Experiment set27S427 for Pseudomonas fluorescens SBW25-INTG

Inosine carbon source

Group: carbon source
Media: MME_noCarbon + Inosine (10 mM)
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C)
By: Andrew Frank on 1/31/23
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 37 genes in this experiment

For carbon source Inosine in Pseudomonas fluorescens SBW25-INTG

For carbon source Inosine across organisms

SEED Subsystems

Subsystem	#Specific
Purine Utilization	5
D-ribose utilization	4
Allantoin Utilization	3
Molybdenum cofactor biosynthesis	2
Purine conversions	2
Terminal cytochrome C oxidases	2
Transport of Molybdenum	2
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Biogenesis of c-type cytochromes	1
Butanol Biosynthesis	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Copper homeostasis	1
De Novo Pyrimidine Synthesis	1
Deoxyribose and Deoxynucleoside Catabolism	1
Experimental tye	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Heme and Siroheme Biosynthesis	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Isoleucine degradation	1
LMPTP YwlE cluster	1
Photorespiration (oxidative C2 cycle)	1
Queuosine-Archaeosine Biosynthesis	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Arginine and proline metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Phenylalanine metabolism
• Tryptophan metabolism
• Glyoxylate and dicarboxylate metabolism
• Pentose phosphate pathway
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Caffeine metabolism
• Pyrimidine metabolism
• Glutamate metabolism
• Tyrosine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Benzoate degradation via hydroxylation
• beta-Alanine metabolism
• Cyanoamino acid metabolism
• Pyruvate metabolism
• Biphenyl degradation
• 1- and 2-Methylnaphthalene degradation
• Fluorene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Styrene degradation
• Butanoate metabolism
• Nicotinate and nicotinamide metabolism
• Porphyrin and chlorophyll metabolism
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate degradation I	1	1	1
pyrimidine nucleobases salvage I	1	1	1
guanosine nucleotides degradation II	4	4	3
superpathway of guanosine nucleotides degradation (plants)	6	5	4
urate conversion to allantoin I	3	2	2
allantoin degradation to glyoxylate I	3	2	2
superpathway of purines degradation in plants	18	14	10
guanosine nucleotides degradation III	4	4	2
guanine and guanosine salvage II	2	2	1
indole-3-acetate biosynthesis III (bacteria)	2	2	1
pyrimidine nucleobases salvage II	2	2	1
acrylonitrile degradation I	2	2	1
indole-3-acetate biosynthesis IV (bacteria)	2	2	1
adenine and adenosine salvage II	2	2	1
adenosine nucleotides degradation I	8	7	4
purine nucleotides degradation I (plants)	12	10	6
guanosine nucleotides degradation I	4	3	2
ribose phosphorylation	2	1	1
arsenite to oxygen electron transfer	2	1	1
allantoin degradation to ureidoglycolate I (urea producing)	2	1	1
ureide biosynthesis	7	6	3
adenosine nucleotides degradation II	5	5	2
superpathway of allantoin degradation in plants	8	4	3
L-alanine degradation II (to D-lactate)	3	3	1
putrescine biosynthesis II	3	3	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
superpathway of allantoin degradation in yeast	6	4	2
superpathway of acrylonitrile degradation	3	2	1
L-arginine degradation X (arginine monooxygenase pathway)	3	2	1
2-deoxy-D-ribose degradation I	3	1	1
ethene biosynthesis IV (engineered)	3	1	1
urate conversion to allantoin II	3	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
urate conversion to allantoin III	3	1	1
purine nucleotides degradation II (aerobic)	11	11	3
superpathway of pyrimidine nucleobases salvage	4	4	1
inosine 5'-phosphate degradation	4	4	1
aerobic respiration I (cytochrome c)	4	3	1
glycolate and glyoxylate degradation I	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
tetrapyrrole biosynthesis II (from glycine)	4	2	1
purine nucleobases degradation II (anaerobic)	24	16	5
allantoin degradation to glyoxylate II	5	1	1
allantoin degradation to glyoxylate III	5	1	1
tetrapyrrole biosynthesis I (from glutamate)	6	5	1
pyruvate fermentation to butanol II (engineered)	6	4	1
Fe(II) oxidation	6	3	1
2-methyl-branched fatty acid β-oxidation	14	11	2
drosopterin and aurodrosopterin biosynthesis	7	5	1
superpathway of glycol metabolism and degradation	7	5	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
4-aminobutanoate degradation V	7	3	1
caffeine degradation III (bacteria, via demethylation)	7	1	1
superpathway of polyamine biosynthesis II	8	6	1
superpathway of heme b biosynthesis from glycine	8	5	1
theophylline degradation	9	1	1
superpathway of heme b biosynthesis from glutamate	10	8	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
superpathway of pyrimidine ribonucleosides salvage	10	6	1
caffeine degradation IV (bacteria, via demethylation and oxidation)	10	1	1
pyruvate fermentation to hexanol (engineered)	11	7	1
indole-3-acetate biosynthesis II	12	5	1
purine nucleobases degradation I (anaerobic)	15	6	1
methylaspartate cycle	19	9	1
superpathway of bacteriochlorophyll a biosynthesis	26	5	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
adenosylcobalamin biosynthesis II (aerobic)	33	30	1
adenosylcobalamin biosynthesis I (anaerobic)	36	27	1