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 : hisp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b3115 b1849 b2296 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b0937 b1982 b0477 b4139 b0261 b0411 b2799 b3945 b1602 b0507 b2913 b2975 b3603 b0529 b2492 b0904 b2954 b1380 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.456723 (mmol/gDw/h)
  Minimum Production Rate : 0.479207 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.569752
  EX_o2_e : 286.867677
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.372239
  EX_pi_e : 0.919765
  EX_so4_e : 0.115012
  EX_k_e : 0.089149
  EX_mg2_e : 0.003962
  EX_cl_e : 0.002377
  EX_ca2_e : 0.002377
  EX_cu2_e : 0.000324
  EX_mn2_e : 0.000316
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992665
  EX_h2o_e : 552.779968
  EX_co2_e : 37.842992
  Auxiliary production reaction : 0.479207
  EX_ac_e : 0.265898
  EX_hxan_e : 0.000511
  DM_5drib_c : 0.000306
  DM_4crsol_c : 0.000102

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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