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 : ap4a_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3553 b1478 b4382 b1241 b4069 b4384 b3752 b2297 b2458 b2925 b2097 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b2690 b0207 b3012 b0937 b1982 b1525 b4139 b1033 b1623 b2661 b4014 b0261 b2976 b0411 b2799 b1602 b0507 b2913 b2492 b0904 b2954 b1781 b3001 b3029 b1380 b0325 b1771 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.413186 (mmol/gDw/h)
  Minimum Production Rate : 0.027426 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.196186
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.738946
  EX_pi_e : 0.508265
  EX_so4_e : 0.104049
  EX_k_e : 0.080651
  EX_mg2_e : 0.003584
  EX_fe2_e : 0.003410
  EX_fe3_e : 0.003226
  EX_ca2_e : 0.002151
  EX_cl_e : 0.002151
  EX_cu2_e : 0.000293
  EX_mn2_e : 0.000286
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 44.595162
  EX_co2_e : 32.940548
  EX_h_e : 8.740765
  EX_ac_e : 4.774152
  Auxiliary production reaction : 0.027426
  EX_ade_e : 0.000462
  DM_5drib_c : 0.000277
  DM_4crsol_c : 0.000092

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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