleosides degradation I	4	1	1
superpathway of purines degradation in plants	18	14	4
purine nucleobases degradation II (anaerobic)	24	16	5
NAD salvage pathway II (PNC IV cycle)	5	5	1
NAD salvage pathway V (PNC V cycle)	5	3	1
superpathway of allantoin degradation in yeast	6	5	1
purine ribonucleosides degradation	6	1	1
superpathway of purine nucleotide salvage	14	12	2
NAD salvage pathway I (PNC VI cycle)	7	5	1
ureide biosynthesis	7	5	1
drosopterin and aurodrosopterin biosynthesis	7	5	1
superpathway of purine deoxyribonucleosides degradation	7	3	1
glyphosate degradation III	7	3	1
caffeine degradation III (bacteria, via demethylation)	7	1	1
(aminomethyl)phosphonate degradation	8	5	1
superpathway of allantoin degradation in plants	8	4	1
superpathway of CDP-glucose-derived O-antigen building blocks biosynthesis	8	1	1
theophylline degradation	9	1	1
caffeine degradation IV (bacteria, via demethylation and oxidation)	10	1	1
NAD salvage (plants)	11	5	1
indole-3-acetate biosynthesis II	12	6	1
superpathway of NAD biosynthesis in eukaryotes	14	9	1
purine nucleobases degradation I (anaerobic)	15	6	1