Experiment set7IT091 for Desulfovibrio vulgaris Hildenborough JW710

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MoLS4 with L-Alanine nitrogen source

Group: nitrogen source
Media: MoLS4_no_ammonium + L-Alanine (20 mM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 2/10/2017
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 36 genes in this experiment

For nitrogen source L-Alanine in Desulfovibrio vulgaris Hildenborough JW710

For nitrogen source L-Alanine across organisms

SEED Subsystems

Subsystem #Specific
Ammonia assimilation 3
Bacterial Chemotaxis 3
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 2
ABC transporter tungstate (TC 3.A.1.6.2) 1
Acetoin, butanediol metabolism 1
Branched-Chain Amino Acid Biosynthesis 1
Folate Biosynthesis 1
Molybdenum cofactor biosynthesis 1
One-carbon metabolism by tetrahydropterines 1
Serine-glyoxylate cycle 1
Transport of Zinc 1
Two-component regulatory systems in Campylobacter 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
L-glutamine degradation I 1 1 1
L-glutamate biosynthesis IV 1 1 1
ammonia assimilation cycle III 3 3 2
glycolate and glyoxylate degradation II 2 2 1
ammonia assimilation cycle I 2 2 1
pyruvate fermentation to (R)-acetoin II 2 1 1
L-glutamate and L-glutamine biosynthesis 7 4 3
pyruvate fermentation to (R)-acetoin I 3 2 1
pyruvate fermentation to (S)-acetoin 3 2 1
superpathway of ammonia assimilation (plants) 3 2 1
glycolate and glyoxylate degradation III 3 1 1
L-valine biosynthesis 4 4 1
L-asparagine biosynthesis III (tRNA-dependent) 4 3 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 3 1
glycolate and glyoxylate degradation I 4 1 1
pyruvate fermentation to isobutanol (engineered) 5 4 1
superpathway of (R,R)-butanediol biosynthesis 5 2 1
L-isoleucine biosynthesis IV 6 4 1
superpathway of 2,3-butanediol biosynthesis 6 2 1
L-isoleucine biosynthesis I (from threonine) 7 6 1
L-isoleucine biosynthesis III 7 4 1
superpathway of glycol metabolism and degradation 7 2 1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales) 8 7 1
L-isoleucine biosynthesis II 8 6 1
L-citrulline biosynthesis 8 5 1
superpathway of branched chain amino acid biosynthesis 17 16 2
photorespiration III 9 6 1
folate transformations III (E. coli) 9 5 1
photorespiration II 10 6 1
folate transformations II (plants) 11 5 1
superpathway of L-citrulline metabolism 12 7 1
superpathway of L-isoleucine biosynthesis I 13 12 1
folate transformations I 13 7 1
superpathway of L-threonine metabolism 18 13 1