Experiment set6IT028 for Desulfovibrio vulgaris Hildenborough JW710

MoLS4 without vitamins with Casamino acids 0.05%

Group: nutrient
Media: MoLS4_no_vitamins + casamino acids (0.5 mg/mL), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 12/12/2016
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)

Specific Phenotypes

For 8 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Coenzyme A Biosynthesis	2
Alanine biosynthesis	1
Aromatic amino acid degradation	1
Auxin biosynthesis	1
Branched-Chain Amino Acid Biosynthesis	1
Glycolate, glyoxylate interconversions	1
Isoleucine degradation	1
Leucine Biosynthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Photorespiration (oxidative C2 cycle)	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Pyruvate Alanine Serine Interconversions	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pantothenate and CoA biosynthesis
• Glyoxylate and dicarboxylate metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Vitamin B6 metabolism
• Indole and ipecac alkaloid biosynthesis
• Alkaloid biosynthesis I
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
phosphopantothenate biosynthesis I	4	4	2
glycolate and glyoxylate degradation II	2	2	1
betaxanthin biosynthesis (via dopamine)	2	2	1
octopamine biosynthesis	2	1	1
L-alanine biosynthesis I	2	1	1
L-dopa degradation II (bacterial)	2	1	1
L-isoleucine biosynthesis V	3	2	1
betaxanthin biosynthesis	3	2	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-tryptophan degradation VI (via tryptamine)	3	1	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	1	1
glycolate and glyoxylate degradation III	3	1	1
L-valine degradation III (oxidative Stickland reaction)	3	1	1
L-valine biosynthesis	4	4	1
superpathway of L-alanine biosynthesis	4	3	1
phosphopantothenate biosynthesis III (archaea)	4	2	1
salidroside biosynthesis	4	2	1
serotonin and melatonin biosynthesis	4	1	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	1	1
glycolate and glyoxylate degradation I	4	1	1
catecholamine biosynthesis	4	1	1
superpathway of coenzyme A biosynthesis I (bacteria)	9	8	2
superpathway of coenzyme A biosynthesis II (plants)	10	5	2
phenylethanol biosynthesis	5	2	1
L-leucine degradation IV (reductive Stickland reaction)	5	1	1
hydroxycinnamic acid tyramine amides biosynthesis	5	1	1
(S)-reticuline biosynthesis I	11	3	2
superpathway of branched chain amino acid biosynthesis	17	16	3
L-leucine biosynthesis	6	6	1
L-isoleucine biosynthesis IV	6	4	1
L-isoleucine degradation I	6	1	1
L-leucine degradation I	6	1	1
beta-carboline biosynthesis	6	1	1
hydroxycinnamic acid serotonin amides biosynthesis	6	1	1
psilocybin biosynthesis	6	1	1
L-isoleucine biosynthesis I (from threonine)	7	6	1
pyridoxal 5'-phosphate biosynthesis I	7	5	1
L-isoleucine biosynthesis III	7	4	1
superpathway of glycol metabolism and degradation	7	2	1
(S)-reticuline biosynthesis II	7	1	1
L-isoleucine biosynthesis II	8	6	1
methanofuran biosynthesis	8	1	1
L-valine degradation I	8	1	1
photorespiration III	9	6	1
photorespiration I	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
photorespiration II	10	6	1
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	9	1
indole-3-acetate biosynthesis II	12	3	1
superpathway of L-isoleucine biosynthesis I	13	12	1
secologanin and strictosidine biosynthesis	17	1	1
superpathway of L-threonine metabolism	18	13	1
Amaryllidacea alkaloids biosynthesis	26	1	1
superpathway of betalain biosynthesis	27	13	1
anteiso-branched-chain fatty acid biosynthesis	34	24	1
even iso-branched-chain fatty acid biosynthesis	34	24	1
odd iso-branched-chain fatty acid biosynthesis	34	24	1