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 : pphn_c
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 207
  Remaining genes: TM0166 TM0333 TM0334 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 TM0428 TM1096 TM1770 TM1693 TM1782 TM1253 TM0402 TM0877 TM0097 TM0882 TM1645 TM1249 TM0446 TM0447 TM0156 TM0259 TM1596 TM1662 TM0857 TM0040 TM1097 TM0332 TM1766 TM0142 TM1828 TM1873 TM0331 TM1629 TM1781 TM1780 TM1432 TM0155 TM1077 TM1523 TM0813 TM0235 TM1155 TM0939 TM1642 TM0547 TM1643 TM0184 TM1400 TM1385 TM0444 TM1043 TM0689 TM1154 TM1042 TM1374 TM1861 TM0862 TM0688 TM1248 TM0917 TM0800 TM0720 TM0883 TM1169 TM0798 TM0801 TM0895 TM0017 TM0558 TM0015 TM0018 TM0016 TM0557 TM1383 TM0239 TM1687 TM0943 TM0167 TM0344 TM1250 TM0139 TM1251 TM1247 TM1035 TM1243 TM1245 TM1246 TM0347 TM1244 TM1037 TM0397 S_0001 TM1217 TM1628 TM0345 TM0290 TM1130 TM0803 TM0741 TM0423 TM0208 TM1585 TM1443 TM1644 TM1516 TM1401 TM1517 TM1522 TM1825 TM1397 TM1827 TM1826 TM1820 TM0343 TM0066 TM0039 TM0551 TM1520 TM0202 TM1521 TM0204 TM1641 TM0203 TM1469 TM1041 TM0804 TM0041 TM0578 TM0881 TM1040 TM1424 TM1425 TM1426 TM1148 TM1038 TM1036 TM1039 TM0140 TM0831 TM1347 TM1444 TM0556 TM0554 TM0555 TM0553 TM1834 TM1839 TM1836 TM_1837 TM0891 TM0647 TM1393 TM1658 TM0269 TM1728 TM1767 TM0270 TM0228 TM0118 TM1718 TM1080 TM0666 TM0356 TM0346 TM0654 TM1519 TM1744 TM0954 TM0953 TM0449 TM0134 TM0137 TM0539 TM0237 TM0108 TM0232 TM0234 TM0231 TM1714 TM1398 TM0236   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.083856 (mmol/gDw/h)
  Minimum Production Rate : 0.102551 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_h2o_e : 9.337831
  EX_malt_e : 2.794000
  EX_hco3_e : 1.130334
  EX_nh4_e : 0.969695
  EX_s_e : 0.232413
  EX_pi_e : 0.064466
  SK_apoACP_c : 0.000234

Product: (mmol/gDw/h)
  EX_h2_e : 19.730008
  EX_co2_e : 11.011111
  EX_ac_e : 9.705977
  EX_h_e : 9.641511
  EX_h2s_e : 0.197760
  Auxiliary production reaction : 0.102551
  SK_5mta_c : 0.014875
  DM_sprm_c : 0.007144
  SK_gcald_c : 0.004193
  SK_pap_c : 0.000234

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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