Experiment set3S240 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 16 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
Ammonia assimilation	1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Cysteine Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycine Biosynthesis	1
Mannose Metabolism	1
Methionine Biosynthesis	1
Soluble cytochromes and functionally related electron carriers	1
Threonine and Homoserine Biosynthesis	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
• Biosynthesis of plant hormones
• Cysteine metabolism
• Arginine and proline metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Nucleotide sugars metabolism
• Biosynthesis of phenylpropanoids
• Urea cycle and metabolism of amino groups
• Glutamate metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Lysine biosynthesis
• Lysine degradation
• Tyrosine metabolism
• Phenylalanine metabolism
• Novobiocin biosynthesis
• Aminophosphonate metabolism
• Selenoamino acid metabolism
• Aminosugars metabolism
• Carbon fixation in photosynthetic organisms
• Caprolactam degradation
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-aspartate degradation I	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
S-methyl-5'-thioadenosine degradation II	1	1	1
L-aspartate biosynthesis	1	1	1
L-glutamine degradation I	1	1	1
L-threonine degradation III (to methylglyoxal)	3	2	2
5'-deoxyadenosine degradation I	3	2	2
L-glutamate biosynthesis I	2	2	1
L-threonine degradation II	2	2	1
malate/L-aspartate shuttle pathway	2	2	1
aminopropanol phosphate biosynthesis II	4	2	2
atromentin biosynthesis	2	1	1
β-alanine degradation III	2	1	1
L-tyrosine degradation II	2	1	1
L-glutamate degradation II	2	1	1
S-methyl-5'-thioadenosine degradation III	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
assimilatory sulfate reduction III	3	3	1
ammonia assimilation cycle III	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-asparagine degradation III (mammalian)	3	2	1
L-phenylalanine degradation II (anaerobic)	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
(R)-cysteate degradation	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
sulfolactate degradation III	3	1	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
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-tyrosine degradation III	4	2	1
diphenyl ethers degradation	4	2	1
L-phenylalanine degradation III	4	2	1
5'-deoxyadenosine degradation II	4	1	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
acridone alkaloid biosynthesis	4	1	1
L-asparagine biosynthesis III (tRNA-dependent)	4	1	1
dimethylsulfoniopropanoate biosynthesis III (algae and phytoplankton)	4	1	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	1	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	6	2
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	8	2
L-tyrosine degradation I	5	4	1
trans-4-hydroxy-L-proline degradation I	5	3	1
uracil degradation III	5	3	1
L-methionine biosynthesis I	5	2	1
4-hydroxy-2(1H)-quinolone biosynthesis	5	2	1
superpathway of plastoquinol biosynthesis	5	2	1
biphenyl degradation	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
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	2
L-methionine salvage cycle II (plants)	11	7	2
superpathway of aromatic amino acid biosynthesis	18	18	3
L-tryptophan biosynthesis	6	6	1
superpathway of L-threonine biosynthesis	6	6	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	10	2
TCA cycle VIII (Chlamydia)	6	5	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
superpathway of sulfolactate degradation	6	2	1
coenzyme M biosynthesis II	6	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	7	1
ethene biosynthesis III (microbes)	7	6	1
L-glutamate and L-glutamine biosynthesis	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	2
L-homomethionine biosynthesis	7	2	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
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	15	2
superpathway of L-threonine metabolism	18	14	2
superpathway of S-adenosyl-L-methionine biosynthesis	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	2	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of quinolone and alkylquinolone biosynthesis	10	2	1
rosmarinic acid biosynthesis I	10	1	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-citrulline metabolism	12	8	1
indole-3-acetate biosynthesis II	12	3	1
aspartate superpathway	25	22	2
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of L-isoleucine biosynthesis I	13	13	1
3-hydroxypropanoate cycle	13	8	1
glyoxylate assimilation	13	6	1
superpathway of rosmarinic acid biosynthesis	14	1	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	12	1
superpathway of anaerobic energy metabolism (invertebrates)	17	13	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
superpathway of the 3-hydroxypropanoate cycle	18	8	1
superpathway of chorismate metabolism	59	39	3
anaerobic aromatic compound degradation (Thauera aromatica)	27	1	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	25	1