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 : pant__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4069 b2744 b3708 b2297 b2458 b2925 b2097 b2883 b2797 b3117 b1814 b4471 b3946 b0825 b2440 b4381 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.761471 (mmol/gDw/h)
  Minimum Production Rate : 0.035274 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.804992
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.223825
  EX_pi_e : 0.734520
  EX_so4_e : 0.191754
  EX_k_e : 0.148634
  EX_fe2_e : 0.012230
  EX_mg2_e : 0.006606
  EX_ca2_e : 0.003963
  EX_cl_e : 0.003963
  EX_cu2_e : 0.000540
  EX_mn2_e : 0.000526
  EX_zn2_e : 0.000260
  EX_ni2_e : 0.000246
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 45.885265
  EX_co2_e : 25.776913
  EX_h_e : 7.786946
  EX_ac_e : 0.443318
  Auxiliary production reaction : 0.346925
  DM_5drib_c : 0.000171
  DM_4crsol_c : 0.000170

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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