MetNetComp Database [1] / Core Genes

A set of core genes for simulation-based growth-coupled production. You can also see minimal gene deletions.

Model : iLJ478 [2].
Target metabolite : udcpp_c
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 301
  Remaining genes: TM0166 TM0333 TM0334 TM0920 TM0335 TM0349 TM0348 TM0161 TM1387 TM0717 TM0550 TM0716 TM1784 TM1783 TM1559 TM0549 TM0548 TM0274 TM0802 TM0292 TM0291 TM1785 TM0692 TM1099 TM1479 TM1689 TM0655 TM0913 TM1733 TM1384 TM0889 TM1095 TM1096 TM1770 TM0645 TM1693 TM1782 TM1253 TM0402 TM0877 TM0273 TM0097 TM1645 TM1249 TM0191 TM0446 TM1433 TM0447 TM0078 TM0156 TM0079 TM1737 TM0259 TM1596 TM0189 TM1662 TM1136 TM0857 TM1135 TM1137 TM0040 TM1878 TM1139 TM1097 TM0332 TM1766 TM0141 TM0540 TM1164 TM0405 TM0142 TM1828 TM1873 TM0331 TM1629 TM1781 TM1780 TM0155 TM1077 TM1523 TM1273 TM0235 TM1155 TM1272 TM0939 TM1642 TM0547 TM0289 TM1518 TM1751 TM1643 TM1752 TM0184 TM1400 TM1385 TM0444 TM1749 TM1043 TM0689 TM1154 TM1042 TM1611 TM1748 TM1747 TM1750 TM1774 TM1616 TM1374 TM1614 TM1613 TM1861 TM1610 TM1612 TM0821 TM1609 TM1262 TM0862 TM1263 TM1203 TM1202 TM1261 TM0261 TM0688 TM1248 TM0917 TM0473 TM1724 TM0148 TM0800 TM0720 TM0883 TM1169 TM0798 TM0801 TM0895 TM0017 TM0558 TM0015 TM0018 TM0016 TM0557 TM1383 TM0587 TM1220 TM0240 TM1222 TM0239 TM1687 TM1219 TM1221 TM0943 TM0167 TM0031 TM0344 TM0029 TM1250 TM0030 TM0027 TM0304 TM0139 TM1251 TM0301 TM0303 TM0300 TM1247 TM1035 TM1243 TM1245 TM1246 TM0347 TM1244 TM1037 TM0397 S_0001 TM1628 TM0345 TM0290 TM1130 TM0803 TM0665 TM1121 TM1120 TM0741 TM1377 TM0423 TM1378 TM1376 TM0208 TM1443 TM1644 TM1516 TM1517 TM1430 TM1522 TM1825 TM1397 TM1827 TM1826 TM0952 TM0217 TM0955 TM0956 TM0959 TM1820 TM0343 TM0128 TM0438 TM1064 TM0039 TM1065 TM0551 TM1066 TM1520 TM0202 TM1063 TM1521 TM0204 TM1641 TM0203 TM1469 TM1041 TM0804 TM0041 TM0578 TM0881 TM1040 TM1424 TM1425 TM1426 TM1148 TM1038 TM1036 TM1039 TM0140 TM0831 TM1347 TM0418 TM0421 TM0420 TM1444 TM0556 TM0554 TM0555 TM0552 TM0553 TM1088 TM1196 TM1199 TM1198 TM1197 TM1834 TM1839 TM1836 TM_1837 TM0891 TM0647 TM1393 TM1658 TM1270 TM0268 TM0269 TM1728 TM1767 TM0270 TM0118 TM1718 TM1080 TM0666 TM0356 TM0346 TM0654 TM1519 TM1744 TM1762 TM0954 TM0953 TM0449 TM0869 TM0134 TM0137 TM0539 TM0237 TM0108 TM0232 TM0234 TM0231 TM1714 TM1398 TM0236 TM0071 TM0074 TM0075 TM0073 TM0060 TM0058 TM0059 TM0057 TM0115 TM0112 TM0123 TM0124   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.097955 (mmol/gDw/h)
  Minimum Production Rate : 0.087151 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_malt_e : 2.794000
  EX_h2o_e : 2.317609
  EX_nh4_e : 1.875491
  EX_hco3_e : 1.729185
  EX_s_e : 0.464405
  EX_pi_e : 0.162455
  SK_apoACP_c : 0.000274

Product: (mmol/gDw/h)
  EX_h2_e : 14.671106
  EX_co2_e : 10.516301
  EX_h_e : 7.210577
  EX_ac_e : 7.158134
  EX_h2s_e : 0.440616
  EX_xtsn_e : 0.214898
  Auxiliary production reaction : 0.087150
  SK_gcald_c : 0.004898
  SK_5mta_c : 0.000686
  SK_pap_c : 0.000274

Visualization
  1. Download JSON file.
  2. Go to Escher site [4].

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 27-Sep-2023
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