Experiment set3IT054 for Pseudomonas fluorescens FW300-N2E2

LB with Doxycycline hyclate 0.0001 mg/ml

Group: stress
Media: LB + Doxycycline hyclate (1e-04 mg/ml)
Culturing: pseudo6_N2E2_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Mark on 3/9/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 1184 E5,E6

Specific Phenotypes

For 26 genes in this experiment

For stress Doxycycline hyclate in Pseudomonas fluorescens FW300-N2E2

For stress Doxycycline hyclate across organisms

SEED Subsystems

Subsystem	#Specific
Alginate metabolism	1
Arginine and Ornithine Degradation	1
Aromatic amino acid degradation	1
Carboxysome	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
DNA-replication	1
DNA repair, bacterial RecFOR pathway	1
De Novo Pyrimidine Synthesis	1
LMPTP YwlE cluster	1
Lipid A modifications	1
Mannose Metabolism	1
Methionine Biosynthesis	1
Methionine Degradation	1
Pentose phosphate pathway	1
Queuosine-Archaeosine Biosynthesis	1
Respiratory dehydrogenases 1	1
Staphylococcal pathogenicity islands SaPI	1
Transport of Zinc	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lipopolysaccharide biosynthesis
• Fructose and mannose metabolism
• Benzoxazinone biosynthesis
• Carotenoid biosynthesis - General
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• Pentose phosphate pathway
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Purine metabolism
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Glutathione metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Nucleotide sugars metabolism
• Keratan sulfate biosynthesis
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Naphthalene and anthracene degradation
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Diterpenoid biosynthesis
• Zeatin biosynthesis
• Phenylpropanoid biosynthesis
• Flavone and flavonol biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyrimidine nucleobases salvage I	1	1	1
3-dehydroquinate biosynthesis I	2	2	1
pyrimidine nucleobases salvage II	2	2	1
NADH to cytochrome bo oxidase electron transfer I	2	2	1
poly-β-1,6-N-acetyl-D-glucosamine biosynthesis	4	3	2
NADH to cytochrome bd oxidase electron transfer I	2	1	1
D-mannose degradation II	2	1	1
D-mannose degradation I	2	1	1
aerobic respiration III (alternative oxidase pathway)	3	3	1
pentose phosphate pathway (oxidative branch) I	3	3	1
β-1,4-D-mannosyl-N-acetyl-D-glucosamine degradation	3	2	1
mannitol biosynthesis	3	1	1
superpathway of pyrimidine nucleobases salvage	4	4	1
GDP-mannose biosynthesis	4	4	1
aerobic respiration I (cytochrome c)	4	3	1
mannitol degradation II	4	2	1
1,5-anhydrofructose degradation	5	2	1
Fe(II) oxidation	6	3	1
NAD(P)/NADPH interconversion	6	3	1
chorismate biosynthesis I	7	7	1
β-(1,4)-mannan degradation	7	2	1
pentose phosphate pathway	8	8	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of pyrimidine ribonucleosides salvage	10	6	1
colanic acid building blocks biosynthesis	11	9	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis	14	7	1
superpathway of glucose and xylose degradation	17	16	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of chorismate metabolism	59	43	1