Experiment set3IT027 for Cupriavidus basilensis FW507-4G11

Sodium nitrite nitrogen source

Group: nitrogen source
Media: RCH2_defined_noNitrogen + Sodium nitrite (20 mM), pH=7
Culturing: cupriavidus_4G11_ML11, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Jayashree on 3/3/2015
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 15 genes in this experiment

For nitrogen source Sodium nitrite in Cupriavidus basilensis FW507-4G11

For nitrogen source Sodium nitrite across organisms

SEED Subsystems

Subsystem	#Specific
Nitrate and nitrite ammonification	3
Ammonia assimilation	2
Branched-Chain Amino Acid Biosynthesis	1
Glycolate, glyoxylate interconversions	1
Leucine Biosynthesis	1
Methionine Biosynthesis	1
Orphan regulatory proteins	1
Photorespiration (oxidative C2 cycle)	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glyoxylate and dicarboxylate metabolism
• Nitrogen metabolism
• Biosynthesis of plant hormones
• Methionine metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine biosynthesis
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Selenoamino acid metabolism
• Pyruvate metabolism
• Sulfur metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycolate and glyoxylate degradation II	2	2	1
alkylnitronates degradation	2	2	1
nitrate reduction V (assimilatory)	2	1	1
glycolate and glyoxylate degradation III	3	1	1
glycolate and glyoxylate degradation I	4	3	1
L-tryptophan biosynthesis	6	6	1
L-leucine biosynthesis	6	6	1
hydrogen sulfide biosynthesis II (mammalian)	6	1	1
3-methylbutanol biosynthesis (engineered)	7	6	1
superpathway of glycol metabolism and degradation	7	5	1
photorespiration III	9	6	1
photorespiration I	9	6	1
photorespiration II	10	6	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of branched chain amino acid biosynthesis	17	17	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of chorismate metabolism	59	45	1