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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4467 b3399 b4069 b2744 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b0675 b2361 b0261 b1602 b2913 b4381 b1727 b0114 b0529 b2492 b0904 b1380 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.465831 (mmol/gDw/h)
  Minimum Production Rate : 0.150961 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.129173
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.684788
  EX_pi_e : 0.751266
  EX_so4_e : 0.117306
  EX_k_e : 0.090927
  EX_fe2_e : 0.007482
  EX_mg2_e : 0.004041
  EX_ca2_e : 0.002425
  EX_cl_e : 0.002425
  EX_cu2_e : 0.000330
  EX_mn2_e : 0.000322
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.015447
  EX_co2_e : 37.283880
  EX_h_e : 5.054333
  EX_12ppd__R_e : 0.493794
  EX_ac_e : 0.271200
  Auxiliary production reaction : 0.150961
  EX_hxan_e : 0.012502
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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