Experiment set27S433 for Pseudomonas fluorescens SBW25-INTG

Xanthosine dihydrate carbon source

Group: carbon source
Media: MME_noCarbon + Xanthosine (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 22 genes in this experiment

For carbon source Xanthosine in Pseudomonas fluorescens SBW25-INTG

For carbon source Xanthosine across organisms

SEED Subsystems

Subsystem	#Specific
D-ribose utilization	4
Purine Utilization	4
Allantoin Utilization	3
Terminal cytochrome C oxidases	2
Biogenesis of c-type cytochromes	1
Copper homeostasis	1
Deoxyribose and Deoxynucleoside Catabolism	1
Flagellar motility	1
Flagellum	1
Molybdenum cofactor biosynthesis	1
Photorespiration (oxidative C2 cycle)	1
Transport of Molybdenum	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Glyoxylate and dicarboxylate metabolism
• Pentose phosphate pathway
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Caffeine metabolism
• Tyrosine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Pyruvate metabolism
• Biphenyl degradation
• 1- and 2-Methylnaphthalene degradation
• Fluorene degradation
• 3-Chloroacrylic acid degradation
• Phenylpropanoid biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
allantoin degradation to glyoxylate I	3	2	2
allantoin degradation to ureidoglycolate I (urea producing)	2	1	1
arsenite to oxygen electron transfer	2	1	1
ribose phosphorylation	2	1	1
adenosine nucleotides degradation II	5	5	2
superpathway of allantoin degradation in plants	8	4	3
superpathway of allantoin degradation in yeast	6	4	2
urate conversion to allantoin I	3	2	1
2-deoxy-D-ribose degradation I	3	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
ureide biosynthesis	7	6	2
superpathway of purines degradation in plants	18	14	5
guanosine nucleotides degradation II	4	4	1
inosine 5'-phosphate degradation	4	4	1
guanosine nucleotides degradation III	4	4	1
adenosine nucleotides degradation I	8	7	2
aerobic respiration I (cytochrome c)	4	3	1
glycolate and glyoxylate degradation I	4	3	1
guanosine nucleotides degradation I	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
allantoin degradation to glyoxylate II	5	1	1
allantoin degradation to glyoxylate III	5	1	1
purine nucleotides degradation II (aerobic)	11	11	2
purine nucleotides degradation I (plants)	12	10	2
superpathway of guanosine nucleotides degradation (plants)	6	5	1
purine nucleobases degradation II (anaerobic)	24	16	4
Fe(II) oxidation	6	3	1
superpathway of glycol metabolism and degradation	7	5	1
caffeine degradation III (bacteria, via demethylation)	7	1	1
theophylline degradation	9	1	1
caffeine degradation IV (bacteria, via demethylation and oxidation)	10	1	1