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 (39 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2836 b3399 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b2779 b2925 b2097 b3617 b0160 b2690 b1982 b2797 b3117 b1814 b4471 b0596 b4374 b0675 b2361 b2291 b0261 b3945 b0507 b3709 b3161 b0112 b2975 b0114 b3603 b2366 b2492 b0904 b1533 b1473   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.408319 (mmol/gDw/h)
  Minimum Production Rate : 1.221812 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.224387
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.853890
  EX_pi_e : 0.393867
  EX_so4_e : 0.102823
  EX_k_e : 0.079701
  EX_fe2_e : 0.006558
  EX_mg2_e : 0.003542
  EX_ca2_e : 0.002125
  EX_cl_e : 0.002125
  EX_cu2_e : 0.000289
  EX_mn2_e : 0.000282
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 45.110550
  EX_co2_e : 24.552567
  EX_h_e : 8.665600
  EX_ac_e : 2.162279
  Auxiliary production reaction : 1.221812
  EX_glyc__R_e : 0.306713
  DM_oxam_c : 0.000457
  DM_5drib_c : 0.000274
  EX_dxylnt_e : 0.000273
  DM_4crsol_c : 0.000091

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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