Experiment set10S433 for Pantoea sp. MT58

Ying_Nucleobase14 rep A; time point 1

Group: carbon source
Media: SDM_noCarbon + 1X Ying_Nucleobase14
Culturing: MT058_ML2, tube, Aerobic, at 28 (C), shaken=180 rpm
By: Ying and Valentine on 09/01/2023
Media components: 1.5 g/L Ammonium chloride, 0.6 g/L Potassium phosphate monobasic, 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)

Ying_Nucleobase14 1x includes: 183 uM 5-methyluridine, 183 uM Adenine, 183 uM Adenosine, 183 uM Cytidine, 183 uM Cytosine, 183 uM Guanine, 183 uM Guanosine, 183 uM Hypoxanthine, 183 uM Inosine, 183 uM Thymine, 183 uM Uracil, 183 uM Uridine, 183 uM Xanthine, 183 uM Xanthosine

Specific Phenotypes

For 6 genes in this experiment

For carbon source Ying_Nucleobase14 in Pantoea sp. MT58

For carbon source Ying_Nucleobase14 across organisms

SEED Subsystems

Subsystem	#Specific
Deoxyribose and Deoxynucleoside Catabolism	3
Adenosyl nucleosidases	1
CytR regulation	1
Purine conversions	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Pyrimidine metabolism
• Pentose phosphate pathway
• Nicotinate and nicotinamide metabolism
• Drug metabolism - other enzymes
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
purine ribonucleosides degradation	6	6	5
purine deoxyribonucleosides degradation I	4	4	3
purine deoxyribonucleosides degradation II	3	3	2
superpathway of purine deoxyribonucleosides degradation	7	7	4
adenine and adenosine salvage III	4	4	2
xanthine and xanthosine salvage	2	2	1
adenine and adenosine salvage I	2	2	1
guanine and guanosine salvage I	2	2	1
pyrimidine ribonucleosides degradation	2	2	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	2
pyrimidine deoxyribonucleosides degradation	3	3	1
adenine and adenosine salvage V	3	3	1
superpathway of guanine and guanosine salvage	3	3	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	3	1
nucleoside and nucleotide degradation (archaea)	10	4	3
purine nucleotides degradation II (aerobic)	11	11	3
inosine 5'-phosphate degradation	4	4	1
guanosine nucleotides degradation III	4	4	1
adenosine nucleotides degradation II	5	5	1
superpathway of pyrimidine ribonucleosides degradation	5	2	1
nucleoside and nucleotide degradation (halobacteria)	6	2	1
fluoroacetate and fluorothreonine biosynthesis	6	1	1
ureide biosynthesis	7	7	1
superpathway of purine nucleotide salvage	14	13	2
salinosporamide A biosynthesis	15	3	1
arsenic detoxification (mammals)	17	8	1