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 : sbt6p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b2744 b0871 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b4374 b2361 b2291 b2799 b3945 b1602 b0153 b0590 b0529 b2492 b0904 b1380 b2660 b1518 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.458666 (mmol/gDw/h)
  Minimum Production Rate : 0.451180 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.963791
  EX_o2_e : 286.352325
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.767989
  EX_pi_e : 0.893611
  EX_so4_e : 0.115501
  EX_k_e : 0.089528
  EX_mg2_e : 0.003979
  EX_ca2_e : 0.002387
  EX_cl_e : 0.002387
  EX_cu2_e : 0.000325
  EX_mn2_e : 0.000317
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992633
  EX_h2o_e : 552.388625
  EX_co2_e : 36.651339
  Auxiliary production reaction : 0.451180
  EX_ade_e : 0.362888
  EX_mththf_e : 0.000205
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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