Experiment set8IT071 for Desulfovibrio vulgaris Hildenborough JW710

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MoLS4 with Spermidine nitrogen source

Group: nitrogen source
Media: MoLS4_no_ammonium + spermidine (20 mM), 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 40 genes in this experiment

For nitrogen source spermidine in Desulfovibrio vulgaris Hildenborough JW710

For nitrogen source spermidine across organisms

SEED Subsystems

Subsystem #Specific
Ammonia assimilation 3
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 3
Peptidoglycan Biosynthesis 2
CMP-N-acetylneuraminate Biosynthesis 1
Flagellar motility 1
Flagellum 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Glycine and Serine Utilization 1
Glycine cleavage system 1
Lactose utilization 1
Lipid A-Ara4N pathway ( Polymyxin resistance ) 1
Lysine Biosynthesis DAP Pathway 1
Photorespiration (oxidative C2 cycle) 1
Serine-glyoxylate cycle 1
Sialic Acid Metabolism 1
Threonine and Homoserine Biosynthesis 1
Translation elongation factor G family 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-glutamate biosynthesis I 2 2 2
L-aspartate degradation I 1 1 1
L-aspartate biosynthesis 1 1 1
L-glutamate biosynthesis IV 1 1 1
L-glutamine degradation I 1 1 1
L-glutamine degradation II 1 1 1
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
ammonia assimilation cycle III 3 3 2
L-glutamate degradation II 2 2 1
ammonia assimilation cycle I 2 2 1
atromentin biosynthesis 2 1 1
L-tyrosine degradation II 2 1 1
L-tryptophan degradation IV (via indole-3-lactate) 2 1 1
malate/L-aspartate shuttle pathway 2 1 1
L-glutamate and L-glutamine biosynthesis 7 4 3
L-phenylalanine biosynthesis I 3 3 1
glycine cleavage 3 3 1
cardiolipin biosynthesis II 3 3 1
L-tyrosine biosynthesis I 3 3 1
glycine biosynthesis II 3 3 1
superpathway of ammonia assimilation (plants) 3 2 1
CMP-N-acetylneuraminate biosynthesis II (bacteria) 3 2 1
L-asparagine degradation III (mammalian) 3 2 1
sulfolactate degradation III 3 1 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
(R)-cysteate degradation 3 1 1
L-phenylalanine degradation II (anaerobic) 3 1 1
indole-3-acetate biosynthesis VI (bacteria) 3 1 1
cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas) 4 3 1
L-asparagine biosynthesis III (tRNA-dependent) 4 3 1
glutaminyl-tRNAgln biosynthesis via transamidation 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-tyrosine degradation I 5 1 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
L-tyrosine degradation V (reductive Stickland reaction) 5 1 1
L-tryptophan degradation XIII (reductive Stickland reaction) 5 1 1
superpathway of plastoquinol biosynthesis 5 1 1
CMP-N-acetylneuraminate 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
TCA cycle VIII (Chlamydia) 6 3 1
superpathway of sulfolactate degradation 6 2 1
peptidoglycan maturation (meso-diaminopimelate containing) 12 3 2
coenzyme M biosynthesis II 6 1 1
L-lysine biosynthesis VI 7 7 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
L-citrulline biosynthesis 8 5 1
superpathway of aromatic amino acid biosynthesis 18 17 2
L-lysine biosynthesis I 9 7 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 13 2
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
rosmarinic acid biosynthesis I 10 1 1
(S)-reticuline biosynthesis I 11 3 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 9 1
superpathway of L-citrulline metabolism 12 7 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 cardiolipin biosynthesis (bacteria) 13 9 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 CMP-sialic acids biosynthesis 15 2 1
peptidoglycan biosynthesis II (staphylococci) 17 12 1
peptidoglycan biosynthesis IV (Enterococcus faecium) 17 12 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