Experiment set2IT082 for Pseudomonas fluorescens GW456-L13

Sodium octanoate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Sodium octanoate (20 mM), pH=7
Culturing: pseudo13_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 3/10/2015
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 78 genes in this experiment

For carbon source Sodium octanoate in Pseudomonas fluorescens GW456-L13

For carbon source Sodium octanoate across organisms

SEED Subsystems

Subsystem	#Specific
Peptidoglycan Biosynthesis	4
ABC transporter oligopeptide (TC 3.A.1.5.1)	3
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	2
Proteolysis in bacteria, ATP-dependent	2
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	1
Ammonia assimilation	1
Arginine and Ornithine Degradation	1
Biogenesis of cbb3-type cytochrome c oxidases	1
Coenzyme A Biosynthesis	1
Experimental tye	1
Flagellar motility	1
Flagellum	1
Glutamate dehydrogenases	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Heme and Siroheme Biosynthesis	1
Hfl operon	1
Iron acquisition in Vibrio	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Lipid A modifications	1
Lysine degradation	1
Multidrug Resistance Efflux Pumps	1
Photorespiration (oxidative C2 cycle)	1
Proteasome bacterial	1
Protein chaperones	1
RNA processing and degradation, bacterial	1
Rhamnose containing glycans	1
Sex pheromones in Enterococcus faecalis and other Firmicutes	1
Teichoic and lipoteichoic acids biosynthesis	1
Transport of Iron	1
Universal GTPases	1
Valine degradation	1
ZZ gjo need homes	1
cAMP signaling in bacteria	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
• Nucleotide sugars metabolism
• Benzoate degradation via CoA ligation
• Nitrogen metabolism
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Purine metabolism
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Thiamine metabolism
• Porphyrin and chlorophyll metabolism
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Fructose and mannose metabolism
• Ubiquinone and menaquinone biosynthesis
• C21-Steroid hormone metabolism
• Puromycin biosynthesis
• Pyrimidine metabolism
• Geraniol degradation
• Arginine and proline metabolism
• Bisphenol A degradation
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Glutathione metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Inositol phosphate metabolism
• Linoleic acid metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Tetrachloroethene degradation
• Trinitrotoluene degradation
• Propanoate metabolism
• Butanoate metabolism
• One carbon pool by folate
• Nicotinate and nicotinamide metabolism
• Pantothenate and CoA biosynthesis
• Retinol metabolism
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Biosynthesis of type II polyketide products
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
hydroxymethylpyrimidine salvage	2	2	2
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation II	1	1	1
L-glutamate degradation I	1	1	1
L-glutamine degradation I	1	1	1
ammonia assimilation cycle III	3	3	2
β-alanine degradation II	2	2	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis I	2	2	1
β-alanine degradation I	2	1	1
oleate biosynthesis II (animals and fungi)	2	1	1
palmitoleate biosynthesis IV (fungi and animals)	2	1	1
thiamine diphosphate salvage II	5	4	2
glycine degradation	3	3	1
glycine cleavage	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
glycine biosynthesis II	3	3	1
NAD salvage pathway III (to nicotinamide riboside)	3	2	1
ethene biosynthesis IV (engineered)	3	1	1
L-glutamate and L-glutamine biosynthesis	7	6	2
UTP and CTP dephosphorylation I	7	5	2
thiamine diphosphate salvage IV (yeast)	7	3	2
purine nucleotides degradation II (aerobic)	11	11	3
guanosine nucleotides degradation II	4	4	1
phosphopantothenate biosynthesis I	4	4	1
guanosine nucleotides degradation III	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
inosine 5'-phosphate degradation	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
adenosine nucleotides degradation I	8	7	2
purine nucleotides degradation I (plants)	12	10	3
tetrapyrrole biosynthesis II (from glycine)	4	3	1
guanosine nucleotides degradation I	4	3	1
phosphopantothenate biosynthesis III (archaea)	4	2	1
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	3	2
adipate degradation	5	5	1
adenosine nucleotides degradation II	5	5	1
L-lysine degradation IV	5	5	1
peptidoglycan recycling II	10	9	2
acrylate degradation I	5	3	1
propanoyl-CoA degradation II	5	3	1
fatty acid salvage	6	6	1
tetrapyrrole biosynthesis I (from glutamate)	6	6	1
superpathway of guanosine nucleotides degradation (plants)	6	5	1
L-lysine degradation X	6	5	1
superpathway of purines degradation in plants	18	14	3
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	2
peptidoglycan recycling I	14	12	2
ureide biosynthesis	7	6	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	3	1
4-aminobutanoate degradation V	7	2	1
2,4-dinitrotoluene degradation	7	1	1
myo-inositol degradation I	7	1	1
L-citrulline biosynthesis	8	7	1
L-valine degradation I	8	6	1
superpathway of heme b biosynthesis from glycine	8	6	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II	8	4	1
sorgoleone biosynthesis	8	2	1
folate transformations III (E. coli)	9	9	1
superpathway of coenzyme A biosynthesis I (bacteria)	9	9	1
photorespiration I	9	6	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
photorespiration III	9	5	1
Escherichia coli serotype O:8 O antigen biosynthesis	9	2	1
tunicamycin biosynthesis	9	2	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
superpathway of heme b biosynthesis from glutamate	10	9	1
superpathway of thiamine diphosphate biosynthesis I	10	7	1
photorespiration II	10	6	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
L-lysine fermentation to acetate and butanoate	10	4	1
myo-, chiro- and scyllo-inositol degradation	10	1	1
folate transformations II (plants)	11	10	1
superpathway of thiamine diphosphate biosynthesis II	11	8	1
NAD salvage (plants)	11	5	1
oleate β-oxidation	35	30	3
superpathway of L-citrulline metabolism	12	9	1
folate transformations I	13	9	1
2-methyl-branched fatty acid β-oxidation	14	11	1
peptidoglycan biosynthesis II (staphylococci)	17	12	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	1
methylaspartate cycle	19	10	1
superpathway of L-lysine degradation	43	17	2
superpathway of bacteriochlorophyll a biosynthesis	26	6	1
adenosylcobalamin biosynthesis II (aerobic)	33	30	1
adenosylcobalamin biosynthesis I (anaerobic)	36	29	1