Experiment set68S101 for Escherichia coli BW25113

LMW_DNA_from_Lysinibacillus_FW301-JW8 7.7 ppm carbon source

Group: carbon source
Media: Chakraborty_Basal + LMW_DNA_from_Lysinibacillus_FW301-JW8 (7.7 ppm), pH=7
Culturing: Keio_ML9a, tube, Aerobic, at 29 (C), shaken=200 rpm
By: Bri Finley on 9/16/24
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 0.3792 g/L Sodium phosphate monobasic, 0.9713 g/L Disodium phosphate, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 23 genes in this experiment

For carbon source LMW_DNA_from_Lysinibacillus_FW301-JW8 in Escherichia coli BW25113

For carbon source LMW_DNA_from_Lysinibacillus_FW301-JW8 across organisms

SEED Subsystems

Subsystem	#Specific
Curli production	5
Glycerol and Glycerol-3-phosphate Uptake and Utilization	2
Polyamine Metabolism	2
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	1
CytR regulation	1
D-ribose utilization	1
Deoxyribose and Deoxynucleoside Catabolism	1
Glycerol fermenation to 1,3-propanediol	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
MLST	1
Thioredoxin-disulfide reductase	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Urea cycle and metabolism of amino groups
• Methionine metabolism
• Arginine and proline metabolism
• Glutathione metabolism
• Pentose phosphate pathway
• beta-Alanine metabolism
• Glycerolipid metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
spermidine biosynthesis I	2	2	2
glycerol degradation I	3	3	2
aminopropylcadaverine biosynthesis	3	3	2
glycerol and glycerophosphodiester degradation	4	4	2
ribose phosphorylation	2	2	1
arsenate detoxification III	2	2	1
spermine biosynthesis	2	1	1
superpathway of polyamine biosynthesis I	8	7	3
2-deoxy-D-ribose degradation I	3	3	1
superpathway of polyamine biosynthesis II	8	4	2
spermidine biosynthesis III	4	2	1
L-methionine salvage cycle III	11	5	2
superpathway of arginine and polyamine biosynthesis	17	16	3
arsenic detoxification (plants)	6	5	1
L-methionine salvage cycle I (bacteria and plants)	12	5	2
arsenic detoxification (yeast)	12	4	1
arsenic detoxification (mammals)	17	8	1