Experiment set5IT066 for Rhodanobacter denitrificans FW104-10B01

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Potassium acetate 20 mM

Group: carbon source
Media: Hans_Basal_Media_plus_0.2x_20AA_mix + Potassium acetate (20 mM)
Culturing: rhodanobacter_10B01_ML12, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 28 (C), shaken=700 rpm
By: Hans Carlson and Trenton Owens on 24-Aug-21
Media components: 0.03 M PIPES sesquisodium salt, 0.1 g/L Potassium Chloride, 0.01 g/L Sodium Chloride, 0.01 g/L Calcium chloride dihydrate, 0.1 g/L Magnesium chloride hexahydrate, 0.1 g/L Sodium sulfate, 0.25 g/L Ammonium chloride, 0.1 g/L Disodium phosphate, 20AA_mix (0.1 mM L-Arginine, 0.1 mM L-Histidine, 0.1 mM L-Lysine, 0.1 mM L-Aspartic Acid, 0.1 mM L-Glutamic acid monopotassium salt monohydrate, 0.1 mM L-Serine, 0.1 mM L-Threonine, 0.1 mM L-Asparagine, 0.1 mM L-Glutamine, 0.1 mM L-Cysteine hydrochloride monohydrate, 0.1 mM Glycine, 0.1 mM L-Proline, 0.1 mM L-Alanine, 0.1 mM L-Valine, 0.1 mM L-Isoleucine, 0.1 mM L-Leucine, 0.1 mM L-Methionine, 0.1 mM L-Phenylalanine, 0.1 mM L-tyrosine disodium salt, 0.1 mM L-Tryptophan), DL vitamins (0.0002 mg/L biotin, 0.0002 mg/L Folic Acid, 0.001 mg/L Pyridoxine HCl, 0.0005 mg/L Riboflavin, 0.0005 mg/L Thiamine HCl, 0.0005 mg/L Nicotinic Acid, 0.0005 mg/L calcium pantothenate, 1e-05 mg/L Cyanocobalamin, 0.0005 mg/L 4-Aminobenzoic acid, 0.0005 mg/L Lipoic acid), Sulfur-free DL minerals (0.0003 g/L Magnesium chloride hexahydrate, 0.00015 g/L Nitrilotriacetic acid disodium salt, 0.0001 g/L Sodium Chloride, 5e-05 g/L Manganese (II) chloride tetrahydrate, 1e-05 g/L Cobalt chloride hexahydrate, 1.3e-05 g/L Zinc chloride, 1e-05 g/L Calcium chloride dihydrate, 1e-05 g/L Iron (II) chloride tetrahydrate, 2.5e-06 g/L Nickel (II) chloride hexahydrate, 2e-06 g/L Aluminum chloride hydrate, 1e-06 g/L copper (II) chloride dihydrate, 1e-06 g/L Boric Acid, 1e-06 g/L Sodium Molybdate Dihydrate, 3e-05 g/L Sodium selenite pentahydrate, 2.5e-05 g/L Sodium tungstate dihydrate)
Growth plate: 1 E3

Specific Phenotypes

For 16 genes in this experiment

For carbon source Potassium acetate in Rhodanobacter denitrificans FW104-10B01

For carbon source Potassium acetate across organisms

SEED Subsystems

Subsystem #Specific
Cysteine Biosynthesis 3
Coenzyme B12 biosynthesis 1
DNA-binding regulatory proteins, strays 1
Dissimilatory nitrite reductase 1
Experimental tye 1
Heme and Siroheme Biosynthesis 1
Ketoisovalerate oxidoreductase 1
Oxidative stress 1
Photorespiration (oxidative C2 cycle) 1
Protein chaperones 1
Proteolysis in bacteria, ATP-dependent 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Serine-glyoxylate cycle 1
Thioredoxin-disulfide reductase 1
Type IV pilus 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
acetate conversion to acetyl-CoA 1 1 1
acetate and ATP formation from acetyl-CoA III 1 1 1
assimilatory sulfate reduction III 3 3 2
assimilatory sulfate reduction I 4 4 2
glycolate and glyoxylate degradation II 2 2 1
chitin deacetylation 4 2 2
factor 430 biosynthesis 7 3 3
glyoxylate cycle 6 6 2
superpathway of acetate utilization and formation 3 3 1
ethanol degradation II 3 3 1
ethanol degradation IV 3 3 1
L-isoleucine biosynthesis V 3 2 1
ethanol degradation III 3 2 1
assimilatory sulfate reduction IV 4 3 1
superpathway of sulfate assimilation and cysteine biosynthesis 9 8 2
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) 10 8 2
2-methylcitrate cycle I 5 4 1
cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion) 15 3 3
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 11 2
superpathway of glyoxylate bypass and TCA 12 10 2
L-isoleucine biosynthesis IV 6 4 1
2-methylcitrate cycle II 6 3 1
superpathway of bitter acids biosynthesis 18 3 3
adlupulone and adhumulone biosynthesis 6 1 1
lupulone and humulone biosynthesis 6 1 1
colupulone and cohumulone biosynthesis 6 1 1
β-alanine biosynthesis II 6 1 1
cob(II)yrinate a,c-diamide biosynthesis II (late cobalt incorporation) 13 2 2
superpathway of glyoxylate cycle and fatty acid degradation 14 11 2
superpathway of glycol metabolism and degradation 7 4 1
D-xylose degradation IV 7 1 1
L-arabinose degradation IV 8 2 1
reductive glycine pathway of autotrophic CO2 fixation 9 5 1
cis-geranyl-CoA degradation 9 2 1
superpathway of coenzyme A biosynthesis II (plants) 10 5 1
adenosylcobalamin biosynthesis I (anaerobic) 36 12 3
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 23 2
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered) 14 2 1
adenosylcobalamin biosynthesis II (aerobic) 33 12 2
superpathway of pentose and pentitol degradation 42 4 1