Experiment set6IT053 for Desulfovibrio vulgaris Miyazaki F

9 day starvation, 37C

Group: starvation
Media: MoLS4
Culturing: Miya_ML3_a, serum bottle, Anaerobic, at 37 (C), shaken=0 rpm
By: Jen on 4/19/2015
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 (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 20 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Alanine biosynthesis	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Branched-Chain Amino Acid Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycogen metabolism	1
Glycolate, glyoxylate interconversions	1
Isoleucine degradation	1
Leucine Biosynthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Maltose and Maltodextrin Utilization	1
Photorespiration (oxidative C2 cycle)	1
Potassium homeostasis	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Pyruvate Alanine Serine Interconversions	1
Thiamin biosynthesis	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Nucleotide sugars metabolism
• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Aminophosphonate metabolism
• Starch and sucrose metabolism
• High-mannose type N-glycan biosynthesis
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Vitamin B6 metabolism
• Pantothenate and CoA biosynthesis
• Biosynthesis of siderophore group nonribosomal peptides
• 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
glycolate and glyoxylate degradation II	2	2	1
L-alanine biosynthesis I	2	1	1
glycogen degradation I	8	6	3
cardiolipin biosynthesis II	3	3	1
glycogen degradation II	6	4	2
L-isoleucine biosynthesis V	3	2	1
L-isoleucine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-valine degradation II	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
glycolate and glyoxylate degradation III	3	1	1
L-valine biosynthesis	4	4	1
starch degradation V	4	3	1
superpathway of L-alanine biosynthesis	4	3	1
cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas)	4	3	1
glycolate and glyoxylate degradation I	4	2	1
starch degradation III	4	2	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
thiazole component of thiamine diphosphate biosynthesis I	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
thiazole component of thiamine diphosphate biosynthesis II	7	5	1
pyridoxal 5'-phosphate biosynthesis I	7	5	1
L-isoleucine biosynthesis III	7	4	1
superpathway of glycol metabolism and degradation	7	4	1
sucrose biosynthesis II	8	6	1
L-isoleucine biosynthesis II	8	6	1
L-valine degradation I	8	2	1
photorespiration III	9	6	1
superpathway of thiamine diphosphate biosynthesis I	10	8	1
glycolysis V (Pyrococcus)	10	7	1
photorespiration II	10	6	1
glycolysis II (from fructose 6-phosphate)	11	10	1
superpathway of thiamine diphosphate biosynthesis II	11	9	1
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	9	1
superpathway of L-isoleucine biosynthesis I	13	12	1
glycolysis I (from glucose 6-phosphate)	13	11	1
gluconeogenesis I	13	10	1
superpathway of cardiolipin biosynthesis (bacteria)	13	8	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	12	1
superpathway of L-threonine metabolism	18	12	1
superpathway of hexitol degradation (bacteria)	18	11	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	15	1
superpathway of anaerobic sucrose degradation	19	15	1
superpathway of N-acetylneuraminate degradation	22	14	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	18	1
odd iso-branched-chain fatty acid biosynthesis	34	24	1
even iso-branched-chain fatty acid biosynthesis	34	24	1
anteiso-branched-chain fatty acid biosynthesis	34	24	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1