Experiment set9IT023 for Desulfovibrio vulgaris Hildenborough JW710

Pyruvate-Sulfite (60-20mM) with Tungstate 2mM

Group: stress
Media: Dv_base_medium + Sodium pyruvate (60 mM) + sodium sulfite (20 mM) + Sodium tungstate dihydrate (2 mM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 4/17/2017
Media components: 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, 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 42 genes in this experiment

For stress Sodium pyruvate in Desulfovibrio vulgaris Hildenborough JW710

For stress Sodium pyruvate across organisms

SEED Subsystems

Subsystem	#Specific
Molybdenum cofactor biosynthesis	3
DNA repair, bacterial MutL-MutS system	2
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	1
CMP-N-acetylneuraminate Biosynthesis	1
Glycogen metabolism	1
Heat shock dnaK gene cluster extended	1
Hydantoin metabolism	1
Potassium homeostasis	1
Protein chaperones	1
Purine Utilization	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Sialic Acid Metabolism	1
Transport of Molybdenum	1
Zinc resistance	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Fructose and mannose metabolism
• Purine metabolism
• Arginine and proline metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Benzoate degradation via CoA ligation
• Carbon fixation in photosynthetic organisms
• 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 histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
CMP-N-acetylneuraminate biosynthesis II (bacteria)	3	2	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	3	2
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
creatinine degradation II	5	1	1
CMP-N-acetylneuraminate biosynthesis I (eukaryotes)	5	1	1
pentose phosphate pathway (non-oxidative branch) II	6	6	1
methylgallate degradation	6	2	1
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	6	2
protocatechuate degradation I (meta-cleavage pathway)	8	3	1
glycolysis IV	10	8	1
starch biosynthesis	10	5	1
superpathway of vanillin and vanillate degradation	10	3	1
syringate degradation	12	3	1
gluconeogenesis I	13	10	1
superpathway of CMP-sialic acids biosynthesis	15	2	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	14	1