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 : ins_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (88 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b4382 b4269 b0493 b3588 b3003 b3011 b4384 b0871 b2925 b2097 b2926 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b3946 b0825 b3945 b1602 b2913 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.370826 (mmol/gDw/h)
  Minimum Production Rate : 0.082838 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.113114
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.336234
  EX_pi_e : 0.357701
  EX_so4_e : 0.093381
  EX_k_e : 0.072383
  EX_fe2_e : 0.005956
  EX_mg2_e : 0.003217
  EX_ca2_e : 0.001930
  EX_cl_e : 0.001930
  EX_cu2_e : 0.000263
  EX_mn2_e : 0.000256
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 43.968770
  EX_co2_e : 28.046822
  EX_h_e : 9.039739
  EX_pyr_e : 5.301096
  EX_ins_e : 0.082838
  DM_mththf_c : 0.000166
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000083

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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