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 : cdg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b3399 b4069 b2744 b2297 b2458 b2779 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b4139 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b4381 b2406 b3915 b0452 b1727 b0114 b0529 b2492 b0904 b2954 b1380 b2660 b0516 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.438546 (mmol/gDw/h)
  Minimum Production Rate : 0.377727 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 39.009553
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.306994
  EX_pi_e : 0.423024
  EX_so4_e : 0.110435
  EX_k_e : 0.085601
  EX_fe3_e : 0.007043
  EX_mg2_e : 0.003804
  EX_cl_e : 0.002283
  EX_ca2_e : 0.002283
  EX_cu2_e : 0.000311
  EX_mn2_e : 0.000303
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 54.258371
  EX_co2_e : 38.784182
  EX_h_e : 6.240356
  Auxiliary production reaction : 0.377727
  EX_ac_e : 0.255315
  EX_ade_e : 0.011966
  DM_5drib_c : 0.000294
  DM_4crsol_c : 0.000098

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