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 : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b3553 b1478 b4382 b0238 b0125 b1241 b0351 b4069 b4384 b2744 b2930 b4232 b3697 b3925 b2297 b2458 b2926 b3617 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b2690 b1982 b0477 b4139 b1033 b0261 b0411 b3945 b1602 b2868 b4064 b4464 b0114 b0509 b3125 b0529 b2492 b0904 b3029 b1380 b2660 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.304890 (mmol/gDw/h)
  Minimum Production Rate : 0.127960 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.726079
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.531755
  EX_pi_e : 0.677977
  EX_so4_e : 0.076777
  EX_k_e : 0.059512
  EX_mg2_e : 0.002645
  EX_fe2_e : 0.002516
  EX_fe3_e : 0.002381
  EX_ca2_e : 0.001587
  EX_cl_e : 0.001587
  EX_cu2_e : 0.000216
  EX_mn2_e : 0.000211
  EX_zn2_e : 0.000104
  EX_ni2_e : 0.000098

Product: (mmol/gDw/h)
  EX_h2o_e : 46.623103
  EX_co2_e : 30.278231
  EX_h_e : 9.386605
  EX_ac_e : 3.727684
  EX_his__L_e : 0.516133
  EX_thymd_e : 0.396574
  Auxiliary production reaction : 0.127960
  EX_ade_e : 0.000341
  DM_5drib_c : 0.000205
  DM_4crsol_c : 0.000068

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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