Experiment set2IT063 for Escherichia coli BW25113

LB with Spectinomycin dihydrochloride pentahydrate 0.0125 mg/ml

Group: stress
Media: LB + Spectinomycin dihydrochloride pentahydrate (0.0125 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 C5,C6

Specific Phenotypes

For 41 genes in this experiment

For stress Spectinomycin dihydrochloride pentahydrate in Escherichia coli BW25113

For stress Spectinomycin dihydrochloride pentahydrate across organisms

SEED Subsystems

Subsystem	#Specific
Deoxyribose and Deoxynucleoside Catabolism	4
Formate hydrogenase	4
Selenocysteine metabolism	3
Formate dehydrogenase	2
Glycogen metabolism	2
Maltose and Maltodextrin Utilization	2
ATP-dependent RNA helicases, bacterial	1
Acid resistance mechanisms	1
Adenosyl nucleosidases	1
Arginine and Ornithine Degradation	1
CytR regulation	1
Folate Biosynthesis	1
Fructose utilization	1
Glycine and Serine Utilization	1
KDO2-Lipid A biosynthesis	1
Molybdenum cofactor biosynthesis	1
Pentose phosphate pathway	1
Polyamine Metabolism	1
Purine conversions	1
Pyruvate Alanine Serine Interconversions	1
Synechocystis experimental	1
Threonine anaerobic catabolism gene cluster	1
Transport of Manganese	1
Triacylglycerol metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Pentose phosphate pathway
• Ubiquinone and menaquinone biosynthesis
• Selenoamino acid metabolism
• Starch and sucrose metabolism
• alpha-Linolenic acid metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• Fatty acid biosynthesis
• Urea cycle and metabolism of amino groups
• Puromycin biosynthesis
• Pyrimidine metabolism
• Arginine and proline metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Nucleotide sugars metabolism
• Glycerophospholipid metabolism
• Naphthalene and anthracene degradation
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Trinitrotoluene degradation
• Methane metabolism
• Nicotinate and nicotinamide metabolism
• Limonene and pinene degradation
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Aminoacyl-tRNA biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from histidine and purine

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
purine ribonucleosides degradation	6	6	5
purine deoxyribonucleosides degradation I	4	4	3
superpathway of purine deoxyribonucleosides degradation	7	7	5
L-selenocysteine biosynthesis I (bacteria)	3	3	2
purine deoxyribonucleosides degradation II	3	3	2
2-deoxy-α-D-ribose 1-phosphate degradation	3	3	2
glycogen degradation I	8	8	4
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	3
adenine and adenosine salvage III	4	4	2
adenine and adenosine salvage I	2	2	1
guanine and guanosine salvage I	2	2	1
polyphosphate metabolism	2	2	1
formate to trimethylamine N-oxide electron transfer	2	2	1
formate to dimethyl sulfoxide electron transfer	2	2	1
putrescine biosynthesis I	2	2	1
nitrate reduction III (dissimilatory)	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
xanthine and xanthosine salvage	2	2	1
starch degradation V	4	3	2
adenine and adenosine salvage V	3	3	1
superpathway of guanine and guanosine salvage	3	3	1
2-deoxy-D-ribose degradation I	3	3	1
pyrimidine deoxyribonucleosides degradation	3	3	1
glycogen degradation II	6	4	2
formate to nitrite electron transfer	3	2	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	1	1
microcin B17 biosynthesis	3	1	1
putrescine biosynthesis II	3	1	1
purine nucleotides degradation II (aerobic)	11	11	3
guanosine nucleotides degradation III	4	4	1
inosine 5'-phosphate degradation	4	4	1
sucrose biosynthesis II	8	6	2
superpathway of putrescine biosynthesis	4	3	1
starch degradation III	4	2	1
spermidine biosynthesis III	4	2	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
L-selenocysteine biosynthesis II (archaea and eukaryotes)	4	2	1
oxalate degradation VI	4	2	1
adenosine nucleotides degradation II	5	5	1
pentose phosphate pathway (non-oxidative branch) I	5	5	1
CMP-3-deoxy-D-manno-octulosonate biosynthesis	5	5	1
nucleoside and nucleotide degradation (archaea)	10	4	2
oxalate degradation III	5	2	1
molybdopterin biosynthesis	6	6	1
ppGpp metabolism	6	6	1
nucleoside and nucleotide degradation (halobacteria)	6	3	1
fluoroacetate and fluorothreonine biosynthesis	6	1	1
superpathway of purine nucleotide salvage	14	13	2
ureide biosynthesis	7	5	1
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis	7	4	1
pentose phosphate pathway	8	8	1
superpathway of polyamine biosynthesis I	8	7	1
superpathway of polyamine biosynthesis II	8	4	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	7	1
starch degradation II	9	1	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
salinosporamide A biosynthesis	15	3	1
superpathway of glucose and xylose degradation	17	17	1
superpathway of (Kdo)2-lipid A biosynthesis	17	17	1
superpathway of arginine and polyamine biosynthesis	17	16	1
arsenic detoxification (mammals)	17	8	1
purine nucleobases degradation II (anaerobic)	24	17	1
superpathway of Kdo2-lipid A biosynthesis	25	24	1