Experiment set9IT019 for Desulfovibrio vulgaris Miyazaki F

MoYLS4 media with NH4 no edta

Group: nitrogen source
Media: MoLS4_no_ammonnia_noEDTA + Ammonium chloride (20 mM), pH=7.2
Culturing: Miya_ML3_a, SerumBottle, Anaerobic, at 30 (C), shaken=0 rpm
By: Wetmore (Baker) on 22-Apr-19
Media components: 30 mM Sodium sulfate, 60 mM Sodium D,L-Lactate, 30 mM Tris hydrochloride, 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 nitrogen source Ammonium chloride in Desulfovibrio vulgaris Miyazaki F

For nitrogen source Ammonium chloride across organisms

SEED Subsystems

Subsystem	#Specific
Carboxysome	1
Cyanate hydrolysis	1
Folate Biosynthesis	1
Zinc resistance	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of alkaloids derived from histidine and purine
• Glycolysis / Gluconeogenesis
• Purine metabolism
• Pyrimidine metabolism
• Nicotinate and nicotinamide metabolism
• Nitrogen metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• 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
CO2 fixation into oxaloacetate (anaplerotic)	2	1	1
NAD salvage pathway III (to nicotinamide riboside)	3	2	1
cyanate degradation	3	2	1
UTP and CTP dephosphorylation I	7	5	2
purine nucleotides degradation II (aerobic)	11	9	3
inosine 5'-phosphate degradation	4	4	1
guanosine nucleotides degradation III	4	3	1
adenosine nucleotides degradation I	8	5	2
purine nucleotides degradation I (plants)	12	6	3
guanosine nucleotides degradation II	4	2	1
guanosine nucleotides degradation I	4	2	1
adenosine nucleotides degradation II	5	4	1
superpathway of purines degradation in plants	18	7	3
superpathway of guanosine nucleotides degradation (plants)	6	2	1
ureide biosynthesis	7	5	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	3	1
tunicamycin biosynthesis	9	1	1
NAD salvage (plants)	11	4	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	4	1
3-hydroxypropanoate cycle	13	5	1
glyoxylate assimilation	13	4	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	6	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
superpathway of the 3-hydroxypropanoate cycle	18	5	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	5	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1