Experiment set1S368 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 7 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
Methionine 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
• Methionine metabolism
• Glutathione metabolism
• Pyruvate metabolism
• One carbon pool by folate
• 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 biosynthesis III	1	1	1
L-glutamate degradation I	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
guanosine deoxyribonucleotides de novo biosynthesis II	4	3	2
adenosine deoxyribonucleotides de novo biosynthesis II	4	3	2
adenosylcobinamide-GDP salvage from cobinamide II	6	4	3
adenosylcobinamide-GDP biosynthesis from cobyrinate a,c-diamide	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
L-methionine salvage from L-homocysteine	3	1	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
L-methionine biosynthesis III	4	3	1
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
L-methionine biosynthesis I	5	3	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
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	5	1
L-glutamate and L-glutamine biosynthesis	7	5	1
L-glutamate degradation XI (reductive Stickland reaction)	7	1	1
4-aminobutanoate degradation V	7	1	1
superpathway of L-homoserine and L-methionine biosynthesis	8	6	1
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	6	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	16	2
folate transformations III (E. coli)	9	8	1
superpathway of S-adenosyl-L-methionine biosynthesis	9	7	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
L-glutamate degradation V (via hydroxyglutarate)	10	1	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	2
folate transformations II (plants)	11	10	1
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
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	9	1
adenosylcobalamin biosynthesis I (anaerobic)	36	10	3
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
folate transformations I	13	9	1
superpathway of purine nucleotide salvage	14	13	1
superpathway of L-methionine salvage and degradation	16	7	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	12	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	8	1
methylaspartate cycle	19	11	1
aspartate superpathway	25	19	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1