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 : forcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b3617 b2407 b0517 b2388 b1982 b0394 b2797 b3117 b1814 b4471 b3449 b0261 b0505 b2406 b0112 b0511 b0837 b0124 b0114 b2366 b2492 b0904 b1533 b0494 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.382358 (mmol/gDw/h)
  Minimum Production Rate : 0.381387 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.094662
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.800859
  EX_pi_e : 1.512987
  EX_so4_e : 0.477673
  EX_k_e : 0.074634
  EX_fe2_e : 0.006141
  EX_mg2_e : 0.003317
  EX_ca2_e : 0.001990
  EX_cl_e : 0.001990
  EX_cu2_e : 0.000271
  EX_mn2_e : 0.000264
  EX_zn2_e : 0.000130
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 48.828738
  EX_co2_e : 31.100117
  EX_h_e : 7.065294
  EX_ac_e : 2.406160
  Auxiliary production reaction : 0.381387
  EX_xan_e : 0.000428
  DM_5drib_c : 0.000257
  DM_4crsol_c : 0.000085

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