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 : forcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4382 b4069 b4384 b3708 b3008 b2297 b2458 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b2406 b2868 b0114 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b3825 b0494 b3447 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.716833 (mmol/gDw/h)
  Minimum Production Rate : 0.182189 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.070453
  EX_o2_e : 273.378240
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.020270
  EX_pi_e : 1.238029
  EX_so4_e : 0.362702
  EX_k_e : 0.139921
  EX_mg2_e : 0.006219
  EX_ca2_e : 0.003731
  EX_cl_e : 0.003731
  EX_cu2_e : 0.000508
  EX_mn2_e : 0.000495
  EX_zn2_e : 0.000244
  EX_ni2_e : 0.000232
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988487
  EX_h2o_e : 547.574932
  EX_co2_e : 25.000104
  EX_ac_e : 0.781709
  Auxiliary production reaction : 0.182189
  EX_hxan_e : 0.000802
  DM_5drib_c : 0.000481
  DM_4crsol_c : 0.000160

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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