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 : dnad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b2779 b0160 b0583 b0121 b1982 b2797 b3117 b1814 b4471 b1623 b3665 b4374 b0675 b2361 b2291 b0261 b0507 b3709 b3161 b0112 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3821 b1473 b4141 b1798 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.489398 (mmol/gDw/h)
  Minimum Production Rate : 0.112334 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.843482
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.962202
  EX_pi_e : 0.696745
  EX_so4_e : 0.123240
  EX_k_e : 0.095527
  EX_fe2_e : 0.007860
  EX_mg2_e : 0.004246
  EX_ca2_e : 0.002547
  EX_cl_e : 0.002547
  EX_cu2_e : 0.000347
  EX_mn2_e : 0.000338
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.725418
  EX_co2_e : 37.549605
  EX_h_e : 4.948861
  Auxiliary production reaction : 0.112334
  EX_ade_e : 0.000548
  DM_5drib_c : 0.000328
  DM_4crsol_c : 0.000109

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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