Experiment set4IT007 for Desulfovibrio vulgaris Miyazaki F

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14 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 20 genes in this experiment

SEED Subsystems

Subsystem #Specific
High affinity phosphate transporter and control of PHO regulon 2
Phosphate metabolism 2
Alanine biosynthesis 1
Branched-Chain Amino Acid Biosynthesis 1
Coenzyme B12 biosynthesis 1
Formate hydrogenase 1
Glycogen metabolism 1
Isoleucine degradation 1
Leucine Biosynthesis 1
Leucine Degradation and HMG-CoA Metabolism 1
Maltose and Maltodextrin Utilization 1
Potassium homeostasis 1
Pyruvate Alanine Serine Interconversions 1
Ribonucleotide reduction 1
Thiamin biosynthesis 1
Translation elongation factor G family 1
Valine degradation 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
long-chain fatty acid activation 1 1 1
adenosine deoxyribonucleotides de novo biosynthesis I 2 2 1
guanosine deoxyribonucleotides de novo biosynthesis I 2 2 1
guanosine deoxyribonucleotides de novo biosynthesis II 4 3 2
adenosine deoxyribonucleotides de novo biosynthesis II 4 3 2
γ-linolenate biosynthesis II (animals) 2 1 1
linoleate biosynthesis II (animals) 2 1 1
L-alanine biosynthesis I 2 1 1
glycogen degradation I 8 6 3
glycogen degradation II 6 4 2
L-isoleucine biosynthesis V 3 2 1
L-valine degradation II 3 2 1
L-leucine degradation III 3 2 1
L-isoleucine degradation II 3 2 1
3-methyl-branched fatty acid α-oxidation 6 3 2
alkane biosynthesis II 3 1 1
L-leucine degradation V (oxidative Stickland reaction) 3 1 1
L-valine degradation III (oxidative Stickland reaction) 3 1 1
L-isoleucine degradation III (oxidative Stickland reaction) 3 1 1
oleate biosynthesis I (plants) 3 1 1
superpathway of adenosine nucleotides de novo biosynthesis II 7 6 2
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli) 14 10 4
L-valine biosynthesis 4 4 1
superpathway of guanosine nucleotides de novo biosynthesis II 8 7 2
superpathway of L-alanine biosynthesis 4 3 1
phytol degradation 4 3 1
starch degradation V 4 3 1
starch degradation III 4 2 1
phosphatidylcholine acyl editing 4 1 1
wax esters biosynthesis II 4 1 1
long chain fatty acid ester synthesis (engineered) 4 1 1
pyrimidine deoxyribonucleotides de novo biosynthesis III 9 9 2
pyrimidine deoxyribonucleotides de novo biosynthesis I 9 8 2
sporopollenin precursors biosynthesis 18 4 4
superpathway of adenosine nucleotides de novo biosynthesis I 5 5 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
octane oxidation 5 2 1
L-leucine degradation IV (reductive Stickland reaction) 5 1 1
superpathway of branched chain amino acid biosynthesis 17 16 3
superpathway of guanosine nucleotides de novo biosynthesis I 6 6 1
L-leucine biosynthesis 6 6 1
stearate biosynthesis II (bacteria and plants) 6 5 1
stearate biosynthesis IV 6 4 1
thiazole component of thiamine diphosphate biosynthesis I 6 4 1
L-isoleucine biosynthesis IV 6 4 1
stearate biosynthesis I (animals) 6 1 1
6-gingerol analog biosynthesis (engineered) 6 1 1
fatty acid salvage 6 1 1
L-isoleucine degradation I 6 1 1
L-leucine degradation I 6 1 1
superpathway of purine nucleotides de novo biosynthesis II 26 23 4
L-isoleucine biosynthesis I (from threonine) 7 6 1
thiazole component of thiamine diphosphate biosynthesis II 7 5 1
pyrimidine deoxyribonucleotides de novo biosynthesis IV 7 5 1
L-isoleucine biosynthesis III 7 4 1
ceramide degradation by α-oxidation 7 2 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
capsaicin biosynthesis 7 1 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
pyrimidine deoxyribonucleotides biosynthesis from CTP 8 6 1
sucrose biosynthesis II 8 6 1
L-isoleucine biosynthesis II 8 6 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
L-valine degradation I 8 2 1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis 18 16 2
superpathway of thiamine diphosphate biosynthesis I 10 8 1
suberin monomers biosynthesis 20 2 2
superpathway of purine nucleotides de novo biosynthesis I 21 21 2
superpathway of fatty acid biosynthesis II (plant) 43 37 4
superpathway of thiamine diphosphate biosynthesis II 11 9 1
superpathway of histidine, purine, and pyrimidine biosynthesis 46 42 4
superpathway of L-isoleucine biosynthesis I 13 12 1
superpathway of purine nucleotide salvage 14 13 1
palmitate biosynthesis II (type II fatty acid synthase) 31 29 2
cutin biosynthesis 16 1 1
superpathway of L-threonine metabolism 18 12 1
superpathway of fatty acids biosynthesis (E. coli) 53 47 2
palmitate biosynthesis III 29 21 1
anteiso-branched-chain fatty acid biosynthesis 34 24 1
odd iso-branched-chain fatty acid biosynthesis 34 24 1
even iso-branched-chain fatty acid biosynthesis 34 24 1
oleate β-oxidation 35 1 1