Experiment set1IT016 for Escherichia coli BW25113

D-Ribose carbon source

Group: carbon source
Media: M9 minimal media_noCarbon + D-Ribose (20 mM)
Culturing: Keio_ML9, tube, Aerobic, at 37 (C), shaken=200 rpm
Growth: about 5.9 generations
By: Kelly on 6/19/2014
Media components: 2 mM Magnesium sulfate, 0.1 mM Calcium chloride, 12.8 g/L Sodium phosphate dibasic heptahydrate, 3 g/L Potassium phosphate monobasic, 0.5 g/L Sodium Chloride, 1 g/L Ammonium chloride

Specific Phenotypes

For 18 genes in this experiment

For carbon source D-Ribose in Escherichia coli BW25113

For carbon source D-Ribose across organisms

SEED Subsystems

Subsystem	#Specific
D-ribose utilization	2
Autoinducer 2 (AI-2) transport and processing (lsrACDBFGE operon)	1
Bacterial Cell Division	1
Bacterial Cytoskeleton	1
CBSS-562.2.peg.5158 SK3 including	1
Calvin-Benson cycle	1
Deoxyribose and Deoxynucleoside Catabolism	1
Entner-Doudoroff Pathway	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Lysine Biosynthesis DAP Pathway	1
Mannitol Utilization	1
Methylcitrate cycle	1
Photorespiration (oxidative C2 cycle)	1
Propionate-CoA to Succinate Module	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Threonine and Homoserine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Glycine, serine and threonine metabolism
• Tyrosine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Fatty acid biosynthesis
• Biosynthesis of steroids
• Purine metabolism
• Lysine biosynthesis
• Lysine degradation
• Benzoate degradation via hydroxylation
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Butanoate metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
ribose phosphorylation	2	2	2
glycolate and glyoxylate degradation II	2	2	1
2-O-α-mannosyl-D-glycerate degradation	2	2	1
L-homoserine biosynthesis	3	3	1
2-deoxy-D-ribose degradation I	3	3	1
autoinducer AI-2 degradation	3	3	1
superpathway of glycol metabolism and degradation	7	7	2
glycolate and glyoxylate degradation I	4	4	1
D-glucarate degradation I	4	4	1
D-galactarate degradation I	4	4	1
chitin deacetylation	4	3	1
dipicolinate biosynthesis	4	3	1
spermidine biosynthesis II	4	2	1
L-methionine biosynthesis IV	4	2	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	2
superpathway of D-glucarate and D-galactarate degradation	5	5	1
2-methylcitrate cycle I	5	5	1
Rubisco shunt	10	9	2
ectoine biosynthesis	5	2	1
glyoxylate cycle	6	6	1
superpathway of L-threonine biosynthesis	6	6	1
norspermidine biosynthesis	6	2	1
L-lysine biosynthesis III	7	6	1
L-lysine biosynthesis VI	7	6	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
3-dehydroquinate biosynthesis II (archaea)	7	3	1
D-xylose degradation IV	7	3	1
cremeomycin biosynthesis	7	2	1
superpathway of L-homoserine and L-methionine biosynthesis	8	8	1
2-deoxy-D-ribose degradation II	8	3	1
superpathway of polyamine biosynthesis III	8	2	1
grixazone biosynthesis	8	2	1
L-arabinose degradation IV	8	2	1
L-lysine biosynthesis I	9	9	1
Entner-Doudoroff pathway I	9	9	1
superpathway of S-adenosyl-L-methionine biosynthesis	9	9	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	9	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	6	1
L-lysine biosynthesis II	9	6	1
photorespiration III	9	5	1
photorespiration I	9	5	1
tunicamycin biosynthesis	9	2	1
glycolysis IV	10	8	1
glycolysis V (Pyrococcus)	10	7	1
photorespiration II	10	6	1
glycolysis III (from glucose)	11	11	1
glycolysis II (from fructose 6-phosphate)	11	11	1
glycolysis VI (from fructose)	11	8	1
homolactic fermentation	12	12	1
superpathway of glyoxylate bypass and TCA	12	11	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	10	1
chorismate biosynthesis II (archaea)	12	8	1
superpathway of L-isoleucine biosynthesis I	13	13	1
glycolysis I (from glucose 6-phosphate)	13	13	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	2
Calvin-Benson-Bassham cycle	13	10	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
formaldehyde assimilation I (serine pathway)	13	8	1
1-butanol autotrophic biosynthesis (engineered)	27	19	2
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	2	1
Bifidobacterium shunt	15	13	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
mixed acid fermentation	16	16	1
glycerol degradation to butanol	16	11	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	1
superpathway of glucose and xylose degradation	17	17	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
oxygenic photosynthesis	17	11	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	1
superpathway of hexitol degradation (bacteria)	18	18	1
heterolactic fermentation	18	16	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	19	1
superpathway of anaerobic sucrose degradation	19	17	1
superpathway of N-acetylneuraminate degradation	22	22	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
aspartate superpathway	25	24	1
ethene biosynthesis V (engineered)	25	18	1
platensimycin biosynthesis	26	6	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	19	1
superpathway of pentose and pentitol degradation	42	18	1