Experiment set2IT026 for Escherichia coli BW25113

LB with Cephalothin sodium salt 0.01 mg/ml

Group: stress
Media: LB + Cephalothin sodium salt (0.01 mg/ml)
Culturing: Keio_ML9, 48 well microplate; Tecan Infinite F200, Aerobic, at 28 (C), shaken=orbital
By: Kelly on 6/24/2014
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 965 A7,A8

Specific Phenotypes

For 49 genes in this experiment

For stress Cephalothin sodium salt in Escherichia coli BW25113

For stress Cephalothin sodium salt across organisms

SEED Subsystems

Subsystem	#Specific
D-ribose utilization	2
Type IV pilus	2
ATP-dependent RNA helicases, bacterial	1
Biogenesis of cytochrome c oxidases	1
CBSS-562.2.peg.5158 SK3 including	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
D-Galacturonate and D-Glucuronate Utilization	1
DNA repair, bacterial	1
DNA topoisomerases, Type I, ATP-independent	1
Deoxyribose and Deoxynucleoside Catabolism	1
Folate Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine and Serine Utilization	1
Heat shock dnaK gene cluster extended	1
KDO2-Lipid A biosynthesis	1
Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes	1
Pentose phosphate pathway	1
Peptidoglycan Biosynthesis	1
Peptidyl-prolyl cis-trans isomerase	1
Polyamine Metabolism	1
Potassium homeostasis	1
Proteasome bacterial	1
Proteolysis in bacteria, ATP-dependent	1
Pyruvate Alanine Serine Interconversions	1
Rhamnose containing glycans	1
Serine-glyoxylate cycle	1
Succinate dehydrogenase	1
TCA Cycle	1
Threonine anaerobic catabolism gene cluster	1
Threonine degradation	1
Trehalose Uptake and Utilization	1
dTDP-rhamnose synthesis	1
linker unit-arabinogalactan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Nucleotide sugars metabolism
• Ascorbate and aldarate metabolism
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Galactose metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Puromycin biosynthesis
• Pyrimidine metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine biosynthesis
• Tryptophan metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Glycerophospholipid metabolism
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Trinitrotoluene degradation
• Butanoate metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Drug metabolism - other enzymes
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of vancomycin group antibiotics
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
S-methyl-5'-thioadenosine degradation II	1	1	1
L-alanine biosynthesis II	1	1	1
L-alanine degradation III	1	1	1
adenine and adenosine salvage III	4	4	3
adenine and adenosine salvage V	3	3	2
purine ribonucleosides degradation	6	6	3
superpathway of L-alanine biosynthesis	4	4	2
L-alanine biosynthesis I	2	2	1
L-alanine degradation V (oxidative Stickland reaction)	2	2	1
glycerol-3-phosphate to fumarate electron transfer	2	2	1
adenine and adenosine salvage I	2	2	1
NADH to fumarate electron transfer	2	2	1
di-trans,poly-cis-undecaprenyl phosphate biosynthesis	2	2	1
hydrogen to fumarate electron transfer	2	1	1
succinate to cytochrome aa3 oxidase electron transfer	2	1	1
adenosine nucleotides degradation II	5	5	2
pyrimidine deoxyribonucleosides salvage	5	4	2
cardiolipin biosynthesis I	3	3	1
cardiolipin biosynthesis III	3	3	1
pentose phosphate pathway (oxidative branch) I	3	3	1
cardiolipin biosynthesis II	3	3	1
pyruvate fermentation to acetate and alanine	3	2	1
L-alanine degradation II (to D-lactate)	3	2	1
peptidoglycan recycling II	10	7	3
dTDP-N-acetylthomosamine biosynthesis	4	4	1
dTDP-β-D-fucofuranose biosynthesis	4	2	1
dTDP-6-deoxy-α-D-allose biosynthesis	4	2	1
dTDP-N-acetylviosamine biosynthesis	4	2	1
superpathway of pyrimidine deoxyribonucleoside salvage	9	8	2
peptidoglycan recycling I	14	14	3
CMP-3-deoxy-D-manno-octulosonate biosynthesis	5	5	1
polyisoprenoid biosynthesis (E. coli)	5	5	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
dTDP-4-O-demethyl-β-L-noviose biosynthesis	5	3	1
dTDP-3-acetamido-3,6-dideoxy-α-D-glucose biosynthesis	5	2	1
dTDP-α-D-mycaminose biosynthesis	5	2	1
dTDP-3-acetamido-α-D-fucose biosynthesis	5	2	1
purine nucleotides degradation II (aerobic)	11	11	2
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	8	2
phosphatidylglycerol biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis II	6	6	1
dTDP-L-daunosamine biosynthesis	6	3	1
dTDP-sibirosamine biosynthesis	6	3	1
dTDP-α-D-ravidosamine and dTDP-4-acetyl-α-D-ravidosamine biosynthesis	6	2	1
dTDP-D-desosamine biosynthesis	6	2	1
L-alanine degradation VI (reductive Stickland reaction)	6	2	1
pyruvate fermentation to propanoate I	7	5	1
incomplete reductive TCA cycle	7	5	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis	7	4	1
dTDP-β-L-digitoxose biosynthesis	7	3	1
dTDP-β-L-olivose biosynthesis	7	3	1
dTDP-β-L-mycarose biosynthesis	7	2	1
pentose phosphate pathway	8	8	1
dTDP-β-L-4-epi-vancosamine biosynthesis	8	3	1
dTDP-β-L-megosamine biosynthesis	8	3	1
TCA cycle VI (Helicobacter)	9	7	1
superpathway of L-alanine fermentation (Stickland reaction)	9	5	1
dTDP-α-D-olivose, dTDP-α-D-oliose and dTDP-α-D-mycarose biosynthesis	9	3	1
dTDP-α-D-forosamine biosynthesis	9	3	1
superpathway of enterobacterial common antigen biosynthesis	10	9	1
nucleoside and nucleotide degradation (archaea)	10	4	1
O-antigen building blocks biosynthesis (E. coli)	11	11	1
reductive TCA cycle I	11	8	1
L-glutamate degradation VIII (to propanoate)	11	5	1
L-methionine salvage cycle III	11	5	1
superpathway of phospholipid biosynthesis III (E. coli)	12	12	1
reductive TCA cycle II	12	8	1
superpathway of cardiolipin biosynthesis (bacteria)	13	11	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
superpathway of purine nucleotide salvage	14	13	1
mixed acid fermentation	16	16	1
superpathway of glucose and xylose degradation	17	17	1
superpathway of (Kdo)2-lipid A biosynthesis	17	17	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	7	1
superpathway of novobiocin biosynthesis	19	4	1
superpathway of erythromycin biosynthesis	19	2	1
superpathway of megalomicin A biosynthesis	22	3	1
superpathway of dTDP-glucose-derived antibiotic building blocks biosynthesis	23	3	1
superpathway of Kdo2-lipid A biosynthesis	25	24	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	2
superpathway of phospholipid biosynthesis II (plants)	28	10	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	14	1