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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (108 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b2836 b1478 b3399 b1241 b4069 b2744 b3708 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b1612 b1611 b2883 b4122 b1779 b2690 b2797 b3117 b1814 b4471 b0675 b0261 b0411 b0822 b4381 b2868 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.377466 (mmol/gDw/h)
  Minimum Production Rate : 0.480949 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.714207
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.076606
  EX_pi_e : 1.326003
  EX_so4_e : 0.095054
  EX_k_e : 0.073679
  EX_fe2_e : 0.006062
  EX_mg2_e : 0.003275
  EX_ca2_e : 0.001965
  EX_cl_e : 0.001965
  EX_cu2_e : 0.000268
  EX_mn2_e : 0.000261
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 51.804987
  EX_co2_e : 40.088006
  EX_h_e : 3.994358
  Auxiliary production reaction : 0.480949
  EX_fum_e : 0.393619
  EX_ac_e : 0.219756
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000084

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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