MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 60
  Gene deletion: b1855 b3553 b1478 b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2779 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b0120 b0207 b3012 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b0411 b2799 b1602 b3709 b0153 b2223 b2406 b3161 b0112 b2789 b3127 b0584 b1539 b2492 b0904 b1781 b3001 b1533 b3821 b1380 b0325 b1473 b2660 b1771 b4141 b1798 b0606 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.389913 (mmol/gDw/h)
  Minimum Production Rate : 0.019543 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.577275
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.217643
  EX_pi_e : 0.434742
  EX_so4_e : 0.117731
  EX_k_e : 0.076108
  EX_fe2_e : 0.006262
  EX_mg2_e : 0.003382
  EX_ca2_e : 0.002029
  EX_cl_e : 0.002029
  EX_cu2_e : 0.000276
  EX_mn2_e : 0.000269
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 51.727668
  EX_co2_e : 34.707059
  EX_h_e : 8.041633
  EX_ac_e : 1.530515
  EX_gsn_e : 0.573613
  Auxiliary production reaction : 0.019543
  EX_hxan_e : 0.000436
  DM_5drib_c : 0.000262
  DM_4crsol_c : 0.000087

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

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.

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Last updated: 21-Sep-2023
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