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 : dgmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b4467 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b3752 b0871 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b0937 b0477 b4139 b3665 b4015 b2799 b3945 b1602 b2913 b4381 b2406 b3654 b3714 b3664 b0529 b2492 b0904 b2954 b1298 b3029 b1380 b3662 b1517 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.465276 (mmol/gDw/h)
  Minimum Production Rate : 0.235925 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.138250
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.204570
  EX_pi_e : 0.684734
  EX_so4_e : 0.117166
  EX_k_e : 0.090819
  EX_mg2_e : 0.004036
  EX_fe2_e : 0.003840
  EX_fe3_e : 0.003633
  EX_cl_e : 0.002422
  EX_ca2_e : 0.002422
  EX_cu2_e : 0.000330
  EX_mn2_e : 0.000322
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.658199
  EX_co2_e : 38.542254
  EX_h_e : 5.458403
  Auxiliary production reaction : 0.235925
  EX_mththf_e : 0.000208
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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