Experiment set4IT086 for Pseudomonas fluorescens FW300-N2E3

LB with Doxycycline hyclate 0.0006 mg/ml

Group: stress
Media: LB + Doxycycline hyclate (6e-04 mg/ml)
Culturing: pseudo3_N2E3_ML2, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Jayashree on 7/1/2014
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 971 D3,D4

Specific Phenotypes

For 23 genes in this experiment

For stress Doxycycline hyclate in Pseudomonas fluorescens FW300-N2E3

For stress Doxycycline hyclate across organisms

SEED Subsystems

Subsystem	#Specific
Oxidative stress	3
DNA repair, bacterial MutL-MutS system	1
Glutathione: Non-redox reactions	1
Glycine and Serine Utilization	1
Methylglyoxal Metabolism	1
Polyamine Metabolism	1
Pyruvate Alanine Serine Interconversions	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Carotenoid biosynthesis - General
• Glycine, serine and threonine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Nucleotide sugars metabolism
• Porphyrin and chlorophyll metabolism
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Galactose metabolism
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• Cysteine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Starch and sucrose metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Streptomycin biosynthesis
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• alpha-Linolenic acid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• Trinitrotoluene degradation
• Diterpenoid biosynthesis
• Zeatin biosynthesis
• Phenylpropanoid biosynthesis
• Flavone and flavonol biosynthesis
• Biosynthesis of siderophore group nonribosomal peptides
• 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
D-serine degradation	3	3	2
L-cysteine degradation II	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
UDP-α-D-glucose biosynthesis	2	2	1
glycine betaine degradation III	7	7	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	6	3
glycine degradation	3	3	1
L-methionine biosynthesis II	6	5	2
GDP-α-D-glucose biosynthesis	3	2	1
methylglyoxal degradation VIII	3	2	1
methylglyoxal degradation I	3	2	1
trehalose degradation V	3	2	1
queuosine biosynthesis I (de novo)	4	4	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
starch degradation V	4	3	1
sucrose degradation IV (sucrose phosphorylase)	4	3	1
L-mimosine degradation	8	4	2
starch degradation III	4	2	1
glutathione-mediated detoxification I	8	3	2
dTDP-β-L-rhamnose biosynthesis	5	5	1
sucrose degradation II (sucrose synthase)	5	4	1
glucose and glucose-1-phosphate degradation	5	4	1
queuosine biosynthesis III (queuosine salvage)	5	3	1
D-galactose degradation I (Leloir pathway)	5	2	1
glucosylglycerol biosynthesis	5	2	1
CDP-6-deoxy-D-gulose biosynthesis	5	1	1
glycogen degradation II	6	5	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
sucrose biosynthesis II	8	6	1
glycogen degradation I	8	6	1
purine nucleobases degradation II (anaerobic)	24	16	3
superpathway of methylglyoxal degradation	8	4	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	3	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
chitin biosynthesis	9	5	1
peptidoglycan recycling II	10	8	1
starch biosynthesis	10	5	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
colanic acid building blocks biosynthesis	11	9	1
peptidoglycan recycling I	14	11	1
streptomycin biosynthesis	18	2	1
superpathway of anaerobic sucrose degradation	19	15	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	5	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	13	1