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 : orot5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (90 of 112: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b0474 b2518 b3831 b3752 b4152 b2297 b2458 b2925 b2097 b2781 b1612 b1611 b4122 b1779 b1759 b3946 b0825 b4161 b4138 b4123 b0621 b2406 b3918 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.422988 (mmol/gDw/h)
  Minimum Production Rate : 0.223399 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.988389
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.168156
  EX_pi_e : 0.631416
  EX_so4_e : 0.106517
  EX_k_e : 0.082564
  EX_fe2_e : 0.006794
  EX_mg2_e : 0.003669
  EX_ca2_e : 0.002202
  EX_cl_e : 0.002202
  EX_cu2_e : 0.000300
  EX_mn2_e : 0.000292
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 47.469611
  EX_co2_e : 32.304723
  EX_h_e : 8.607085
  EX_succ_e : 1.824943
  EX_ac_e : 0.246258
  Auxiliary production reaction : 0.223399
  EX_ura_e : 0.076562
  EX_for_e : 0.001038
  DM_5drib_c : 0.000095
  DM_4crsol_c : 0.000094

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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