Selected Cell
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Metadata
Organism_Sample
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nomenclature
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| Metadata | Values (examples) | ||||||||
| Asset Title | Timecourse data for glycolytic oscillation in yeast extracts | ||||||||
| Uploader | Franco du Preez | ||||||||
| Uploader SEEK ID | 355 | ||||||||
| Project | SysMO-DB | ||||||||
| ASSAY | |||||||||
| Assay SEEK ID | 220 | ||||||||
| Assay Title | Metabolite concentrations in yeast glycolytic oscillations | ||||||||
| Assay_type | discontinuousEnzymatic | ||||||||
| Technology_type | enzymatic activity measurements | ||||||||
| Description | Concentration of glycolytic intermediates were determined by enzymatic assays | ||||||||
| Experimentalist | Joachim Das and Heinrich-Gustav Busse | ||||||||
| Date | 1991 | ||||||||
| SOP | |||||||||
| Publication (optional) | Das, J. and Busse, H.G. (1991) Biopyshical Journal 60:369-379 | ||||||||
| Experimental_conditions | |||||||||
| Item | temperature | pH | |||||||
| Compound (if concentration) | |||||||||
| Unit | |||||||||
| Start_value (optional) | 25 | 6.5 | |||||||
| End_value (optional) | 25 | 6.5 | |||||||
| Comments | |||||||||
| Culture growth | Batch | ||||||||
| FACTORS_STUDIED | |||||||||
| Item | concentration | ||||||||
| Compound (if concentration) | Glucose | ||||||||
| Unit | umol/ml | ||||||||
| Start_value (optional) | 50 | ||||||||
| End_value (optional) | 50 | ||||||||
| SD (optional) | |||||||||
| Comments | Semi-aerobic. Cultures were harvested in the early stationary phase. The oscillations were induced and sustained by continuous feeding of the extract with 50 umol glucose/ml extract/h(or 0.83 umol/ml/ min) from a stock solution of 3M glucose in 0.1M potassium phosphate buffer(pH6 .5) by an autoburette | ||||||||
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| Sample Name | Treatments (Factors Studied) | ||||||||
| Organism | NCBI_ID | Strain | Genotype | Phenotype | Respiration | concentration | |||
| sample | Saccharomyces cerevisiae | 4932 | ATCC 9080 | semi-aerobic | Glucose 30uM/ml | ||||
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| Metabolites | Steady state data | measured unit: mM | ||||||||||||||||||||||||||||||||||
| timeseries (minutes) | ||||||||||||||||||||||||||||||||||||
| 1.083 | 2.083 | 2.167 | 2.5 | 3.083 | 3.167 | 3.2915 | 4.167 | 4.833 | 5 | 5.167 | 6.333 | 6.417 | 6.5 | 6.833 | 6.9585 | 7.375 | 7.666666666666667 | 7.917 | 8.0415 | 8.333 | 8.4585 | 8.583 | 8.8335 | 9.875 | 10.333400000000001 | 10.8195 | 11.167 | 11.167 | 11.333 | 11.333 | 11.610999999999999 | 11.833 | 11.833 | 12.833333333333334 | 15.125 | |
| 1,3-biphosphoglycerate | ||||||||||||||||||||||||||||||||||||
| 2-phospho-D-glyceric acid | ||||||||||||||||||||||||||||||||||||
| 3-phospho-D-glyceric acid | ||||||||||||||||||||||||||||||||||||
| acetaldehyde | ||||||||||||||||||||||||||||||||||||
| ADP | - | - | - | - | - | - | - | - | - | - | - | - | 0.433 | - | - | - | - | - | - | - | - | 0.417 | - | - | - | - | 0.467 | - | - | - | - | - | - | - | - | - |
| alpha, alpha-trehalose | ||||||||||||||||||||||||||||||||||||
| alpha, alpha-trehalose 6-phosphate | ||||||||||||||||||||||||||||||||||||
| alpha, alpha-trehalose_out | ||||||||||||||||||||||||||||||||||||
| ATP | - | - | 0.7 | - | - | - | 0.617 | - | 0.783 | - | - | - | 0.7 | - | - | 0.667 | 0.567 | 0.2 | - | 0.083 | - | - | 0.05 | - | 0.283 | 0.567 | 0.667 | - | - | - | - | - | - | - | - | - |
| beta-D-glucose 6-phosphate | ||||||||||||||||||||||||||||||||||||
| carbon dioxide | ||||||||||||||||||||||||||||||||||||
| D-fructose 1,6-biphosphate | - | 1.37 | - | - | 1.082 | - | - | - | - | 0.384 | - | 0.384 | - | - | - | 0.384 | 0.671 | 1.904 | - | 2.192 | - | 2.562 | - | - | 3.548 | 3.466 | 3.219 | - | - | - | - | - | - | - | - | - |
| D-fructose 2,6-biphosphate | ||||||||||||||||||||||||||||||||||||
| D-fructose 6-phosphate | 0.219 | 0.466 | - | - | 0.425 | - | - | - | - | - | 0.589 | 0.795 | - | - | - | 0.918 | 0.795 | 0.466 | - | 0.425 | - | - | 0.466 | |||||||||||||
| D-glucose | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | 0.155 | - | - | - | 0.138 | 0.017 | - | - | - | - | - | - | - | - | - |
| D-glucose 1-phosphate | ||||||||||||||||||||||||||||||||||||
| D-glucose 6-phosphate | 0.878 | 1.245 | - | - | - | 1.694 | - | - | 2.469 | - | - | 2.755 | - | - | - | 3.082 | 2.837 | 2.102 | 1.735 | - | - | 1.49 | - | - | 0.714 | 0.551 | 0.796 | - | - | - | - | - | - | - | - | - |
| D-glucose_out | ||||||||||||||||||||||||||||||||||||
| dihydroxyacetone phosphate | - | 0.552 | - | - | - | 0.483 | - | - | - | 0.241 | - | - | - | 0.328 | 0.241 | - | - | 0.603 | - | 0.862 | - | 0.862 | - | |||||||||||||
| diphosphate | ||||||||||||||||||||||||||||||||||||
| ethanol | ||||||||||||||||||||||||||||||||||||
| ethanol_out | ||||||||||||||||||||||||||||||||||||
| fructose 1,6-biphosphate | ||||||||||||||||||||||||||||||||||||
| fructose 6-phosphate | ||||||||||||||||||||||||||||||||||||
| glucose 6-phosphate | ||||||||||||||||||||||||||||||||||||
| glyceraldehyde 3-phosphate | - | 0.069 | - | - | - | - | 0.069 | - | - | 0.069 | - | - | 0.069 | - | - | 0.034 | 0.052 | 0.155 | - | 0.172 | - | 0.155 | - | - | 0.414 | - | 0.241 | - | - | - | - | - | - | - | 0.138 | 0.138 |
| glycerol | ||||||||||||||||||||||||||||||||||||
| glycerol_out | ||||||||||||||||||||||||||||||||||||
| glycerone phosphate | ||||||||||||||||||||||||||||||||||||
| H+ | ||||||||||||||||||||||||||||||||||||
| H+_out | ||||||||||||||||||||||||||||||||||||
| NAD(+) | ||||||||||||||||||||||||||||||||||||
| NADH | - | - | - | 0.073 | - | - | - | 0.098 | - | - | - | - | - | 0.195 | - | - | 0.244 | - | - | 0.341 | 0.463 | 0.683 | 0.951 | 1 | - | 0.854 | - | 0.707 | - | 0.61 | - | 0.341 | 0.098 | - | - | - |
| phosphate | ||||||||||||||||||||||||||||||||||||
| phosphoenolpyruvate | ||||||||||||||||||||||||||||||||||||
| pyruvate | ||||||||||||||||||||||||||||||||||||
| pyruvate_out | ||||||||||||||||||||||||||||||||||||
| sn-glycerol 3-phosphate | ||||||||||||||||||||||||||||||||||||
| UDP | ||||||||||||||||||||||||||||||||||||
| UDP-D-glucose | ||||||||||||||||||||||||||||||||||||
| UTP | ||||||||||||||||||||||||||||||||||||
| water | ||||||||||||||||||||||||||||||||||||
| AMP | - | - | - | - | - | - | - | - | - | - | - | - | - | 0.217 | - | - | - | - | - | - | - | - | 0.883 | - | - | - | 0.233 | - | - | - | - | - | - | - | - | - |
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| This is sheet displays the nomenclature of the genes, reaction, etc, that needs to be used for this excel file | |||||||||
| Name | Gene(s) | Gene Names | Reaction | Metabolites | Notes | ||||
| Hexose transport | YDL245C | HXT15 | D-glucose_out = D-glucose | D-glucose_out | In the minimal model we add only one reaction, but later should one for each permease. These permeases also transport other hexoses, like fructose. | ||||
| YDR342C | HXT7 | D-glucose | |||||||
| YDR343C | HXT6 | ||||||||
| YDR345C | HXT3 | ||||||||
| YDR536W | STL1 | ||||||||
| YEL069C | HXT13 | ||||||||
| YFL011W | HXT10 | ||||||||
| YHR092C | HXT4 | ||||||||
| YHR094C | HXT1 | ||||||||
| YHR096C | HXT5 | ||||||||
| YJL214W | HXT8 | ||||||||
| YJL219W | HXT9 | ||||||||
| YJR158W | HXT16 | ||||||||
| YLR081W | GAL2 | ||||||||
| YMR011W | HXT2 | ||||||||
| YNR072W | HXT17 | ||||||||
| YOL156W | HXT11 | ||||||||
| Glucokinase | YCL040W | GLK1 | ATP + D-glucose = ADP + beta-D-glucose 6-phosphate + H+ | ATP | |||||
| ADP | |||||||||
| D-glucose | |||||||||
| beta-D-glucose 6-phosphate | |||||||||
| H+ | |||||||||
| Hexokinase 1 | YFR053C | HXK1 | ATP + D-glucose = ADP + beta-D-glucose 6-phosphate + H+ | ATP | |||||
| ADP | |||||||||
| D-glucose | |||||||||
| beta-D-glucose 6-phosphate | |||||||||
| H+ | |||||||||
| Hexokinase 2 | YGL253W | HXK2 | ATP + D-glucose = ADP + beta-D-glucose 6-phosphate + H+ | ATP | |||||
| ADP | |||||||||
| D-glucose | |||||||||
| beta-D-glucose 6-phosphate | |||||||||
| H+ | |||||||||
| Phosphoglucose isomerase | YBR196C | PGI1 | glucose 6-phosphate = fructose 6-phosphate | glucose 6-phosphate | |||||
| fructose 6-phosphate | |||||||||
| Phosphofructokinase | YGR240C | PFK1 | ATP + fructose 6-phosphate -> ADP + fructose 1,6-bisphosphate" + H+ | ATP | The enzyme is a hetero-multimer (octamer) of two different polypeptides (2 genes). The binding of these polypeptides could be represented in the model | ||||
| YMR205C | PFK2 | ADP | |||||||
| fructose 6-phosphate | |||||||||
| fructose 1,6-biphosphate | |||||||||
| H+ | |||||||||
| Fructosebisphosphate aldolase | YKL060C | FBA1 | fructose 1,6-bisphosphate = dihydroxyacetone phosphate + glyceraldehyde 3-phosphate | fructose 1,6-biphosphate | |||||
| dihydroxyacetone phosphate | |||||||||
| glyceraldehyde 3-phosphate | |||||||||
| Triosephosphate isomerase | YDR050C | TPI1 | dihydroxyacetone phosphate = glyceraldehyde 3-phosphate | dihydroxyacetone phosphate | |||||
| glyceraldehyde 3-phosphate | |||||||||
| Glyceraldehyde phosphate dehydrogenase | YJL052W | TDH1 | glyceraldehyde 3-phosphate + NAD + phosphate = 1,3-bisphosphoglycerate + NADH + H+ | glyceraldehyde 3-phosphate | |||||
| NAD | |||||||||
| phosphate | |||||||||
| 1,3-biphosphoglycerate | |||||||||
| NADH | |||||||||
| H+ | |||||||||
| Glyceraldehyde phosphate dehydrogenase | YJR009C | TDH2 | glyceraldehyde 3-phosphate + NAD + phosphate = 1,3-bisphosphoglycerate + NADH + H+ | glyceraldehyde 3-phosphate | |||||
| NAD | |||||||||
| phosphate | |||||||||
| 1,3-biphosphoglycerate | |||||||||
| NADH | |||||||||
| H+ | |||||||||
| Glyceraldehyde phosphate dehydrogenase | YGR192C | TDH3 | glyceraldehyde 3-phosphate + NAD + phosphate = 1,3-bisphosphoglycerate + NADH + H+ | glyceraldehyde 3-phosphate | |||||
| NAD | |||||||||
| phosphate | |||||||||
| 1,3-biphosphoglycerate | |||||||||
| NADH | |||||||||
| H+ | |||||||||
| Phosphoglycerate kinase | YCR012W | PGK1 | 1,3-bisphosphoglycerate + ADP = 3-phospho-D-glyceric acid + ATP | 1,3-biphosphoglycerate | |||||
| ADP | |||||||||
| 3-phospho-D-glyceric acid | |||||||||
| ATP | |||||||||
| Phosphoglycerate mutase | YKL152C | GPM1 | 3-phospho-D-glyceric acid = 2-phospho-D-glyceric acid | 3-phospho-D-glyceric acid | This enzyme also catalyzes a reaction of 1,3-bisphosphoglycerate to 2,3- bisphosphoglycerate | ||||
| 2-phospho-D-glyceric acid | |||||||||
| Enolase | YGR254W | ENO1 | 2-phospho-D-glyceric acid = phosphoenolpyruvate + water | 2-phospho-D-glyceric acid | |||||
| phosphoenolpyruvate | |||||||||
| water | |||||||||
| Enolase | YHR174W | ENO2 | 2-phospho-D-glyceric acid = phosphoenolpyruvate + water | 2-phospho-D-glyceric acid | |||||
| phosphoenolpyruvate | |||||||||
| water | |||||||||
| pyruvate kinase | YAL038W | PYK1 | ADP + H+ + phosphoenolpyruvate = ATP + pyruvate | ATP | |||||
| ADP | |||||||||
| H+ | |||||||||
| phosphoenolpyruvate | |||||||||
| pyruvate | |||||||||
| Pyruvate kinase | YOR347C | PYK2 | ADP + H+ + phosphoenolpyruvate = ATP + pyruvate | ATP | |||||
| ADP |
