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 : q8h2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b1478 b4382 b1241 b3831 b3708 b3008 b4152 b0871 b2925 b2097 b2926 b2407 b1612 b1611 b4122 b2690 b2920 b2797 b3117 b1814 b4471 b3449 b0675 b0822 b4138 b4123 b0621 b4381 b2239 b2406 b2868 b0114 b0728 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b1517 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.365449 (mmol/gDw/h)
  Minimum Production Rate : 0.040444 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.290194
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.465127
  EX_pi_e : 0.352514
  EX_so4_e : 0.092027
  EX_k_e : 0.071333
  EX_fe2_e : 0.005869
  EX_mg2_e : 0.003170
  EX_ca2_e : 0.001902
  EX_cl_e : 0.001902
  EX_cu2_e : 0.000259
  EX_mn2_e : 0.000253
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 51.046505
  EX_co2_e : 39.082418
  EX_h_e : 5.022065
  EX_succ_e : 0.572932
  EX_ura_e : 0.259157
  DM_mththf_c : 0.121496
  Auxiliary production reaction : 0.040444
  DM_5drib_c : 0.000082
  DM_4crsol_c : 0.000081

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
Contact