Experiment set6IT002 for Klebsiella michiganensis M5al

L-Histidine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + L-Histidine (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: 1808 A2

Specific Phenotypes

For 8 genes in this experiment

For nitrogen source L-Histidine in Klebsiella michiganensis M5al

For nitrogen source L-Histidine across organisms

SEED Subsystems

Subsystem	#Specific
Histidine Degradation	3
Arginine Biosynthesis extended	1
DNA-binding regulatory proteins, strays	1
Glycine and Serine Utilization	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Serine Biosynthesis	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:

• Histidine metabolism
• Glycine, serine and threonine metabolism
• Glyoxylate and dicarboxylate metabolism
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Glutathione metabolism
• Pyruvate metabolism
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-histidine degradation I	4	4	3
L-histidine degradation II	5	4	2
L-serine biosynthesis I	3	3	1
L-histidine degradation III	6	4	2
L-cysteine biosynthesis IX (Trichomonas vaginalis)	3	2	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
L-histidine degradation VI	8	7	2
L-serine biosynthesis II	4	3	1
L-ornithine biosynthesis I	5	5	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
formaldehyde assimilation I (serine pathway)	13	8	1
superpathway of arginine and polyamine biosynthesis	17	16	1