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-leucine degradation III	3	2	1
L-isoleucine biosynthesis V	3	2	1
betaxanthin biosynthesis	3	2	1
L-valine degradation II	3	2	1
L-isoleucine degradation II	3	2	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	1	1
L-tryptophan degradation VI (via tryptamine)	3	1	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
L-valine degradation III (oxidative Stickland reaction)	3	1	1
glycolate and glyoxylate degradation III	3	1	1
L-valine biosynthesis	4	4	1
superpathway of L-alanine biosynthesis	4	3	1
salidroside biosynthesis	4	2	1
phosphopantothenate biosynthesis III (archaea)	4	2	1
serotonin and melatonin biosynthesis	4	1	1
glycolate and glyoxylate degradation I	4	1	1
catecholamine biosynthesis	4	1	1
L-tryptophan degradation X (mammalian, via tryptamine)	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
hydroxycinnamic acid tyramine amides biosynthesis	5	1	1
L-leucine degradation IV (reductive Stickland reaction)	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
psilocybin biosynthesis	6	1	1
L-leucine degradation I	6	1	1
beta-carboline biosynthesis	6	1	1
L-isoleucine degradation I	6	1	1
hydroxycinnamic acid serotonin amides 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
L-valine degradation I	8	1	1
methanofuran biosynthesis	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
odd iso-branched-chain fatty acid biosynthesis	34	24	1
anteiso-branched-chain fatty acid biosynthesis	34	24	1
even iso-branched-chain fatty acid biosynthesis	34	24	1