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 : 2dr5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2836 b3831 b3614 b0910 b4152 b0871 b2925 b2097 b0030 b1612 b1611 b4122 b0651 b2162 b1779 b3946 b0825 b4138 b4123 b0621 b4381 b0114 b0529 b2492 b0904 b1380 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.548669 (mmol/gDw/h)
  Minimum Production Rate : 0.289777 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.068519
  EX_o2_e : 276.840547
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.703758
  EX_pi_e : 0.819027
  EX_so4_e : 0.138166
  EX_k_e : 0.107096
  EX_mg2_e : 0.004760
  EX_ca2_e : 0.002856
  EX_cl_e : 0.002856
  EX_cu2_e : 0.000389
  EX_mn2_e : 0.000379
  EX_zn2_e : 0.000187
  EX_ni2_e : 0.000177
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991188
  EX_h2o_e : 545.560006
  EX_co2_e : 26.309403
  EX_pyr_e : 1.958803
  EX_succ_e : 0.572148
  EX_ura_e : 0.389088
  Auxiliary production reaction : 0.289777
  DM_5drib_c : 0.000123
  DM_4crsol_c : 0.000122

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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