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 : q8h2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4069 b4384 b2744 b3708 b2297 b2458 b2926 b2407 b1612 b1611 b4122 b2797 b3117 b1814 b4471 b3616 b3589 b1623 b3665 b2406 b0114 b2366 b2492 b0904 b1533 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.496295 (mmol/gDw/h)
  Minimum Production Rate : 0.087398 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.745112
  EX_o2_e : 274.335794
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.672589
  EX_pi_e : 0.478729
  EX_so4_e : 0.124977
  EX_k_e : 0.096873
  EX_mg2_e : 0.004305
  EX_cl_e : 0.002583
  EX_ca2_e : 0.002583
  EX_cu2_e : 0.000352
  EX_mn2_e : 0.000343
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992029
  EX_h2o_e : 544.515422
  EX_co2_e : 25.741777
  EX_acald_e : 1.116057
  EX_fum_e : 1.042590
  EX_ac_e : 0.288936
  EX_ade_e : 0.262529
  DM_mththf_c : 0.262417
  Auxiliary production reaction : 0.087398
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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
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