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 : hxan_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4467 b1241 b0351 b4069 b3115 b1849 b2296 b3617 b1004 b3713 b1109 b0046 b3236 b1602 b2913 b4381 b1727 b0114 b0529 b2492 b0904 b1380 b0515 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.421473 (mmol/gDw/h)
  Minimum Production Rate : 0.796995 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.608997
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.785096
  EX_pi_e : 0.406555
  EX_so4_e : 0.106135
  EX_k_e : 0.082268
  EX_fe2_e : 0.006769
  EX_mg2_e : 0.003656
  EX_ca2_e : 0.002194
  EX_cl_e : 0.002194
  EX_cu2_e : 0.000299
  EX_mn2_e : 0.000291
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.892350
  EX_co2_e : 34.487660
  EX_h_e : 9.191060
  EX_ac_e : 2.085173
  EX_hxan_e : 0.808307
  DM_mththf_c : 0.000189
  DM_5drib_c : 0.000095
  DM_4crsol_c : 0.000094

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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