Experiment set2H37 for Shewanella amazonensis SB2B

Minimal media with Thymidine as carbon source

Group: carbon source
Media: ShewMM_noCarbon + Thymidine (10 mM), pH=7
Culturing: SB2B_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Jake on 4/15/2013
Media components: 1.5 g/L Ammonium chloride, 1.75 g/L Sodium Chloride, 0.61 g/L Magnesium chloride hexahydrate, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)
Growth plate: 508 B3,B4

Specific Phenotypes

For 5 genes in this experiment

For carbon source Thymidine in Shewanella amazonensis SB2B

For carbon source Thymidine across organisms

SEED Subsystems

Subsystem	#Specific
Chitin and N-acetylglucosamine utilization	1
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methylglyoxal Metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Pyrimidine metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Nicotinate and nicotinamide metabolism
• Limonene and pinene degradation
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
putrescine degradation V	2	2	1
putrescine degradation I	2	1	1
ethylene glycol degradation	2	1	1
phenylethylamine degradation II	2	1	1
phenylethylamine degradation I	2	1	1
phenylethanol degradation	2	1	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
NAD salvage pathway III (to nicotinamide riboside)	3	2	1
ethanol degradation III	3	2	1
putrescine degradation IV	3	2	1
hypotaurine degradation	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
histamine degradation	3	1	1
styrene degradation	3	1	1
UTP and CTP dephosphorylation I	7	5	2
purine nucleotides degradation II (aerobic)	11	8	3
phytol degradation	4	3	1
inosine 5'-phosphate degradation	4	3	1
guanosine nucleotides degradation III	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
adenosine nucleotides degradation I	8	3	2
purine nucleotides degradation I (plants)	12	4	3
guanosine nucleotides degradation II	4	1	1
guanosine nucleotides degradation I	4	1	1
D-arabinose degradation II	4	1	1
putrescine degradation III	4	1	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	1	1
mitochondrial NADPH production (yeast)	5	3	1
adenosine nucleotides degradation II	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
dopamine degradation	5	1	1
3-methyl-branched fatty acid α-oxidation	6	3	1
superpathway of purines degradation in plants	18	4	3
superpathway of guanosine nucleotides degradation (plants)	6	1	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	4	2
superpathway of glycol metabolism and degradation	7	5	1
ureide biosynthesis	7	3	1
serotonin degradation	7	3	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
superpathway of ornithine degradation	8	6	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
aromatic biogenic amine degradation (bacteria)	8	1	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
tunicamycin biosynthesis	9	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	1
superpathway of phenylethylamine degradation	11	3	1
NAD salvage (plants)	11	3	1
superpathway of L-arginine and L-ornithine degradation	13	8	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	2	1
superpathway of pentose and pentitol degradation	42	6	1