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 : pgp120_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 67: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b3831 b3614 b0910 b3752 b4152 b2779 b2781 b3844 b1612 b1611 b4122 b1759 b4138 b4123 b0621 b0153 b4381 b2239 b2406 b0591 b2197 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.547076 (mmol/gDw/h)
  Minimum Production Rate : 0.288891 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.336461
  EX_o2_e : 271.564216
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.684293
  EX_pi_e : 1.105496
  EX_so4_e : 0.137765
  EX_k_e : 0.106785
  EX_mg2_e : 0.004746
  EX_ca2_e : 0.002848
  EX_cl_e : 0.002848
  EX_cu2_e : 0.000388
  EX_mn2_e : 0.000378
  EX_zn2_e : 0.000187
  EX_ni2_e : 0.000177
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991213
  EX_h2o_e : 542.863839
  EX_co2_e : 25.044510
  EX_succ_e : 0.570487
  EX_ura_e : 0.387958
  Auxiliary production reaction : 0.288891
  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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