Experiment set7IT089 for Desulfovibrio vulgaris Hildenborough JW710

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 34 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	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Serine-glyoxylate cycle	2
Acetoin, butanediol metabolism	1
Branched-Chain Amino Acid Biosynthesis	1
Folate Biosynthesis	1
Molybdenum cofactor biosynthesis	1
One-carbon metabolism by tetrahydropterines	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:

• Glutamate metabolism
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Valine, leucine and isoleucine biosynthesis
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• C5-Branched dibasic acid metabolism
• One carbon pool by folate
• Pantothenate and CoA biosynthesis
• Limonene and pinene degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

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-glutamate biosynthesis IV	1	1	1
L-glutamine degradation I	1	1	1
ammonia assimilation cycle III	3	3	2
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
L-valine biosynthesis	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	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
L-isoleucine biosynthesis II	8	6	1
L-citrulline biosynthesis	8	5	1
superpathway of branched chain amino acid biosynthesis	17	16	2
folate transformations III (E. coli)	9	5	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