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 : 2dr5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3831 b3614 b0910 b3752 b4152 b0871 b2925 b2097 b2926 b3617 b1612 b1611 b4122 b3962 b3616 b3589 b3946 b0825 b4267 b2799 b4138 b4123 b0621 b4381 b2406 b0114 b0509 b3125 b0306 b3605 b2492 b0904 b1380 b4266 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.357409 (mmol/gDw/h)
  Minimum Production Rate : 0.144212 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.701324
  EX_o2_e : 279.726755
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.366902
  EX_pi_e : 0.488971
  EX_so4_e : 0.090003
  EX_k_e : 0.069764
  EX_mg2_e : 0.003101
  EX_cl_e : 0.001860
  EX_ca2_e : 0.001860
  EX_cu2_e : 0.000253
  EX_mn2_e : 0.000247
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994260
  EX_h2o_e : 543.666401
  EX_co2_e : 27.690287
  EX_pyr_e : 4.756598
  EX_succ_e : 0.372704
  Auxiliary production reaction : 0.144212
  EX_thym_e : 0.144212
  EX_ura_e : 0.109244
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000080

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