Experiment set42IT067 for Escherichia coli BW25113

LB + carbenicillin regrowth after 48hr

Group: stress
Media: LB + Carbenicillin disodium salt (0.0044 mg/mL), pH=7
Culturing: Keio_ML9a, 50mL bottle, Anaerobic, at 37 (C), shaken=0 rpm
By: Charlotte Brannon/Becca Culver on 21-Oct-20
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 15 genes in this experiment

For stress Carbenicillin disodium salt in Escherichia coli BW25113

For stress Carbenicillin disodium salt across organisms

SEED Subsystems

Subsystem	#Specific
DNA repair, bacterial	3
DNA-replication	1
DNA repair, bacterial UvrD and related helicases	1
Heat shock dnaK gene cluster extended	1
Lysine degradation	1
Serine-glyoxylate cycle	1
Succinate dehydrogenase	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Citrate cycle (TCA cycle)
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Lysine degradation
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Thiamine metabolism
• Folate biosynthesis
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
cadaverine biosynthesis	1	1	1
NADH to fumarate electron transfer	2	2	1
glycerol-3-phosphate to fumarate electron transfer	2	2	1
succinate to cytochrome aa3 oxidase electron transfer	2	1	1
hydrogen to fumarate electron transfer	2	1	1
aminopropylcadaverine biosynthesis	3	3	1
UTP and CTP dephosphorylation I	7	5	2
desferrioxamine E biosynthesis	5	1	1
bisucaberin biosynthesis	5	1	1
desferrioxamine B biosynthesis	5	1	1
lupanine biosynthesis	5	1	1
L-lysine degradation X	6	5	1
L-lysine degradation I	7	7	1
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	6	1
incomplete reductive TCA cycle	7	5	1
pyruvate fermentation to propanoate I	7	5	1
superpathway of polyamine biosynthesis I	8	7	1
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	6	1
pyrimidine deoxyribonucleotides de novo biosynthesis I	9	9	1
pyrimidine deoxyribonucleotides de novo biosynthesis III	9	8	1
TCA cycle VI (Helicobacter)	9	7	1
peptidoglycan recycling II	10	7	1
reductive TCA cycle I	11	8	1
L-glutamate degradation VIII (to propanoate)	11	5	1
reductive TCA cycle II	12	8	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	14	1
peptidoglycan recycling I	14	14	1
mixed acid fermentation	16	16	1
superpathway of arginine and polyamine biosynthesis	17	16	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	18	1
superpathway of L-lysine degradation	43	14	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1