Experiment set13IT031 for Desulfovibrio vulgaris Hildenborough JW710

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MoLS4 with Thymine nitrogen source

Group: nitrogen source
Media: MoLS4_no_ammonium + Thymine (20 mM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 6/14/2017
Media components: 30 mM Sodium sulfate, 60 mM Sodium D,L-Lactate, 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, Desulfovibrio trace elements (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 nitrogen source Thymine in Desulfovibrio vulgaris Hildenborough JW710

For nitrogen source Thymine across organisms

SEED Subsystems

Subsystem #Specific
Ammonia assimilation 2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 2
Glycerol and Glycerol-3-phosphate Uptake and Utilization 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

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-glutamate biosynthesis IV 1 1 1
L-glutamine degradation II 1 1 1
ammonia assimilation cycle III 3 3 2
glycerol-3-phosphate shuttle 2 2 1
ammonia assimilation cycle I 2 2 1
L-glutamate and L-glutamine biosynthesis 7 4 3
superpathway of ammonia assimilation (plants) 3 2 1
CDP-diacylglycerol biosynthesis I 4 4 1
CDP-diacylglycerol biosynthesis II 4 4 1
L-asparagine biosynthesis III (tRNA-dependent) 4 3 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 3 1
phosphatidate biosynthesis (yeast) 5 3 1
CDP-diacylglycerol biosynthesis III 5 3 1
glucosylglycerol biosynthesis 5 2 1
phosphatidylglycerol biosynthesis I 6 6 1
phosphatidylglycerol biosynthesis II 6 6 1
L-citrulline biosynthesis 8 5 1
1,3-propanediol biosynthesis (engineered) 9 4 1
superpathway of phospholipid biosynthesis III (E. coli) 12 10 1
superpathway of L-citrulline metabolism 12 7 1
superpathway of cardiolipin biosynthesis (bacteria) 13 9 1
superpathway of phospholipid biosynthesis II (plants) 28 10 1