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 : h2mb4p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b1241 b0351 b3831 b3614 b0910 b3752 b2930 b4232 b3697 b3925 b4152 b0871 b1612 b1611 b4122 b2690 b3616 b3589 b3945 b4138 b4123 b0621 b4381 b0114 b0529 b2492 b0904 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.485920 (mmol/gDw/h)
  Minimum Production Rate : 0.121791 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.257322
  EX_o2_e : 277.922691
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.937073
  EX_pi_e : 0.712304
  EX_so4_e : 0.122364
  EX_k_e : 0.094848
  EX_mg2_e : 0.004215
  EX_ca2_e : 0.002529
  EX_cl_e : 0.002529
  EX_cu2_e : 0.000345
  EX_mn2_e : 0.000336
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992196
  EX_h2o_e : 545.289503
  EX_co2_e : 27.164281
  EX_pyr_e : 2.689233
  EX_succ_e : 0.506714
  EX_ura_e : 0.209744
  EX_thymd_e : 0.134845
  Auxiliary production reaction : 0.121791
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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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