Experiment set13IT033 for Desulfovibrio vulgaris Hildenborough JW710

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MoLS4 with Thymine nitrogen source

Group: nitrogen source
Media: MoLS4_no_ammonium + Thymine (20 mM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 6/14/2017
Media components: 30 mM Sodium sulfate, 60 mM Sodium D,L-Lactate, 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 31 genes in this experiment

For nitrogen source Thymine in Desulfovibrio vulgaris Hildenborough JW710

For nitrogen source Thymine across organisms

SEED Subsystems

Subsystem #Specific
Ammonia assimilation 3
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 2
Glycine and Serine Utilization 2
Glycine cleavage system 2
Photorespiration (oxidative C2 cycle) 2
Bacterial Chemotaxis 1
Fermentations: Lactate 1
Fermentations: Mixed acid 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Hydrogenases 1
Lipoic acid metabolism 1
Serine-glyoxylate cycle 1
Translation elongation factor G family 1
Transport of Zinc 1
Two-component regulatory systems in Campylobacter 1
Zinc resistance 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
L-glutamate biosynthesis I 2 2 2
L-glutamine degradation II 1 1 1
pyruvate fermentation to (S)-lactate 1 1 1
L-glutamate biosynthesis IV 1 1 1
L-glutamine degradation I 1 1 1
ammonia assimilation cycle III 3 3 2
lipoate biosynthesis and incorporation I 2 2 1
ammonia assimilation cycle I 2 2 1
L-histidine degradation V 2 1 1
L-glutamate and L-glutamine biosynthesis 7 4 3
lipoate biosynthesis and incorporation IV (yeast) 7 4 3
cardiolipin biosynthesis II 3 3 1
glycine cleavage 3 3 1
glycine biosynthesis II 3 3 1
lipoate biosynthesis and incorporation III (Bacillus) 3 2 1
superpathway of ammonia assimilation (plants) 3 2 1
lipoate biosynthesis and incorporation V (mammals) 3 2 1
methylglyoxal degradation V 3 1 1
lipoate biosynthesis and incorporation II 3 1 1
pyruvate fermentation to acetate and lactate II 4 4 1
pyruvate fermentation to acetate and (S)-lactate I 4 3 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 3 1
L-asparagine biosynthesis III (tRNA-dependent) 4 3 1
cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas) 4 3 1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales) 8 7 1
L-citrulline biosynthesis 8 5 1
tRNA-uridine 2-thiolation and selenation (bacteria) 11 2 1
homolactic fermentation 12 11 1
superpathway of L-citrulline metabolism 12 7 1
superpathway of cardiolipin biosynthesis (bacteria) 13 9 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