Experiment set1IT032 for Escherichia coli BW25113

Sodium D-Lactate carbon source

Group: carbon source
Media: M9 minimal media_noCarbon + Sodium D-Lactate (20 mM)
Culturing: Keio_ML9, tube, Aerobic, at 37 (C), shaken=200 rpm
Growth: about 5.5 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 9 genes in this experiment

For carbon source Sodium D-Lactate in Escherichia coli BW25113

For carbon source Sodium D-Lactate across organisms

SEED Subsystems

Subsystem	#Specific
Lactate utilization	3
Autoinducer 2 (AI-2) transport and processing (lsrACDBFGE operon)	1
CBSS-562.2.peg.5158 SK3 including	1
DNA-binding regulatory proteins, strays	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Methylcitrate cycle	1
Propionate-CoA to Succinate Module	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Respiratory dehydrogenases 1	1
Ribosomal protein S5p acylation	1
Ribosome biogenesis bacterial	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Tyrosine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Fatty acid biosynthesis
• Lysine degradation
• Benzoate degradation via hydroxylation
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyruvate fermentation to (R)-lactate	1	1	1
D-lactate to cytochrome bo oxidase electron transfer	2	1	1
autoinducer AI-2 degradation	3	3	1
L-alanine degradation II (to D-lactate)	3	2	1
2-chloroacrylate degradation I	3	2	1
vancomycin resistance I	3	2	1
2-methylcitrate cycle I	5	5	1
L-alanine degradation VI (reductive Stickland reaction)	6	2	1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	5	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	8	1
superpathway of L-alanine fermentation (Stickland reaction)	9	5	1
glycolysis V (Pyrococcus)	10	7	1
glycolysis II (from fructose 6-phosphate)	11	11	1
glycolysis I (from glucose 6-phosphate)	13	13	1
gluconeogenesis I	13	13	1
mixed acid fermentation	16	16	1
superpathway of glucose and xylose degradation	17	17	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	1
superpathway of hexitol degradation (bacteria)	18	18	1
heterolactic fermentation	18	16	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	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 glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1