Experiment set10IT046 for Escherichia coli BW25113

LB Aerobic with Ramoplanin 0.000125 mM

Group: stress
Media: LB + Ramoplanin (0.125 mM)
Culturing: Keio_ML9a, 96 deep-well microplate; Multitron, Aerobic, at 37 (C), shaken=750 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 62 genes in this experiment

For stress Ramoplanin in Escherichia coli BW25113

For stress Ramoplanin across organisms

SEED Subsystems

Subsystem	#Specific
Oxidative stress	3
Peptidoglycan Biosynthesis	3
ATP-dependent RNA helicases, bacterial	1
Biogenesis of cytochrome c oxidases	1
Capsular heptose biosynthesis	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
D-Galacturonate and D-Glucuronate Utilization	1
D-allose utilization	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
LOS core oligosaccharide biosynthesis	1
Multidrug Resistance Efflux Pumps	1
Periplasmic disulfide interchange	1
Type IV pilus	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose and glucuronate interconversions
• Ubiquinone and menaquinone biosynthesis
• Nucleotide sugars metabolism
• Peptidoglycan biosynthesis
• Glycerophospholipid metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Aminophosphonate metabolism
• Starch and sucrose metabolism
• High-mannose type N-glycan biosynthesis
• Glycosaminoglycan degradation
• Glycerolipid metabolism
• Inositol phosphate metabolism
• Sphingolipid metabolism
• Naphthalene and anthracene degradation
• Biotin metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of ansamycins
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
di-trans,poly-cis-undecaprenyl phosphate biosynthesis	2	2	1
L-tryptophan degradation II (via pyruvate)	3	3	1
D-serine degradation	3	3	1
L-serine degradation	3	3	1
cardiolipin biosynthesis II	3	3	1
cardiolipin biosynthesis I	3	3	1
L-cysteine degradation II	3	2	1
L-methionine degradation II	3	2	1
alkane biosynthesis I	3	1	1
pectin degradation I	3	1	1
heptadecane biosynthesis	3	1	1
peptidoglycan recycling II	10	7	3
cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas)	4	3	1
GDP-D-glycero-α-D-manno-heptose biosynthesis	4	1	1
peptidoglycan recycling I	14	14	3
polyisoprenoid biosynthesis (E. coli)	5	5	1
ADP-L-glycero-β-D-manno-heptose biosynthesis	5	5	1
pectin degradation II	5	3	1
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	1
L-threonine degradation I	6	6	1
L-methionine biosynthesis II	6	5	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	6	2
superpathway of cardiolipin biosynthesis (bacteria)	13	11	2
L-isoleucine biosynthesis I (from threonine)	7	7	1
lipoprotein posttranslational modification (Gram-negative bacteria)	7	6	1
glycine betaine degradation III	7	4	1
L-mimosine degradation	8	4	1
glycine betaine degradation I	8	4	1
glutathione-mediated detoxification I	8	3	1
mycobactin biosynthesis	11	3	1
superpathway of phospholipid biosynthesis III (E. coli)	12	12	1
superpathway of L-isoleucine biosynthesis I	13	13	1
hypoglycin biosynthesis	14	4	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
superpathway of branched chain amino acid biosynthesis	17	17	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	1
peptidoglycan biosynthesis II (staphylococci)	17	12	1
superpathway of L-threonine metabolism	18	16	1
purine nucleobases degradation II (anaerobic)	24	17	1