Experiment set13IT032 for Desulfovibrio vulgaris Hildenborough JW710

MoLS4 with Thymine nitrogen source

Group: nitrogen source
Media: MoLS4_no_ammonium + Thymine (20 mM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 6/14/2017
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 34 genes in this experiment

For nitrogen source Thymine in Desulfovibrio vulgaris Hildenborough JW710

For nitrogen source Thymine across organisms

SEED Subsystems

Subsystem	#Specific
Ammonia assimilation	3
Glycine cleavage system	3
Photorespiration (oxidative C2 cycle)	3
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Glycine and Serine Utilization	2
Bacterial Chemotaxis	1
DNA repair, bacterial UvrD and related helicases	1
Fermentations: Lactate	1
Fermentations: Mixed acid	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
High affinity phosphate transporter and control of PHO regulon	1
Hydrogenases	1
Leucine Degradation and HMG-CoA Metabolism	1
Lipoic acid metabolism	1
Phosphate metabolism	1
Serine-glyoxylate cycle	1
TCA Cycle	1
Translation elongation factor G family	1
Transport of Zinc	1
Two-component regulatory systems in Campylobacter	1
Zinc resistance	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
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Glycolysis / Gluconeogenesis
• Glutamate metabolism
• Pyruvate metabolism
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine degradation
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• One carbon pool by folate
• Lipoic acid metabolism
• Folate biosynthesis
• Limonene and pinene degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycine biosynthesis II	3	3	3
glycine cleavage	3	3	3
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation II	1	1	1
pyruvate fermentation to (S)-lactate	1	1	1
L-glutamine degradation I	1	1	1
L-glutamate biosynthesis IV	1	1	1
ammonia assimilation cycle III	3	3	2
ammonia assimilation cycle I	2	2	1
lipoate biosynthesis and incorporation I	2	2	1
glycerol-3-phosphate shuttle	2	2	1
L-histidine degradation V	2	1	1
L-glutamate and L-glutamine biosynthesis	7	4	3
lipoate biosynthesis and incorporation IV (yeast)	7	4	3
superpathway of ammonia assimilation (plants)	3	2	1
lipoate biosynthesis and incorporation III (Bacillus)	3	2	1
lipoate biosynthesis and incorporation V (mammals)	3	2	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	1	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	1	1
methylglyoxal degradation V	3	1	1
lipoate biosynthesis and incorporation II	3	1	1
pyruvate decarboxylation to acetyl CoA I	3	1	1
CDP-diacylglycerol biosynthesis II	4	4	1
pyruvate fermentation to acetate and lactate II	4	4	1
CDP-diacylglycerol biosynthesis I	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	3	1
pyruvate fermentation to acetate and (S)-lactate I	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
phosphatidate biosynthesis (yeast)	5	3	1
CDP-diacylglycerol biosynthesis III	5	3	1
glucosylglycerol biosynthesis	5	2	1
phosphatidylglycerol biosynthesis II	6	6	1
phosphatidylglycerol biosynthesis I	6	6	1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	7	1
L-citrulline biosynthesis	8	5	1
1,3-propanediol biosynthesis (engineered)	9	4	1
homolactic fermentation	12	11	1
superpathway of phospholipid biosynthesis III (E. coli)	12	10	1
superpathway of L-citrulline metabolism	12	7	1
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	7	1
Bifidobacterium shunt	15	13	1
superpathway of glucose and xylose degradation	17	12	1
heterolactic fermentation	18	13	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	16	1
superpathway of anaerobic sucrose degradation	19	15	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	14	1
superpathway of phospholipid biosynthesis II (plants)	28	10	1