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 : 12ppd__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (89 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b2836 b3553 b1478 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b0871 b3617 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b3908 b1656 b4139 b1033 b1623 b3665 b3945 b1602 b2913 b3915 b3654 b3714 b3664 b1297 b0509 b3125 b2492 b0904 b2954 b1380 b1511 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.488697 (mmol/gDw/h)
  Minimum Production Rate : 0.048500 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.668793
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.277882
  EX_pi_e : 0.471400
  EX_so4_e : 0.123065
  EX_k_e : 0.095390
  EX_fe3_e : 0.007851
  EX_mg2_e : 0.004239
  EX_ca2_e : 0.002544
  EX_cl_e : 0.002544
  EX_cu2_e : 0.000346
  EX_mn2_e : 0.000338
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.021351
  EX_co2_e : 38.168647
  EX_h_e : 4.498190
  EX_acald_e : 0.813009
  EX_12ppd__S_e : 0.048497
  DM_mththf_c : 0.000219
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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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