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 : 12ppd__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4467 b1478 b1241 b4069 b3115 b1849 b2296 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b3946 b0825 b1602 b0507 b2492 b0904 b1380 b2660 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.462237 (mmol/gDw/h)
  Minimum Production Rate : 2.655398 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.476254
  EX_o2_e : 278.879223
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.992116
  EX_pi_e : 0.445876
  EX_so4_e : 0.116400
  EX_k_e : 0.090225
  EX_mg2_e : 0.004010
  EX_cl_e : 0.002406
  EX_ca2_e : 0.002406
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992576
  EX_h2o_e : 542.070181
  EX_co2_e : 32.522900
  EX_12ppd__R_e : 2.655398
  EX_ac_e : 0.269108
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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