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 : ipdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4467 b4069 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1779 b1602 b2913 b4381 b3915 b1727 b0114 b0529 b2492 b0904 b1380 b1771 b1518 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.489118 (mmol/gDw/h)
  Minimum Production Rate : 0.011992 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.335776
  EX_o2_e : 287.667776
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.171824
  EX_pi_e : 0.495790
  EX_so4_e : 0.123170
  EX_k_e : 0.095472
  EX_mg2_e : 0.004243
  EX_cl_e : 0.002546
  EX_ca2_e : 0.002546
  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_fe3_e : 999.992144
  EX_h2o_e : 553.119082
  EX_co2_e : 38.181643
  EX_ac_e : 0.284758
  EX_hxan_e : 0.222348
  Auxiliary production reaction : 0.011992
  DM_mththf_c : 0.000219
  DM_5drib_c : 0.000110
  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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