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__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3553 b0474 b2518 b4069 b3926 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1033 b1602 b2342 b3845 b2913 b3915 b0755 b3612 b2492 b0904 b1380 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.494688 (mmol/gDw/h)
  Minimum Production Rate : 0.255237 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.158664
  EX_o2_e : 287.040721
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.342588
  EX_pi_e : 0.477179
  EX_so4_e : 0.124572
  EX_k_e : 0.096560
  EX_mg2_e : 0.004291
  EX_ca2_e : 0.002575
  EX_cl_e : 0.002575
  EX_cu2_e : 0.000351
  EX_mn2_e : 0.000342
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992055
  EX_h2o_e : 551.157752
  EX_co2_e : 38.353619
  EX_ac_e : 0.288000
  EX_12ppd__R_e : 0.255237
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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