Experiment set2S446 for Bacteroides ovatus ATCC 8483

Peptone 2.5 mg/mL carbon source complex media

Group: carbon source complex media
Media: Varel_Bryant_medium + Bacto Peptone (2.5 mg/mL)
Culturing: Bovatus_ATCC8483_ML6, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya on 10/30/24
Media components: 15 uM Hemin, 134 uM L-Methionine, 15 uM Iron (II) sulfate heptahydrate, 8.25 mM L-Cysteine, 23.8 mM Sodium bicarbonate, Mineral 3B solution (6.6 mM Potassium phosphate monobasic, 15.4 mM Sodium Chloride, 98 uM Magnesium chloride hexahydrate, 176.5 uM Calcium chloride dihydrate, 4.2 uM Cobalt chloride hexahydrate, 50.5 uM Manganese (II) chloride tetrahydrate, 9.3 mM Ammonium chloride, 1.75 mM Sodium sulfate)

Specific Phenotypes

For 6 genes in this experiment

For carbon source complex media Bacto Peptone in Bacteroides ovatus ATCC 8483

For carbon source complex media Bacto Peptone across organisms

SEED Subsystems

Subsystem	#Specific
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Ribonucleotide reduction	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• Arginine and proline metabolism
• Nitrogen metabolism
• Citrate cycle (TCA cycle)
• Purine metabolism
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Glutathione metabolism
• Pyruvate metabolism
• Porphyrin and chlorophyll metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate degradation I	1	1	1
L-glutamate biosynthesis III	1	1	1
adenosylcobalamin salvage from cobalamin	5	5	4
adenosylcobinamide-GDP salvage from cobinamide I	5	5	3
guanosine deoxyribonucleotides de novo biosynthesis I	2	2	1
adenosine deoxyribonucleotides de novo biosynthesis I	2	2	1
adenosine deoxyribonucleotides de novo biosynthesis II	4	3	2
guanosine deoxyribonucleotides de novo biosynthesis II	4	3	2
adenosylcobinamide-GDP biosynthesis from cobyrinate a,c-diamide	6	4	3
adenosylcobinamide-GDP salvage from cobinamide II	6	4	3
cobalamin salvage (eukaryotic)	8	4	4
superpathway of adenosylcobalamin salvage from cobinamide I	8	8	3
superpathway of adenosylcobalamin salvage from cobinamide II	9	7	3
L-alanine degradation II (to D-lactate)	3	2	1
ethene biosynthesis IV (engineered)	3	1	1
superpathway of adenosine nucleotides de novo biosynthesis II	7	6	2
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	10	4
superpathway of guanosine nucleotides de novo biosynthesis II	8	7	2
pyrimidine deoxyribonucleotides de novo biosynthesis I	9	8	2
pyrimidine deoxyribonucleotides de novo biosynthesis III	9	7	2
superpathway of adenosine nucleotides de novo biosynthesis I	5	5	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
superpathway of purine nucleotides de novo biosynthesis II	26	23	4
incomplete reductive TCA cycle	7	6	1
L-glutamate and L-glutamine biosynthesis	7	5	1
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	5	1
4-aminobutanoate degradation V	7	1	1
L-glutamate degradation XI (reductive Stickland reaction)	7	1	1
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	6	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	16	2
L-glutamate degradation V (via hydroxyglutarate)	10	1	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	2
reductive TCA cycle I	11	9	1
adenosylcobalamin biosynthesis II (aerobic)	33	11	3
superpathway of histidine, purine, and pyrimidine biosynthesis	46	42	4
gluconeogenesis III	12	10	1
adenosylcobalamin biosynthesis I (anaerobic)	36	10	3
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
superpathway of purine nucleotide salvage	14	13	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	8	1
methylaspartate cycle	19	11	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1