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 : cph4_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 43: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b4382 b0238 b0125 b4069 b4384 b2744 b2297 b2458 b2779 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1982 b0477 b4139 b1033 b0261 b0411 b3945 b1602 b0153 b2913 b2868 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b2954 b0591 b3927 b3029 b1380 b3662 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.448091 (mmol/gDw/h)
  Minimum Production Rate : 0.206791 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.365522
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.875804
  EX_pi_e : 0.432231
  EX_so4_e : 0.112838
  EX_k_e : 0.087464
  EX_mg2_e : 0.003887
  EX_fe2_e : 0.003698
  EX_fe3_e : 0.003499
  EX_cl_e : 0.002332
  EX_ca2_e : 0.002332
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000310
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.605119
  EX_co2_e : 37.434615
  EX_h_e : 5.624860
  EX_12ppd__S_e : 0.733509
  EX_ac_e : 0.260872
  Auxiliary production reaction : 0.206791
  EX_ade_e : 0.000501
  DM_5drib_c : 0.000301
  DM_4crsol_c : 0.000100

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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