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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (11 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b2836 b3399 b1241 b0351 b4069 b2502 b2744 b3708 b2297 b2458 b3617 b1238 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b4381 b2406 b0112 b2868 b0114 b1539 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.520354 (mmol/gDw/h)
  Minimum Production Rate : 0.519018 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.894894
  EX_o2_e : 270.597081
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.255811
  EX_pi_e : 1.539972
  EX_so4_e : 0.650053
  EX_k_e : 0.101569
  EX_mg2_e : 0.004514
  EX_ca2_e : 0.002708
  EX_cl_e : 0.002708
  EX_cu2_e : 0.000369
  EX_mn2_e : 0.000360
  EX_zn2_e : 0.000177
  EX_ni2_e : 0.000168
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991643
  EX_h2o_e : 545.312360
  EX_co2_e : 22.227294
  EX_ac_e : 2.755567
  Auxiliary production reaction : 0.519018
  EX_ade_e : 0.000582
  DM_5drib_c : 0.000349
  DM_4crsol_c : 0.000116

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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