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 : dcmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b4384 b2744 b2297 b2458 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b1623 b4374 b2361 b2291 b0261 b2799 b3945 b1602 b0153 b2913 b2406 b0529 b2492 b0904 b0591 b1380 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.370795 (mmol/gDw/h)
  Minimum Production Rate : 1.166352 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.870441
  EX_o2_e : 284.223275
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.505274
  EX_pi_e : 1.524024
  EX_so4_e : 0.093374
  EX_k_e : 0.072377
  EX_mg2_e : 0.003217
  EX_ca2_e : 0.001930
  EX_cl_e : 0.001930
  EX_cu2_e : 0.000263
  EX_mn2_e : 0.000256
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994045
  EX_h2o_e : 552.971994
  EX_co2_e : 33.848742
  Auxiliary production reaction : 1.166352
  EX_ac_e : 0.215872
  EX_hxan_e : 0.000415
  DM_5drib_c : 0.000249
  DM_4crsol_c : 0.000083

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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