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 : ckdo_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b2836 b4382 b0474 b2518 b3831 b4069 b4384 b3752 b4152 b2297 b2458 b2926 b2781 b2407 b3844 b1612 b1611 b4122 b1759 b4161 b4138 b4123 b0621 b2406 b0114 b0529 b2492 b0904 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.579161 (mmol/gDw/h)
  Minimum Production Rate : 0.305834 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.996817
  EX_o2_e : 277.351987
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.382140
  EX_pi_e : 0.864496
  EX_so4_e : 0.145844
  EX_k_e : 0.113048
  EX_mg2_e : 0.005024
  EX_ca2_e : 0.003015
  EX_cl_e : 0.003015
  EX_cu2_e : 0.000411
  EX_mn2_e : 0.000400
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990698
  EX_h2o_e : 546.995345
  EX_co2_e : 27.519298
  EX_succ_e : 0.603944
  EX_ac_e : 0.337179
  Auxiliary production reaction : 0.305834
  EX_ura_e : 0.104876
  DM_5drib_c : 0.000130
  DM_4crsol_c : 0.000129

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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