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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3399 b4069 b2744 b3708 b2297 b2458 b2925 b2097 b2926 b2883 b2690 b2797 b3117 b1814 b4471 b2440 b1623 b3665 b0675 b0411 b0822 b4381 b2239 b3654 b3714 b3664 b1727 b0114 b2366 b0529 b2492 b0904 b2954 b1533 b3927 b1912 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.610893 (mmol/gDw/h)
  Minimum Production Rate : 0.389321 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.895677
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.765557
  EX_pi_e : 0.978592
  EX_so4_e : 0.153835
  EX_k_e : 0.119242
  EX_fe2_e : 0.009812
  EX_mg2_e : 0.005299
  EX_cl_e : 0.003180
  EX_ca2_e : 0.003180
  EX_cu2_e : 0.000433
  EX_mn2_e : 0.000422
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.277939
  EX_co2_e : 27.810014
  EX_h_e : 8.391618
  EX_ac_e : 1.999846
  Auxiliary production reaction : 0.389321
  DM_mththf_c : 0.000274
  DM_5drib_c : 0.000137
  DM_4crsol_c : 0.000136

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