Experiment set6IT037 for Klebsiella michiganensis M5al

Sodium nitrate nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Sodium nitrate (20 mM), pH=7
Culturing: Koxy_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 27-Apr-17
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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)
Growth plate: 1810 D2

Specific Phenotypes

For 6 genes in this experiment

For nitrogen source Sodium nitrate in Klebsiella michiganensis M5al

For nitrogen source Sodium nitrate across organisms

SEED Subsystems

Subsystem	#Specific
Nitrate and nitrite ammonification	3
Ammonia assimilation	1
Coenzyme B12 biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Porphyrin and chlorophyll metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Ubiquinone and menaquinone biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Benzoxazinone biosynthesis
• Naphthalene and anthracene degradation
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
alkylnitronates degradation	2	2	1
nitrate reduction V (assimilatory)	2	1	1
L-tryptophan biosynthesis	6	6	1
cob(II)yrinate a,c-diamide biosynthesis II (late cobalt incorporation)	13	10	2
cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion)	15	14	2
superpathway of L-tryptophan biosynthesis	13	13	1
adenosylcobalamin biosynthesis II (aerobic)	33	29	2
superpathway of aromatic amino acid biosynthesis	18	18	1
adenosylcobalamin biosynthesis I (anaerobic)	36	31	2
superpathway of chorismate metabolism	59	54	1