Experiment set53IT058 for Escherichia coli BW25113

M9 no stress control; Anaerobic 48 hr

Group: no stress control anaerobic
Media: M9
Culturing: Keio_ML9a_ucsf, tube, Anaerobic, at 37 (C), shaken=200 rpm
By: Ben Guthrie on 8/11/21
Media components: 4 g/L D-Glucose, 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 10 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Succinate dehydrogenase	4
Serine-glyoxylate cycle	2
TCA Cycle	2
Arginine Biosynthesis extended	1
Coenzyme A Biosynthesis	1
Glycolate, glyoxylate interconversions	1
Lysine Biosynthesis DAP Pathway	1
Orphan regulatory proteins	1
Photorespiration (oxidative C2 cycle)	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lysine biosynthesis
• Arginine and proline metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Citrate cycle (TCA cycle)
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• C21-Steroid hormone metabolism
• Oxidative phosphorylation
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Bisphenol A degradation
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Linoleic acid metabolism
• Tetrachloroethene degradation
• Glyoxylate and dicarboxylate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Pantothenate and CoA biosynthesis
• Retinol metabolism
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide products
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
NADH to fumarate electron transfer	2	2	1
succinate to cytochrome bd oxidase electron transfer	2	2	1
glycerol-3-phosphate to fumarate electron transfer	2	2	1
glycolate and glyoxylate degradation II	2	2	1
succinate to cytochrome bo oxidase electron transfer	2	1	1
hydrogen to fumarate electron transfer	2	1	1
succinate to cytochrome aa3 oxidase electron transfer	2	1	1
aerobic respiration III (alternative oxidase pathway)	3	2	1
glycolate and glyoxylate degradation III	3	1	1
phosphopantothenate biosynthesis I	4	4	1
glycolate and glyoxylate degradation I	4	4	1
aerobic respiration I (cytochrome c)	4	2	1
aerobic respiration II (cytochrome c) (yeast)	4	2	1
phosphopantothenate biosynthesis III (archaea)	4	2	1
L-ornithine biosynthesis I	5	5	1
L-arginine degradation II (AST pathway)	5	5	1
superpathway of glycol metabolism and degradation	7	7	1
incomplete reductive TCA cycle	7	5	1
pyruvate fermentation to propanoate I	7	5	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
superpathway of coenzyme A biosynthesis I (bacteria)	9	9	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
TCA cycle VI (Helicobacter)	9	7	1
photorespiration I	9	5	1
photorespiration III	9	5	1
L-lysine degradation V	9	2	1
L-arginine biosynthesis II (acetyl cycle)	10	9	1
TCA cycle III (animals)	10	8	1
photorespiration II	10	6	1
superpathway of coenzyme A biosynthesis II (plants)	10	5	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
mixed acid fermentation	16	16	1
superpathway of arginine and polyamine biosynthesis	17	16	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	1
aspartate superpathway	25	24	1
superpathway of L-lysine degradation	43	14	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1