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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 69
  Gene deletion: b3942 b1732 b1241 b0351 b4069 b4384 b2744 b3708 b1479 b3115 b1849 b2296 b2779 b3617 b0030 b2407 b3844 b3236 b1779 b2463 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3449 b2210 b4267 b0596 b4374 b2361 b2291 b1415 b3551 b1014 b0261 b0411 b2799 b3945 b3709 b2913 b4219 b1832 b1778 b3161 b0112 b2789 b3127 b2868 b4265 b2975 b0114 b3603 b1539 b2492 b0904 b1533 b3927 b1380 b1710 b2480 b0508 b1473 b0494 b4266 b3662 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.279549 (mmol/gDw/h)
  Minimum Production Rate : 0.267928 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.659837
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.196827
  EX_pi_e : 1.073438
  EX_so4_e : 0.638985
  EX_k_e : 0.054566
  EX_fe2_e : 0.004490
  EX_mg2_e : 0.002425
  EX_ca2_e : 0.001455
  EX_cl_e : 0.001455
  EX_cu2_e : 0.000198
  EX_mn2_e : 0.000193
  EX_zn2_e : 0.000095
  EX_ni2_e : 0.000090

Product: (mmol/gDw/h)
  EX_h2o_e : 48.448289
  EX_co2_e : 33.179248
  EX_h_e : 7.046333
  EX_ac_e : 2.048937
  EX_fum_e : 0.827993
  EX_met__L_e : 0.300662
  Auxiliary production reaction : 0.267928
  EX_ade_e : 0.000313
  DM_5drib_c : 0.000188
  EX_dxylnt_e : 0.000187
  DM_4crsol_c : 0.000062

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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