Experiment set5H12 for Phaeobacter inhibens DSM 17395

D-Xylose carbon source

Group: carbon source
Media: DinoMM_noCarbon_HighNutrient + D-Xylose (20 mM), pH=7
Culturing: Phaeo_ML1, tube, Aerobic, at 25 (C), shaken=200 rpm
Growth: about 5.1 generations
By: Adam on marchapr14
Media components: 20 g/L Sea salts, 0.3 g/L Ammonium Sulfate, 0.1 g/L Potassium phosphate monobasic, 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)

Specific Phenotypes

For 12 genes in this experiment

For carbon source D-Xylose in Phaeobacter inhibens DSM 17395

For carbon source D-Xylose across organisms

SEED Subsystems

Subsystem	#Specific
Xylose utilization	3
Isobutyryl-CoA to Propionyl-CoA Module	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Pyrimidine utilization	1
Redox-dependent regulation of nucleus processes	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	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
• Pentose and glucuronate interconversions
• Fatty acid metabolism
• Lysine degradation
• Benzoate degradation via hydroxylation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Ethylbenzene degradation
• Butanoate metabolism
• Biosynthesis of unsaturated fatty acids
• Fructose and mannose metabolism
• Fatty acid biosynthesis
• Fatty acid elongation in mitochondria
• Synthesis and degradation of ketone bodies
• Geraniol degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Taurine and hypotaurine metabolism
• Lipopolysaccharide biosynthesis
• Inositol phosphate metabolism
• Glycerophospholipid metabolism
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Nicotinate and nicotinamide metabolism
• Terpenoid biosynthesis
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-xylose degradation I	2	2	2
taurine degradation I	1	1	1
3-oxoadipate degradation	2	2	1
acetoacetate degradation (to acetyl CoA)	2	1	1
β-alanine degradation II	2	1	1
D-arabinitol degradation I	2	1	1
xylitol degradation I	2	1	1
β-alanine degradation I	2	1	1
5,6-dehydrokavain biosynthesis (engineered)	10	6	4
hypotaurine degradation	3	3	1
benzoyl-CoA biosynthesis	3	3	1
ketolysis	3	3	1
polyhydroxybutanoate biosynthesis	3	2	1
(2S)-ethylmalonyl-CoA biosynthesis	4	3	1
oleate β-oxidation	35	30	8
valproate β-oxidation	9	6	2
phenylacetate degradation I (aerobic)	9	6	2
2-methyl-branched fatty acid β-oxidation	14	10	3
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	5	1
adipate degradation	5	5	1
NAD salvage pathway V (PNC V cycle)	5	4	1
adipate biosynthesis	5	4	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
ketogenesis	5	3	1
propanoyl-CoA degradation II	5	3	1
glutaryl-CoA degradation	5	3	1
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast)	10	4	2
4-hydroxybenzoate biosynthesis III (plants)	5	2	1
pyruvate fermentation to acetone	5	1	1
ethylbenzene degradation (anaerobic)	5	1	1
fatty acid β-oxidation VII (yeast peroxisome)	5	1	1
isopropanol biosynthesis (engineered)	5	1	1
pyruvate fermentation to hexanol (engineered)	11	7	2
superpathway of phenylethylamine degradation	11	6	2
fatty acid salvage	6	6	1
catechol degradation III (ortho-cleavage pathway)	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
superpathway of taurine degradation	6	4	1
L-isoleucine degradation I	6	4	1
propanoate fermentation to 2-methylbutanoate	6	3	1
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast)	6	1	1
4-ethylphenol degradation (anaerobic)	6	1	1
jasmonic acid biosynthesis	19	4	3
myo-inositol degradation I	7	7	1
NAD salvage pathway I (PNC VI cycle)	7	6	1
superpathway of salicylate degradation	7	5	1
fatty acid β-oxidation I (generic)	7	5	1
acetyl-CoA fermentation to butanoate	7	4	1
4-methylcatechol degradation (ortho cleavage)	7	4	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	1
pyruvate fermentation to butanoate	7	3	1
benzoyl-CoA degradation I (aerobic)	7	3	1
mevalonate pathway I (eukaryotes and bacteria)	7	2	1
mevalonate pathway II (haloarchaea)	7	2	1
2,4-dinitrotoluene degradation	7	1	1
L-valine degradation I	8	5	1
pyruvate fermentation to butanol I	8	3	1
2-deoxy-D-ribose degradation II	8	3	1
mevalonate pathway IV (archaea)	8	2	1
isoprene biosynthesis II (engineered)	8	2	1
mevalonate pathway III (Thermoplasma)	8	2	1
2-methylpropene degradation	8	2	1
androstenedione degradation I (aerobic)	25	6	3
superpathway of glucose and xylose degradation	17	14	2
aromatic compounds degradation via β-ketoadipate	9	7	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
4-oxopentanoate degradation	9	2	1
superpathway of testosterone and androsterone degradation	28	6	3
myo-, chiro- and scyllo-inositol degradation	10	7	1
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)	10	5	1
3-phenylpropanoate degradation	10	4	1
L-glutamate degradation V (via hydroxyglutarate)	10	4	1
L-lysine fermentation to acetate and butanoate	10	3	1
methyl tert-butyl ether degradation	10	2	1
superpathway of cholesterol degradation I (cholesterol oxidase)	42	8	4
toluene degradation III (aerobic) (via p-cresol)	11	7	1
ethylmalonyl-CoA pathway	11	7	1
NAD salvage (plants)	11	6	1
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	5	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	9	4
L-glutamate degradation VII (to butanoate)	12	4	1
10-cis-heptadecenoyl-CoA degradation (yeast)	12	2	1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	2	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
androstenedione degradation II (anaerobic)	27	4	2
superpathway of glyoxylate cycle and fatty acid degradation	14	10	1
superpathway of NAD biosynthesis in eukaryotes	14	8	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
L-tryptophan degradation III (eukaryotic)	15	5	1
glycerol degradation to butanol	16	9	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	4	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	4	1
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	2	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
mandelate degradation to acetyl-CoA	18	7	1
toluene degradation VI (anaerobic)	18	4	1
sitosterol degradation to androstenedione	18	1	1
superpathway of pentose and pentitol degradation	42	11	2
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	3	1
superpathway of cholesterol degradation III (oxidase)	49	5	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	20	1
platensimycin biosynthesis	26	6	1
superpathway of ergosterol biosynthesis I	26	4	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
superpathway of aerobic toluene degradation	30	11	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	14	1
superpathway of cholesterol biosynthesis	38	4	1
superpathway of L-lysine degradation	43	10	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1