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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2836 b4382 b3846 b2341 b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b0507 b3709 b2406 b3161 b0112 b2975 b0114 b3603 b1539 b2492 b0904 b2947 b2578 b1533 b3927 b1473 b0594 b4141 b1798 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.527719 (mmol/gDw/h)
  Minimum Production Rate : 0.670621 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.891147
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.370529
  EX_pi_e : 0.509041
  EX_so4_e : 0.132890
  EX_k_e : 0.103007
  EX_fe2_e : 0.008476
  EX_mg2_e : 0.004578
  EX_ca2_e : 0.002747
  EX_cl_e : 0.002747
  EX_cu2_e : 0.000374
  EX_mn2_e : 0.000365
  EX_zn2_e : 0.000180
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 46.965179
  EX_co2_e : 31.687163
  EX_h_e : 6.498544
  Auxiliary production reaction : 0.670621
  EX_ac_e : 0.307230
  DM_oxam_c : 0.000591
  DM_5drib_c : 0.000354
  DM_4crsol_c : 0.000118

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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