Experiment set2IT024 for Desulfovibrio vulgaris Miyazaki F

Compare to:

6 days starvation

Group: starvation
Media: MoYLS4, pH=7.2
Culturing: Miya_ML3, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Jen on 11/23/2014
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

SEED Subsystems

Subsystem #Specific
Thiamin biosynthesis 2
Bacterial Chemotaxis 1
Glycolate, glyoxylate interconversions 1
Photorespiration (oxidative C2 cycle) 1
Pyridoxin (Vitamin B6) Biosynthesis 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-glutamate biosynthesis IV 1 1 1
L-glutamine degradation II 1 1 1
L-glutamine degradation I 1 1 1
ammonia assimilation cycle III 3 3 2
ammonia assimilation cycle I 2 2 1
glycolate and glyoxylate degradation II 2 2 1
L-glutamate and L-glutamine biosynthesis 7 4 3
thiazole component of thiamine diphosphate biosynthesis I 6 4 2
superpathway of ammonia assimilation (plants) 3 2 1
glycolate and glyoxylate degradation III 3 1 1
thiazole component of thiamine diphosphate biosynthesis II 7 5 2
L-asparagine biosynthesis III (tRNA-dependent) 4 4 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 3 1
glycolate and glyoxylate degradation I 4 2 1
superpathway of thiamine diphosphate biosynthesis I 10 8 2
superpathway of thiamine diphosphate biosynthesis II 11 9 2
pyridoxal 5'-phosphate biosynthesis I 7 5 1
superpathway of glycol metabolism and degradation 7 4 1
L-citrulline biosynthesis 8 5 1
photorespiration III 9 6 1
photorespiration II 10 6 1
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage 12 9 1
superpathway of L-citrulline metabolism 12 7 1