Experiment set3S239 for Rhodanobacter sp000427505 FW510-R12

defined media with L-Serine

Group: nutrient
Media: NLDM_defined_nocarbon + D-Glucose (20 mM) + L-Serine (1 mM)
Culturing: rhodanobacter_R12_ML3, tube, Aerobic, at 23 (C), shaken=200 rpm
By: Hira on 03/23/2025
Media components: 1 mM Ammonium chloride, 3.3 mM Potassium Chloride, 0.812 mM Magnesium Sulfate Heptahydrate, 0.68 mM Calcium chloride dihydrate, 4.05 mM Disodium phosphate, 0.95 mM Sodium phosphate monobasic, ATCC Wolfe's mineral mix (5 mg/L EDTA, 3 mg/L Magnesium Sulfate Heptahydrate, 5 mg/L Manganese (II) sulfate monohydrate, 10 mg/L Sodium Chloride, 1 mg/L Iron (II) sulfate heptahydrate, 1 mg/L Cobalt(II) nitrate hexahydrate, 1 mg/L Calcium chloride dihydrate, 1 mg/L Zinc sulfate heptahydrate, 0.1 mg/L Copper (II) sulfate pentahydrate, 0.1 mg/L Aluminum potassium sulfate dodecahydrate, 0.1 mg/L Boric Acid, 0.1 mg/L Sodium Molybdate Dihydrate, 0.01 mg/L Sodium selenite pentahydrate, 0.1 mg/L Sodium tungstate dihydrate, 0.2 mg/L Nickel (II) chloride hexahydrate), ATCC Wolfe's vitamin mix (20 ug/L Folic Acid, 100 ug/L Pyridoxine HCl, 50 ug/L Riboflavin, 20 ug/L biotin, 50 ug/L Thiamine HCl, 50 ug/L Nicotinic Acid, 50 ug/L calcium pantothenate, 1 ug/L Cyanocobalamin, 50 ug/L 4-Aminobenzoic acid, 50 ug/L Lipoic acid)

Specific Phenotypes

For 13 genes in this experiment

For nutrient D-Glucose in Rhodanobacter sp000427505 FW510-R12

For nutrient D-Glucose across organisms

SEED Subsystems

Subsystem	#Specific
Methionine Salvage	3
Aromatic amino acid degradation	1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Cysteine Biosynthesis	1
Folate Biosynthesis	1
Glycine Biosynthesis	1
Methionine Biosynthesis	1
Pterin biosynthesis	1
Soluble cytochromes and functionally related electron carriers	1
Threonine degradation	1
Tryptophan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Methionine metabolism
• Sulfur metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Biosynthesis of plant hormones
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Phenylalanine metabolism
• Selenoamino acid metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine degradation I	1	1	1
S-methyl-5'-thioadenosine degradation II	1	1	1
L-phenylalanine degradation I (aerobic)	1	1	1
L-tyrosine biosynthesis IV	1	1	1
5'-deoxyadenosine degradation I	3	2	2
L-threonine degradation III (to methylglyoxal)	3	2	2
L-threonine degradation II	2	2	1
L-glutamate biosynthesis I	2	2	1
aminopropanol phosphate biosynthesis II	4	2	2
S-methyl-5'-thioadenosine degradation III	2	1	1
β-alanine degradation III	2	1	1
assimilatory sulfate reduction III	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
ammonia assimilation cycle III	3	3	1
L-phenylalanine degradation V	3	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation I	7	6	2
L-methionine salvage cycle III	11	10	3
assimilatory sulfate reduction I	4	4	1
homocysteine and cysteine interconversion	4	3	1
assimilatory sulfate reduction IV	4	3	1
diphenyl ethers degradation	4	2	1
L-asparagine biosynthesis III (tRNA-dependent)	4	1	1
acridone alkaloid biosynthesis	4	1	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	1	1
5'-deoxyadenosine degradation II	4	1	1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	8	2
uracil degradation III	5	3	1
4-hydroxy-2(1H)-quinolone biosynthesis	5	2	1
biphenyl degradation	5	2	1
L-methionine biosynthesis I	5	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III	5	1	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II	5	1	1
L-methionine salvage cycle II (plants)	11	7	2
L-tryptophan biosynthesis	6	6	1
L-methionine salvage cycle I (bacteria and plants)	12	9	2
L-methionine biosynthesis II	6	4	1
superpathway of L-cysteine biosynthesis (fungi)	6	4	1
L-glutamate and L-glutamine biosynthesis	7	5	1
L-citrulline biosynthesis	8	6	1
superpathway of L-homoserine and L-methionine biosynthesis	8	5	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
folate transformations III (E. coli)	9	9	1
superpathway of L-threonine metabolism	18	14	2
superpathway of S-adenosyl-L-methionine biosynthesis	9	6	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	6	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
superpathway of quinolone and alkylquinolone biosynthesis	10	2	1
folate transformations II (plants)	11	10	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	10	1
superpathway of L-citrulline metabolism	12	8	1
superpathway of L-tryptophan biosynthesis	13	13	1
3-hydroxypropanoate cycle	13	8	1
glyoxylate assimilation	13	6	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	12	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	15	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
superpathway of the 3-hydroxypropanoate cycle	18	8	1
aspartate superpathway	25	22	1
superpathway of chorismate metabolism	59	39	2