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 : xtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b1241 b0351 b4384 b3708 b3008 b0871 b0030 b2407 b2388 b1982 b0394 b2797 b3117 b1814 b4471 b3616 b3589 b0261 b4381 b2406 b0452 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b3437 b4268 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.520001 (mmol/gDw/h)
  Minimum Production Rate : 0.119275 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.973955
  EX_o2_e : 286.708062
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.093651
  EX_pi_e : 0.859421
  EX_so4_e : 0.130947
  EX_k_e : 0.101501
  EX_mg2_e : 0.004511
  EX_ca2_e : 0.002707
  EX_cl_e : 0.002707
  EX_cu2_e : 0.000369
  EX_mn2_e : 0.000359
  EX_zn2_e : 0.000177
  EX_ni2_e : 0.000168
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991648
  EX_h2o_e : 552.740621
  EX_co2_e : 37.461262
  Auxiliary production reaction : 0.119275
  DM_oxam_c : 0.000582
  DM_5drib_c : 0.000349
  DM_4crsol_c : 0.000116

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