Experiment set2IT005 for Pseudomonas fluorescens FW300-N2E3

LB with Cisplatin 0.006 mg/ml

Group: stress
Media: LB + Cisplatin (0.006 mg/ml)
Culturing: pseudo3_N2E3_ML2, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Jayashree on 4/28/2014
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 891 E5,E6

Specific Phenotypes

For 29 genes in this experiment

For stress Cisplatin in Pseudomonas fluorescens FW300-N2E3

For stress Cisplatin across organisms

SEED Subsystems

Subsystem	#Specific
DNA-replication	3
DNA repair, UvrABC system	2
DNA repair, bacterial DinG and relatives	2
2-phosphoglycolate salvage	1
Alanine biosynthesis	1
Carboxysome	1
Copper homeostasis: copper tolerance	1
Cyanate hydrolysis	1
DNA Repair Base Excision	1
DNA repair, bacterial RecFOR pathway	1
Entner-Doudoroff Pathway	1
Glutathione: Redox cycle	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycolate, glyoxylate interconversions	1
Iron acquisition in Vibrio	1
Methionine Biosynthesis	1
Methionine Degradation	1
Methylglyoxal Metabolism	1
Phosphate metabolism	1
Photorespiration (oxidative C2 cycle)	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Transcription factors bacterial	1
Twin-arginine translocation system	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tryptophan metabolism
• Limonene and pinene degradation
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• 1- and 2-Methylnaphthalene degradation
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Phenylalanine metabolism
• Lipopolysaccharide biosynthesis
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Pyrimidine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Tyrosine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• beta-Alanine metabolism
• Cyanoamino acid metabolism
• Glutathione metabolism
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• Toluene and xylene degradation
• 1,4-Dichlorobenzene degradation
• Glyoxylate and dicarboxylate metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Ethylbenzene degradation
• Styrene degradation
• Methane metabolism
• Thiamine metabolism
• Folate biosynthesis
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Isoflavonoid biosynthesis
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-cysteine degradation IV	1	1	1
L-alanine biosynthesis III	1	1	1
putrescine degradation I	2	2	1
ethylene glycol degradation	2	2	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
salicylate biosynthesis I	2	2	1
putrescine degradation V	2	2	1
cytidylyl molybdenum cofactor sulfurylation	2	1	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
cyanate degradation	3	3	1
salicylate biosynthesis II	3	2	1
putrescine degradation IV	3	2	1
glutathione-peroxide redox reactions	3	2	1
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
2,3-dihydroxybenzoate biosynthesis	3	2	1
bis(guanylyl molybdopterin) cofactor sulfurylation	3	1	1
histamine degradation	3	1	1
microcin B17 biosynthesis	3	1	1
thiazole component of thiamine diphosphate biosynthesis II	7	5	2
superpathway of L-alanine biosynthesis	4	4	1
L-arginine degradation IX (arginine:pyruvate transaminase pathway)	4	4	1
L-arginine degradation VIII (arginine oxidase pathway)	4	3	1
phytol degradation	4	3	1
putrescine degradation III	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
D-arabinose degradation II	4	1	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	1	1
tRNA-uridine 2-thiolation (yeast mitochondria)	4	1	1
aerobactin biosynthesis	4	1	1
tRNA-uridine 2-thiolation (mammalian mitochondria)	4	1	1
octane oxidation	5	4	1
mitochondrial NADPH production (yeast)	5	4	1
[2Fe-2S] iron-sulfur cluster biosynthesis	10	4	2
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	1	1
tRNA-uridine 2-thiolation (thermophilic bacteria)	5	1	1
superpathway of thiamine diphosphate biosynthesis II	11	9	2
thiazole component of thiamine diphosphate biosynthesis I	6	4	1
molybdopterin biosynthesis	6	4	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	4	2
superpathway of glycol metabolism and degradation	7	7	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
serotonin degradation	7	3	1
2-carboxy-1,4-naphthoquinol biosynthesis	7	2	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of ornithine degradation	8	7	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
anguibactin biosynthesis	8	2	1
tRNA-uridine 2-thiolation (cytoplasmic)	8	1	1
aromatic biogenic amine degradation (bacteria)	8	1	1
pseudomonine biosynthesis	9	6	1
photorespiration I	9	5	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
photorespiration III	9	5	1
superpathway of demethylmenaquinol-8 biosynthesis I	9	3	1
acinetobactin biosynthesis	9	3	1
vibriobactin biosynthesis	9	2	1
superpathway of demethylmenaquinol-6 biosynthesis I	9	2	1
superpathway of demethylmenaquinol-9 biosynthesis	9	2	1
superpathway of thiamine diphosphate biosynthesis I	10	8	1
photorespiration II	10	6	1
superpathway of menaquinol-8 biosynthesis I	10	4	1
superpathway of menaquinol-7 biosynthesis	10	3	1
superpathway of menaquinol-9 biosynthesis	10	3	1
superpathway of menaquinol-13 biosynthesis	10	3	1
superpathway of menaquinol-6 biosynthesis	10	3	1
superpathway of menaquinol-11 biosynthesis	10	3	1
superpathway of menaquinol-12 biosynthesis	10	3	1
superpathway of menaquinol-10 biosynthesis	10	3	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	1
enterobactin biosynthesis	11	5	1
tRNA-uridine 2-thiolation and selenation (bacteria)	11	4	1
mycobactin biosynthesis	11	2	1
bacillibactin biosynthesis	12	4	1
superpathway of L-arginine and L-ornithine degradation	13	11	1
3-hydroxypropanoate cycle	13	5	1
glyoxylate assimilation	13	4	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1
superpathway of phylloquinol biosynthesis	15	3	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	8	1
superpathway of the 3-hydroxypropanoate cycle	18	5	1
superpathway of pentose and pentitol degradation	42	8	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1
superpathway of chorismate metabolism	59	43	1