Experiment set3H24 for Shewanella amazonensis SB2B

L-Histidine nitrogen source

Group: nitrogen source
Media: ShewMM_noNitrogen + L-Histidine (20 mM), pH=7
Culturing: SB2B_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Jake on 4/24/2013
Media components: 1.75 g/L Sodium Chloride, 0.61 g/L Magnesium chloride hexahydrate, 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)
Growth plate: 511 A3,A4

Specific Phenotypes

For 12 genes in this experiment

For nitrogen source L-Histidine in Shewanella amazonensis SB2B

For nitrogen source L-Histidine across organisms

SEED Subsystems

Subsystem	#Specific
Histidine Degradation	3
ATP-dependent RNA helicases, bacterial	1
Phosphate metabolism	1
PnuC-like transporters	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Serine-glyoxylate cycle	1
Thiamin biosynthesis	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:

• Histidine metabolism
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• gamma-Hexachlorocyclohexane degradation
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Pyruvate metabolism
• Carbon fixation in photosynthetic organisms
• Folate biosynthesis
• Nitrogen metabolism
• Biosynthesis of siderophore group nonribosomal peptides

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-histidine degradation I	4	4	3
diethylphosphate degradation	2	1	1
L-histidine degradation II	5	3	2
L-histidine degradation III	6	4	2
L-histidine degradation VI	8	7	2
gluconeogenesis I	13	13	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1