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 : nmn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b2242 b3831 b3614 b0910 b2781 b0030 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b0651 b2162 b1759 b3449 b2210 b4138 b4123 b0621 b4381 b2406 b0306 b3605 b2492 b0904 b2197 b3028 b3918 b0789 b1249 b0494 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.561649 (mmol/gDw/h)
  Minimum Production Rate : 0.296632 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.329644
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.862345
  EX_pi_e : 0.838402
  EX_so4_e : 0.141434
  EX_k_e : 0.109630
  EX_fe2_e : 0.009021
  EX_mg2_e : 0.004872
  EX_cl_e : 0.002923
  EX_ca2_e : 0.002923
  EX_cu2_e : 0.000398
  EX_mn2_e : 0.000388
  EX_zn2_e : 0.000192
  EX_ni2_e : 0.000181
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 49.233202
  EX_co2_e : 30.934566
  EX_h_e : 6.831973
  EX_succ_e : 0.585683
  Auxiliary production reaction : 0.296632
  EX_ura_e : 0.101660
  DM_5drib_c : 0.000126
  DM_4crsol_c : 0.000125

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