Experiment set3H4 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: 510 A3,A4

Specific Phenotypes

For 10 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
DNA repair, bacterial	1
Purine conversions	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
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Puromycin biosynthesis
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Naphthalene and anthracene degradation
• Trinitrotoluene degradation
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Drug metabolism - other enzymes
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-histidine degradation I	4	4	3
guanine and guanosine salvage I	2	2	1
xanthine and xanthosine salvage	2	2	1
guanine and guanosine salvage II	2	1	1
L-histidine degradation II	5	3	2
superpathway of guanine and guanosine salvage	3	3	1
L-histidine degradation III	6	4	2
adenine salvage	3	2	1
adenine and adenosine salvage III	4	4	1
L-histidine degradation VI	8	7	2
putrescine degradation II	4	3	1
superpathway of ornithine degradation	8	6	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	1
superpathway of L-arginine and L-ornithine degradation	13	8	1
superpathway of purine nucleotide salvage	14	13	1