Experiment set4IT050 for Desulfovibrio vulgaris Miyazaki F

MoYLS4 with Vanillin 10 mM

Group: stress
Media: MoYLS4 + Vanillin (10 mM), 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 5 genes in this experiment

For stress Vanillin in Desulfovibrio vulgaris Miyazaki F

For stress Vanillin across organisms

SEED Subsystems

Subsystem	#Specific
Ammonia assimilation	1
Biogenesis of c-type cytochromes	1
DNA repair, UvrABC system	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Periplasmic disulfide interchange	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate 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 II	1	1	1
L-glutamine degradation I	1	1	1
ammonia assimilation cycle III	3	3	2
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
L-citrulline biosynthesis	8	5	1
superpathway of L-citrulline metabolism	12	7	1