Experiment set16IT095 for Desulfovibrio vulgaris Hildenborough JW710

MoLS4 with L-Cysteine 1mM as nitrogen source

Group: nitrogen source
Media: MoLS4_no_ammonium + L-Cysteine (1 mM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 11/2/2017
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 23 genes in this experiment

For nitrogen source L-Cysteine in Desulfovibrio vulgaris Hildenborough JW710

For nitrogen source L-Cysteine across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	5
Anaerobic respiratory reductases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Hfl operon	1
Hydrogenases	1
One-carbon metabolism by tetrahydropterines	1
Potassium homeostasis	1
Protein degradation	1
Queuosine-Archaeosine Biosynthesis	1
Threonine and Homoserine Biosynthesis	1
Universal GTPases	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• Alanine and aspartate metabolism
• Cysteine metabolism
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Glycerophospholipid metabolism
• Glyoxylate and dicarboxylate metabolism
• One carbon pool by folate
• Carbon fixation in photosynthetic organisms
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-aspartate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
glycerol-3-phosphate shuttle	2	2	1
L-glutamate degradation II	2	2	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
glutathione degradation (DUG pathway)	2	1	1
atromentin biosynthesis	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
L-tyrosine degradation II	2	1	1
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-asparagine degradation III (mammalian)	3	2	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
L-phenylalanine degradation II (anaerobic)	3	1	1
(R)-cysteate degradation	3	1	1
sulfolactate degradation III	3	1	1
formaldehyde oxidation VII (THF pathway)	4	4	1
CDP-diacylglycerol biosynthesis I	4	4	1
CDP-diacylglycerol biosynthesis II	4	4	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
phosphatidate biosynthesis (yeast)	5	3	1
CDP-diacylglycerol biosynthesis III	5	3	1
trans-4-hydroxy-L-proline degradation I	5	2	1
glucosylglycerol biosynthesis	5	2	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-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tyrosine degradation I	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	4	2
phosphatidylglycerol biosynthesis I	6	6	1
superpathway of L-threonine biosynthesis	6	6	1
phosphatidylglycerol biosynthesis II	6	6	1
TCA cycle VIII (Chlamydia)	6	3	1
superpathway of sulfolactate degradation	6	2	1
γ-glutamyl cycle	6	1	1
coenzyme M biosynthesis II	6	1	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 L-methionine biosynthesis (transsulfuration)	9	6	1
1,3-propanediol biosynthesis (engineered)	9	4	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
rosmarinic acid biosynthesis I	10	1	1
(S)-reticuline biosynthesis I	11	3	1
superpathway of phospholipid biosynthesis III (E. coli)	12	10	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	9	1
indole-3-acetate biosynthesis II	12	3	1
superpathway of L-isoleucine biosynthesis I	13	12	1
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
folate transformations I	13	7	1
superpathway of rosmarinic acid biosynthesis	14	1	1
purine nucleobases degradation I (anaerobic)	15	5	1
superpathway of anaerobic energy metabolism (invertebrates)	17	6	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	13	1
purine nucleobases degradation II (anaerobic)	24	16	1
aspartate superpathway	25	20	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	2	1
superpathway of phospholipid biosynthesis II (plants)	28	10	1
superpathway of chorismate metabolism	59	31	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1