Experiment set7IT069 for Desulfovibrio vulgaris Hildenborough JW710

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MoLS4 with L-Threonine nitrogen source

Group: nitrogen source
Media: MoLS4_no_ammonium + L-Threonine (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 40 genes in this experiment

For nitrogen source L-Threonine in Desulfovibrio vulgaris Hildenborough JW710

For nitrogen source L-Threonine across organisms

SEED Subsystems

Subsystem #Specific
Molybdenum cofactor biosynthesis 6
ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 5
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 3
Ammonia assimilation 2
Bacterial Chemotaxis 2
CMP-N-acetylneuraminate Biosynthesis 1
Cobalamin synthesis 1
Coenzyme B12 biosynthesis 1
Experimental tye 1
Fermentations: Lactate 1
Fermentations: Mixed acid 1
Flagellar motility 1
Heme and Siroheme Biosynthesis 1
Queuosine-Archaeosine Biosynthesis 1
Sialic Acid Metabolism 1
Threonine and Homoserine Biosynthesis 1
Transport of Zinc 1
Two-component regulatory systems in Campylobacter 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:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-glutamate biosynthesis I 2 2 2
L-aspartate biosynthesis 1 1 1
pyruvate fermentation to (S)-lactate 1 1 1
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
L-aspartate degradation I 1 1 1
L-glutamine degradation I 1 1 1
L-glutamate biosynthesis IV 1 1 1
L-glutamine degradation II 1 1 1
glycine biosynthesis IV 1 1 1
ammonia assimilation cycle III 3 3 2
siroheme biosynthesis 4 4 2
ammonia assimilation cycle I 2 2 1
L-threonine degradation IV 2 2 1
L-glutamate degradation II 2 2 1
L-histidine degradation V 2 1 1
malate/L-aspartate shuttle pathway 2 1 1
L-tyrosine degradation II 2 1 1
atromentin biosynthesis 2 1 1
L-tryptophan degradation IV (via indole-3-lactate) 2 1 1
L-glutamate and L-glutamine biosynthesis 7 4 3
L-phenylalanine biosynthesis I 3 3 1
L-tyrosine biosynthesis I 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
(R)-cysteate degradation 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
sulfolactate degradation III 3 1 1
methylglyoxal degradation V 3 1 1
pyruvate fermentation to acetate and lactate II 4 4 1
queuosine biosynthesis I (de novo) 4 3 1
superpathway of L-aspartate and L-asparagine biosynthesis 4 3 1
pyruvate fermentation to acetate and (S)-lactate I 4 3 1
L-asparagine biosynthesis III (tRNA-dependent) 4 3 1
glutaminyl-tRNAgln biosynthesis via transamidation 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
queuosine biosynthesis III (queuosine salvage) 5 2 1
CMP-N-acetylneuraminate 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-tyrosine degradation I 5 1 1
L-tryptophan degradation XIII (reductive Stickland reaction) 5 1 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
superpathway of plastoquinol biosynthesis 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
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales) 8 7 1
L-citrulline biosynthesis 8 5 1
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
homolactic fermentation 12 11 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
superpathway of L-isoleucine biosynthesis I 13 12 1
(S)-lactate fermentation to propanoate, acetate and hydrogen 13 7 1
superpathway of rosmarinic acid biosynthesis 14 1 1
Bifidobacterium shunt 15 13 1
superpathway of CMP-sialic acids biosynthesis 15 2 1
superpathway of glucose and xylose degradation 17 12 1
superpathway of anaerobic energy metabolism (invertebrates) 17 6 1
adenosylcobalamin biosynthesis I (anaerobic) 36 29 2
superpathway of L-threonine metabolism 18 13 1
heterolactic fermentation 18 13 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 13 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 16 1
superpathway of anaerobic sucrose degradation 19 15 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