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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b1478 b4382 b0238 b0125 b1241 b0351 b4069 b4384 b3708 b2297 b2458 b3617 b1004 b3713 b1109 b0046 b3236 b2883 b1982 b0477 b2797 b3117 b1814 b4471 b1033 b0411 b1602 b2913 b2868 b4064 b4464 b0114 b2366 b2492 b0904 b1380 b1511 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.439060 (mmol/gDw/h)
  Minimum Production Rate : 0.438141 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.317354
  EX_o2_e : 284.853780
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.934000
  EX_pi_e : 0.423520
  EX_so4_e : 0.110564
  EX_k_e : 0.085702
  EX_mg2_e : 0.003809
  EX_ca2_e : 0.002285
  EX_cl_e : 0.002285
  EX_cu2_e : 0.000311
  EX_mn2_e : 0.000303
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992948
  EX_h2o_e : 551.109772
  EX_co2_e : 34.696415
  EX_ac_e : 1.449148
  Auxiliary production reaction : 0.438141
  EX_ade_e : 0.000295
  DM_mththf_c : 0.000197
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000098

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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