Experiment set5IT080 for Dinoroseobacter shibae DFL-12

marine broth with Thallium(I) acetate 0.004 mg/ml

Group: stress
Media: marine_broth_2216 + Thallium(I) acetate (0.004 mg/ml)
Culturing: Dino_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Adam on 5/14/2014
Media components: 5 g/L Bacto Peptone, 1 g/L Yeast Extract, 0.1 g/L Ferric citrate, 19.45 g/L Sodium Chloride, 5.9 g/L Magnesium chloride hexahydrate, 3.24 g/L Magnesium sulfate, 1.8 g/L Calcium chloride, 0.55 g/L Potassium Chloride, 0.16 g/L Sodium bicarbonate, 0.08 g/L Potassium bromide, 34 mg/L Strontium chloride, 22 mg/L Boric Acid, 4 mg/L Sodium metasilicate, 2.4 mg/L sodium fluoride, 8 mg/L Disodium phosphate
Growth plate: 917 B1,B2

Specific Phenotypes

For 21 genes in this experiment

For stress Thallium(I) acetate in Dinoroseobacter shibae DFL-12

For stress Thallium(I) acetate across organisms

SEED Subsystems

Subsystem	#Specific
Transport of Manganese	3
Mannitol Utilization	2
Arsenic resistance	1
DNA-replication	1
Fructose utilization	1
Glutathione: Redox cycle	1
Isoprenoid Biosynthesis	1
Potassium homeostasis	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
RNA processing and degradation, bacterial	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Ribonucleotide reduction	1
Ribosome biogenesis bacterial	1
Sucrose utilization	1
Sucrose utilization Shewanella	1
Thiamin biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Pyrimidine metabolism
• Glutathione metabolism
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Taurine and hypotaurine metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Ether lipid metabolism
• Nicotinate and nicotinamide metabolism
• Terpenoid biosynthesis
• Drug metabolism - other enzymes
• Biosynthesis of terpenoids and steroids
• 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
taurine degradation I	1	1	1
guanosine deoxyribonucleotides de novo biosynthesis I	2	2	1
adenosine deoxyribonucleotides de novo biosynthesis I	2	2	1
guanosine deoxyribonucleotides de novo biosynthesis II	4	3	2
adenosine deoxyribonucleotides de novo biosynthesis II	4	3	2
D-sorbitol degradation I	3	3	1
hypotaurine degradation	3	3	1
glutathione-peroxide redox reactions	3	2	1
sucrose degradation I (sucrose phosphotransferase)	3	1	1
superpathway of adenosine nucleotides de novo biosynthesis II	7	6	2
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	11	4
sucrose degradation IV (sucrose phosphorylase)	4	4	1
sucrose degradation III (sucrose invertase)	4	4	1
superpathway of guanosine nucleotides de novo biosynthesis II	8	7	2
sucrose degradation VII (sucrose 3-dehydrogenase)	4	1	1
pyrimidine deoxyribonucleotides de novo biosynthesis III	9	9	2
pyrimidine deoxyribonucleotides de novo biosynthesis I	9	8	2
tRNA processing	10	10	2
superpathway of adenosine nucleotides de novo biosynthesis I	5	5	1
sucrose degradation II (sucrose synthase)	5	4	1
mannitol cycle	5	3	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
superpathway of taurine degradation	6	3	1
thiazole component of thiamine diphosphate biosynthesis I	6	3	1
superpathway of purine nucleotides de novo biosynthesis II	26	23	4
pyridoxal 5'-phosphate biosynthesis I	7	6	1
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	5	1
thiazole component of thiamine diphosphate biosynthesis II	7	5	1
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	5	1
methylerythritol phosphate pathway II	9	9	1
methylerythritol phosphate pathway I	9	9	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	16	2
isoprene biosynthesis I	10	9	1
superpathway of thiamine diphosphate biosynthesis I	10	6	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	2
superpathway of thiamine diphosphate biosynthesis II	11	8	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	42	4
superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP)	12	12	1
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	7	1
taxadiene biosynthesis (engineered)	13	12	1
superpathway of purine nucleotide salvage	14	13	1
heterolactic fermentation	18	12	1
superpathway of anaerobic sucrose degradation	19	14	1
superpathway of ergosterol biosynthesis II	26	11	1