Experiment set6IT008 for Desulfovibrio vulgaris Miyazaki F

L-Serine carbon source

Group: carbon source
Media: MoLS4_no_lactate + L-Serine (20 mM)
Culturing: Miya_ML3_a, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Jen on 4/19/2015
Media components: 30 mM Sodium sulfate, 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, 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 2 genes in this experiment

For carbon source L-Serine in Desulfovibrio vulgaris Miyazaki F

For carbon source L-Serine across organisms

SEED Subsystems

Subsystem	#Specific
Alanine biosynthesis	1
Branched-Chain Amino Acid Biosynthesis	1
Isoleucine degradation	1
Leucine Biosynthesis	1
Leucine Degradation and HMG-CoA Metabolism	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:

• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Pantothenate and CoA biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-alanine biosynthesis I	2	1	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine biosynthesis V	3	2	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	1	1
L-valine degradation III (oxidative Stickland reaction)	3	1	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
L-valine biosynthesis	4	4	1
superpathway of L-alanine biosynthesis	4	3	1
L-leucine degradation IV (reductive Stickland reaction)	5	1	1
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
L-isoleucine biosynthesis I (from threonine)	7	6	1
L-isoleucine biosynthesis III	7	4	1
L-isoleucine biosynthesis II	8	6	1
L-valine degradation I	8	2	1
superpathway of L-isoleucine biosynthesis I	13	12	1
superpathway of L-threonine metabolism	18	12	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