Experiment set6IT054 for Desulfovibrio vulgaris Miyazaki F

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10 day starvation, 37C

Group: starvation
Media: MoLS4
Culturing: Miya_ML3_a, serum bottle, Anaerobic, at 37 (C), shaken=0 rpm
By: Jen on 4/19/2015
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), 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 26 genes in this experiment

SEED Subsystems

Subsystem #Specific
Respiratory Complex I 3
Energy-conserving hydrogenase (ferredoxin) 2
Thiamin biosynthesis 2
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Glycogen metabolism 1
Maltose and Maltodextrin Utilization 1
Molybdenum cofactor biosynthesis 1
NiFe hydrogenase maturation 1
Potassium homeostasis 1
Pyridoxin (Vitamin B6) Biosynthesis 1
Transport of Molybdenum 1
Zinc resistance 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
ethanol degradation I 2 2 2
hydrogen production III 1 1 1
methanol oxidation to formaldehyde II 1 1 1
acetaldehyde biosynthesis I 1 1 1
hydrogen production VIII 1 1 1
pyruvate fermentation to ethanol III 3 3 2
pyruvate fermentation to ethanol I 3 2 2
L-threonine degradation IV 2 2 1
hydrogen production VI 2 2 1
thiamine diphosphate biosynthesis I (E. coli) 2 2 1
thiamine diphosphate biosynthesis II (Bacillus) 2 2 1
NADH to cytochrome bd oxidase electron transfer I 2 1 1
NADH to cytochrome bo oxidase electron transfer I 2 1 1
pyruvate fermentation to ethanol II 2 1 1
superpathway of hydrogen production 2 1 1
ethanolamine utilization 5 5 2
acetylene degradation (anaerobic) 5 4 2
glycogen degradation I 8 6 3
ethanol degradation II 3 3 1
cardiolipin biosynthesis II 3 3 1
thiamine diphosphate salvage V 3 3 1
superpathway of fermentation (Chlamydomonas reinhardtii) 9 6 3
glycogen degradation II 6 4 2
L-leucine degradation III 3 2 1
2-aminoethylphosphonate degradation I 3 2 1
L-isoleucine degradation II 3 2 1
L-valine degradation II 3 2 1
aerobic respiration III (alternative oxidase pathway) 3 2 1
thiamine diphosphate biosynthesis IV (eukaryotes) 3 1 1
2-deoxy-α-D-ribose 1-phosphate degradation 3 1 1
L-methionine degradation III 3 1 1
sulfoacetaldehyde degradation IV 3 1 1
2-hydroxypenta-2,4-dienoate degradation 3 1 1
2-deoxy-D-ribose degradation I 3 1 1
thiamine diphosphate biosynthesis III (Staphylococcus) 3 1 1
aerobic respiration I (cytochrome c) 4 3 1
starch degradation V 4 3 1
phytol degradation 4 3 1
cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas) 4 3 1
L-tyrosine degradation III 4 2 1
L-phenylalanine degradation III 4 2 1
starch degradation III 4 2 1
salidroside biosynthesis 4 2 1
thiamine diphosphate salvage II 5 5 1
superpathway of thiamine diphosphate biosynthesis I 10 8 2
pyruvate fermentation to isobutanol (engineered) 5 4 1
(S)-propane-1,2-diol degradation 5 3 1
phenylethanol biosynthesis 5 2 1
catechol degradation I (meta-cleavage pathway) 5 1 1
superpathway of thiamine diphosphate biosynthesis II 11 9 2
thiazole component of thiamine diphosphate biosynthesis I 6 4 1
superpathway of pyrimidine deoxyribonucleosides degradation 6 2 1
superpathway of photosynthetic hydrogen production 6 2 1
Fe(II) oxidation 6 2 1
NAD(P)/NADPH interconversion 6 2 1
methanol oxidation to carbon dioxide 6 2 1
triethylamine degradation 6 1 1
noradrenaline and adrenaline degradation 13 4 2
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 4 2
3-methylbutanol biosynthesis (engineered) 7 6 1
thiazole component of thiamine diphosphate biosynthesis II 7 5 1
pyridoxal 5'-phosphate biosynthesis I 7 5 1
superpathway of purine deoxyribonucleosides degradation 7 4 1
thiamine diphosphate salvage IV (yeast) 7 4 1
superpathway of thiamine diphosphate biosynthesis III (eukaryotes) 7 3 1
serotonin degradation 7 3 1
catechol degradation II (meta-cleavage pathway) 7 2 1
toluene degradation V (aerobic) (via toluene-cis-diol) 7 1 1
toluene degradation I (aerobic) (via o-cresol) 7 1 1
sucrose biosynthesis II 8 6 1
mixed acid fermentation 16 11 2
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast) 8 4 1
butanol and isobutanol biosynthesis (engineered) 8 3 1
3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation 8 1 1
p-cumate degradation 8 1 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 8 2
heterolactic fermentation 18 13 2
hexitol fermentation to lactate, formate, ethanol and acetate 19 15 2
meta cleavage pathway of aromatic compounds 10 2 1
superpathway of N-acetylneuraminate degradation 22 14 2
p-cymene degradation 11 1 1
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage 12 9 1
L-glutamate degradation VII (to butanoate) 12 4 1
naphthalene degradation to acetyl-CoA 12 1 1
L-tryptophan degradation IX 12 1 1
L-tryptophan degradation XII (Geobacillus) 12 1 1
superpathway of cardiolipin biosynthesis (bacteria) 13 8 1
toluene degradation IV (aerobic) (via catechol) 13 2 1
L-tryptophan degradation V (side chain pathway) 13 1 1
superpathway of L-threonine metabolism 18 12 1
mandelate degradation to acetyl-CoA 18 1 1
superpathway of anaerobic sucrose degradation 19 15 1
superpathway of aerobic toluene degradation 30 3 1
superpathway of aromatic compound degradation via 3-oxoadipate 35 3 1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate 42 4 1