Experiment set15IT027 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 35 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)	7
Molybdenum cofactor biosynthesis	3
Choline and Betaine Uptake and Betaine Biosynthesis	2
Hfl operon	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
Isoleucine degradation	1
Potassium homeostasis	1
Proteasome bacterial	1
Protein degradation	1
Proteolysis in bacteria, ATP-dependent	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:

• Butanoate metabolism
• Purine metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Cysteine metabolism
• Lysine degradation
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Peptidoglycan biosynthesis
• 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
L-aspartate biosynthesis	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
L-glutamate degradation II	2	2	1
glutathione degradation (DUG pathway)	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-tyrosine degradation II	2	1	1
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
CMP-N-acetylneuraminate biosynthesis II (bacteria)	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
sulfolactate degradation III	3	1	1
L-phenylalanine degradation II (anaerobic)	3	1	1
(R)-cysteate degradation	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
pyruvate fermentation to butanoate	7	3	2
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
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	2
(S)-propane-1,2-diol degradation	5	3	1
trans-4-hydroxy-L-proline degradation I	5	2	1
superpathway of plastoquinol biosynthesis	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
CMP-N-acetylneuraminate biosynthesis I (eukaryotes)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tyrosine degradation I	5	1	1
L-tryptophan degradation XIII (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
L-threonine degradation I	6	5	1
TCA cycle VIII (Chlamydia)	6	3	1
L-glutamate degradation VII (to butanoate)	12	4	2
superpathway of sulfolactate degradation	6	2	1
coenzyme M biosynthesis II	6	1	1
γ-glutamyl cycle	6	1	1
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis	7	5	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	6	2
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	8	2
superpathway of aromatic amino acid biosynthesis	18	17	2
superpathway of L-methionine biosynthesis (transsulfuration)	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
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
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 anaerobic energy metabolism (invertebrates)	17	6	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	13	1
superpathway of L-threonine metabolism	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