Experiment set17IT081 for Desulfovibrio vulgaris Hildenborough JW710

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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 58 genes in this experiment

For respiratory growth H2 in Desulfovibrio vulgaris Hildenborough JW710

For respiratory growth H2 across organisms

SEED Subsystems

Subsystem #Specific
Type IV pilus 6
Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes 4
Energy-conserving hydrogenase (ferredoxin) 3
Molybdenum cofactor biosynthesis 3
Zinc resistance 3
Anaerobic respiratory reductases 2
Formate hydrogenase 2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 2
2-phosphoglycolate salvage 1
ABC transporter alkylphosphonate (TC 3.A.1.9.1) 1
ABC transporter dipeptide (TC 3.A.1.5.2) 1
Bacterial Chemotaxis 1
Biogenesis of c-type cytochromes 1
Cyanophycin Metabolism 1
Flagellar motility 1
Flagellum 1
Folate Biosynthesis 1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 1
Glycolate, glyoxylate interconversions 1
High affinity phosphate transporter and control of PHO regulon 1
Ketoisovalerate oxidoreductase 1
NiFe hydrogenase maturation 1
Periplasmic disulfide interchange 1
Phosphate metabolism 1
Photorespiration (oxidative C2 cycle) 1
Two-component regulatory systems in Campylobacter 1
ZZ gjo need homes 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:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
hydrogen production III 1 1 1
thiosulfate disproportionation II (cytochrome) 1 1 1
hydrogen production VIII 1 1 1
formate oxidation to CO2 1 1 1
L-asparagine biosynthesis I 1 1 1
L-glutamine degradation I 1 1 1
acetate conversion to acetyl-CoA 1 1 1
acetate and ATP formation from acetyl-CoA III 1 1 1
L-glutamate biosynthesis I 2 2 1
hydrogen production VI 2 1 1
superpathway of L-asparagine biosynthesis 2 1 1
superpathway of hydrogen production 2 1 1
superpathway of acetate utilization and formation 3 3 1
ammonia assimilation cycle III 3 3 1
ethanol degradation II 3 2 1
L-isoleucine biosynthesis V 3 2 1
ethanol degradation IV 3 2 1
ethanol degradation III 3 1 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 3 1
L-asparagine biosynthesis III (tRNA-dependent) 4 3 1
chitin deacetylation 4 2 1
oxalate degradation VI 4 1 1
2-methylcitrate cycle I 5 1 1
oxalate degradation III 5 1 1
L-isoleucine biosynthesis IV 6 4 1
superpathway of photosynthetic hydrogen production 6 2 1
superpathway of bitter acids biosynthesis 18 3 3
adlupulone and adhumulone biosynthesis 6 1 1
β-alanine biosynthesis II 6 1 1
2-methylcitrate cycle II 6 1 1
lupulone and humulone biosynthesis 6 1 1
colupulone and cohumulone biosynthesis 6 1 1
L-glutamate and L-glutamine biosynthesis 7 4 1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales) 8 7 1
L-citrulline biosynthesis 8 5 1
superpathway of fermentation (Chlamydomonas reinhardtii) 9 7 1
photorespiration I 9 6 1
photorespiration III 9 6 1
reductive glycine pathway of autotrophic CO2 fixation 9 6 1
cis-geranyl-CoA degradation 9 1 1
photorespiration II 10 6 1
superpathway of coenzyme A biosynthesis II (plants) 10 5 1
superpathway of L-citrulline metabolism 12 7 1
L-glutamate degradation VII (to butanoate) 12 4 1
superpathway of C1 compounds oxidation to CO2 12 2 1
purine nucleobases degradation I (anaerobic) 15 5 1
purine nucleobases degradation II (anaerobic) 24 16 1