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 : imacp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3553 b4382 b1241 b0351 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b3617 b2407 b1004 b3713 b1109 b0046 b1982 b2797 b3117 b1814 b4471 b2210 b1033 b0261 b1602 b2406 b0114 b2366 b2492 b0904 b1533 b1380 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.423634 (mmol/gDw/h)
  Minimum Production Rate : 1.267673 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.783147
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.110556
  EX_pi_e : 1.676313
  EX_so4_e : 0.106679
  EX_k_e : 0.082690
  EX_fe2_e : 0.006804
  EX_mg2_e : 0.003675
  EX_cl_e : 0.002205
  EX_ca2_e : 0.002205
  EX_cu2_e : 0.000300
  EX_mn2_e : 0.000293
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.846485
  EX_co2_e : 33.053448
  EX_h_e : 7.403536
  Auxiliary production reaction : 1.267673
  EX_ac_e : 0.975673
  DM_5drib_c : 0.000284
  DM_4crsol_c : 0.000094

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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