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 (81 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b4069 b4384 b3752 b0871 b3115 b1849 b2296 b2925 b2097 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b1982 b0261 b2799 b3945 b1602 b4381 b2406 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b2660 b3662 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.323753 (mmol/gDw/h)
  Minimum Production Rate : 0.448228 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.612680
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.394770
  EX_fe3_e : 1.140298
  EX_pi_e : 0.760522
  EX_so4_e : 0.081527
  EX_k_e : 0.063194
  EX_mg2_e : 0.002809
  EX_ca2_e : 0.001685
  EX_cl_e : 0.001685
  EX_cu2_e : 0.000230
  EX_mn2_e : 0.000224
  EX_zn2_e : 0.000110
  EX_ni2_e : 0.000105

Product: (mmol/gDw/h)
  EX_h2o_e : 43.691732
  EX_co2_e : 27.707929
  EX_h_e : 10.513366
  EX_pyr_e : 5.311546
  EX_fe2_e : 1.135099
  Auxiliary production reaction : 0.448228
  EX_ac_e : 0.188484
  EX_ade_e : 0.000362
  DM_5drib_c : 0.000217
  DM_4crsol_c : 0.000072

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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