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 : h2mb4p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b2502 b2744 b2930 b4232 b3697 b3925 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b2937 b4139 b3946 b0825 b1623 b3665 b4374 b2361 b2291 b1493 b3517 b4015 b0411 b2799 b3945 b1602 b3915 b3654 b3714 b3664 b2492 b0904 b2954 b3029 b1380 b2660 b0515 b1518 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.413647 (mmol/gDw/h)
  Minimum Production Rate : 0.219980 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.940313
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.467355
  EX_pi_e : 0.838967
  EX_so4_e : 0.104165
  EX_k_e : 0.080741
  EX_fe3_e : 0.006644
  EX_mg2_e : 0.003588
  EX_ca2_e : 0.002153
  EX_cl_e : 0.002153
  EX_cu2_e : 0.000293
  EX_mn2_e : 0.000286
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 44.514595
  EX_co2_e : 33.154676
  EX_h_e : 7.970507
  EX_ac_e : 4.383088
  Auxiliary production reaction : 0.219980
  DM_mththf_c : 0.000185
  DM_5drib_c : 0.000093
  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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