Experiment set9IT064 for Desulfovibrio vulgaris Hildenborough JW710

Formate/Acetate-Sulfite (60/30-40 mM) + 0.1% Yeast Extract

Group: respiratory growth
Media: Dv_base_Y_medium + Sodium Formate (60 mM) + Sodium acetate (30 mM) + sodium sulfite (40 mM), pH=7.2
Culturing: DvH_JW710, 15 mL tube, 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, 1 g/L Yeast Extract, 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 30 genes in this experiment

For respiratory growth Sodium Formate in Desulfovibrio vulgaris Hildenborough JW710

For respiratory growth Sodium Formate across organisms

SEED Subsystems

Subsystem	#Specific
Molybdenum cofactor biosynthesis	3
Anaerobic respiratory reductases	2
Hydantoin metabolism	2
Bacterial Chemotaxis	1
Cysteine Biosynthesis	1
DNA-replication	1
DNA Repair Base Excision	1
DNA repair, bacterial RecFOR pathway	1
Glycine reductase, sarcosine reductase and betaine reductase	1
Ketoisovalerate oxidoreductase	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1
Peptidoglycan Biosynthesis	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Thioredoxin-disulfide reductase	1
Transport of Zinc	1
Two-component regulatory systems in Campylobacter	1
Wyeosine-MimG 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:

• Glycolysis / Gluconeogenesis
• Puromycin biosynthesis
• Pyrimidine metabolism
• Arginine and proline metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Trinitrotoluene degradation
• Propanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate conversion to acetyl-CoA	1	1	1
thiosulfate disproportionation II (cytochrome)	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
thioredoxin pathway	2	1	1
superpathway of acetate utilization and formation	3	3	1
L-isoleucine biosynthesis V	3	2	1
ethanol degradation II	3	2	1
ethanol degradation IV	3	2	1
ethanol degradation III	3	1	1
chitin deacetylation	4	2	1
creatinine degradation II	5	1	1
2-methylcitrate cycle I	5	1	1
L-isoleucine biosynthesis IV	6	4	1
superpathway of bitter acids biosynthesis	18	3	3
2-methylcitrate cycle II	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
β-alanine biosynthesis II	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
lupulone and humulone biosynthesis	6	1	1
reductive glycine pathway of autotrophic CO2 fixation	9	6	1
cis-geranyl-CoA degradation	9	1	1
superpathway of coenzyme A biosynthesis II (plants)	10	5	1