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 (78 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3553 b1478 b1241 b4069 b2930 b4232 b3697 b3925 b2297 b2458 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b0937 b1033 b4015 b2799 b3945 b1602 b2913 b4381 b2492 b0904 b1380 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.400647 (mmol/gDw/h)
  Minimum Production Rate : 0.633155 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.828604
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.326954
  EX_pi_e : 0.386467
  EX_so4_e : 0.100891
  EX_k_e : 0.078204
  EX_fe2_e : 0.006435
  EX_mg2_e : 0.003476
  EX_ca2_e : 0.002085
  EX_cl_e : 0.002085
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000129
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 42.896729
  EX_co2_e : 32.316748
  EX_h_e : 8.034260
  EX_ac_e : 3.719799
  Auxiliary production reaction : 0.633155
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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