Experiment set10IT090 for Phaeobacter inhibens DSM 17395

No vitamins, timepoint 1

Group: vitamin
Media: DinoMM_L_lactateCarbon_HighNutrient_noVitamin
Culturing: Phaeo_ML1, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 6.2 generations
By: Adam on 29-Jun-16
Media components: 20 g/L Sea salts, 0.3 g/L Ammonium Sulfate, 0.1 g/L Potassium phosphate monobasic, 20 mM Sodium L-Lactate, 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)

Specific Phenotypes

For 41 genes in this experiment

SEED Subsystems

Subsystem	#Specific
ABC transporter tungstate (TC 3.A.1.6.2)	3
Biotin biosynthesis	3
Formate hydrogenase	3
NAD and NADP cofactor biosynthesis global	2
NAD regulation	2
Acid resistance mechanisms	1
Adenosyl nucleosidases	1
Arginine and Ornithine Degradation	1
Branched-Chain Amino Acid Biosynthesis	1
Deoxyribose and Deoxynucleoside Catabolism	1
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Lipopolysaccharide-related cluster in Alphaproteobacteria	1
Methylglyoxal Metabolism	1
Molybdenum cofactor biosynthesis	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Polyamine Metabolism	1
Purine conversions	1
Pyrimidine utilization	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Synechocystis experimental	1
Threonine degradation	1
Triacylglycerol metabolism	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Biotin metabolism
• Purine metabolism
• Valine, leucine and isoleucine degradation
• Propanoate metabolism
• Nicotinate and nicotinamide metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Oxidative phosphorylation
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Taurine and hypotaurine metabolism
• Glutathione metabolism
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Inositol phosphate metabolism
• Glycerophospholipid metabolism
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Methane metabolism
• Folate biosynthesis
• 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
bis(guanylyl molybdenum cofactor) biosynthesis	2	2	2
taurine degradation I	1	1	1
formate oxidation to CO2	1	1	1
arginine dependent acid resistance	1	1	1
guanylyl molybdenum cofactor biosynthesis	1	1	1
bis(guanylyl tungstenpterin) cofactor biosynthesis	1	1	1
cadaverine biosynthesis	1	1	1
purine deoxyribonucleosides degradation I	4	3	3
hypotaurine degradation	3	3	2
L-methionine degradation II	3	3	2
purine ribonucleosides degradation	6	5	4
purine deoxyribonucleosides degradation II	3	2	2
superpathway of putrescine biosynthesis	4	4	2
biotin biosynthesis from 8-amino-7-oxononanoate I	4	4	2
xanthine and xanthosine salvage	2	2	1
putrescine degradation V	2	2	1
adenine and adenosine salvage I	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
putrescine biosynthesis III	2	2	1
putrescine biosynthesis I	2	2	1
guanine and guanosine salvage I	2	2	1
L-threonine degradation I	6	5	3
adenine and adenosine salvage III	4	3	2
8-amino-7-oxononanoate biosynthesis II	2	1	1
ethylene glycol degradation	2	1	1
β-alanine degradation I	2	1	1
β-alanine degradation II	2	1	1
8-amino-7-oxononanoate biosynthesis III	2	1	1
putrescine degradation I	2	1	1
L-threonine degradation V	2	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	3
superpathway of purine deoxyribonucleosides degradation	7	6	3
superpathway of polyamine biosynthesis I	8	8	3
NAD de novo biosynthesis I	6	6	2
ethanol degradation II	3	3	1
aminopropylcadaverine biosynthesis	3	3	1
pyrimidine deoxyribonucleosides degradation	3	3	1
ethanol degradation IV	3	3	1
NAD de novo biosynthesis III	6	5	2
NAD de novo biosynthesis IV (anaerobic)	6	5	2
biotin biosynthesis II	6	4	2
superpathway of guanine and guanosine salvage	3	2	1
putrescine degradation IV	3	2	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	2	1
ethanol degradation III	3	2	1
putrescine biosynthesis II	3	2	1
histamine degradation	3	1	1
adenine and adenosine salvage V	3	1	1
purine nucleotides degradation II (aerobic)	11	10	3
inosine 5'-phosphate degradation	4	4	1
NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde	4	4	1
guanosine nucleotides degradation III	4	4	1
superpathway of polyamine biosynthesis II	8	6	2
phytol degradation	4	3	1
biotin biosynthesis from 8-amino-7-oxononanoate II	4	3	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
D-arabinose degradation II	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
spermidine biosynthesis III	4	2	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
superpathway of ornithine degradation	8	3	2
putrescine degradation III	4	1	1
oxalate degradation VI	4	1	1
superpathway of L-isoleucine biosynthesis I	13	12	3
superpathway of L-arginine and L-ornithine degradation	13	7	3
nicotine biosynthesis	9	3	2
hypoglycin biosynthesis	14	4	3
biotin biosynthesis I	15	13	3
adenosine nucleotides degradation II	5	4	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
octane oxidation	5	3	1
propanoyl-CoA degradation II	5	3	1
biotin biosynthesis from 8-amino-7-oxononanoate III	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
mitochondrial NADPH production (yeast)	5	2	1
nucleoside and nucleotide degradation (archaea)	10	3	2
oxalate degradation III	5	1	1
dopamine degradation	5	1	1
desferrioxamine B biosynthesis	5	1	1
desferrioxamine E biosynthesis	5	1	1
bisucaberin biosynthesis	5	1	1
lupanine biosynthesis	5	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	5	2
superpathway of branched chain amino acid biosynthesis	17	17	3
superpathway of arginine and polyamine biosynthesis	17	17	3
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	1
superpathway of L-threonine metabolism	18	15	3
superpathway of taurine degradation	6	4	1
3-methyl-branched fatty acid α-oxidation	6	3	1
L-lysine degradation X	6	3	1
superpathway of nicotine biosynthesis	12	4	2
nucleoside and nucleotide degradation (halobacteria)	6	2	1
fluoroacetate and fluorothreonine biosynthesis	6	1	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	4	2
myo-inositol degradation I	7	7	1
superpathway of purine nucleotide salvage	14	13	2
ureide biosynthesis	7	6	1
superpathway of glycol metabolism and degradation	7	4	1
serotonin degradation	7	3	1
ceramide degradation by α-oxidation	7	2	1
L-lysine degradation I	7	2	1
sulfur oxidation IV (intracellular sulfur)	7	2	1
2,4-dinitrotoluene degradation	7	1	1
limonene degradation IV (anaerobic)	7	1	1
L-valine degradation I	8	5	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
aromatic biogenic amine degradation (bacteria)	8	1	1
NAD de novo biosynthesis II (from tryptophan)	9	6	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	4	1
myo-, chiro- and scyllo-inositol degradation	10	7	1
8-amino-7-oxononanoate biosynthesis I	11	9	1
superpathway of C1 compounds oxidation to CO2	12	4	1
superpathway of sulfide oxidation (phototrophic sulfur bacteria)	12	3	1
aspartate superpathway	25	23	2
superpathway of NAD biosynthesis in eukaryotes	14	8	1
purine nucleobases degradation I (anaerobic)	15	5	1
salinosporamide A biosynthesis	15	3	1
cyclosporin A biosynthesis	15	2	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	4	1
arsenic detoxification (mammals)	17	8	1
purine nucleobases degradation II (anaerobic)	24	15	1
superpathway of pentose and pentitol degradation	42	11	1
superpathway of L-lysine degradation	43	10	1