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 : ins_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 38: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4384 b2744 b3708 b3008 b3752 b0871 b2407 b1982 b2797 b3117 b1814 b4471 b2440 b4381 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b2413 b0515 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.577832 (mmol/gDw/h)
  Minimum Production Rate : 0.131110 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.053226
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.773995
  EX_pi_e : 0.557380
  EX_so4_e : 0.145510
  EX_k_e : 0.112789
  EX_fe2_e : 0.009281
  EX_mg2_e : 0.005013
  EX_ca2_e : 0.003008
  EX_cl_e : 0.003008
  EX_cu2_e : 0.000410
  EX_mn2_e : 0.000399
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.537741
  EX_co2_e : 34.951917
  EX_h_e : 5.842810
  Auxiliary production reaction : 0.131110
  EX_alltn_e : 0.002256
  DM_mththf_c : 0.001868
  DM_5drib_c : 0.000388
  DM_4crsol_c : 0.000129

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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