Experiment set8IT054 for Desulfovibrio vulgaris Hildenborough JW710

MoLS4 with N2 gas nitrogen source

Group: nitrogen source
Media: MoLS4_no_ammonium + N2 (90 %atm), 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 27 genes in this experiment

For nitrogen source N2 in Desulfovibrio vulgaris Hildenborough JW710

For nitrogen source N2 across organisms

SEED Subsystems

Subsystem	#Specific
Glycine and Serine Utilization	4
Glycine cleavage system	4
Photorespiration (oxidative C2 cycle)	4
Ammonia assimilation	1
Bacterial Chemotaxis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	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

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• 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
• Glyoxylate and dicarboxylate metabolism
• One carbon pool by folate
• Carbon fixation in photosynthetic organisms
• Lipoic acid metabolism
• Nitrogen 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
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
glycine cleavage	3	3	2
glycine biosynthesis II	3	3	2
L-glutamate degradation II	2	2	1
lipoate biosynthesis and incorporation I	2	2	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
lipoate biosynthesis and incorporation IV (yeast)	7	4	3
L-tyrosine biosynthesis I	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
L-phenylalanine degradation II (anaerobic)	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
lipoate biosynthesis and incorporation II	3	1	1
(R)-cysteate degradation	3	1	1
sulfolactate degradation III	3	1	1
superpathway of L-aspartate and L-asparagine biosynthesis	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
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation I	5	1	1
superpathway of plastoquinol biosynthesis	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	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
superpathway of L-methionine biosynthesis (transsulfuration)	9	6	1
L-lysine biosynthesis II	9	6	1
photorespiration I	9	6	1
photorespiration III	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
photorespiration II	10	6	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 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