Experiment set17IT082 for Desulfovibrio vulgaris Hildenborough JW710

Hydrogen/Acetate-Thiosulfate (90%atm/5mM-20mM) with 0.1% Yeast Extract

Group: respiratory growth
Media: Dv_base_Y_medium + H2 (90 %atm) + Sodium acetate (5 mM) + Sodium thiosulfate (20 mM), pH=7.2
Culturing: DvH_JW710, 15 mL tube, Anaerobic, at 30 (C), shaken=0 rpm
By: Kara on 5/22/2018
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 34 genes in this experiment

For respiratory growth H2 in Desulfovibrio vulgaris Hildenborough JW710

For respiratory growth H2 across organisms

SEED Subsystems

Subsystem	#Specific
Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes	4
Flagellum	3
Anaerobic respiratory reductases	2
Molybdenum cofactor biosynthesis	2
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	1
Flagellar motility	1
Flagellum in Campylobacter	1
Glycine reductase, sarcosine reductase and betaine reductase	1
Membrane-bound Ni, Fe-hydrogenase	1
Phosphate metabolism	1
Thioredoxin-disulfide reductase	1
Wyeosine-MimG Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Puromycin biosynthesis
• Pyrimidine metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Glyoxylate and dicarboxylate metabolism
• Trinitrotoluene degradation
• Methane metabolism
• 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
hydrogen production VIII	1	1	1
thiosulfate disproportionation II (cytochrome)	1	1	1
hydrogen production III	1	1	1
superpathway of hydrogen production	2	1	1
thioredoxin pathway	2	1	1
hydrogen production VI	2	1	1
superpathway of photosynthetic hydrogen production	6	2	1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	7	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	7	1
L-glutamate degradation VII (to butanoate)	12	4	1