Experiment set3H13 for Pseudomonas stutzeri RCH2

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Sodium nitrite nitrogen source

Group: nitrogen source
Media: RCH2_defined_noNitrogen + Sodium nitrite (5 mM), pH=7.2
Culturing: psRCH2_ML7, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Kelly on 6/20/2013
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)
Growth plate: 553 E7,E8

Specific Phenotypes

For 30 genes in this experiment

For nitrogen source Sodium nitrite in Pseudomonas stutzeri RCH2

For nitrogen source Sodium nitrite across organisms

SEED Subsystems

Subsystem #Specific
Nitrate and nitrite ammonification 3
Arginine Deiminase Pathway 1
Arginine and Ornithine Degradation 1
Central meta-cleavage pathway of aromatic compound degradation 1
Coenzyme A Biosynthesis 1
Coenzyme B12 biosynthesis 1
Dissimilatory nitrite reductase 1
Ectoine biosynthesis and regulation 1
Experimental tye 1
Heme and Siroheme Biosynthesis 1
Isoleucine degradation 1
MLST 1
Polyamine Metabolism 1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 1
Ribosome biogenesis bacterial 1
Rubrerythrin 1
SigmaB stress responce regulation 1
Thioredoxin-disulfide reductase 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
β-alanine biosynthesis III 1 1 1
siroheme biosynthesis 4 4 3
L-methionine degradation II 3 2 2
alkylnitronates degradation 2 2 1
nitrate reduction V (assimilatory) 2 1 1
factor 430 biosynthesis 7 3 3
L-serine biosynthesis I 3 3 1
L-citrulline degradation 3 3 1
L-threonine degradation I 6 5 2
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis 3 1 1
L-isoleucine biosynthesis I (from threonine) 7 7 2
L-arginine degradation V (arginine deiminase pathway) 4 4 1
superpathway of L-serine and glycine biosynthesis I 4 4 1
adipate degradation 5 5 1
ectoine biosynthesis 5 5 1
cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion) 15 4 3
fatty acid salvage 6 6 1
superpathway of L-isoleucine biosynthesis I 13 13 2
cob(II)yrinate a,c-diamide biosynthesis II (late cobalt incorporation) 13 3 2
hypoglycin biosynthesis 14 4 2
superpathway of CDP-glucose-derived O-antigen building blocks biosynthesis 8 1 1
superpathway of branched chain amino acid biosynthesis 17 17 2
superpathway of coenzyme A biosynthesis I (bacteria) 9 9 1
superpathway of sulfate assimilation and cysteine biosynthesis 9 9 1
superpathway of L-threonine metabolism 18 13 2
allantoin degradation IV (anaerobic) 9 2 1
methyl tert-butyl ether degradation 10 3 1
oleate β-oxidation 35 30 3
adenosylcobalamin biosynthesis I (anaerobic) 36 20 3
guadinomine B biosynthesis 13 2 1
2-methyl-branched fatty acid β-oxidation 14 10 1
adenosylcobalamin biosynthesis II (aerobic) 33 21 2