Experiment set9IT043 for Escherichia coli BW25113

LB Anaerobic with Amoxicillin 0.0000078125 mM

Group: stress
Media: LB + Amoxicillin (7.81E-03 mM)
Culturing: Keio_ML9a, 96 deep-well microplate; Multitron, Anaerobic, at 37 (C), shaken=0 rpm
By: Hans_Hualan on 7/20/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 13 genes in this experiment

For stress Amoxicillin in Escherichia coli BW25113

For stress Amoxicillin across organisms

SEED Subsystems

Subsystem	#Specific
Entner-Doudoroff Pathway	2
Glycolysis and Gluconeogenesis	2
Glycolysis and Gluconeogenesis, including Archaeal enzymes	2
Beta-lactamase	1
CBSS-562.2.peg.5158 SK3 including	1
DNA repair, bacterial	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Tn552	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Penicillin and cephalosporin biosynthesis
• beta-Lactam resistance
• Tryptophan metabolism
• D-Alanine metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Peptidoglycan biosynthesis
• Pyruvate metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of siderophore group nonribosomal peptides

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-aspartate degradation II (aerobic)	3	3	1
L-aspartate degradation III (anaerobic)	3	3	1
peptidoglycan recycling II	10	7	3
Entner-Doudoroff pathway III (semi-phosphorylative)	9	6	2
peptidoglycan recycling I	14	14	3
Rubisco shunt	10	9	2
glycolysis IV	10	8	2
glycolysis V (Pyrococcus)	10	7	2
glycolysis III (from glucose)	11	11	2
glycolysis II (from fructose 6-phosphate)	11	11	2
glycolysis VI (from fructose)	11	8	2
homolactic fermentation	12	12	2
glycolysis I (from glucose 6-phosphate)	13	13	2
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
Bifidobacterium shunt	15	13	2
UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-diaminopimelate containing)	8	8	1
UDP-N-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)	8	7	1
UDP-N-acetylmuramoyl-pentapeptide biosynthesis III (meso-diaminopimelate containing)	8	6	1
glycerol degradation to butanol	16	11	2
superpathway of glucose and xylose degradation	17	17	2
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	2
superpathway of hexitol degradation (bacteria)	18	18	2
Entner-Doudoroff pathway I	9	9	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	19	2
superpathway of anaerobic sucrose degradation	19	17	2
photorespiration II	10	6	1
superpathway of N-acetylneuraminate degradation	22	22	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	12	1
gluconeogenesis I	13	13	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
1-butanol autotrophic biosynthesis (engineered)	27	19	2
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
mixed acid fermentation	16	16	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
peptidoglycan biosynthesis II (staphylococci)	17	12	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	1
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	1
heterolactic fermentation	18	16	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
ethene biosynthesis V (engineered)	25	18	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1