Experiment set2IT062 for Escherichia coli BW25113

LB with Spectinomycin dihydrochloride pentahydrate 0.00625 mg/ml

Group: stress
Media: LB + Spectinomycin dihydrochloride pentahydrate (0.00625 mg/ml)
Culturing: Keio_ML9, 48 well microplate; Tecan Infinite F200, Aerobic, at 28 (C), shaken=orbital
By: Kelly on 6/30/2014
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 959 C3,C4

Specific Phenotypes

For 20 genes in this experiment

For stress Spectinomycin dihydrochloride pentahydrate in Escherichia coli BW25113

For stress Spectinomycin dihydrochloride pentahydrate across organisms

SEED Subsystems

Subsystem	#Specific
Formate hydrogenase	3
Selenocysteine metabolism	3
Deoxyribose and Deoxynucleoside Catabolism	2
Formate dehydrogenase	2
Acid resistance mechanisms	1
Arginine and Ornithine Degradation	1
CytR regulation	1
Folate Biosynthesis	1
Fructose utilization	1
Glycine and Serine Utilization	1
Glycogen metabolism	1
Maltose and Maltodextrin Utilization	1
Pentose phosphate pathway	1
Polyamine Metabolism	1
Pyruvate Alanine Serine Interconversions	1
Threonine anaerobic catabolism gene cluster	1
Transport of Manganese	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Selenoamino acid metabolism
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Starch and sucrose metabolism
• Glyoxylate and dicarboxylate metabolism
• Methane metabolism
• Aminoacyl-tRNA biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
formate oxidation to CO2	1	1	1
arginine dependent acid resistance	1	1	1
L-selenocysteine biosynthesis I (bacteria)	3	3	2
formate to dimethyl sulfoxide electron transfer	2	2	1
formate to trimethylamine N-oxide electron transfer	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
putrescine biosynthesis I	2	2	1
nitrate reduction III (dissimilatory)	2	2	1
2-deoxy-D-ribose degradation I	3	3	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	3	1
formate to nitrite electron transfer	3	2	1
putrescine biosynthesis II	3	1	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	1	1
heme b biosynthesis I (aerobic)	4	4	1
heme b biosynthesis II (oxygen-independent)	4	4	1
heme b biosynthesis V (aerobic)	4	4	1
starch degradation V	4	3	1
superpathway of putrescine biosynthesis	4	3	1
oxalate degradation VI	4	2	1
L-selenocysteine biosynthesis II (archaea and eukaryotes)	4	2	1
spermidine biosynthesis III	4	2	1
pentose phosphate pathway (non-oxidative branch) I	5	5	1
oxalate degradation III	5	2	1
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	6	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	1
superpathway of purine deoxyribonucleosides degradation	7	7	1
glycogen degradation I	8	8	1
pentose phosphate pathway	8	8	1
superpathway of heme b biosynthesis from glycine	8	7	1
superpathway of polyamine biosynthesis I	8	7	1
sucrose biosynthesis II	8	6	1
superpathway of polyamine biosynthesis II	8	4	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	7	1
starch degradation II	9	1	1
superpathway of heme b biosynthesis from glutamate	10	10	1
Rubisco shunt	10	9	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	11	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
superpathway of C1 compounds oxidation to CO2	12	4	1
superpathway of L-arginine and L-ornithine degradation	13	13	1
Bifidobacterium shunt	15	13	1
purine nucleobases degradation I (anaerobic)	15	6	1
superpathway of glucose and xylose degradation	17	17	1
superpathway of arginine and polyamine biosynthesis	17	16	1
purine nucleobases degradation II (anaerobic)	24	17	1