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 : prbatp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b2836 b3553 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b0871 b2926 b3617 b0030 b2407 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b1602 b4381 b2406 b1727 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b1380 b2660 b4141 b1798 b3662 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.400491 (mmol/gDw/h)
  Minimum Production Rate : 0.142561 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.027239
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.078493
  EX_pi_e : 0.956542
  EX_so4_e : 0.100852
  EX_k_e : 0.078173
  EX_fe2_e : 0.006434
  EX_mg2_e : 0.003474
  EX_cl_e : 0.002085
  EX_ca2_e : 0.002085
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000129
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 51.783094
  EX_co2_e : 35.677485
  EX_h_e : 6.147982
  EX_etoh_e : 0.832038
  EX_his__L_e : 0.680147
  Auxiliary production reaction : 0.142556
  DM_5drib_c : 0.000269
  DM_4crsol_c : 0.000089

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