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 : dgtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b3942 b1732 b0474 b2518 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b2925 b2097 b3236 b2883 b1779 b2690 b2797 b3117 b1814 b4471 b3616 b3589 b2210 b0411 b3945 b4381 b0114 b2366 b2492 b0904 b1533 b0516 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.544192 (mmol/gDw/h)
  Minimum Production Rate : 0.541880 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.078455
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.595124
  EX_pi_e : 2.150572
  EX_so4_e : 0.137038
  EX_k_e : 0.106222
  EX_fe2_e : 0.008740
  EX_mg2_e : 0.004721
  EX_ca2_e : 0.002833
  EX_cl_e : 0.002833
  EX_cu2_e : 0.000386
  EX_mn2_e : 0.000376
  EX_zn2_e : 0.000186
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.850491
  EX_co2_e : 26.878697
  EX_h_e : 9.312496
  EX_ac_e : 2.678107
  Auxiliary production reaction : 0.541880
  EX_alltn_e : 0.002125
  DM_mththf_c : 0.000244
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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.

Last updated: 21-Sep-2023
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