Experiment set7IT021 for Rhodanobacter denitrificans FW104-10B01

Anaerobic, acetate donor; nitrate electron acceptor

Group: anaerobic
Media: Hans_Basal_Media_bicarb_nitrate + Potassium acetate (5 mM), pH=7
Culturing: rhodanobacter_10B01_ML12, tube, Anaerobic, at 30 (C)
By: Hans Carlson on 22-Sep-21
Media components: 2.5 g/L Sodium bicarbonate, 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, 10 mM Sodium nitrate, 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)

Specific Phenotypes

For 21 genes in this experiment

For anaerobic Potassium acetate in Rhodanobacter denitrificans FW104-10B01

For anaerobic Potassium acetate across organisms

SEED Subsystems

Subsystem	#Specific
Molybdenum cofactor biosynthesis	6
Transport of Molybdenum	3
Formate hydrogenase	2
Nitrate and nitrite ammonification	2
Experimental tye	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Heme and Siroheme Biosynthesis	1
Hydrogenases	1
Methionine Biosynthesis	1
Methionine Degradation	1
Photorespiration (oxidative C2 cycle)	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Serine-glyoxylate cycle	1
Thiamin biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Puromycin biosynthesis
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Porphyrin and chlorophyll metabolism
• Oxidative phosphorylation
• Methionine metabolism
• Selenoamino acid metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• alpha-Linolenic acid metabolism
• Trinitrotoluene degradation
• Reductive carboxylate cycle (CO2 fixation)
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Alkaloid biosynthesis I
• Insect hormone biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
nitrate reduction IX (dissimilatory)	2	2	1
glycolate and glyoxylate degradation II	2	2	1
nitrate reduction VIII (dissimilatory)	2	1	1
nitrate reduction III (dissimilatory)	2	1	1
NADH to nitrate electron transfer	2	1	1
nitrate reduction VIIIb (dissimilatory)	2	1	1
glyoxylate cycle	6	6	2
S-adenosyl-L-methionine salvage II	3	3	1
L-methionine degradation I (to L-homocysteine)	3	2	1
heme b biosynthesis II (oxygen-independent)	4	3	1
chitin deacetylation	4	2	1
nitrate reduction I (denitrification)	5	4	1
nitrate reduction VII (denitrification)	5	4	1
superpathway of L-cysteine biosynthesis (mammalian)	5	4	1
superpathway of glyoxylate bypass and TCA	12	10	2
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	4	1
thiazole component of thiamine diphosphate biosynthesis I	6	3	1
molybdopterin biosynthesis	6	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
thiazole component of thiamine diphosphate biosynthesis II	7	4	1
superpathway of glycol metabolism and degradation	7	4	1
D-xylose degradation IV	7	1	1
L-arabinose degradation IV	8	2	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	3
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)	9	2	1
glycolysis V (Pyrococcus)	10	7	1
superpathway of thiamine diphosphate biosynthesis I	10	5	1
glycolysis II (from fructose 6-phosphate)	11	11	1
superpathway of thiamine diphosphate biosynthesis II	11	6	1
glycolysis I (from glucose 6-phosphate)	13	12	1
gluconeogenesis I	13	11	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	2	1
superpathway of L-methionine salvage and degradation	16	8	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	16	1
superpathway of hexitol degradation (bacteria)	18	14	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	8	1
superpathway of anaerobic sucrose degradation	19	16	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of N-acetylneuraminate degradation	22	16	1
superpathway of bacteriochlorophyll a biosynthesis	26	5	1
superpathway of pentose and pentitol degradation	42	4	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	25	1