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 : uri_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b3846 b2341 b1241 b0351 b3831 b3708 b3614 b0910 b3752 b3926 b4152 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1779 b1759 b1033 b0411 b1602 b4138 b4123 b0621 b4381 b0529 b2492 b0904 b1380 b3918 b2660 b1206 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.467240 (mmol/gDw/h)
  Minimum Production Rate : 0.020128 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.188670
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.708833
  EX_pi_e : 0.450702
  EX_so4_e : 0.117660
  EX_k_e : 0.091202
  EX_fe3_e : 0.007504
  EX_mg2_e : 0.004053
  EX_cl_e : 0.002432
  EX_ca2_e : 0.002432
  EX_cu2_e : 0.000331
  EX_mn2_e : 0.000323
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.945843
  EX_co2_e : 37.447016
  EX_h_e : 5.937840
  EX_succ_e : 0.487234
  EX_ura_e : 0.311214
  Auxiliary production reaction : 0.020128
  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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