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 (90 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b0871 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b1033 b2799 b3945 b1602 b0153 b2913 b4381 b0529 b2492 b0904 b3035 b1380 b1511 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.405368 (mmol/gDw/h)
  Minimum Production Rate : 0.519823 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.512362
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.458600
  EX_pi_e : 0.391021
  EX_so4_e : 0.102080
  EX_k_e : 0.079125
  EX_fe2_e : 0.006511
  EX_mg2_e : 0.003517
  EX_ca2_e : 0.002110
  EX_cl_e : 0.002110
  EX_cu2_e : 0.000287
  EX_mn2_e : 0.000280
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 51.599562
  EX_co2_e : 35.693947
  EX_h_e : 5.805342
  EX_acald_e : 1.233522
  EX_ins_e : 0.519823
  EX_ade_e : 0.000273
  DM_mththf_c : 0.000182
  DM_5drib_c : 0.000091
  DM_4crsol_c : 0.000090

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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