Experiment set15IT064 for Desulfovibrio vulgaris Hildenborough JW710

MoYLS4 with Molybdate 100uM and Tungstate 2mM

Group: stress
Media: MoYLS4 + Sodium molybdate (100 uM) + Sodium tungstate dihydrate (2 mM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 10/26/2017
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 77 genes in this experiment

For stress Sodium molybdate in Desulfovibrio vulgaris Hildenborough JW710

For stress Sodium molybdate across organisms

SEED Subsystems

Subsystem	#Specific
Molybdenum cofactor biosynthesis	4
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	3
Zinc resistance	3
Bacterial Cell Division	2
Energy-conserving hydrogenase (ferredoxin)	2
Hfl operon	2
Hydrogenases	2
Multidrug Resistance Efflux Pumps	2
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	2
Peptidoglycan Biosynthesis	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
CMP-N-acetylneuraminate Biosynthesis	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Fatty Acid Biosynthesis FASII	1
Lactate utilization	1
NiFe hydrogenase maturation	1
Protein chaperones	1
Ribonucleotide reduction	1
Rrf2 family transcriptional regulators	1
Sialic Acid Metabolism	1
Transport of Molybdenum	1
Transport of Zinc	1
mycolic acid synthesis	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Peptidoglycan biosynthesis
• Pentose phosphate pathway
• Fatty acid biosynthesis
• Fatty acid metabolism
• Oxidative phosphorylation
• Purine metabolism
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Lysine degradation
• Tyrosine metabolism
• Glutathione metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Methane metabolism
• Biotin metabolism
• Retinol metabolism
• Alkaloid biosynthesis II
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Drug metabolism - other enzymes

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
ethanol degradation I	2	2	2
methylsalicylate degradation	2	2	2
hydrogen production VIII	1	1	1
acetaldehyde biosynthesis I	1	1	1
methanol oxidation to formaldehyde II	1	1	1
hydrogen production III	1	1	1
pyruvate fermentation to ethanol I	3	3	2
pyruvate fermentation to ethanol III	3	3	2
adenosine deoxyribonucleotides de novo biosynthesis I	2	2	1
guanosine deoxyribonucleotides de novo biosynthesis I	2	2	1
L-threonine degradation IV	2	2	1
adenosine deoxyribonucleotides de novo biosynthesis II	4	3	2
guanosine deoxyribonucleotides de novo biosynthesis II	4	3	2
superpathway of hydrogen production	2	1	1
hydrogen production VI	2	1	1
methyl indole-3-acetate interconversion	2	1	1
pyruvate fermentation to ethanol II	2	1	1
aspartame degradation	2	1	1
acetylene degradation (anaerobic)	5	4	2
ethanolamine utilization	5	4	2
superpathway of fermentation (Chlamydomonas reinhardtii)	9	7	3
L-leucine degradation III	3	2	1
ethanol degradation II	3	2	1
CMP-N-acetylneuraminate biosynthesis II (bacteria)	3	2	1
L-isoleucine degradation II	3	2	1
sulfoacetaldehyde degradation IV	3	2	1
L-valine degradation II	3	2	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	1	1
2-hydroxypenta-2,4-dienoate degradation	3	1	1
2-deoxy-D-ribose degradation I	3	1	1
L-methionine degradation III	3	1	1
2-aminoethylphosphonate degradation I	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
gondoate biosynthesis (anaerobic)	4	4	1
superpathway of guanosine nucleotides de novo biosynthesis II	8	7	2
phytol degradation	4	2	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
salidroside biosynthesis	4	2	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
pyrimidine deoxyribonucleotides de novo biosynthesis III	9	9	2
pyrimidine deoxyribonucleotides de novo biosynthesis I	9	8	2
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	2
oleate biosynthesis IV (anaerobic)	14	13	3
superpathway of fatty acids biosynthesis (E. coli)	53	47	11
8-amino-7-oxononanoate biosynthesis IV	5	5	1
superpathway of adenosine nucleotides de novo biosynthesis I	5	5	1
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	17	4
cis-vaccenate biosynthesis	5	4	1
fatty acid elongation -- saturated	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
(S)-propane-1,2-diol degradation	5	3	1
phenylethanol biosynthesis	5	2	1
superpathway of methylsalicylate metabolism	5	1	1
catechol degradation I (meta-cleavage pathway)	5	1	1
superpathway of fatty acid biosynthesis II (plant)	43	37	8
8-amino-7-oxononanoate biosynthesis I	11	9	2
anteiso-branched-chain fatty acid biosynthesis	34	24	6
even iso-branched-chain fatty acid biosynthesis	34	24	6
odd iso-branched-chain fatty acid biosynthesis	34	24	6
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
stearate biosynthesis II (bacteria and plants)	6	5	1
(5Z)-dodecenoate biosynthesis I	6	5	1
(5Z)-dodecenoate biosynthesis II	6	4	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	2	1
methanol oxidation to carbon dioxide	6	2	1
superpathway of photosynthetic hydrogen production	6	2	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	3	2
triethylamine degradation	6	1	1
superpathway of purine nucleotides de novo biosynthesis II	26	23	4
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	2
noradrenaline and adrenaline degradation	13	2	2
streptorubin B biosynthesis	34	20	5
3-methylbutanol biosynthesis (engineered)	7	6	1
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	5	1
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis	7	5	1
superpathway of purine deoxyribonucleosides degradation	7	4	1
catechol degradation II (meta-cleavage pathway)	7	2	1
serotonin degradation	7	2	1
toluene degradation I (aerobic) (via o-cresol)	7	1	1
toluene degradation V (aerobic) (via toluene-cis-diol)	7	1	1
retinol biosynthesis	7	1	1
biotin biosynthesis I	15	13	2
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	7	1
superpathway of fatty acid biosynthesis I (E. coli)	16	12	2
mixed acid fermentation	16	12	2
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	6	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
p-cumate degradation	8	1	1
3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation	8	1	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	8	2
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	16	2
heterolactic fermentation	18	13	2
hexitol fermentation to lactate, formate, ethanol and acetate	19	16	2
meta cleavage pathway of aromatic compounds	10	2	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	2
superpathway of N-acetylneuraminate degradation	22	15	2
p-cymene degradation	11	1	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	42	4
L-glutamate degradation VII (to butanoate)	12	4	1
L-tryptophan degradation IX	12	1	1
naphthalene degradation to acetyl-CoA	12	1	1
L-tryptophan degradation XII (Geobacillus)	12	1	1
toluene degradation IV (aerobic) (via catechol)	13	2	1
L-tryptophan degradation V (side chain pathway)	13	1	1
superpathway of purine nucleotide salvage	14	13	1
superpathway of CMP-sialic acids biosynthesis	15	2	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	1
peptidoglycan biosynthesis II (staphylococci)	17	12	1
superpathway of L-threonine metabolism	18	13	1
mandelate degradation to acetyl-CoA	18	1	1
superpathway of anaerobic sucrose degradation	19	15	1
superpathway of aerobic toluene degradation	30	2	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	2	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	4	1
mycolate biosynthesis	205	17	4
superpathway of mycolate biosynthesis	239	18	4