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 : grdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (30 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0945 b1241 b0351 b3831 b4069 b4384 b3752 b2297 b2458 b2407 b1612 b1611 b4122 b1779 b1982 b2498 b3616 b3589 b4388 b0114 b0529 b2492 b0904 b0723 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.473351 (mmol/gDw/h)
  Minimum Production Rate : 0.738628 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.101485
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.787571
  EX_pi_e : 1.933854
  EX_so4_e : 0.119199
  EX_k_e : 0.092395
  EX_fe2_e : 0.007602
  EX_mg2_e : 0.004106
  EX_cl_e : 0.002464
  EX_ca2_e : 0.002464
  EX_cu2_e : 0.000336
  EX_mn2_e : 0.000327
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 43.211028
  EX_co2_e : 26.312456
  EX_h_e : 7.046363
  EX_ac_e : 1.771745
  Auxiliary production reaction : 0.738628
  EX_succ_e : 0.494244
  EX_ura_e : 0.337708
  DM_mththf_c : 0.000212
  DM_5drib_c : 0.000107
  DM_4crsol_c : 0.000106

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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