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 : bmoco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (100 of 137: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2779 b3617 b2407 b1238 b1779 b1982 b2797 b3117 b1814 b4471 b3449 b0261 b4381 b2406 b0112 b2789 b3127 b2975 b0114 b3603 b1539 b2492 b0904 b1533 b0494 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.453050 (mmol/gDw/h)
  Minimum Production Rate : 0.225950 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.825325
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.282650
  EX_pi_e : 1.114863
  EX_so4_e : 1.017885
  EX_mobd_e : 0.225953
  EX_k_e : 0.088432
  EX_fe2_e : 0.007276
  EX_mg2_e : 0.003930
  EX_ca2_e : 0.002358
  EX_cl_e : 0.002358
  EX_cu2_e : 0.000321
  EX_mn2_e : 0.000313
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.472123
  EX_co2_e : 27.565534
  EX_h_e : 8.370835
  EX_ac_e : 3.529170
  Auxiliary production reaction : 0.225950
  DM_oxam_c : 0.000507
  DM_5drib_c : 0.000304
  DM_4crsol_c : 0.000101

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