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 : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b3399 b4382 b1241 b0351 b4069 b2502 b2744 b3708 b0871 b2297 b2458 b2925 b2097 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b3946 b0825 b1033 b0675 b2361 b0261 b0507 b4381 b2406 b0112 b2943 b0114 b1539 b2492 b0904 b1533 b3821 b2413 b0594   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.480783 (mmol/gDw/h)
  Minimum Production Rate : 0.063119 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.610320
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.682178
  EX_so4_e : 1.471477
  EX_pi_e : 0.463766
  EX_k_e : 0.093845
  EX_fe2_e : 0.007722
  EX_mg2_e : 0.004171
  EX_ca2_e : 0.002502
  EX_cl_e : 0.002502
  EX_cu2_e : 0.000341
  EX_mn2_e : 0.000332
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 40.952316
  EX_co2_e : 25.024164
  EX_h_e : 7.103822
  EX_ac_e : 3.883805
  EX_met__L_e : 1.350406
  EX_trp__L_e : 0.063119
  DM_oxam_c : 0.013118
  DM_5drib_c : 0.000323
  EX_glyclt_e : 0.000322
  DM_4crsol_c : 0.000107

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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