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 : 10fthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 46: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b1478 b1241 b4069 b4384 b2744 b2297 b2458 b2926 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b0937 b1982 b0477 b4139 b1033 b4014 b0261 b2976 b0411 b2799 b3945 b1602 b0507 b4381 b0529 b1539 b2492 b0904 b1300 b2954 b3029 b1380 b2660 b3662 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.412165 (mmol/gDw/h)
  Minimum Production Rate : 0.288303 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.818924
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.471774
  EX_pi_e : 0.397577
  EX_so4_e : 0.103791
  EX_k_e : 0.080452
  EX_mg2_e : 0.003576
  EX_fe2_e : 0.003402
  EX_fe3_e : 0.003218
  EX_ca2_e : 0.002145
  EX_cl_e : 0.002145
  EX_cu2_e : 0.000292
  EX_mn2_e : 0.000285
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 53.198223
  EX_co2_e : 36.833325
  EX_h_e : 6.627345
  Auxiliary production reaction : 0.288303
  EX_ac_e : 0.239957
  EX_ade_e : 0.000461
  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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