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 : mmcoa__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2836 b4382 b0586 b4069 b4384 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b0030 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b0261 b3945 b2406 b0511 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b0516 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.721680 (mmol/gDw/h)
  Minimum Production Rate : 0.037340 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.382127
  EX_o2_e : 274.043910
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.788924
  EX_pi_e : 0.808157
  EX_so4_e : 0.584188
  EX_k_e : 0.140867
  EX_mg2_e : 0.006261
  EX_ca2_e : 0.003756
  EX_cl_e : 0.003756
  EX_cu2_e : 0.000512
  EX_mn2_e : 0.000499
  EX_zn2_e : 0.000246
  EX_ni2_e : 0.000233
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988409
  EX_h2o_e : 547.272060
  EX_co2_e : 25.968411
  EX_ac_e : 0.822607
  EX_cgly_e : 0.365115
  Auxiliary production reaction : 0.037340
  EX_xan_e : 0.000808
  DM_5drib_c : 0.000484
  DM_4crsol_c : 0.000161

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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