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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b4382 b3942 b1732 b1241 b0351 b4069 b4384 b2744 b3752 b3926 b3115 b1849 b2296 b2925 b2097 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b3616 b3589 b0261 b0411 b3945 b1602 b0114 b0529 b2492 b0904 b1380 b3662 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.322638 (mmol/gDw/h)
  Minimum Production Rate : 0.952403 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.843795
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.911616
  EX_pi_e : 3.168428
  EX_so4_e : 0.081247
  EX_k_e : 0.062977
  EX_fe2_e : 0.005182
  EX_mg2_e : 0.002799
  EX_ca2_e : 0.001679
  EX_cl_e : 0.001679
  EX_cu2_e : 0.000229
  EX_mn2_e : 0.000223
  EX_zn2_e : 0.000110
  EX_ni2_e : 0.000104

Product: (mmol/gDw/h)
  EX_h2o_e : 49.189710
  EX_co2_e : 29.436952
  EX_h_e : 7.438667
  EX_ac_e : 2.951794
  Auxiliary production reaction : 0.952403
  EX_thymd_e : 0.284251
  EX_hxan_e : 0.000361
  DM_5drib_c : 0.000216
  DM_4crsol_c : 0.000072

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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