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 : glx_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2502 b2744 b3708 b3008 b1479 b0512 b0871 b3236 b1779 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b4374 b0675 b2361 b2291 b1014 b0261 b0822 b2799 b2913 b0112 b1745 b2975 b0114 b3603 b0306 b1539 b3605 b2492 b0904 b1533 b3821 b1380 b0508 b4042 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.409224 (mmol/gDw/h)
  Minimum Production Rate : 0.034651 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.343870
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.017699
  EX_so4_e : 0.561828
  EX_pi_e : 0.394740
  EX_k_e : 0.079878
  EX_fe2_e : 0.006573
  EX_mg2_e : 0.003550
  EX_ca2_e : 0.002130
  EX_cl_e : 0.002130
  EX_cu2_e : 0.000290
  EX_mn2_e : 0.000283
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 49.998139
  EX_co2_e : 37.892491
  EX_h_e : 3.475325
  EX_acald_e : 1.197395
  EX_met__L_e : 0.458777
  EX_alltn_e : 0.034835
  DM_5drib_c : 0.034652
  Auxiliary production reaction : 0.034651
  DM_4crsol_c : 0.034468

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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