Experiment set15IT065 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 98 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	5
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	4
Multidrug Resistance Efflux Pumps	3
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	3
Zinc resistance	3
CMP-N-acetylneuraminate Biosynthesis	2
Energy-conserving hydrogenase (ferredoxin)	2
Hfl operon	2
High affinity phosphate transporter and control of PHO regulon	2
Peptidoglycan Biosynthesis	2
Phosphate metabolism	2
Photorespiration (oxidative C2 cycle)	2
Sialic Acid Metabolism	2
Transport of Zinc	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
ABC transporter oligopeptide (TC 3.A.1.5.1)	1
Bacterial Cell Division	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Cobalamin synthesis	1
Coenzyme B12 biosynthesis	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
DNA repair, bacterial	1
Experimental tye	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Heat shock dnaK gene cluster extended	1
Heme and Siroheme Biosynthesis	1
Hydrogenases	1
Lactate utilization	1
Lipid A-Ara4N pathway ( Polymyxin resistance )	1
Membrane-bound Ni, Fe-hydrogenase	1
Methionine Salvage	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1
NiFe hydrogenase maturation	1
Protein chaperones	1
Pyruvate Alanine Serine Interconversions	1
Ribonucleotide reduction	1
Serine-glyoxylate cycle	1
Sex pheromones in Enterococcus faecalis and other Firmicutes	1
Terminal cytochrome d ubiquinol oxidases	1
Terminal cytochrome oxidases	1
Transport of Molybdenum	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Nucleotide sugars metabolism
• Porphyrin and chlorophyll metabolism
• Methionine metabolism
• Lysine degradation
• Aminosugars metabolism
• Peptidoglycan biosynthesis
• Glyoxylate and dicarboxylate metabolism
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Oxidative phosphorylation
• Purine metabolism
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Aminophosphonate metabolism
• Glutathione metabolism
• Glycerophospholipid metabolism
• Pyruvate metabolism
• Methane metabolism
• Biotin metabolism
• Caprolactam degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
hydrogen production III	1	1	1
glycine biosynthesis III	1	1	1
hydrogen production VIII	1	1	1
CMP-N-acetylneuraminate biosynthesis II (bacteria)	3	2	2
siroheme biosynthesis	4	4	2
adenosine deoxyribonucleotides de novo biosynthesis I	2	2	1
guanosine deoxyribonucleotides de novo biosynthesis I	2	2	1
glycerol-3-phosphate shuttle	2	2	1
glycolate and glyoxylate degradation II	2	2	1
adenosine deoxyribonucleotides de novo biosynthesis II	4	3	2
L-serine biosynthesis II	4	3	2
guanosine deoxyribonucleotides de novo biosynthesis II	4	3	2
hydrogen production VI	2	1	1
superpathway of hydrogen production	2	1	1
3,8-divinyl-chlorophyllide a biosynthesis III (aerobic, light independent)	9	3	3
3,8-divinyl-chlorophyllide a biosynthesis I (aerobic, light-dependent)	9	3	3
5'-deoxyadenosine 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
CDP-diacylglycerol biosynthesis I	4	4	1
CDP-diacylglycerol biosynthesis II	4	4	1
superpathway of guanosine nucleotides de novo biosynthesis II	8	7	2
chitin deacetylation	4	2	1
5'-deoxyadenosine degradation II	4	1	1
pyrimidine deoxyribonucleotides de novo biosynthesis III	9	9	2
pyrimidine deoxyribonucleotides de novo biosynthesis I	9	8	2
superpathway of adenosine nucleotides de novo biosynthesis I	5	5	1
CDP-diacylglycerol biosynthesis III	5	3	1
phosphatidate biosynthesis (yeast)	5	3	1
glucosylglycerol biosynthesis	5	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III	5	1	1
CMP-N-acetylneuraminate biosynthesis I (eukaryotes)	5	1	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II	5	1	1
phosphatidylglycerol biosynthesis I	6	6	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis II	6	6	1
glyoxylate cycle	6	4	1
superpathway of photosynthetic hydrogen production	6	2	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	3	2
superpathway of purine nucleotides de novo biosynthesis II	26	23	4
formaldehyde assimilation I (serine pathway)	13	7	2
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	5	1
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis	7	5	1
factor 430 biosynthesis	7	3	1
superpathway of glycol metabolism and degradation	7	2	1
D-xylose degradation IV	7	1	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation I	7	1	1
cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion)	15	13	2
superpathway of CMP-sialic acids biosynthesis	15	2	2
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	7	1
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	6	1
L-arabinose degradation IV	8	2	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	16	2
superpathway of fermentation (Chlamydomonas reinhardtii)	9	7	1
photorespiration III	9	6	1
photorespiration I	9	6	1
1,3-propanediol biosynthesis (engineered)	9	4	1
photorespiration II	10	6	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	2
L-methionine salvage cycle III	11	2	1
L-methionine salvage cycle II (plants)	11	2	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	42	4
superpathway of phospholipid biosynthesis III (E. coli)	12	10	1
superpathway of glyoxylate bypass and TCA	12	7	1
L-glutamate degradation VII (to butanoate)	12	4	1
L-methionine salvage cycle I (bacteria and plants)	12	2	1
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
superpathway of purine nucleotide salvage	14	13	1
superpathway of glyoxylate cycle and fatty acid degradation	14	5	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	1	1
peptidoglycan biosynthesis II (staphylococci)	17	12	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	1
adenosylcobalamin biosynthesis I (anaerobic)	36	29	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	18	1
superpathway of phospholipid biosynthesis II (plants)	28	10	1
superpathway of pentose and pentitol degradation	42	4	1