Experiment set15IT025 for Desulfovibrio vulgaris Hildenborough JW710

MoLS4 with L-Cysteine 5mM as nutrient

Group: nutrient
Media: MoLS4 + L-Cysteine (5 mM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 10/26/2017
Media components: 30 mM Sodium sulfate, 60 mM Sodium D,L-Lactate, 20 mM Ammonium chloride, 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 30 genes in this experiment

For nutrient L-Cysteine in Desulfovibrio vulgaris Hildenborough JW710

For nutrient L-Cysteine across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	6
Molybdenum cofactor biosynthesis	3
Choline and Betaine Uptake and Betaine Biosynthesis	2
Acetyl-CoA fermentation to Butyrate	1
Arginine and Ornithine Degradation	1
CMP-N-acetylneuraminate Biosynthesis	1
Coenzyme A Biosynthesis	1
DNA repair, bacterial MutL-MutS system	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Hfl operon	1
Isoleucine degradation	1
Potassium homeostasis	1
Sialic Acid Metabolism	1
Threonine and Homoserine Biosynthesis	1
Valine degradation	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lysine degradation
• Purine metabolism
• 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
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Peptidoglycan biosynthesis
• Butanoate metabolism
• Carbon fixation in photosynthetic organisms
• Biotin metabolism
• 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
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
L-glutamate degradation II	2	2	1
L-tyrosine degradation II	2	1	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-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-asparagine degradation III (mammalian)	3	2	1
CMP-N-acetylneuraminate biosynthesis II (bacteria)	3	2	1
(R)-cysteate degradation	3	1	1
sulfolactate degradation III	3	1	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
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
spermidine biosynthesis II	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
(S)-propane-1,2-diol degradation	5	3	1
trans-4-hydroxy-L-proline degradation I	5	2	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-tyrosine degradation I	5	1	1
CMP-N-acetylneuraminate biosynthesis I (eukaryotes)	5	1	1
superpathway of plastoquinol biosynthesis	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	4	2
superpathway of L-threonine biosynthesis	6	6	1
L-threonine degradation I	6	5	1
TCA cycle VIII (Chlamydia)	6	3	1
superpathway of sulfolactate degradation	6	2	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
pyruvate fermentation to butanoate	7	3	1
superpathway of polyamine biosynthesis III	8	3	1
superpathway of aromatic amino acid biosynthesis	18	17	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	6	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
L-lysine biosynthesis IV	9	3	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
L-glutamate degradation VII (to butanoate)	12	4	1
indole-3-acetate biosynthesis II	12	3	1
superpathway of L-isoleucine biosynthesis I	13	12	1
superpathway of rosmarinic acid biosynthesis	14	1	1
superpathway of CMP-sialic acids biosynthesis	15	2	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	8	1
superpathway of anaerobic energy metabolism (invertebrates)	17	6	1
superpathway of L-threonine metabolism	18	13	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	13	1
aspartate superpathway	25	20	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	2	1
superpathway of chorismate metabolism	59	31	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1