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 : ditp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4382 b1241 b0351 b4384 b3752 b0871 b3115 b1849 b2296 b2925 b2097 b3617 b2407 b0907 b2690 b3665 b3945 b3654 b3714 b3664 b0114 b0755 b3612 b0529 b2492 b0904 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.612892 (mmol/gDw/h)
  Minimum Production Rate : 0.123512 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.031764
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.113229
  EX_pi_e : 0.961736
  EX_so4_e : 0.154338
  EX_k_e : 0.119632
  EX_fe2_e : 0.009844
  EX_mg2_e : 0.005317
  EX_cl_e : 0.003190
  EX_ca2_e : 0.003190
  EX_cu2_e : 0.000435
  EX_mn2_e : 0.000424
  EX_zn2_e : 0.000209
  EX_ni2_e : 0.000198
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.986266
  EX_co2_e : 26.989500
  EX_h_e : 8.084847
  EX_pyr_e : 2.206328
  Auxiliary production reaction : 0.123512
  DM_5drib_c : 0.000138
  DM_4crsol_c : 0.000137

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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