Experiment set1IT004 for Caulobacter crescentus NA1000

D-Xylose carbon source

Group: carbon source
Media: M2_noCarbon + D-Xylose (20 mM)
Culturing: Caulo_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 5.3 generations
By: Jayashree on 22-Mar-17
Media components: 1.74 g/L Disodium phosphate, 1.06 g/L Potassium phosphate monobasic, 0.5 g/L Ammonium chloride, 0.5 mM Magnesium sulfate, 0.5 mM Calcium chloride, 0.01 mM Iron (II) sulfate heptahydrate, 0.008 mM EDTA
Growth plate: 1521 A4

Specific Phenotypes

For 7 genes in this experiment

For carbon source D-Xylose in Caulobacter crescentus NA1000

For carbon source D-Xylose across organisms

SEED Subsystems

Subsystem	#Specific
Xylose utilization	4
D-Galacturonate and D-Glucuronate Utilization	2
Proline, 4-hydroxyproline uptake and utilization	2

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose and glucuronate interconversions
• Ascorbate and aldarate metabolism
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• 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
• Pantothenate and CoA biosynthesis
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-xylose degradation V	5	5	4
D-xylose degradation III	5	4	3
pyruvate fermentation to acetate VIII	2	1	1
mitochondrial NADPH production (yeast)	5	3	2
D-xylose degradation VI	5	2	2
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	3
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
ethanol degradation III	3	2	1
L-lyxonate degradation	3	2	1
hypotaurine degradation	3	2	1
histamine degradation	3	1	1
D-galactarate degradation II	3	1	1
L-carnitine degradation II	3	1	1
D-glucarate degradation II	3	1	1
D-xylose degradation IV	7	4	2
L-valine biosynthesis	4	4	1
phytol degradation	4	3	1
1,2-dichloroethane degradation	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
putrescine degradation III	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
D-xylose degradation to ethylene glycol (engineered)	4	1	1
trans-4-hydroxy-L-proline degradation II	4	1	1
cytosolic NADPH production (yeast)	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	2	1
octane oxidation	5	2	1
D-glucuronate degradation II	5	2	1
D-galacturonate degradation II	5	1	1
L-isoleucine biosynthesis IV	6	4	1
D-arabinose degradation III	6	3	1
L-arabinose degradation III	6	3	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
L-isoleucine biosynthesis I (from threonine)	7	7	1
serotonin degradation	7	4	1
L-isoleucine biosynthesis III	7	4	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
L-isoleucine biosynthesis II	8	6	1
aromatic biogenic amine degradation (bacteria)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
superpathway of pentose and pentitol degradation	42	12	5
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-threonine metabolism	18	9	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	13	1