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 : dgtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3942 b1732 b1241 b0351 b4069 b3708 b1479 b2297 b2458 b2926 b3844 b1238 b3236 b2463 b2797 b3117 b1814 b4471 b3616 b3589 b2210 b3551 b4219 b1832 b1778 b4381 b2406 b0114 b1539 b2492 b0904 b1533 b1710 b2480 b1518 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.393005 (mmol/gDw/h)
  Minimum Production Rate : 0.392358 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.090685
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.206207
  EX_pi_e : 1.556169
  EX_so4_e : 0.098966
  EX_k_e : 0.076712
  EX_fe2_e : 0.006312
  EX_mg2_e : 0.003409
  EX_ca2_e : 0.002046
  EX_cl_e : 0.002046
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 51.620294
  EX_co2_e : 34.147823
  EX_h_e : 7.686498
  EX_ac_e : 1.297049
  EX_fum_e : 0.800646
  Auxiliary production reaction : 0.392358
  EX_mththf_e : 0.000176
  DM_5drib_c : 0.000088
  DM_4crsol_c : 0.000088

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