Experiment set8IT053 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 24 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	3
Glycine cleavage system	3
Photorespiration (oxidative C2 cycle)	3
Ammonia assimilation	1
Bacterial Chemotaxis	1
Cysteine Biosynthesis	1
DNA structural proteins, bacterial	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Lysine Biosynthesis DAP Pathway	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1
O-Methyl Phosphoramidate Capsule Modification in Campylobacter	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:

• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Purine metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Selenoamino acid metabolism
• Glyoxylate and dicarboxylate metabolism
• Carbon fixation in photosynthetic organisms
• Sulfur 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 biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
glycine cleavage	3	3	2
glycine biosynthesis II	3	3	2
L-glutamate degradation II	2	2	1
sulfate activation for sulfonation	2	2	1
malate/L-aspartate shuttle pathway	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-asparagine degradation III (mammalian)	3	2	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
sulfolactate degradation III	3	1	1
(R)-cysteate degradation	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
L-phenylalanine degradation II (anaerobic)	3	1	1
assimilatory sulfate reduction I	4	3	1
assimilatory sulfate reduction IV	4	3	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-tyrosine degradation III	4	2	1
L-phenylalanine 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
superpathway of plastoquinol biosynthesis	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation I	5	1	1
L-phenylalanine degradation VI (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
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	9	2
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
superpathway of sulfate assimilation and cysteine biosynthesis	9	7	1
L-lysine biosynthesis I	9	7	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	13	2
photorespiration III	9	6	1
photorespiration I	9	6	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	6	1
L-lysine biosynthesis II	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
superpathway of L-tyrosine biosynthesis	10	9	1
superpathway of L-phenylalanine biosynthesis	10	9	1
photorespiration II	10	6	1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	3	1
rosmarinic acid biosynthesis I	10	1	1
(S)-reticuline biosynthesis I	11	3	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