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 : ipdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1241 b0351 b3831 b4069 b0910 b3752 b4152 b2297 b2458 b2925 b2097 b3617 b1612 b1611 b4122 b1779 b3946 b0825 b4138 b4123 b0621 b4381 b2406 b0114 b2492 b0904 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.541381 (mmol/gDw/h)
  Minimum Production Rate : 0.285928 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.737285
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.614710
  EX_pi_e : 1.094075
  EX_so4_e : 0.136331
  EX_k_e : 0.105674
  EX_fe2_e : 0.008695
  EX_mg2_e : 0.004696
  EX_ca2_e : 0.002818
  EX_cl_e : 0.002818
  EX_cu2_e : 0.000384
  EX_mn2_e : 0.000374
  EX_zn2_e : 0.000185
  EX_ni2_e : 0.000175
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 44.150647
  EX_co2_e : 26.798266
  EX_h_e : 9.271981
  EX_ac_e : 2.686548
  EX_succ_e : 0.564548
  EX_thym_e : 0.383919
  Auxiliary production reaction : 0.285928
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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