Experiment set8IT055 for Desulfovibrio vulgaris Hildenborough JW710

MoLS4 with L-Arginine nitrogen source

Group: nitrogen source
Media: MoLS4_no_ammonium + L-Arginine (20 mM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 3/3/2017
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 22 genes in this experiment

For nitrogen source L-Arginine in Desulfovibrio vulgaris Hildenborough JW710

For nitrogen source L-Arginine across organisms

SEED Subsystems

Subsystem	#Specific
Ammonia assimilation	1
Bacterial Chemotaxis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Lipoic acid metabolism	1
Lysine Biosynthesis DAP Pathway	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1
Threonine and Homoserine Biosynthesis	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:

• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Glutamate metabolism
• Alanine and aspartate metabolism
• Cysteine metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Aminophosphonate metabolism
• High-mannose type N-glycan biosynthesis
• Nucleotide sugars metabolism
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• Carbon fixation in photosynthetic organisms
• Lipoic acid metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-aspartate biosynthesis	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
lipoate biosynthesis and incorporation I	2	2	1
L-glutamate degradation II	2	2	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
lipoate biosynthesis and incorporation IV (yeast)	7	4	3
L-tyrosine biosynthesis I	3	3	1
cardiolipin biosynthesis II	3	3	1
L-phenylalanine biosynthesis I	3	3	1
lipoate biosynthesis and incorporation III (Bacillus)	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
lipoate biosynthesis and incorporation V (mammals)	3	2	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
(R)-cysteate degradation	3	1	1
lipoate biosynthesis and incorporation II	3	1	1
sulfolactate degradation III	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
L-phenylalanine degradation II (anaerobic)	3	1	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas)	4	3	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
trans-4-hydroxy-L-proline degradation I	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-tyrosine degradation I	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
superpathway of plastoquinol biosynthesis	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	4	2
superpathway of L-threonine biosynthesis	6	6	1
TCA cycle VIII (Chlamydia)	6	3	1
superpathway of sulfolactate degradation	6	2	1
coenzyme M biosynthesis II	6	1	1
L-lysine biosynthesis VI	7	7	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	6	2
superpathway of aromatic amino acid biosynthesis	18	17	2
L-lysine biosynthesis I	9	7	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	13	2
L-lysine biosynthesis II	9	6	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
superpathway of L-phenylalanine biosynthesis	10	9	1
superpathway of L-tyrosine biosynthesis	10	9	1
rosmarinic acid biosynthesis I	10	1	1
(S)-reticuline biosynthesis I	11	3	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	9	1
indole-3-acetate biosynthesis II	12	3	1
aspartate superpathway	25	20	2
superpathway of L-isoleucine biosynthesis I	13	12	1
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
superpathway of rosmarinic acid biosynthesis	14	1	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
superpathway of anaerobic energy metabolism (invertebrates)	17	6	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	2	1
superpathway of chorismate metabolism	59	31	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1