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 : idp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b2744 b3115 b1849 b2296 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b4374 b2361 b2291 b0261 b0411 b2799 b3945 b1602 b2913 b3915 b0529 b2492 b0904 b1380 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.392061 (mmol/gDw/h)
  Minimum Production Rate : 0.615223 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.044587
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.696441
  EX_pi_e : 1.608631
  EX_so4_e : 0.098729
  EX_k_e : 0.076528
  EX_fe3_e : 0.006297
  EX_mg2_e : 0.003401
  EX_ca2_e : 0.002041
  EX_cl_e : 0.002041
  EX_cu2_e : 0.000278
  EX_mn2_e : 0.000271
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 52.428362
  EX_co2_e : 34.692938
  EX_h_e : 6.986299
  EX_glyclt_e : 1.302345
  Auxiliary production reaction : 0.615223
  EX_ac_e : 0.228253
  EX_ade_e : 0.000264
  DM_5drib_c : 0.000088
  DM_4crsol_c : 0.000087

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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