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 : mal__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (14 of 14: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b3553 b3942 b1732 b1241 b0351 b4069 b4384 b1479 b3752 b2297 b2458 b2779 b3617 b2407 b3844 b3236 b0517 b1779 b2463 b3962 b0104 b2210 b4267 b1033 b1415 b3551 b1014 b0261 b3945 b4138 b4123 b0621 b4219 b1832 b1778 b4381 b0112 b3915 b0114 b0529 b1539 b2492 b0904 b3927 b1380 b0325 b1710 b2480 b4266 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.387242 (mmol/gDw/h)
  Minimum Production Rate : 0.706022 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.541354
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.182177
  EX_pi_e : 0.373536
  EX_so4_e : 0.097515
  EX_k_e : 0.075587
  EX_fe3_e : 0.006219
  EX_mg2_e : 0.003359
  EX_ca2_e : 0.002016
  EX_cl_e : 0.002016
  EX_cu2_e : 0.000275
  EX_mn2_e : 0.000268
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 49.592033
  EX_co2_e : 38.663139
  EX_h_e : 6.285147
  EX_ac_e : 1.308494
  EX_mal__L_e : 0.706022
  EX_dxylnt_e : 0.000259
  DM_5drib_c : 0.000087
  DM_4crsol_c : 0.000086

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.

Last updated: 21-Sep-2023
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