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 (105 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3553 b4382 b3942 b1732 b0474 b2518 b4069 b4384 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b2463 b2210 b1033 b3551 b2799 b3945 b1602 b4219 b1832 b1778 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b1710 b2480 b1517 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.319291 (mmol/gDw/h)
  Minimum Production Rate : 0.147541 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.962583
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.039553
  EX_fe3_e : 1.417030
  EX_pi_e : 0.307990
  EX_so4_e : 0.080404
  EX_k_e : 0.062323
  EX_mg2_e : 0.002770
  EX_ca2_e : 0.001662
  EX_cl_e : 0.001662
  EX_cu2_e : 0.000226
  EX_mn2_e : 0.000221
  EX_zn2_e : 0.000109
  EX_ni2_e : 0.000103

Product: (mmol/gDw/h)
  EX_h2o_e : 42.905184
  EX_co2_e : 27.553101
  EX_h_e : 11.279376
  EX_pyr_e : 5.189600
  EX_fe2_e : 1.411902
  EX_fum_e : 0.480925
  EX_ac_e : 0.185887
  EX_ins_e : 0.147541
  EX_ade_e : 0.000215
  DM_mththf_c : 0.000143
  DM_5drib_c : 0.000072
  DM_4crsol_c : 0.000071

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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