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 : q8_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b4069 b3708 b0871 b2297 b2458 b2925 b2097 b1004 b3713 b1109 b0046 b1779 b2690 b2797 b3117 b1814 b4471 b2210 b3945 b1602 b4381 b0114 b2366 b2492 b0904 b1533 b1380 b1695 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.368047 (mmol/gDw/h)
  Minimum Production Rate : 0.011567 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.097858
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.974875
  EX_pi_e : 0.355020
  EX_so4_e : 0.092682
  EX_k_e : 0.071840
  EX_fe2_e : 0.005911
  EX_mg2_e : 0.003193
  EX_ca2_e : 0.001916
  EX_cl_e : 0.001916
  EX_cu2_e : 0.000261
  EX_mn2_e : 0.000254
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 43.496814
  EX_co2_e : 28.509343
  EX_h_e : 8.725604
  EX_pyr_e : 5.129571
  EX_ac_e : 0.214272
  Auxiliary production reaction : 0.011567
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000082

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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