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 : g3pg_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (107 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b1478 b1241 b3831 b4069 b3614 b0910 b3752 b4152 b2297 b2458 b2781 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b0907 b1759 b3449 b0411 b1602 b4138 b4123 b0621 b4381 b2239 b0529 b1380 b3918 b0789 b1249 b2660 b1206 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.496399 (mmol/gDw/h)
  Minimum Production Rate : 0.262171 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.016568
  EX_o2_e : 283.282467
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.361065
  EX_pi_e : 0.741000
  EX_so4_e : 0.125003
  EX_k_e : 0.096894
  EX_mg2_e : 0.004306
  EX_cl_e : 0.002584
  EX_ca2_e : 0.002584
  EX_cu2_e : 0.000352
  EX_mn2_e : 0.000343
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992027
  EX_h2o_e : 547.969201
  EX_co2_e : 34.347025
  EX_succ_e : 0.517641
  EX_3hpp_e : 0.352020
  EX_ac_e : 0.288996
  EX_g3pg_e : 0.262171
  EX_glyclt_e : 0.000221
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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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