Experiment set7IT087 for Desulfovibrio vulgaris Hildenborough JW710

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MoLS4 with L-Glycine nitrogen source

Group: nitrogen source
Media: MoLS4_no_ammonium + Glycine (20 mM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 2/10/2017
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 35 genes in this experiment

For nitrogen source Glycine in Desulfovibrio vulgaris Hildenborough JW710

For nitrogen source Glycine across organisms

SEED Subsystems

Subsystem #Specific
Glycine cleavage system 5
Photorespiration (oxidative C2 cycle) 5
Anaerobic respiratory reductases 4
Glycine and Serine Utilization 4
H2:CoM-S-S-HTP oxidoreductase 3
Methanogenesis 3
Bacterial Chemotaxis 2
Lipoic acid metabolism 2
ABC transporter tungstate (TC 3.A.1.6.2) 1
Cobalamin synthesis 1
Coenzyme B12 biosynthesis 1
DNA structural proteins, bacterial 1
Experimental tye 1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 1
Heme and Siroheme Biosynthesis 1
Hfl operon 1
Hydrogenases 1
Leucine Degradation and HMG-CoA Metabolism 1
Methionine Biosynthesis 1
Molybdenum cofactor biosynthesis 1
TCA Cycle 1
Threonine and Homoserine Biosynthesis 1
Two-component regulatory systems in Campylobacter 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
glycine cleavage 3 3 3
glycine biosynthesis II 3 3 3
lipoate biosynthesis and incorporation I 2 2 2
L-aspartate biosynthesis 1 1 1
L-aspartate degradation I 1 1 1
coenzyme B/coenzyme M regeneration IV (H2-dependent) 1 1 1
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
lipoate biosynthesis and incorporation V (mammals) 3 2 2
lipoate biosynthesis and incorporation III (Bacillus) 3 2 2
lipoate biosynthesis and incorporation IV (yeast) 7 4 4
siroheme biosynthesis 4 4 2
L-glutamate degradation II 2 2 1
L-tryptophan degradation IV (via indole-3-lactate) 2 1 1
malate/L-aspartate shuttle pathway 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
L-asparagine degradation III (mammalian) 3 2 1
lipoate biosynthesis and incorporation II 3 1 1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA 3 1 1
pyruvate decarboxylation to acetyl CoA I 3 1 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
(R)-cysteate degradation 3 1 1
sulfolactate degradation III 3 1 1
L-phenylalanine degradation II (anaerobic) 3 1 1
2-oxoglutarate decarboxylation to succinyl-CoA 3 1 1
indole-3-acetate biosynthesis VI (bacteria) 3 1 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
coenzyme B/coenzyme M regeneration I (methanophenazine-dependent) 4 1 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
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
L-tryptophan degradation XIII (reductive Stickland reaction) 5 1 1
L-tyrosine degradation I 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
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
factor 430 biosynthesis 7 3 1
cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion) 15 13 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 anaerobic energy metabolism (invertebrates) 17 6 1
adenosylcobalamin biosynthesis I (anaerobic) 36 29 2
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 13 1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle 22 14 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