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SEDML
cfeMnRec
cfeMnRec2
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| Metadata | Values (examples) | ||||||||
| Asset Title | Cell Free Extract analysis | ||||||||
| Uploader | Jacky Snoep | ||||||||
| Uploader SEEK ID | 49 | ||||||||
| Project | Computational pathway design for biotechnology | ||||||||
| ASSAY | |||||||||
| Assay SEEK ID | 993 | ||||||||
| Assay Title | Cell Free Extract analysis | ||||||||
| Assay_type | enzymaticAssay | ||||||||
| Technology_type | Cell Free Extract analysis | ||||||||
| Description | Cell Free Extract analysis for the Weimberg pathway in Caulobacter crescentus, with Mn (0.15 mM), and NAD recycling, metabolites measured enzymatically. | ||||||||
| Experimentalist | Lu Shen | ||||||||
| Date | |||||||||
| SOP | |||||||||
| Publication (optional) | |||||||||
| Experimental_conditions | |||||||||
| Item | temperature | ||||||||
| Compound (if concentration) | |||||||||
| Unit | degrees celcius | ||||||||
| Start_value (optional) | 37 | ||||||||
| End_value (optional) | 37 | ||||||||
| Comments | |||||||||
| Culture growth | CultureGrowth | ||||||||
| FACTORS_STUDIED | |||||||||
| Item | concentration | concentration | |||||||
| Compound (if concentration) | Xyl | NAD | |||||||
| Unit | mM | mM | |||||||
| Start_value (optional) | 5 | 12 | |||||||
| End_value (optional) | |||||||||
| SD (optional) | |||||||||
| Comments | |||||||||
| ENZYME IDENTITY | |||||||||
| Enzyme Name (IUBMB) | Xylose dehydrogenase | D-Xylono-1,4-lactonase | D-Xylonate dehydratase | 2-keto-3-deoxy-D-xylonate dehydratase | α-ketoglutarate semialdehyde dehydrogenase | ||||
| EC Number | 1.1.1.175 | 3.1.1.68 | 4.2.1.82 | ||||||
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| time | NADH | XYL | KGSA | KDX | XA | PYR | KG | NADH2 | XYL2 | KGSA2 | KDX2 | XA2 | PYR2 | KG2 | |
| min | mM | mM | mM | mM | mM | mM | mM | mM | mM | mM | mM | mM | mM | mM | |
| 0 | 0.004093763337856239 | 5.305140050776079 | 0.0040068637532333015 | -9.620934171835731E-4 | -6.326645723331529E-4 | 15.830051798014265 | -0.1695603822116496 | 0 | 5.426849762315596 | -0.020116113146730927 | 0.08812129209701017 | -0.06456645488640145 | 14.996598853422022 | -0.07683229502774865 | |
| 8 | 0.001289817003617644 | 1.8941624375621022 | 12.488269699794564 | -0.010963105387504717 | 2.8314909565127633 | 13.714235031994336 | |||||||||
| 16 | 0.0033647401910985517 | 0.3965246507789245 | 10.717298284177563 | -0.017154703131049515 | 1.017750090254922 | 11.26665914539322 | |||||||||
| 24 | 8.131461380949572E-4 | -0.010516246048139253 | 9.603812850770291 | -0.00744127821619615 | -0.005851804924946878 | 9.79408223971561 | |||||||||
| 30 | 8.131461380949572E-4 | -0.003486672277432325 | 0.10405795802734796 | 0.045467197422422986 | 4.318003973134549 | 9.089488559044508 | 0.010849496148080805 | -0.07969662553383541 | 0.004548555175277351 | 0.14595598832666143 | 4.197333613602214 | 8.990400874264461 | |||
| 60 | 0.0028319894171124783 | 1.9683158514323049E-4 | 0.05103472927851453 | 0.10021366727873714 | 3.1516280290468 | 8.443930808285417 | 0.5601851821497629 | 0.005765571560109803 | -0.12457151330986016 | -0.003956550938956634 | 0.17232170321865659 | 3.367236701639958 | 8.562106084750363 | 0.7505910123211835 | |
| 100 | 0.0012337370951542572 | 2.530649909419664E-4 | 0.0072907038292904566 | 0.1753739695885012 | 2.4371412660733416 | 6.40916904692214 | 1.397280505409946 | -0.010054248400922765 | -0.09844181146259406 | 0.07939346363339671 | 0.01837952334885147 | 2.4495377923588815 | 7.099607613365102 | 2.3522456698383847 | |
| 150 | 0.0016823680064452506 | -0.003542905683231061 | -0.009941904772036138 | 0.2867224734239243 | 2.1856792812479613 | 5.114079943919512 | 2.520833425913674 | -0.016047034207678054 | -0.08537691821693769 | 0.003698158625984261 | 0.09152325850128348 | 1.349829815010319 | 6.1447639993598635 | 4.237588669391389 | |
| 165 | 0.002803949462880785 | -0.019483654449418686 | |||||||||||||
| 230 | 0.0037572911939261584 | -3.0930258669717436E-4 | -0.00596510335791782 | 0.0566021031133907 | 0.02644531459819617 | 4.243175406737712 | 4.198205941874119 | -0.02326109817722872 | -0.005851889568993442 | -0.026920299426678413 | 0.12384263638823276 | 0.1336021753888604 | 4.887592884913559 | 4.790189249295715 | |
| 260 | 0.0037012112854627717 | -0.001124730965321813 | -0.04043012303405178 | 0.09557406562893239 | -0.0018417519312877786 | 3.842850780284794 | 4.787037442265836 | ||||||||
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| time (min) | NADH (mM) | D-xylose (mM) | KGSA (mM) | KDX (mM) | D-xylonate (mM) | Pyruvate (mM) | KG (mM) | ||
| 0 | 0.004093763337856239 | 5.305140050776079 | 0.0040068637532333015 | -9.620934171835731E-4 | -6.326645723331529E-4 | 15.830051798014265 | -0.1695603822116496 | ||
| 8 | 0.001289817003617644 | 1.8941624375621022 | 12.488269699794564 | ||||||
| 16 | 0.0033647401910985517 | 0.3965246507789245 | 10.717298284177563 | ||||||
| 24 | 8.131461380949572E-4 | -0.010516246048139253 | 9.603812850770291 | ||||||
| 30 | 8.131461380949572E-4 | -0.003486672277432325 | 0.10405795802734796 | 0.045467197422422986 | 4.318003973134549 | 9.089488559044508 | |||
| 60 | 0.0028319894171124783 | 1.9683158514323049E-4 | 0.05103472927851453 | 0.10021366727873714 | 3.1516280290468 | 8.443930808285417 | 0.5601851821497629 | ||
| 100 | 0.0012337370951542572 | 2.530649909419664E-4 | 0.0072907038292904566 | 0.1753739695885012 | 2.4371412660733416 | 6.40916904692214 | 1.397280505409946 | ||
| 150 | 0.0016823680064452506 | -0.003542905683231061 | -0.009941904772036138 | 0.2867224734239243 | 2.1856792812479613 | 5.114079943919512 | 2.520833425913674 | ||
| 165 | 0.002803949462880785 | ||||||||
| 230 | 0.0037572911939261584 | -3.0930258669717436E-4 | -0.00596510335791782 | 0.0566021031133907 | 0.02644531459819617 | 4.243175406737712 | 4.198205941874119 | ||
| 260 | 0.0037012112854627717 | -0.001124730965321813 | -0.04043012303405178 | 0.09557406562893239 | -0.0018417519312877786 | 3.842850780284794 | 4.787037442265836 | ||
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| Time min | NADH | D-xylose | KGSA | KDX | D-xylonate | Pyruvate | KG | ||
| 0 | 0 | 5.426849762315596 | -0.020116113146730927 | 0.08812129209701017 | -0.06456645488640145 | 14.996598853422022 | -0.07683229502774865 | ||
| 8 | -0.010963105387504717 | 2.8314909565127633 | 13.714235031994336 | ||||||
| 16 | -0.017154703131049515 | 1.017750090254922 | 11.26665914539322 | ||||||
| 24 | -0.00744127821619615 | -0.005851804924946878 | 9.79408223971561 | ||||||
| 30 | 0.010849496148080805 | -0.07969662553383541 | 0.004548555175277351 | 0.14595598832666143 | 4.197333613602214 | 8.990400874264461 | |||
| 60 | 0.005765571560109803 | -0.12457151330986016 | -0.003956550938956634 | 0.17232170321865659 | 3.367236701639958 | 8.562106084750363 | 0.7505910123211835 | ||
| 100 | -0.010054248400922765 | -0.09844181146259406 | 0.07939346363339671 | 0.01837952334885147 | 2.4495377923588815 | 7.099607613365102 | 2.3522456698383847 | ||
| 150 | -0.016047034207678054 | -0.08537691821693769 | 0.003698158625984261 | 0.09152325850128348 | 1.349829815010319 | 6.1447639993598635 | 4.237588669391389 | ||
| 165 | -0.019483654449418686 | ||||||||
| 230 | -0.02326109817722872 | -0.005851889568993442 | -0.026920299426678413 | 0.12384263638823276 | 0.1336021753888604 | 4.887592884913559 | 4.790189249295715 | ||
