Experiment set3S242 for Rhodanobacter sp000427505 FW510-R12

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defined media with D-Glucose

Group: nutrient
Media: NLDM_defined_nocarbon + D-Glucose (20 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 9 genes in this experiment

For nutrient D-Glucose in Rhodanobacter sp000427505 FW510-R12

For nutrient D-Glucose across organisms

SEED Subsystems

Subsystem #Specific
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. 1
Coenzyme B12 biosynthesis 1
Cysteine Biosynthesis 1
Dissimilatory nitrite reductase 1
Experimental tye 1
Heme and Siroheme Biosynthesis 1
Mannose Metabolism 1
Methionine Biosynthesis 1
Tryptophan synthesis 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
siroheme biosynthesis 4 4 4
L-glutamine degradation I 1 1 1
L-glutamate biosynthesis I 2 2 1
factor 430 biosynthesis 7 3 3
ammonia assimilation cycle III 3 3 1
assimilatory sulfate reduction III 3 3 1
assimilatory sulfate reduction I 4 4 1
homocysteine and cysteine interconversion 4 3 1
assimilatory sulfate reduction IV 4 3 1
acridone alkaloid biosynthesis 4 1 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 1 1
L-asparagine biosynthesis III (tRNA-dependent) 4 1 1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) 10 8 2
4-hydroxy-2(1H)-quinolone biosynthesis 5 2 1
L-methionine biosynthesis I 5 2 1
cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion) 15 3 3
L-tryptophan biosynthesis 6 6 1
L-methionine biosynthesis II 6 4 1
superpathway of L-cysteine biosynthesis (fungi) 6 4 1
cob(II)yrinate a,c-diamide biosynthesis II (late cobalt incorporation) 13 2 2
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
superpathway of S-adenosyl-L-methionine biosynthesis 9 6 1
superpathway of L-methionine biosynthesis (transsulfuration) 9 6 1
superpathway of quinolone and alkylquinolone biosynthesis 10 2 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 10 1
superpathway of L-citrulline metabolism 12 8 1
adenosylcobalamin biosynthesis I (anaerobic) 36 12 3
superpathway of L-tryptophan biosynthesis 13 13 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 12 1
adenosylcobalamin biosynthesis II (aerobic) 33 12 2
superpathway of aromatic amino acid biosynthesis 18 18 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 15 1
aspartate superpathway 25 22 1
superpathway of chorismate metabolism 59 39 1