Experiment set27S428 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 43 genes in this experiment

For carbon source Inosine in Pseudomonas fluorescens SBW25-INTG

For carbon source Inosine across organisms

SEED Subsystems

Subsystem	#Specific
D-ribose utilization	4
Purine Utilization	4
Allantoin Utilization	3
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Biogenesis of c-type cytochromes	1
Butanol Biosynthesis	1
Catechol branch of beta-ketoadipate pathway	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
Glycine cleavage system	1
Heme and Siroheme Biosynthesis	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Isoleucine degradation	1
LMPTP YwlE cluster	1
Molybdenum cofactor biosynthesis	1
Muconate lactonizing enzyme family	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Orphan regulatory proteins	1
Phenylpropanoid compound degradation	1
Photorespiration (oxidative C2 cycle)	1
Terminal cytochrome C oxidases	1
Transport of Molybdenum	1
Ubiquinone 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
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Benzoate degradation via hydroxylation
• Glyoxylate and dicarboxylate metabolism
• Porphyrin and chlorophyll metabolism
• Pentose phosphate pathway
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Caffeine metabolism
• Pyrimidine metabolism
• Glutamate metabolism
• Arginine and proline metabolism
• Tyrosine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Phenylalanine metabolism
• Fluorobenzoate degradation
• Tryptophan metabolism
• beta-Alanine metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Biphenyl degradation
• Toluene and xylene degradation
• 2,4-Dichlorobenzoate degradation
• 1- and 2-Methylnaphthalene degradation
• 1,4-Dichlorobenzene degradation
• Fluorene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Folate biosynthesis
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Biosynthesis of unsaturated fatty acids
• 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
urate conversion to allantoin I	3	2	2
allantoin degradation to glyoxylate I	3	2	2
pyrimidine nucleobases salvage II	2	2	1
ribose phosphorylation	2	1	1
allantoin degradation to ureidoglycolate I (urea producing)	2	1	1
arsenite to oxygen electron transfer	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
superpathway of purines degradation in plants	18	14	6
superpathway of allantoin degradation in yeast	6	4	2
polymyxin resistance	6	3	2
2-deoxy-D-ribose degradation I	3	1	1
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis	3	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
ethene biosynthesis IV (engineered)	3	1	1
urate conversion to allantoin III	3	1	1
urate conversion to allantoin II	3	1	1
inosine 5'-phosphate degradation	4	4	1
catechol degradation to β-ketoadipate	4	4	1
superpathway of pyrimidine nucleobases salvage	4	4	1
guanosine nucleotides degradation III	4	4	1
guanosine nucleotides degradation II	4	4	1
adenosine nucleotides degradation I	8	7	2
aerobic respiration II (cytochrome c) (yeast)	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
glycolate and glyoxylate degradation I	4	3	1
guanosine nucleotides degradation I	4	3	1
oleate β-oxidation (isomerase-dependent, yeast)	4	2	1
tetrapyrrole biosynthesis II (from glycine)	4	2	1
fatty acid β-oxidation V (unsaturated, odd number, di-isomerase-dependent)	5	4	1
fatty acid β-oxidation II (plant peroxisome)	5	4	1
propanoyl-CoA degradation II	5	4	1
fatty acid β-oxidation VII (yeast peroxisome)	5	3	1
allantoin degradation to glyoxylate III	5	1	1
allantoin degradation to glyoxylate II	5	1	1
purine nucleotides degradation II (aerobic)	11	11	2
(5Z)-dodecenoate biosynthesis II	6	6	1
catechol degradation III (ortho-cleavage pathway)	6	6	1
purine nucleotides degradation I (plants)	12	10	2
tetrapyrrole biosynthesis I (from glutamate)	6	5	1
superpathway of guanosine nucleotides degradation (plants)	6	5	1
purine nucleobases degradation II (anaerobic)	24	16	4
methyl ketone biosynthesis (engineered)	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
Fe(II) oxidation	6	3	1
6-gingerol analog biosynthesis (engineered)	6	3	1
10-cis-heptadecenoyl-CoA degradation (yeast)	12	4	2
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	4	2
jasmonic acid biosynthesis	19	7	3
superpathway of salicylate degradation	7	7	1
2-methyl-branched fatty acid β-oxidation	14	11	2
superpathway of glycol metabolism and degradation	7	5	1
fatty acid β-oxidation VI (mammalian peroxisome)	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 heme b biosynthesis from glycine	8	5	1
superpathway of CDP-glucose-derived O-antigen building blocks biosynthesis	8	1	1
aromatic compounds degradation via β-ketoadipate	9	9	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
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast)	10	5	1
caffeine degradation IV (bacteria, via demethylation and oxidation)	10	1	1
pyruvate fermentation to hexanol (engineered)	11	7	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	3	1
superpathway of glyoxylate cycle and fatty acid degradation	14	12	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	3	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	2	1
mandelate degradation to acetyl-CoA	18	7	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
superpathway of aromatic compound degradation via 3-oxoadipate	35	19	1
adenosylcobalamin biosynthesis I (anaerobic)	36	27	1