Experiment set3S182 for Desulfovibrio vulgaris Hildenborough JW710

Compare to:

MoLS4 without Biotin with Avidin

Group: nutrient
Media: MoLS4_no_Biotin + Avidin (0.2 U/mL), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 5/5/2016
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 minus biotin (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 Folic Acid, 0.0001 mg/L Cyanocobalamin, 0.2 mg/L Choline chloride)

Specific Phenotypes

For 10 genes in this experiment

SEED Subsystems

Subsystem #Specific
Biotin biosynthesis 4
Fatty Acid Biosynthesis FASII 2
mycolic acid synthesis 2
Ammonia assimilation 1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 1
Glycerolipid and Glycerophospholipid Metabolism 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
biotin biosynthesis from 8-amino-7-oxononanoate I 4 4 4
biotin biosynthesis from 8-amino-7-oxononanoate II 4 4 4
L-glutamate biosynthesis I 2 2 2
L-glutamine degradation I 1 1 1
L-glutamine degradation II 1 1 1
biotin biosynthesis II 6 5 5
ammonia assimilation cycle III 3 3 2
biotin biosynthesis I 15 13 9
biotin biosynthesis from 8-amino-7-oxononanoate III 5 3 3
gondoate biosynthesis (anaerobic) 4 4 2
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast) 12 9 6
8-amino-7-oxononanoate biosynthesis II 2 1 1
8-amino-7-oxononanoate biosynthesis III 2 1 1
8-amino-7-oxononanoate biosynthesis I 11 9 5
palmitate biosynthesis III 29 21 13
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate) 9 8 4
tetradecanoate biosynthesis (mitochondria) 25 17 11
oleate biosynthesis IV (anaerobic) 14 13 6
palmitate biosynthesis II (type II fatty acid synthase) 31 29 13
8-amino-7-oxononanoate biosynthesis IV 5 5 2
fatty acid elongation -- saturated 5 4 2
superpathway of fatty acids biosynthesis (E. coli) 53 47 20
superpathway of unsaturated fatty acids biosynthesis (E. coli) 20 17 7
superpathway of fatty acid biosynthesis II (plant) 43 37 15
(5Z)-dodecenoate biosynthesis I 6 5 2
stearate biosynthesis II (bacteria and plants) 6 5 2
stearate biosynthesis IV 6 4 2
(5Z)-dodecenoate biosynthesis II 6 4 2
superpathway of fatty acid biosynthesis I (E. coli) 16 12 5
L-glutamate and L-glutamine biosynthesis 7 4 2
streptorubin B biosynthesis 34 20 9
L-asparagine biosynthesis III (tRNA-dependent) 4 3 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 3 1
fatty acid biosynthesis initiation (mitochondria) 4 2 1
cis-vaccenate biosynthesis 5 4 1
superpathway of fatty acid biosynthesis initiation 5 3 1
anteiso-branched-chain fatty acid biosynthesis 34 24 6
odd iso-branched-chain fatty acid biosynthesis 34 24 6
even iso-branched-chain fatty acid biosynthesis 34 24 6
petroselinate biosynthesis 6 2 1
L-citrulline biosynthesis 8 5 1
2-allylmalonyl-CoA biosynthesis 8 2 1
superpathway of L-citrulline metabolism 12 7 1
mycolate biosynthesis 205 17 9
superpathway of mycolate biosynthesis 239 18 9