Experiment set1H35 for Desulfovibrio vulgaris Miyazaki F

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MoYLS4 with Nalidixic acid sodium salt 0.0078125 mg/ml

Group: stress
Media: MoYLS4 + Nalidixic acid sodium salt (0.0078125 mg/ml), pH=7.2
Culturing: Miya_ML3, hungate, Anaerobic, at 30 (C), shaken=0 rpm
Growth: about 3.4 generations
By: Jen on 3/20/2014
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 53 genes in this experiment

For stress Nalidixic acid sodium salt in Desulfovibrio vulgaris Miyazaki F

For stress Nalidixic acid sodium salt across organisms

SEED Subsystems

Subsystem #Specific
DNA repair, bacterial 3
Campylobacter Iron Metabolism 1
DNA-replication 1
Folate Biosynthesis 1
Fructose utilization 1
Glycine reductase, sarcosine reductase and betaine reductase 1
Pentose phosphate pathway 1
Phage capsid proteins 1
Proteasome bacterial 1
Proteolysis in bacteria, ATP-dependent 1
TCA Cycle 1
Thioredoxin-disulfide reductase 1
Wyeosine-MimG Biosynthesis 1
Zinc resistance 1
tRNA aminoacylation, Asp and Asn 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
thioredoxin pathway 2 1 1
pentose phosphate pathway (non-oxidative branch) I 5 5 1
TCA cycle VIII (Chlamydia) 6 3 1
incomplete reductive TCA cycle 7 6 1
pyruvate fermentation to propanoate I 7 2 1
pentose phosphate pathway 8 6 1
partial TCA cycle (obligate autotrophs) 8 5 1
TCA cycle V (2-oxoglutarate synthase) 9 7 1
TCA cycle VI (Helicobacter) 9 7 1
TCA cycle VII (acetate-producers) 9 6 1
formaldehyde assimilation II (assimilatory RuMP Cycle) 9 6 1
TCA cycle II (plants and fungi) 9 5 1
TCA cycle IV (2-oxoglutarate decarboxylase) 9 5 1
Rubisco shunt 10 8 1
TCA cycle I (prokaryotic) 10 6 1
TCA cycle III (animals) 10 6 1
anaerobic energy metabolism (invertebrates, mitochondrial) 10 3 1
reductive TCA cycle I 11 9 1
L-glutamate degradation VIII (to propanoate) 11 2 1
formaldehyde assimilation III (dihydroxyacetone cycle) 12 10 1
superpathway of glyoxylate bypass and TCA 12 7 1
reductive TCA cycle II 12 7 1
(S)-lactate fermentation to propanoate, acetate and hydrogen 13 6 1
superpathway of glyoxylate cycle and fatty acid degradation 14 5 1
Bifidobacterium shunt 15 13 1
mixed acid fermentation 16 11 1
superpathway of glucose and xylose degradation 17 12 1
superpathway of anaerobic energy metabolism (invertebrates) 17 7 1
methylaspartate cycle 19 8 1
tRNA charging 21 21 1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle 22 15 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 18 1
colibactin biosynthesis 38 7 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 21 1