Experiment set10H39 for Pseudomonas stutzeri RCH2

Compare to:

Sodium propionate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Sodium propionate (20 mM), pH=7.2
Culturing: psRCH2_ML7c, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.5 generations
By: Kelly on 2/24/2014
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 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)

Specific Phenotypes

For 20 genes in this experiment

For carbon source Sodium propionate in Pseudomonas stutzeri RCH2

For carbon source Sodium propionate across organisms

SEED Subsystems

Subsystem #Specific
Fermentations: Mixed acid 3
Ethanolamine utilization 2
Fermentations: Lactate 2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 2
Threonine anaerobic catabolism gene cluster 2
Bacterial hemoglobins 1
DNA-replication 1
Glycogen metabolism 1
MLST 1
Nudix proteins (nucleoside triphosphate hydrolases) 1
Propanediol utilization 1
Pyruvate metabolism I: anaplerotic reactions, PEP 1
Ribosome activity modulation 1
Transcription factors bacterial 1
Trehalose Biosynthesis 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
acetate and ATP formation from acetyl-CoA I 2 2 2
L-glutamine biosynthesis I 1 1 1
acetate formation from acetyl-CoA (succinate) 1 1 1
superpathway of acetate utilization and formation 3 3 2
pyruvate fermentation to acetate II 3 3 2
pyruvate fermentation to acetate I 3 2 2
pyruvate fermentation to acetate IV 3 2 2
pyruvate fermentation to acetate VII 3 2 2
pyruvate fermentation to acetate and (S)-lactate I 4 4 2
ammonia assimilation cycle I 2 2 1
CO2 fixation into oxaloacetate (anaplerotic) 2 2 1
pyruvate fermentation to acetate and lactate II 4 3 2
sulfoacetaldehyde degradation I 2 1 1
glycine degradation (reductive Stickland reaction) 2 1 1
ammonia assimilation cycle II 2 1 1
ethanolamine utilization 5 5 2
acetylene degradation (anaerobic) 5 4 2
(S)-propane-1,2-diol degradation 5 3 2
ammonia assimilation cycle III 3 3 1
pyruvate fermentation to acetate V 3 3 1
L-threonine degradation I 6 5 2
L-aspartate degradation II (aerobic) 3 2 1
superpathway of ammonia assimilation (plants) 3 2 1
pyruvate fermentation to acetate VI 3 2 1
L-aspartate degradation III (anaerobic) 3 2 1
methanogenesis from acetate 6 2 2
acetyl-CoA fermentation to butanoate 7 4 2
putrescine degradation II 4 3 1
glycogen biosynthesis I (from ADP-D-Glucose) 4 3 1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales) 8 3 2
sulfolactate degradation II 4 1 1
glycogen biosynthesis II (from UDP-D-Glucose) 4 1 1
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 5 2
superpathway of fermentation (Chlamydomonas reinhardtii) 9 5 2
superpathway of L-alanine fermentation (Stickland reaction) 9 4 2
starch biosynthesis 10 5 2
L-lysine fermentation to acetate and butanoate 10 3 2
mixed acid fermentation 16 12 3
gallate degradation III (anaerobic) 11 5 2
superpathway of sulfolactate degradation 6 2 1
superpathway of taurine degradation 6 1 1
(S)-lactate fermentation to propanoate, acetate and hydrogen 13 5 2
L-glutamate and L-glutamine biosynthesis 7 5 1
C4 photosynthetic carbon assimilation cycle, NADP-ME type 7 4 1
succinate fermentation to butanoate 7 2 1
partial TCA cycle (obligate autotrophs) 8 8 1
superpathway of ornithine degradation 8 6 1
nitrogen remobilization from senescing leaves 8 5 1
glycogen biosynthesis III (from α-maltose 1-phosphate) 8 4 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 8 2
TCA cycle VII (acetate-producers) 9 8 1
superpathway of L-threonine metabolism 18 13 2
reductive glycine pathway of autotrophic CO2 fixation 9 5 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 16 2
L-arginine biosynthesis II (acetyl cycle) 10 10 1
anaerobic energy metabolism (invertebrates, mitochondrial) 10 5 1
superpathway of methanogenesis 21 2 2
superpathway of N-acetylneuraminate degradation 22 14 2
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 6 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 6 1
purine nucleobases degradation II (anaerobic) 24 16 2
superpathway of L-arginine and L-ornithine degradation 13 8 1
formaldehyde assimilation I (serine pathway) 13 5 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 9 1
Bifidobacterium shunt 15 15 1
purine nucleobases degradation I (anaerobic) 15 6 1
superpathway of anaerobic energy metabolism (invertebrates) 17 9 1
heterolactic fermentation 18 15 1
gluconeogenesis II (Methanobacterium thermoautotrophicum) 18 9 1
superpathway of L-lysine degradation 43 11 2
ethene biosynthesis V (engineered) 25 18 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 21 1