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 : imp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b4382 b3942 b1732 b0474 b2518 b1241 b0351 b4069 b4384 b2744 b1479 b2297 b2458 b3617 b2407 b3844 b3236 b1779 b2463 b2210 b3665 b3551 b4219 b1832 b1778 b0114 b0529 b2492 b0904 b1710 b2480 b1518 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.352396 (mmol/gDw/h)
  Minimum Production Rate : 0.347037 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.385844
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.509410
  EX_pi_e : 0.686961
  EX_so4_e : 0.088740
  EX_k_e : 0.068785
  EX_fe2_e : 0.005660
  EX_mg2_e : 0.003057
  EX_cl_e : 0.001834
  EX_ca2_e : 0.001834
  EX_cu2_e : 0.000250
  EX_mn2_e : 0.000244
  EX_zn2_e : 0.000120
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 50.723003
  EX_co2_e : 32.227510
  EX_h_e : 7.573902
  EX_fum_e : 0.713612
  EX_thymd_e : 0.657113
  Auxiliary production reaction : 0.347037
  EX_ac_e : 0.205160
  EX_ade_e : 0.000237
  DM_mththf_c : 0.000158
  DM_5drib_c : 0.000079
  DM_4crsol_c : 0.000079

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