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 : trp__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b2779 b2925 b2097 b3617 b0160 b0583 b0907 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b3449 b4374 b0675 b2361 b2291 b0261 b0822 b3709 b3161 b0112 b2789 b3127 b1727 b2975 b0114 b3603 b2366 b2492 b0904 b1533 b1912 b1473 b0494   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.410723 (mmol/gDw/h)
  Minimum Production Rate : 1.229040 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.279720
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.894318
  EX_pi_e : 0.396186
  EX_so4_e : 0.103428
  EX_k_e : 0.080170
  EX_fe2_e : 0.006597
  EX_mg2_e : 0.003563
  EX_ca2_e : 0.002138
  EX_cl_e : 0.002138
  EX_cu2_e : 0.000291
  EX_mn2_e : 0.000284
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 45.449355
  EX_co2_e : 24.770043
  EX_h_e : 8.657800
  EX_ac_e : 2.424726
  Auxiliary production reaction : 1.229040
  DM_oxam_c : 0.000460
  DM_5drib_c : 0.000276
  EX_dxylnt_e : 0.000183
  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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