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 : gsn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b3617 b1238 b3236 b2883 b1982 b2210 b0675 b2361 b0411 b4381 b2868 b0114 b0529 b2492 b0904 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.593746 (mmol/gDw/h)
  Minimum Production Rate : 0.965461 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.882084
  EX_nh4_e : 11.241707
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.572731
  EX_so4_e : 0.149517
  EX_k_e : 0.115895
  EX_fe2_e : 0.009536
  EX_mg2_e : 0.005151
  EX_cl_e : 0.003090
  EX_ca2_e : 0.003090
  EX_cu2_e : 0.000421
  EX_mn2_e : 0.000410
  EX_zn2_e : 0.000202
  EX_ni2_e : 0.000192
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 49.298972
  EX_co2_e : 22.995719
  EX_h_e : 10.284876
  EX_acald_e : 1.487901
  EX_gsn_e : 0.965461
  EX_ade_e : 0.000400
  DM_mththf_c : 0.000266
  DM_5drib_c : 0.000134
  DM_4crsol_c : 0.000132

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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