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 : pgp161_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3831 b3614 b0910 b3752 b4152 b2925 b2097 b2781 b3617 b1612 b1611 b4122 b0907 b1779 b2690 b1759 b3962 b4267 b3945 b4138 b4123 b0621 b4381 b2406 b0509 b3125 b2197 b3825 b3918 b0325 b0789 b1249 b0494 b4266 b1206 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.401085 (mmol/gDw/h)
  Minimum Production Rate : 0.211831 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.561600
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.900539
  EX_pi_e : 0.810551
  EX_so4_e : 0.101001
  EX_k_e : 0.078289
  EX_fe2_e : 0.006442
  EX_mg2_e : 0.003479
  EX_ca2_e : 0.002088
  EX_cl_e : 0.002088
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 45.238477
  EX_co2_e : 31.747390
  EX_h_e : 5.343668
  EX_ac_e : 0.464819
  EX_succ_e : 0.418248
  EX_ura_e : 0.284429
  Auxiliary production reaction : 0.211831
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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