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 : his__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b2297 b2458 b0030 b2407 b1779 b1982 b3616 b3589 b4374 b2361 b2291 b0411 b0112 b0114 b0529 b2492 b0904 b0516 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.385194 (mmol/gDw/h)
  Minimum Production Rate : 1.474455 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.857732
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.589441
  EX_pi_e : 0.371560
  EX_so4_e : 0.097000
  EX_k_e : 0.075187
  EX_fe2_e : 0.006187
  EX_mg2_e : 0.003342
  EX_ca2_e : 0.002005
  EX_cl_e : 0.002005
  EX_cu2_e : 0.000273
  EX_mn2_e : 0.000266
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 53.230025
  EX_co2_e : 34.200863
  EX_h_e : 8.533128
  Auxiliary production reaction : 1.474455
  EX_ac_e : 0.564433
  EX_alltn_e : 0.001504
  DM_mththf_c : 0.001245
  DM_5drib_c : 0.000258
  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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