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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b3708 b3008 b0871 b3617 b3236 b3962 b2797 b3117 b1814 b4471 b4267 b1033 b2799 b3945 b4381 b2868 b0114 b0755 b3612 b1539 b2492 b0904 b4266 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.498419 (mmol/gDw/h)
  Minimum Production Rate : 0.392181 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.399247
  EX_o2_e : 282.351965
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.395959
  EX_pi_e : 0.480778
  EX_so4_e : 0.125512
  EX_k_e : 0.097288
  EX_mg2_e : 0.004324
  EX_cl_e : 0.002594
  EX_ca2_e : 0.002594
  EX_cu2_e : 0.000353
  EX_mn2_e : 0.000344
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991995
  EX_h2o_e : 550.618471
  EX_co2_e : 33.029229
  EX_acald_e : 1.262404
  Auxiliary production reaction : 0.392181
  EX_xan_e : 0.013042
  DM_mththf_c : 0.000223
  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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