Experiment set3S239 for Rhodanobacter sp000427505 FW510-R12

Compare to:

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 23-Mar-25
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 10 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
Folate Biosynthesis 1
Glycine Biosynthesis 1
Pterin biosynthesis 1
Soluble cytochromes and functionally related electron carriers 1
Threonine degradation 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-tyrosine biosynthesis IV 1 1 1
S-methyl-5'-thioadenosine degradation II 1 1 1
L-phenylalanine degradation I (aerobic) 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
aminopropanol phosphate biosynthesis II 4 2 2
β-alanine degradation III 2 1 1
S-methyl-5'-thioadenosine degradation III 2 1 1
dTMP de novo biosynthesis (mitochondrial) 3 3 1
tetrahydrofolate biosynthesis I 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
diphenyl ethers degradation 4 2 1
5'-deoxyadenosine degradation II 4 1 1
uracil degradation III 5 3 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
L-methionine salvage cycle II (plants) 11 7 2
L-methionine salvage cycle I (bacteria and plants) 12 9 2
folate transformations III (E. coli) 9 9 1
superpathway of L-threonine metabolism 18 14 2
superpathway of tetrahydrofolate biosynthesis 10 8 1
folate transformations II (plants) 11 10 1
superpathway of tetrahydrofolate biosynthesis and salvage 12 10 1
3-hydroxypropanoate cycle 13 8 1
glyoxylate assimilation 13 6 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 11 1
superpathway of the 3-hydroxypropanoate cycle 18 8 1
superpathway of chorismate metabolism 59 39 1