Experiment set13IT007 for Desulfovibrio vulgaris Hildenborough JW710
MoLS4 with Pantothenic acid
Group: nutrientMedia: MoLS4_no_vitamins + calcium pantothenate (210 uM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 6/14/2017
Media components: 30 mM Sodium sulfate, 60 mM Sodium D,L-Lactate, 20 mM Ammonium chloride, 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, Desulfovibrio trace elements (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)
Specific Phenotypes
For 5 genes in this experiment
For nutrient calcium pantothenate in Desulfovibrio vulgaris Hildenborough JW710
For nutrient calcium pantothenate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Biotin biosynthesis | 1 |
| Glycolate, glyoxylate interconversions | 1 |
| Photorespiration (oxidative C2 cycle) | 1 |
| Pyridoxin (Vitamin B6) Biosynthesis | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| biotin biosynthesis from 8-amino-7-oxononanoate I | 4 | 4 | 2 |
| biotin biosynthesis from 8-amino-7-oxononanoate II | 4 | 4 | 2 |
| glycolate and glyoxylate degradation II | 2 | 2 | 1 |
| biotin biosynthesis from 8-amino-7-oxononanoate III | 5 | 3 | 2 |
| biotin biosynthesis II | 6 | 5 | 2 |
| glycolate and glyoxylate degradation III | 3 | 1 | 1 |
| glycolate and glyoxylate degradation I | 4 | 1 | 1 |
| pyridoxal 5'-phosphate biosynthesis I | 7 | 5 | 1 |
| superpathway of glycol metabolism and degradation | 7 | 2 | 1 |
| biotin biosynthesis I | 15 | 13 | 2 |
| photorespiration I | 9 | 6 | 1 |
| photorespiration III | 9 | 6 | 1 |
| photorespiration II | 10 | 6 | 1 |
| superpathway of pyridoxal 5'-phosphate biosynthesis and salvage | 12 | 9 | 1 |