Experiment set5IT065 for Rhodanobacter denitrificans FW104-10B01

D-Glucose-6-Phosphate sodium salt 20 mM

Group: carbon source
Media: Hans_Basal_Media_plus_0.2x_20AA_mix + D-Glucose-6-Phosphate sodium salt (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 D3

Specific Phenotypes

For 9 genes in this experiment

For carbon source D-Glucose-6-Phosphate sodium salt in Rhodanobacter denitrificans FW104-10B01

For carbon source D-Glucose-6-Phosphate sodium salt across organisms

SEED Subsystems

Subsystem	#Specific
Protein chaperones	2
Campylobacter Iron Metabolism	1
DNA-binding regulatory proteins, strays	1
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Mannose Metabolism	1
Methylglyoxal Metabolism	1
Oxidative stress	1
Proteolysis in bacteria, ATP-dependent	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Thioredoxin-disulfide reductase	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Limonene and pinene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
putrescine degradation V	2	1	1
ethylene glycol degradation	2	1	1
putrescine degradation I	2	1	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
putrescine degradation IV	3	2	1
hypotaurine degradation	3	2	1
ethanol degradation III	3	2	1
histamine degradation	3	1	1
phytol degradation	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	1	1
D-arabinose degradation II	4	1	1
putrescine degradation III	4	1	1
4-methylphenol degradation to protocatechuate	4	1	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
mitochondrial NADPH production (yeast)	5	2	1
octane oxidation	5	2	1
dopamine degradation	5	1	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
4-hydroxymandelate degradation	6	1	1
noradrenaline and adrenaline degradation	13	4	2
superpathway of glycol metabolism and degradation	7	4	1
serotonin degradation	7	3	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
2,4-xylenol degradation to protocatechuate	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
superpathway of ornithine degradation	8	2	1
aromatic biogenic amine degradation (bacteria)	8	1	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	4	1
toluene degradation III (aerobic) (via p-cresol)	11	5	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	3	1
superpathway of L-arginine and L-ornithine degradation	13	4	1
superpathway of aerobic toluene degradation	30	7	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	11	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	8	1
superpathway of pentose and pentitol degradation	42	4	1