Experiment set6IT012 for Desulfovibrio vulgaris Hildenborough JW710

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MoYLS4 with peroxynitrite 200uM

Group: stress
Media: MoYLS4 + peroxynitrite (200 uM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 12/12/2016
Media components: 1 g/L Yeast Extract, 30 mM Sodium sulfate, 60 mM Sodium D,L-Lactate, 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, 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 9 genes in this experiment

For stress peroxynitrite in Desulfovibrio vulgaris Hildenborough JW710

For stress peroxynitrite across organisms

SEED Subsystems

Subsystem #Specific
Glycerol and Glycerol-3-phosphate Uptake and Utilization 2
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 2
Lactate utilization 2
Nitrate and nitrite ammonification 2
Glycine reductase, sarcosine reductase and betaine reductase 1
L-rhamnose utilization 1
MLST 1
Respiratory dehydrogenases 1 1
Soluble cytochromes and functionally related electron carriers 1
Thioredoxin-disulfide reductase 1
Wyeosine-MimG Biosynthesis 1
YcfH 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
pyruvate fermentation to (S)-lactate 1 1 1
glycerol degradation I 3 2 2
glycerol-3-phosphate shuttle 2 2 1
glycerol-3-phosphate to fumarate electron transfer 2 2 1
glycerophosphodiester degradation 2 2 1
glycerol and glycerophosphodiester degradation 4 3 2
thioredoxin pathway 2 1 1
glycerol-3-phosphate to hydrogen peroxide electron transport 2 1 1
nitrate reduction IX (dissimilatory) 2 1 1
glycerol-3-phosphate to cytochrome bo oxidase electron transfer 2 1 1
glycerol 3-phosphate to cytochrome aa3 oxidase electron transfer 2 1 1
nitrate reduction IV (dissimilatory) 2 1 1
formate to nitrite electron transfer 3 1 1
sn-glycerol 3-phosphate anaerobic respiration 3 1 1
pyruvate fermentation to acetate and lactate II 4 4 1
pyruvate fermentation to acetate and (S)-lactate I 4 3 1
homolactic fermentation 12 11 1
(S)-lactate fermentation to propanoate, acetate and hydrogen 13 7 1
Bifidobacterium shunt 15 13 1
superpathway of glucose and xylose degradation 17 12 1
heterolactic fermentation 18 13 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 16 1
superpathway of anaerobic sucrose degradation 19 15 1