Experiment set10S452 for Pantoea sp. MT58

Ying_Nucleobase14 rep B; time point 2

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 1-Sep-23
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 11 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
Thiamin biosynthesis	3
Adenosyl nucleosidases	1
CytR regulation	1
Purine conversions	1
Transport of Zinc	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Thiamine metabolism
• 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
hydroxymethylpyrimidine salvage	2	2	2
glyphosate degradation II	1	1	1
purine ribonucleosides degradation	6	6	5
purine deoxyribonucleosides degradation I	4	4	3
purine deoxyribonucleosides degradation II	3	3	2
thiamine diphosphate salvage II	5	5	3
superpathway of purine deoxyribonucleosides degradation	7	7	4
adenine and adenosine salvage III	4	4	2
pyrimidine ribonucleosides degradation	2	2	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis I	2	2	1
thiamine diphosphate biosynthesis I (E. coli)	2	2	1
thiamine diphosphate biosynthesis II (Bacillus)	2	2	1
xanthine and xanthosine salvage	2	2	1
guanine and guanosine salvage I	2	2	1
adenine and adenosine salvage I	2	2	1
thiamine diphosphate salvage IV (yeast)	7	5	3
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	4	3
superpathway of thiamine diphosphate biosynthesis II	11	9	4
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	2
pyrimidine deoxyribonucleosides degradation	3	3	1
superpathway of guanine and guanosine salvage	3	3	1
thiamine diphosphate salvage V	3	3	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	3	1
adenine and adenosine salvage V	3	3	1
thiamine diphosphate biosynthesis III (Staphylococcus)	3	1	1
thiamine diphosphate biosynthesis IV (eukaryotes)	3	1	1
superpathway of thiamine diphosphate biosynthesis I	10	8	3
nucleoside and nucleotide degradation (archaea)	10	4	3
thiazole component of thiamine diphosphate biosynthesis II	7	5	2
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	3	2
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
thiazole component of thiamine diphosphate biosynthesis I	6	4	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
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II	8	5	1
butanol and isobutanol biosynthesis (engineered)	8	4	1
salinosporamide A biosynthesis	15	3	1
arsenic detoxification (mammals)	17	8	1