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 (10 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b0469 b4069 b4384 b2744 b3708 b2297 b2458 b2779 b2926 b2407 b0517 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b2789 b3127 b0452 b0114 b1539 b2492 b0904 b1533 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.496734 (mmol/gDw/h)
  Minimum Production Rate : 0.079156 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.775052
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.364682
  EX_pi_e : 0.479152
  EX_so4_e : 0.125087
  EX_k_e : 0.096959
  EX_fe2_e : 0.007978
  EX_mg2_e : 0.004309
  EX_cl_e : 0.002585
  EX_ca2_e : 0.002585
  EX_cu2_e : 0.000352
  EX_mn2_e : 0.000343
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.912877
  EX_co2_e : 38.795514
  EX_h_e : 4.932535
  EX_ac_e : 0.289191
  Auxiliary production reaction : 0.079156
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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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