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 : g3pg_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (101 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b2242 b0474 b2518 b2744 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b0907 b1779 b1759 b2210 b4374 b4161 b0675 b2361 b2291 b1415 b4138 b4123 b0621 b2239 b3453 b2492 b0904 b3825 b3028 b3918 b0789 b1249 b1695 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445376 (mmol/gDw/h)
  Minimum Production Rate : 0.061920 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.228433
  EX_o2_e : 286.170230
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.326158
  EX_pi_e : 0.491532
  EX_so4_e : 0.112154
  EX_k_e : 0.086934
  EX_mg2_e : 0.003864
  EX_ca2_e : 0.002318
  EX_cl_e : 0.002318
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.935079
  EX_h2o_e : 551.189331
  EX_co2_e : 36.954891
  EX_succ_e : 0.464434
  EX_ura_e : 0.142534
  EX_g3pg_e : 0.061920
  EX_pheme_e : 0.057768
  EX_dxylnt_e : 0.000199
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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