Experiment set4IT004 for Desulfovibrio vulgaris Miyazaki F

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2 days starvation 37C

Group: starvation
Media: MoYLS4, pH=7.2
Culturing: Miya_ML3_a, 15 mL falcon, Anaerobic, at 37 (C), shaken=0 rpm
By: Jen on 1/9/2015
Media components: 1 g/L Yeast Extract, 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, 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 17 genes in this experiment

SEED Subsystems

Subsystem #Specific
Respiratory Complex I 4
High affinity phosphate transporter and control of PHO regulon 2
Phosphate metabolism 2
ABC transporter alkylphosphonate (TC 3.A.1.9.1) 1
Carbon monoxide induced hydrogenase 1
Carboxysome 1
Coenzyme B12 biosynthesis 1
Cyanate hydrolysis 1
Energy-conserving hydrogenase (ferredoxin) 1
Potassium homeostasis 1
SigmaB stress responce regulation 1
trimethylamine N-oxide (TMAO) reductase 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
NADH to cytochrome bd oxidase electron transfer I 2 1 1
CO2 fixation into oxaloacetate (anaplerotic) 2 1 1
NADH to cytochrome bo oxidase electron transfer I 2 1 1
aerobic respiration III (alternative oxidase pathway) 3 2 1
cyanate degradation 3 2 1
aerobic respiration I (cytochrome c) 4 3 1
Fe(II) oxidation 6 2 1
NAD(P)/NADPH interconversion 6 2 1
C4 photosynthetic carbon assimilation cycle, NADP-ME type 7 3 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 4 1
3-hydroxypropanoate cycle 13 5 1
glyoxylate assimilation 13 4 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 6 1
gluconeogenesis II (Methanobacterium thermoautotrophicum) 18 9 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 5 1
superpathway of the 3-hydroxypropanoate cycle 18 5 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 21 1