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 : udpLa4n_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b1241 b0351 b3831 b4069 b1278 b3614 b0910 b3752 b4152 b2297 b2458 b2779 b2781 b3617 b1612 b1611 b4122 b0907 b1759 b0411 b4138 b4123 b0621 b4381 b0529 b3821 b3918 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.577398 (mmol/gDw/h)
  Minimum Production Rate : 0.304950 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.523132
  EX_o2_e : 275.387437
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.359726
  EX_pi_e : 1.166862
  EX_so4_e : 0.145400
  EX_k_e : 0.112704
  EX_mg2_e : 0.005009
  EX_cl_e : 0.003005
  EX_ca2_e : 0.003005
  EX_cu2_e : 0.000409
  EX_mn2_e : 0.000399
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000186
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990726
  EX_h2o_e : 545.123713
  EX_co2_e : 25.706691
  EX_ac_e : 1.748992
  EX_succ_e : 0.602106
  Auxiliary production reaction : 0.304950
  EX_ura_e : 0.104511
  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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