Experiment set9IT088 for Escherichia coli BW25113

LB Anaerobic with Cephalothin sodium salt 0.0000078125 mM

Group: stress
Media: LB + Cephalothin sodium salt (7.81E-03 mM)
Culturing: Keio_ML9a, 96 deep-well microplate; Multitron, Anaerobic, at 37 (C), shaken=0 rpm
By: Hans_Hualan on 7/20/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 78 genes in this experiment

For stress Cephalothin sodium salt in Escherichia coli BW25113

For stress Cephalothin sodium salt across organisms

SEED Subsystems

Subsystem	#Specific
NiFe hydrogenase maturation	4
D-ribose utilization	3
Flagellum	3
Hydrogenases	3
Transport of Nickel and Cobalt	3
Bacterial Cell Division	2
Bacterial Cytoskeleton	2
Conserved gene cluster associated with Met-tRNA formyltransferase	2
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Membrane-bound Ni, Fe-hydrogenase	2
Peptidoglycan Biosynthesis	2
Peptidyl-prolyl cis-trans isomerase	2
Potassium homeostasis	2
Rhamnose containing glycans	2
dTDP-rhamnose synthesis	2
linker unit-arabinogalactan synthesis	2
ATP-dependent RNA helicases, bacterial	1
Anaerobic respiratory reductases	1
Bacterial Chemotaxis	1
Beta-lactamase	1
CBSS-214092.1.peg.3450	1
CBSS-562.2.peg.5158 SK3 including	1
Capsular heptose biosynthesis	1
D-Galacturonate and D-Glucuronate Utilization	1
DNA repair, bacterial	1
DNA topoisomerases, Type I, ATP-independent	1
Fermentations: Mixed acid	1
Flagellar motility	1
Folate Biosynthesis	1
Glutaredoxins	1
Glutathione: Redox cycle	1
Glycine Biosynthesis	1
Glycine and Serine Utilization	1
Oxidative stress	1
Polyamine Metabolism	1
Tn552	1
Transport of Zinc	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Ubiquinone and menaquinone biosynthesis
• Pyrimidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Cysteine metabolism
• Lysine degradation
• Penicillin and cephalosporin biosynthesis
• beta-Lactam resistance
• Histidine metabolism
• Benzoxazinone biosynthesis
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Trinitrotoluene degradation
• 3-Chloroacrylic acid degradation
• Biotin metabolism
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Metabolism of xenobiotics by cytochrome P450
• Insect hormone biosynthesis
• Drug metabolism - cytochrome P450
• Drug metabolism - other enzymes
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of vancomycin group antibiotics
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
acetaldehyde biosynthesis I	1	1	1
hydrogen oxidation I (aerobic)	1	1	1
NiFe(CO)(CN)2 cofactor biosynthesis	10	9	8
L-tryptophan degradation II (via pyruvate)	3	3	2
D-serine degradation	3	3	2
L-cysteine degradation II	3	2	2
L-threonine degradation II	2	2	1
pseudouridine degradation	2	2	1
ethanol degradation I	2	2	1
di-trans,poly-cis-undecaprenyl phosphate biosynthesis	2	2	1
pyruvate fermentation to ethanol II	2	1	1
glycine betaine degradation III	7	4	3
dTDP-β-L-rhamnose biosynthesis	5	5	2
pyrimidine deoxyribonucleosides salvage	5	4	2
peptidoglycan recycling II	10	7	4
dTDP-4-O-demethyl-β-L-noviose biosynthesis	5	3	2
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	4	3
ethanol degradation II	3	3	1
cardiolipin biosynthesis III	3	3	1
cardiolipin biosynthesis II	3	3	1
pyruvate fermentation to ethanol III	3	3	1
pyruvate fermentation to ethanol I	3	3	1
glycine degradation	3	3	1
cardiolipin biosynthesis I	3	3	1
L-methionine biosynthesis II	6	5	2
L-valine degradation II	3	2	1
acrylate degradation II	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine degradation II	3	2	1
dTDP-sibirosamine biosynthesis	6	3	2
dTDP-L-daunosamine biosynthesis	6	3	2
L-methionine degradation III	3	1	1
peptidoglycan recycling I	14	14	4
dTDP-N-acetylthomosamine biosynthesis	4	4	1
phytol degradation	4	3	1
L-mimosine degradation	8	4	2
dTDP-6-deoxy-α-D-allose biosynthesis	4	2	1
salidroside biosynthesis	4	2	1
dTDP-β-D-fucofuranose biosynthesis	4	2	1
dTDP-N-acetylviosamine biosynthesis	4	2	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
glutathione-mediated detoxification I	8	3	2
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
superpathway of pyrimidine deoxyribonucleoside salvage	9	8	2
ethanolamine utilization	5	5	1
polyisoprenoid biosynthesis (E. coli)	5	5	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
acetylene degradation (anaerobic)	5	4	1
(S)-propane-1,2-diol degradation	5	3	1
dTDP-3-acetamido-α-D-fucose biosynthesis	5	2	1
phenylethanol biosynthesis	5	2	1
dTDP-3-acetamido-3,6-dideoxy-α-D-glucose biosynthesis	5	2	1
dTDP-α-D-mycaminose biosynthesis	5	2	1
O-antigen building blocks biosynthesis (E. coli)	11	11	2
phosphatidylglycerol biosynthesis II	6	6	1
phosphatidylglycerol biosynthesis I	6	6	1
dTDP-D-desosamine biosynthesis	6	2	1
dTDP-α-D-ravidosamine and dTDP-4-acetyl-α-D-ravidosamine biosynthesis	6	2	1
noradrenaline and adrenaline degradation	13	4	2
3-methylbutanol biosynthesis (engineered)	7	6	1
lipoprotein posttranslational modification (Gram-negative bacteria)	7	6	1
dTDP-β-L-digitoxose biosynthesis	7	3	1
serotonin degradation	7	3	1
dTDP-β-L-olivose biosynthesis	7	3	1
dTDP-β-L-mycarose biosynthesis	7	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
purine nucleobases degradation II (anaerobic)	24	17	3
dTDP-β-L-megosamine biosynthesis	8	3	1
dTDP-β-L-4-epi-vancosamine biosynthesis	8	3	1
butanol and isobutanol biosynthesis (engineered)	8	2	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	8	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
tunicamycin biosynthesis	9	2	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	7	2
superpathway of novobiocin biosynthesis	19	4	2
superpathway of enterobacterial common antigen biosynthesis	10	9	1
superpathway of phospholipid biosynthesis III (E. coli)	12	12	1
superpathway of cardiolipin biosynthesis (bacteria)	13	11	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	7	1
3-hydroxypropanoate cycle	13	7	1
glyoxylate assimilation	13	5	1
L-tryptophan degradation V (side chain pathway)	13	1	1
mixed acid fermentation	16	16	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	14	2
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	9	1
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	1
superpathway of L-threonine metabolism	18	16	1
heterolactic fermentation	18	16	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	10	1
superpathway of the 3-hydroxypropanoate cycle	18	7	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	19	1
superpathway of anaerobic sucrose degradation	19	17	1
superpathway of erythromycin biosynthesis	19	2	1
superpathway of N-acetylneuraminate degradation	22	22	1
superpathway of megalomicin A biosynthesis	22	3	1
superpathway of dTDP-glucose-derived antibiotic building blocks biosynthesis	23	3	1
superpathway of phospholipid biosynthesis II (plants)	28	10	1