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 : coa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 58
  Gene deletion: b4467 b2836 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b3831 b4384 b3708 b3008 b3614 b0910 b3752 b0871 b2779 b2925 b2097 b2781 b1004 b3713 b1109 b0046 b3236 b2690 b1759 b1982 b2797 b3117 b1814 b4471 b2210 b0261 b0411 b2799 b3945 b1602 b2913 b2223 b4381 b2406 b3915 b4064 b4464 b2366 b2492 b0904 b1533 b1380 b3918 b4141 b1798 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.377303 (mmol/gDw/h)
  Minimum Production Rate : 0.068216 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 41.658865
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.827178
  EX_pi_e : 0.568496
  EX_so4_e : 0.163196
  EX_k_e : 0.073647
  EX_fe3_e : 0.006061
  EX_mg2_e : 0.003273
  EX_ca2_e : 0.001964
  EX_cl_e : 0.001964
  EX_cu2_e : 0.000268
  EX_mn2_e : 0.000261
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 54.338851
  EX_co2_e : 42.396290
  EX_h_e : 3.952480
  EX_thym_e : 0.136475
  Auxiliary production reaction : 0.068183
  EX_ade_e : 0.000422
  DM_5drib_c : 0.000253
  DM_4crsol_c : 0.000084

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