Experiment set8IT011 for Pseudomonas simiae WCS417

2-Deoxy-D-Ribose 10 mM carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 2-Deoxy-D-Ribose (10 mM), pH=7
Culturing: fluoroDangl_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 5/2/18
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)
Growth plate: WCS417_deoxyribosePlus_plate D1

Specific Phenotypes

For 9 genes in this experiment

For carbon source 2-Deoxy-D-Ribose in Pseudomonas simiae WCS417

For carbon source 2-Deoxy-D-Ribose across organisms

SEED Subsystems

Subsystem	#Specific
N-heterocyclic aromatic compound degradation	2
Allantoin Utilization	1
D-galactarate, D-glucarate and D-glycerate catabolism	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine and Serine Utilization	1
Molybdenum cofactor biosynthesis	1
Nitrate and nitrite ammonification	1
Photorespiration (oxidative C2 cycle)	1
Serine-glyoxylate cycle	1
Soluble cytochromes and functionally related electron carriers	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Glycerolipid metabolism
• Glyoxylate and dicarboxylate metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
2-O-α-mannosyl-D-glycerate degradation	2	1	1
2-deoxy-D-ribose degradation II	8	7	3
glycolate and glyoxylate degradation I	4	3	1
D-glucarate degradation I	4	3	1
D-galactarate degradation I	4	3	1
glucose degradation (oxidative)	5	5	1
superpathway of D-glucarate and D-galactarate degradation	5	4	1
superpathway of glycol metabolism and degradation	7	5	1
L-ascorbate biosynthesis VIII (engineered pathway)	7	5	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
photorespiration I	9	5	1
photorespiration III	9	5	1
photorespiration II	10	6	1
formaldehyde assimilation I (serine pathway)	13	6	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	13	1