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 : 12ppd__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (23 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3553 b1478 b1241 b0351 b0871 b2925 b2097 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b3946 b0825 b1033 b1493 b3517 b3945 b1602 b0507 b2913 b2492 b0904 b1380 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.409755 (mmol/gDw/h)
  Minimum Production Rate : 3.157192 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.678249
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.425318
  EX_pi_e : 0.395252
  EX_so4_e : 0.103184
  EX_k_e : 0.079981
  EX_fe2_e : 0.006581
  EX_mg2_e : 0.003555
  EX_ca2_e : 0.002133
  EX_cl_e : 0.002133
  EX_cu2_e : 0.000291
  EX_mn2_e : 0.000283
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 41.373170
  EX_co2_e : 33.709867
  EX_h_e : 3.764992
  EX_12ppd__S_e : 3.157192
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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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