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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b2297 b2458 b2925 b2097 b3617 b0030 b2407 b1238 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b4381 b2406 b0511 b0114 b2366 b2492 b0904 b1533 b0515 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.510819 (mmol/gDw/h)
  Minimum Production Rate : 0.465145 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.616869
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.175627
  EX_pi_e : 0.957883
  EX_so4_e : 0.128634
  EX_k_e : 0.099708
  EX_fe2_e : 0.008204
  EX_mg2_e : 0.004431
  EX_ca2_e : 0.002659
  EX_cl_e : 0.002659
  EX_cu2_e : 0.000362
  EX_mn2_e : 0.000353
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 47.379431
  EX_co2_e : 26.106977
  EX_h_e : 9.993820
  EX_ac_e : 1.176241
  EX_his__L_e : 1.064103
  Auxiliary production reaction : 0.465145
  EX_xan_e : 0.000344
  DM_mththf_c : 0.000229
  DM_5drib_c : 0.000115
  DM_4crsol_c : 0.000114

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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