From 8071d592be1ff3a5692553ad32c9286fe76cfac5 Mon Sep 17 00:00:00 2001
From: Kang Wang <888666wang4286@gmail.com>
Date: Mon, 30 Sep 2024 08:27:55 +0000
Subject: [PATCH] Update file model.tsx
---
src/contents/model.tsx | 136 +++++++++++++++++++++++++++++++----------
1 file changed, 103 insertions(+), 33 deletions(-)
diff --git a/src/contents/model.tsx b/src/contents/model.tsx
index 7bd035d..051952b 100644
--- a/src/contents/model.tsx
+++ b/src/contents/model.tsx
@@ -968,63 +968,133 @@ export function Model() {
<p>In COBRApy, the default unit for flux is mmol/(gDW*hr), which represents the millimoles of a substance produced or consumed per gram dry cell weight per hour.</p>
</div>
<p>To identify knockout targets, we ran FBA optimization on iDK1463, yielding the flux values for various metabolic reactions in the optimized strain. Next, we filtered out the reactions related to ammonia, excluding those with a flux of zero under normal physiological conditions. The biomass reaction and reactions linearly related to it were considered essential and not selected as targets. Ultimately, among the **6 reactions identified**, the flux of ammonia-producing reactions will be minimized, while the flux of ammonia-consuming reactions will be maximized.</p>
-<table border="1">
+<table>
<thead>
<tr>
<th>ID</th>
<th>Name</th>
<th>Formula</th>
<th>Flux [mmol/(gDW*hr)]</th>
- <th>Strategy</th>
+ <th>Strategy </th>
+ <th></th>
+ <th></th>
+ <th></th>
+ <th></th>
+ <th></th>
</tr>
</thead>
<tbody>
<tr>
- <td align="center">CBMKr</td>
- <td align="center">Carbamate kinase</td>
- <td align="center">atp_c + co2_c + nh4_c ↔ adp_c + cbp_c + 2.0 h_c</td>
- <td align="center">0.551604</td>
- <td align="center">Maximize</td>
+ <td>CBMKr</td>
+ <td>Carbamate kinase</td>
+ <td>atp_c + co2_c + nh4_c <=> adp_c + cbp_c + 2.0 h_c</td>
+ <td>0.551604</td>
+ <td>Maximize </td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>GMPS</td>
+ <td>GMP synthase</td>
+ <td>atp_c + nh4_c + xmp_c --> amp_c + gmp_c + 2.0 h_c + ppi_c</td>
+ <td>0.214121</td>
+ <td>Maximize </td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>ASNS2</td>
+ <td>Asparagine synthetase</td>
+ <td>asp__L_c + atp_c + nh4_c --> amp_c + asn__L_c + h_c + ppi_c</td>
+ <td>0.212208</td>
+ <td>Maximize </td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>GLYCL</td>
+ <td>Glycine Cleavage System</td>
+ <td>gly_c + nad_c + thf_c --> co2_c + mlthf_c + nadh_c + nh4_c</td>
+ <td>0.047647</td>
+ <td>Minimize </td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
</tr>
<tr>
- <td align="center">GMPS</td>
- <td align="center">GMP synthase</td>
- <td align="center">atp_c + nh4_c + xmp_c → amp_c + gmp_c + 2.0 h_c + ppi_c</td>
- <td align="center">0.214121</td>
- <td align="center">Maximize</td>
+ <td>TRPAS2</td>
+ <td>Tryptophanase (L-tryptophan)</td>
+ <td>h2o_c + trp__L_c <=> indole_c + nh4_c + pyr_c</td>
+ <td>-0.05004</td>
+ <td>Minimize </td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
</tr>
<tr>
- <td align="center">ASNS2</td>
- <td align="center">Asparagine synthetase</td>
- <td align="center">asp_L_c + atp_c + nh4_c → amp_c + asn_L_c + h_c + ppi_c</td>
- <td align="center">0.212208</td>
- <td align="center">Maximize</td>
+ <td>GLUDy</td>
+ <td>Glutamate dehydrogenase (NADP)</td>
+ <td>glu__L_c + h2o_c + nadp_c <=> akg_c + h_c + nadph_c + nh4_c</td>
+ <td>-7.52748</td>
+ <td>Minimize </td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
</tr>
<tr>
- <td align="center">GLYCL</td>
- <td align="center">Glycine Cleavage System</td>
- <td align="center">gly_c + nad_c + thf_c → co2_c + mlthf_c + nadh_c + nh4_c</td>
- <td align="center">0.047647</td>
- <td align="center">Minimize</td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
</tr>
<tr>
- <td align="center">TRPAS2</td>
- <td align="center">Tryptophanase (L-tryptophan)</td>
- <td align="center">h2o_c + trp__L_c ↔ indole_c + nh4_c + pyr_c</td>
- <td align="center">-0.050040</td>
- <td align="center">Minimize</td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
</tr>
<tr>
- <td align="center">GLUDy</td>
- <td align="center">Glutamate dehydrogenase (NADP)</td>
- <td align="center">glu__L_c + h2o_c + nadp_c ↔ akg_c + h_c + nadph_c + nh4_c</td>
- <td align="center">-7.527480</td>
- <td align="center">Minimize</td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
</tr>
</tbody>
</table>
-
</div>
<img
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