Experiment set58S331 for Escherichia coli BW25113

retron_Ec_48_control

Group: retron_ec_48_control
Media: LB + Kanamycin sulfate (0.05 mg/mL) + Chloramphenicol (34 0.034)
Culturing: Keio_ML9a, bioassay_dish, Aerobic, at 37 (C), (Solid)
By: Kate Miller/Brady Cress/Ben Adler on 10-Apr-23
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 16 genes in this experiment

For retron_ec_48_control Kanamycin sulfate in Escherichia coli BW25113

For retron_ec_48_control Kanamycin sulfate across organisms

SEED Subsystems

Subsystem	#Specific
DNA-replication	2
Cysteine Biosynthesis	1
D-gluconate and ketogluconates metabolism	1
DNA repair, bacterial	1
Formate hydrogenase	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycerol fermenation to 1,3-propanediol	1
Glycine and Serine Utilization	1
Peptidoglycan Biosynthesis	1
Potassium homeostasis	1
Pyruvate Alanine Serine Interconversions	1
Threonine anaerobic catabolism gene cluster	1
Type IV pilus	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Peptidoglycan biosynthesis
• Fructose and mannose metabolism
• Glycolysis / Gluconeogenesis
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Lysine degradation
• Cyanoamino acid metabolism
• Starch and sucrose metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Biotin metabolism
• Carotenoid biosynthesis - General
• Zeatin biosynthesis
• Nitrogen metabolism
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
hydrogen production V	1	1	1
hydrogen production III	1	1	1
hydrogen production VIII	1	1	1
L-asparagine biosynthesis II	1	1	1
D-serine degradation	3	3	2
L-tryptophan degradation II (via pyruvate)	3	3	2
L-cysteine degradation II	3	2	2
superpathway of L-asparagine biosynthesis	2	2	1
arsenate detoxification III	2	2	1
superpathway of hydrogen production	2	1	1
hydrogen production VI	2	1	1
glycine betaine degradation III	7	4	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	4	3
glycerol degradation I	3	3	1
glycine degradation	3	3	1
L-methionine biosynthesis II	6	5	2
superpathway of L-aspartate and L-asparagine biosynthesis	4	4	1
glycerol and glycerophosphodiester degradation	4	4	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	6	3
L-mimosine degradation	8	4	2
glutathione-mediated detoxification I	8	3	2
arsenic detoxification (plants)	6	5	1
superpathway of photosynthetic hydrogen production	6	3	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
purine nucleobases degradation II (anaerobic)	24	17	3
peptidoglycan biosynthesis II (staphylococci)	17	12	2
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	2
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
superpathway of fermentation (Chlamydomonas reinhardtii)	9	8	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	12	1
L-glutamate degradation VII (to butanoate)	12	5	1
arsenic detoxification (yeast)	12	4	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
mixed acid fermentation	16	16	1
arsenic detoxification (mammals)	17	8	1