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 : glyc__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (11 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b2779 b3617 b0160 b0517 b1779 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b2913 b2789 b3127 b0114 b2366 b2492 b0904 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.427868 (mmol/gDw/h)
  Minimum Production Rate : 0.320469 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.472526
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.620941
  EX_pi_e : 0.412724
  EX_so4_e : 0.107746
  EX_k_e : 0.083517
  EX_fe2_e : 0.006872
  EX_mg2_e : 0.003712
  EX_ca2_e : 0.002227
  EX_cl_e : 0.002227
  EX_cu2_e : 0.000303
  EX_mn2_e : 0.000296
  EX_zn2_e : 0.000146
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.524190
  EX_co2_e : 38.225372
  EX_h_e : 5.877491
  EX_ac_e : 1.625598
  Auxiliary production reaction : 0.320469
  DM_5drib_c : 0.000096
  DM_4crsol_c : 0.000095

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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