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SEDML
cfeNoMnRec
cfeNoMnRec2
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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 | 995 | ||||||||
| 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, without added Mn, but with 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 | 0.0052714205245471095 | 5.255033459106698 | -0.0016730454289568542 | -0.07701607383540421 | -9.98204754785537E-4 | 15.87114442499422 | -0.30092584590117166 | 0.0052714205245471095 | 5.337100240695687 | -0.11909396164616046 | 0.04138280031929154 | -0.031210418792629237 | 15.48283769490986 | 0.2234037209909792 | |
| 8 | -8.411819141186001E-4 | 1.847767435033521 | 13.34459377744502 | -0.005027124200461381 | 2.9365778100989477 | 13.409389987771542 | |||||||||
| 16 | -0.0011776571866908706 | 0.5375660520988432 | 11.329714245413662 | -0.012752421283014974 | 1.2767747546510118 | 12.032549573289243 | |||||||||
| 24 | -7.290262753998772E-4 | -7.591949728258975E-4 | 10.54364719027248 | -0.003436620241740629 | 0.12934081995620025 | 10.246310588903627 | |||||||||
| 30 | -2.8039118590083255E-4 | -0.0014621523498965922 | 0.04308132397679721 | 0.039899813711220915 | 4.9777445427888205 | 10.234788403764728 | 0.011275530795920474 | 0.002100672546633618 | -0.11823309023431007 | 0.05946058685748804 | 4.643242585068374 | 9.95280387711388 | |||
| 60 | 8.411986269507999E-5 | -0.0016027463392846112 | 0.04838372586228834 | 0.042683574701103684 | 4.939700224066113 | 9.798671972005184 | -0.1938656593362491 | 0.014456530248957308 | 0.008349011426855367 | -0.1509456907739629 | 0.07753875822868053 | 4.8240222463376545 | 10.267724352296145 | 0.08156027917884484 | |
| 100 | -2.8035776023642087E-5 | -0.0025306499094196657 | -0.09610455272563073 | 0.01484651787652971 | 5.135487818705219 | 9.984252087466983 | -0.07060201217730855 | -0.002953789438593677 | -0.0035797047805152735 | -0.14405884775682526 | 0.12660753076049439 | 4.6552941434459525 | 9.52702888388117 | -0.043735236422671776 | |
| 150 | 6.729505451445409E-4 | -0.0013496771583861727 | 0.05368593022126005 | -9.279894642426918E-4 | 5.008365222334714 | 9.662138481404618 | 0.016782432794570923 | -0.012468402416657531 | -0.09219338793832563 | -0.03903420312072929 | -0.01973817197842742 | 4.757736302124163 | 9.66055556179839 | 0.16312035826644716 | |
| 165 | 0.0020749231874809078 | -0.016217443834611586 | |||||||||||||
| 230 | 0.00319650046570839 | 4.7801118400632794E-4 | 0.10140655955808305 | -0.01763014059784901 | 4.452549932144743 | 9.668765891181925 | -0.005208335264965447 | -0.01783634587098598 | -0.016076467185005473 | -0.12339831870541229 | 0.12402504480260856 | 4.740518873887155 | 9.568598014191956 | 0.1382981237226626 | |
| 260 | 0.004738672879203225 | -0.003852208269928239 | -0.02982551678958902 | 0.022269603979090176 | 4.717003354663831 | 10.00281167922532 | -0.019097286793920754 | ||||||||
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| time (min) | NADH (mM) | D-xylose (mM) | KGSA (mM) | KDX (mM) | D-xylonate (mM) | Pyruvate (mM) | KG (mM) | ||
| 0 | 0.0052714205245471095 | 5.255033459106698 | -0.0016730454289568542 | -0.07701607383540421 | -9.98204754785537E-4 | 15.87114442499422 | -0.30092584590117166 | ||
| 8 | -8.411819141186001E-4 | 1.847767435033521 | 13.34459377744502 | ||||||
| 16 | -0.0011776571866908706 | 0.5375660520988432 | 11.329714245413662 | ||||||
| 24 | -7.290262753998772E-4 | -7.591949728258975E-4 | 10.54364719027248 | ||||||
| 30 | -2.8039118590083255E-4 | -0.0014621523498965922 | 0.04308132397679721 | 0.039899813711220915 | 4.9777445427888205 | 10.234788403764728 | |||
| 60 | 8.411986269507999E-5 | -0.0016027463392846112 | 0.04838372586228834 | 0.042683574701103684 | 4.939700224066113 | 9.798671972005184 | -0.1938656593362491 | ||
| 100 | -2.8035776023642087E-5 | -0.0025306499094196657 | -0.09610455272563073 | 0.01484651787652971 | 5.135487818705219 | 9.984252087466983 | -0.07060201217730855 | ||
| 150 | 6.729505451445409E-4 | -0.0013496771583861727 | 0.05368593022126005 | -9.279894642426918E-4 | 5.008365222334714 | 9.662138481404618 | 0.016782432794570923 | ||
| 165 | 0.0020749231874809078 | ||||||||
| 230 | 0.00319650046570839 | 4.7801118400632794E-4 | 0.10140655955808305 | -0.01763014059784901 | 4.452549932144743 | 9.668765891181925 | -0.005208335264965447 | ||
| 260 | 0.004738672879203225 | -0.003852208269928239 | -0.02982551678958902 | 0.022269603979090176 | 4.717003354663831 | 10.00281167922532 | -0.019097286793920754 | ||
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| Time min | NADH | D-xylose | KGSA | KDX | D-xylonate | Pyruvate | KG | ||
| 0 | 0.0052714205245471095 | 5.337100240695687 | -0.11909396164616046 | 0.04138280031929154 | -0.031210418792629237 | 15.48283769490986 | 0.2234037209909792 | ||
| 8 | -0.005027124200461381 | 2.9365778100989477 | 13.409389987771542 | ||||||
| 16 | -0.012752421283014974 | 1.2767747546510118 | 12.032549573289243 | ||||||
| 24 | -0.003436620241740629 | 0.12934081995620025 | 10.246310588903627 | ||||||
| 30 | 0.011275530795920474 | 0.002100672546633618 | -0.11823309023431007 | 0.05946058685748804 | 4.643242585068374 | 9.95280387711388 | |||
| 60 | 0.014456530248957308 | 0.008349011426855367 | -0.1509456907739629 | 0.07753875822868053 | 4.8240222463376545 | 10.267724352296145 | 0.08156027917884484 | ||
| 100 | -0.002953789438593677 | -0.0035797047805152735 | -0.14405884775682526 | 0.12660753076049439 | 4.6552941434459525 | 9.52702888388117 | -0.043735236422671776 | ||
| 150 | -0.012468402416657531 | -0.09219338793832563 | -0.03903420312072929 | -0.01973817197842742 | 4.757736302124163 | 9.66055556179839 | 0.16312035826644716 | ||
| 165 | -0.016217443834611586 | ||||||||
| 230 | -0.01783634587098598 | -0.016076467185005473 | -0.12339831870541229 | 0.12402504480260856 | 4.740518873887155 | 9.568598014191956 | 0.1382981237226626 | ||
