Experiment set2IT067 for Pseudomonas simiae WCS417

D-Galacturonic Acid monohydrate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Galacturonic Acid monohydrate (20 mM), pH=7
Culturing: fluoroDangl_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 2/18/2015
Media components: 0.25 g/L Ammonium chloride, 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)

Specific Phenotypes

For 6 genes in this experiment

For carbon source D-Galacturonic Acid monohydrate in Pseudomonas simiae WCS417

For carbon source D-Galacturonic Acid monohydrate across organisms

SEED Subsystems

Subsystem	#Specific
D-galactarate, D-glucarate and D-glycerate catabolism	3
D-Galacturonate and D-Glucuronate Utilization	2
Entner-Doudoroff Pathway	1
L-Arabinose utilization	1
Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway	1
Lactose and Galactose Uptake and Utilization	1
N-linked Glycosylation in Bacteria	1
Rhamnose containing glycans	1
Xylose utilization	1
linker unit-arabinogalactan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ascorbate and aldarate metabolism
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Galactose metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Nucleotide sugars metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Caprolactam degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-galactarate degradation II	3	3	3
UDP-α-D-galactose biosynthesis	1	1	1
UDP-N-acetyl-D-galactosamine biosynthesis I	1	1	1
D-glucarate degradation II	3	3	2
D-glucuronate degradation II	5	4	3
D-galacturonate degradation II	5	3	3
D-glucuronate degradation III	2	2	1
D-galacturonate degradation III	2	1	1
UDP-α-D-galactofuranose biosynthesis	2	1	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
sorbitol biosynthesis II	3	2	1
ethanol degradation III	3	2	1
L-lyxonate degradation	3	2	1
hypotaurine degradation	3	2	1
D-galactose detoxification	3	1	1
histamine degradation	3	1	1
trans-4-hydroxy-L-proline degradation II	4	4	1
D-galactarate degradation I	4	3	1
phytol degradation	4	3	1
putrescine degradation III	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	1	1
L-ascorbate biosynthesis VI (plants, myo-inositol pathway)	4	1	1
glucose degradation (oxidative)	5	5	1
superpathway of D-glucarate and D-galactarate degradation	5	4	1
octane oxidation	5	4	1
glucose and glucose-1-phosphate degradation	5	4	1
mitochondrial NADPH production (yeast)	5	4	1
D-galactose degradation I (Leloir pathway)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
D-xylose degradation V	5	1	1
dopamine degradation	5	1	1
D-xylose degradation III	5	1	1
L-arabinose degradation III	6	5	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
L-ascorbate biosynthesis IV (animals, D-glucuronate pathway)	6	3	1
3-methyl-branched fatty acid α-oxidation	6	3	1
D-arabinose degradation III	6	2	1
alkane oxidation	6	1	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	13	5
noradrenaline and adrenaline degradation	13	4	2
L-ascorbate biosynthesis VIII (engineered pathway)	7	5	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
serotonin degradation	7	3	1
ceramide degradation by α-oxidation	7	2	1
stachyose degradation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
aromatic biogenic amine degradation (bacteria)	8	2	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	7	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
teichuronic acid biosynthesis (B. subtilis 168)	9	2	1
UDP-sugars interconversion	9	2	1
colanic acid building blocks biosynthesis	11	8	1
mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	18	1	1
superpathway of pentose and pentitol degradation	42	16	2
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1