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 : glyc__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b2836 b0474 b2518 b1241 b0351 b3831 b4069 b4384 b1278 b3708 b3752 b2930 b4232 b3697 b3925 b0512 b2297 b2458 b2779 b2781 b2407 b2690 b1759 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b4161 b0261 b3945 b4381 b2406 b0112 b0114 b1539 b2492 b0904 b1533 b3918 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.466674 (mmol/gDw/h)
  Minimum Production Rate : 0.074803 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.021467
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.834993
  EX_pi_e : 0.450157
  EX_so4_e : 0.117518
  EX_k_e : 0.091092
  EX_fe2_e : 0.007495
  EX_mg2_e : 0.004048
  EX_ca2_e : 0.002429
  EX_cl_e : 0.002429
  EX_cu2_e : 0.000331
  EX_mn2_e : 0.000322
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 45.547414
  EX_co2_e : 26.238028
  EX_h_e : 8.888580
  EX_ac_e : 1.730837
  EX_alltn_e : 0.656484
  DM_5drib_c : 0.656274
  DM_4crsol_c : 0.656065
  EX_thym_e : 0.084507
  EX_glyc__R_e : 0.074803

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