Experiment set1IT056 for Pseudomonas fluorescens FW300-N2E3

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D-Ribose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Ribose (20 mM), pH=7
Culturing: pseudo3_N2E3_ML2, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.5 generations
By: Jayashree on 4/28/2014
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 9 genes in this experiment

For carbon source D-Ribose in Pseudomonas fluorescens FW300-N2E3

For carbon source D-Ribose across organisms

SEED Subsystems

Subsystem #Specific
D-ribose utilization 4
Cluster-based Subsystem Grouping Hypotheticals - perhaps Proteosome Related 1
Deoxyribose and Deoxynucleoside Catabolism 1
Fructose utilization 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
UDP-α-D-glucose biosynthesis 2 2 1
ribose phosphorylation 2 1 1
2-deoxy-D-ribose degradation I 3 2 1
GDP-α-D-glucose biosynthesis 3 2 1
trehalose degradation V 3 2 1
starch degradation V 4 3 1
sucrose degradation IV (sucrose phosphorylase) 4 3 1
glycogen biosynthesis I (from ADP-D-Glucose) 4 3 1
starch degradation III 4 2 1
dTDP-β-L-rhamnose biosynthesis 5 5 1
sucrose degradation II (sucrose synthase) 5 4 1
glucose and glucose-1-phosphate degradation 5 4 1
glucosylglycerol biosynthesis 5 2 1
D-galactose degradation I (Leloir pathway) 5 2 1
CDP-6-deoxy-D-gulose biosynthesis 5 1 1
glycogen degradation II 6 5 1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis 6 4 1
glycogen degradation I 8 6 1
sucrose biosynthesis II 8 6 1
glycogen biosynthesis III (from α-maltose 1-phosphate) 8 3 1
sucrose biosynthesis I (from photosynthesis) 9 7 1
chitin biosynthesis 9 5 1
starch biosynthesis 10 5 1
O-antigen building blocks biosynthesis (E. coli) 11 10 1
colanic acid building blocks biosynthesis 11 9 1
streptomycin biosynthesis 18 2 1
superpathway of anaerobic sucrose degradation 19 15 1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis 19 5 1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis 33 13 1