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 : nadphx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2779 b3617 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3124 b3236 b1982 b0261 b0411 b1602 b0153 b2913 b4381 b0590 b2789 b3127 b1727 b2975 b0114 b3603 b0529 b2492 b0904 b1380 b0514 b1771 b3662 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.328072 (mmol/gDw/h)
  Minimum Production Rate : 0.297234 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.312596
  EX_o2_e : 283.333579
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.614298
  EX_pi_e : 1.208163
  EX_so4_e : 0.082615
  EX_k_e : 0.064037
  EX_mg2_e : 0.002846
  EX_ca2_e : 0.001708
  EX_cl_e : 0.001708
  EX_cu2_e : 0.000233
  EX_mn2_e : 0.000227
  EX_zn2_e : 0.000112
  EX_ni2_e : 0.000106

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994731
  EX_h2o_e : 551.214973
  EX_co2_e : 33.728572
  EX_etoh_e : 1.100508
  EX_his__L_e : 0.663013
  Auxiliary production reaction : 0.297234
  EX_ac_e : 0.190999
  EX_hxan_e : 0.000367
  DM_5drib_c : 0.000220
  DM_4crsol_c : 0.000073

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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