Experiment set7IT068 for Desulfovibrio vulgaris Miyazaki F
casamino acids nitrogen source
Group: nitrogen sourceMedia: MoLS4_no_ammonia + casamino acids (2 mg/ml)
Culturing: Miya_ML3_a, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Jen on 4/6/2015
Media components: 30 mM Sodium sulfate, 60 mM Sodium D,L-Lactate, 30 mM Tris hydrochloride, 0.12 mM EDTA, 1 mM Sodium sulfide nonahydrate, 8 mM Magnesium chloride hexahydrate, 0.6 mM Calcium chloride, 2 mM Potassium phosphate dibasic, 60 uM Iron (II) chloride tetrahydrate, 15 uM Manganese (II) chloride tetrahydrate, 7.8 uM Cobalt chloride hexahydrate, 9 uM Zinc chloride, 1.26 uM Sodium molybdate, 1.92 uM Boric Acid, 2.28 uM Nickel (II) sulfate hexahydrate, 0.06 uM copper (II) chloride dihydrate, 0.21 uM Sodium selenite pentahydrate, 0.144 uM Sodium tungstate dihydrate, Thauer's vitamin mix (0.01 mg/L Pyridoxine HCl, 0.005 mg/L 4-Aminobenzoic acid, 0.005 mg/L Lipoic acid, 0.005 mg/L Nicotinic Acid, 0.005 mg/L Riboflavin, 0.005 mg/L Thiamine HCl, 0.005 mg/L calcium pantothenate, 0.002 mg/L biotin, 0.002 mg/L Folic Acid, 0.0001 mg/L Cyanocobalamin, 0.2 mg/L Choline chloride)
Specific Phenotypes
For 3 genes in this experiment
For nitrogen source casamino acids in Desulfovibrio vulgaris Miyazaki F
For nitrogen source casamino acids across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Chorismate Synthesis | 1 |
| Phenylalanine and Tyrosine Branches from Chorismate | 1 |
| Universal GTPases | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Phenylalanine, tyrosine and tryptophan biosynthesis
- Biosynthesis of phenylpropanoids
- Biosynthesis of alkaloids derived from shikimate pathway
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| L-tyrosine biosynthesis I | 3 | 3 | 1 |
| L-phenylalanine biosynthesis I | 3 | 3 | 1 |
| L-tyrosine biosynthesis III | 4 | 2 | 1 |
| L-phenylalanine biosynthesis II | 4 | 1 | 1 |
| L-tyrosine biosynthesis II | 4 | 1 | 1 |
| chorismate biosynthesis from 3-dehydroquinate | 5 | 5 | 1 |
| superpathway of L-tyrosine biosynthesis | 10 | 9 | 2 |
| superpathway of L-phenylalanine biosynthesis | 10 | 9 | 2 |
| superpathway of L-phenylalanine and L-tyrosine biosynthesis | 5 | 1 | 1 |
| chorismate biosynthesis I | 7 | 6 | 1 |
| superpathway of aromatic amino acid biosynthesis | 18 | 17 | 2 |
| bacilysin biosynthesis | 10 | 1 | 1 |
| chorismate biosynthesis II (archaea) | 12 | 9 | 1 |
| superpathway of L-tryptophan biosynthesis | 13 | 12 | 1 |
| salinosporamide A biosynthesis | 15 | 3 | 1 |
| superpathway of chorismate metabolism | 59 | 31 | 2 |