Experiment set9IT022 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 64 genes in this experiment

For stress Sodium pyruvate in Desulfovibrio vulgaris Hildenborough JW710

For stress Sodium pyruvate across organisms

SEED Subsystems

Subsystem	#Specific
High affinity phosphate transporter and control of PHO regulon	4
Phosphate metabolism	4
Glycogen metabolism	2
Potassium homeostasis	2
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	1
CMP-N-acetylneuraminate Biosynthesis	1
Calvin-Benson cycle	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Entner-Doudoroff Pathway	1
Folate Biosynthesis	1
Glycolysis and Gluconeogenesis	1
Hydantoin metabolism	1
Hydrogenases	1
Maltose and Maltodextrin Utilization	1
Molybdenum cofactor biosynthesis	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Redox-dependent regulation of nucleus processes	1
Sialic Acid Metabolism	1
TCA Cycle	1
Transport of Molybdenum	1
ZZ gjo need homes	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:

• Lysine biosynthesis
• Arginine and proline metabolism
• Starch and sucrose metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Methionine metabolism
• Geraniol degradation
• Lysine degradation
• Tryptophan metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• One carbon pool by folate
• Reductive carboxylate cycle (CO2 fixation)
• Limonene and pinene degradation
• Aminoacyl-tRNA biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycogen degradation I	8	6	3
glycogen degradation II	6	4	2
CMP-N-acetylneuraminate biosynthesis II (bacteria)	3	2	1
starch degradation V	4	3	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
spermidine biosynthesis II	4	3	1
starch degradation III	4	2	1
arsenic detoxification (bacteria)	4	2	1
CMP-N-acetylneuraminate biosynthesis I (eukaryotes)	5	1	1
creatinine degradation II	5	1	1
TCA cycle VIII (Chlamydia)	6	3	1
arsenate detoxification I	6	3	1
incomplete reductive TCA cycle	7	6	1
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis	7	5	1
pyridoxal 5'-phosphate biosynthesis I	7	5	1
pyruvate fermentation to propanoate I	7	2	1
sucrose biosynthesis II	8	6	1
partial TCA cycle (obligate autotrophs)	8	5	1
superpathway of polyamine biosynthesis III	8	3	1
TCA cycle V (2-oxoglutarate synthase)	9	7	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
TCA cycle VI (Helicobacter)	9	7	1
TCA cycle VII (acetate-producers)	9	6	1
Entner-Doudoroff pathway I	9	6	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	5	1
TCA cycle II (plants and fungi)	9	5	1
L-lysine biosynthesis IV	9	3	1
glycolysis IV	10	8	1
TCA cycle I (prokaryotic)	10	6	1
TCA cycle III (animals)	10	6	1
starch biosynthesis	10	5	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	2	1
glycolysis II (from fructose 6-phosphate)	11	10	1
glycolysis III (from glucose)	11	10	1
reductive TCA cycle I	11	9	1
glycolysis VI (from fructose)	11	8	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	14	2
tRNA-uridine 2-thiolation and selenation (bacteria)	11	2	1
L-glutamate degradation VIII (to propanoate)	11	2	1
homolactic fermentation	12	11	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	9	1
gluconeogenesis III	12	9	1
reductive TCA cycle II	12	7	1
superpathway of glyoxylate bypass and TCA	12	7	1
glycolysis I (from glucose 6-phosphate)	13	11	1
gluconeogenesis I	13	10	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	18	2
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	7	1
superpathway of glyoxylate cycle and fatty acid degradation	14	5	1
Bifidobacterium shunt	15	13	1
superpathway of CMP-sialic acids biosynthesis	15	2	1
mixed acid fermentation	16	12	1
glycerol degradation to butanol	16	9	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	12	1
superpathway of glucose and xylose degradation	17	12	1
superpathway of anaerobic energy metabolism (invertebrates)	17	6	1
heterolactic fermentation	18	13	1
superpathway of hexitol degradation (bacteria)	18	11	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	16	1
superpathway of anaerobic sucrose degradation	19	15	1
methylaspartate cycle	19	6	1
superpathway of N-acetylneuraminate degradation	22	15	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1