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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2744 b1479 b0871 b2297 b2458 b2925 b2097 b3617 b3236 b2463 b3946 b2210 b0825 b1623 b3665 b0675 b2361 b2913 b4381 b0114 b0529 b2492 b0904 b0515 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.412833 (mmol/gDw/h)
  Minimum Production Rate : 0.520439 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.888146
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.625791
  EX_pi_e : 0.918660
  EX_so4_e : 0.103960
  EX_k_e : 0.080582
  EX_fe2_e : 0.006631
  EX_mg2_e : 0.003581
  EX_cl_e : 0.002149
  EX_ca2_e : 0.002149
  EX_cu2_e : 0.000293
  EX_mn2_e : 0.000285
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 46.925742
  EX_co2_e : 26.649140
  EX_h_e : 10.752728
  EX_pyr_e : 2.010289
  EX_ac_e : 1.781935
  EX_alltn_e : 0.531241
  Auxiliary production reaction : 0.520439
  EX_ade_e : 0.000278
  DM_mththf_c : 0.000185
  DM_5drib_c : 0.000093
  DM_4crsol_c : 0.000092

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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