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 : 2omph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1478 b4382 b1241 b0351 b4069 b4384 b2297 b2458 b2779 b2925 b2097 b0030 b2407 b2690 b1982 b3616 b3589 b0675 b0822 b4388 b0114 b0529 b2492 b0904 b4042 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.510094 (mmol/gDw/h)
  Minimum Production Rate : 0.010404 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.172912
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.445618
  EX_pi_e : 0.492039
  EX_so4_e : 0.128452
  EX_k_e : 0.099567
  EX_fe2_e : 0.008193
  EX_mg2_e : 0.004425
  EX_ca2_e : 0.002655
  EX_cl_e : 0.002655
  EX_cu2_e : 0.000362
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 42.491303
  EX_co2_e : 27.033393
  EX_h_e : 9.052472
  EX_ac_e : 2.492059
  DM_oxam_c : 0.936649
  DM_mththf_c : 0.936306
  Auxiliary production reaction : 0.010404
  DM_5drib_c : 0.000342
  EX_glyc__R_e : 0.000171
  DM_4crsol_c : 0.000114

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