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 : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b1478 b4382 b1241 b0351 b4384 b3752 b0871 b2925 b2097 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b3946 b0825 b1033 b0261 b2799 b3945 b1602 b0153 b2913 b0590 b2406 b0529 b2492 b0904 b3927 b3821 b1380 b3662 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.377663 (mmol/gDw/h)
  Minimum Production Rate : 0.014463 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.391106
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.182080
  EX_pi_e : 0.407684
  EX_so4_e : 0.095103
  EX_k_e : 0.073717
  EX_fe2_e : 0.006066
  EX_mg2_e : 0.003276
  EX_ca2_e : 0.001966
  EX_cl_e : 0.001966
  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 : 44.055989
  EX_co2_e : 28.544823
  EX_h_e : 8.745807
  EX_pyr_e : 5.215725
  Auxiliary production reaction : 0.014463
  EX_ade_e : 0.000423
  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