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 : mal__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (29 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b0871 b3844 b1004 b3713 b1109 b0046 b1779 b2463 b0207 b3012 b0937 b2210 b1033 b3551 b0261 b2799 b1602 b4219 b1832 b1778 b4381 b1727 b0114 b0529 b2492 b0904 b1781 b3001 b1380 b0325 b1710 b2480 b1771 b1206 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.442422 (mmol/gDw/h)
  Minimum Production Rate : 1.475989 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.171472
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.253370
  EX_pi_e : 0.426763
  EX_so4_e : 0.111411
  EX_k_e : 0.086358
  EX_fe2_e : 0.007106
  EX_mg2_e : 0.003838
  EX_cl_e : 0.002303
  EX_ca2_e : 0.002303
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.571033
  EX_co2_e : 35.342590
  EX_h_e : 7.492377
  Auxiliary production reaction : 1.475989
  EX_hxan_e : 0.118812
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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