Experiment set4IT035 for Desulfovibrio vulgaris Miyazaki F

MoYLS4 with Rifampicin 0.2 mg/ml

Group: stress
Media: MoYLS4 + Rifampicin (0.2 mg/ml), pH=7.2
Culturing: Miya_ML3_a, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Jen on 1/20/2015
Media components: 1 g/L Yeast Extract, 30 mM Sodium sulfate, 60 mM Sodium D,L-Lactate, 20 mM Ammonium chloride, 30 mM Tris hydrochloride, 0.12 mM EDTA, 1 mM Sodium sulfide nonahydrate, 8 mM Magnesium chloride hexahydrate, 0.6 mM Calcium chloride, 2 mM Potassium phosphate dibasic, 60 uM Iron (II) chloride tetrahydrate, 15 uM Manganese (II) chloride tetrahydrate, 7.8 uM Cobalt chloride hexahydrate, 9 uM Zinc chloride, 1.26 uM Sodium molybdate, 1.92 uM Boric Acid, 2.28 uM Nickel (II) sulfate hexahydrate, 0.06 uM copper (II) chloride dihydrate, 0.21 uM Sodium selenite pentahydrate, 0.144 uM Sodium tungstate dihydrate, Thauer's vitamin mix (0.01 mg/L Pyridoxine HCl, 0.005 mg/L 4-Aminobenzoic acid, 0.005 mg/L Lipoic acid, 0.005 mg/L Nicotinic Acid, 0.005 mg/L Riboflavin, 0.005 mg/L Thiamine HCl, 0.005 mg/L calcium pantothenate, 0.002 mg/L biotin, 0.002 mg/L Folic Acid, 0.0001 mg/L Cyanocobalamin, 0.2 mg/L Choline chloride)

Specific Phenotypes

For 14 genes in this experiment

For stress Rifampicin in Desulfovibrio vulgaris Miyazaki F

For stress Rifampicin across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter oligopeptide (TC 3.A.1.5.1)	1
ATP-dependent RNA helicases, bacterial	1
Ammonia assimilation	1
Biogenesis of c-type cytochromes	1
Dihydroxyacetone kinases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
MLST	1
Periplasmic disulfide interchange	1
Protein chaperones	1
Proteolysis in bacteria, ATP-dependent	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Glutamate metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Glycerolipid metabolism
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation I	1	1	1
L-glutamine degradation II	1	1	1
ammonia assimilation cycle III	3	3	2
NADH to dimethyl sulfoxide electron transfer	2	2	1
hydrogen to dimethyl sulfoxide electron transfer	2	1	1
formate to dimethyl sulfoxide electron transfer	2	1	1
glycerol degradation V	2	1	1
glycerol degradation I	3	2	1
L-glutamate and L-glutamine biosynthesis	7	4	2
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
glycerol and glycerophosphodiester degradation	4	3	1
L-citrulline biosynthesis	8	5	1
superpathway of L-citrulline metabolism	12	7	1