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 : hpyr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b4384 b2744 b3115 b1849 b2296 b0160 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b1982 b4139 b1033 b0675 b2361 b4014 b0261 b2976 b2799 b3945 b1602 b3915 b0509 b3125 b0529 b2492 b0904 b1300 b2954 b3029 b1380 b2660 b0221 b2285 b1378 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.417865 (mmol/gDw/h)
  Minimum Production Rate : 0.153376 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.221028
  EX_o2_e : 286.098242
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.049006
  EX_pi_e : 0.403075
  EX_so4_e : 0.105227
  EX_k_e : 0.081564
  EX_mg2_e : 0.003625
  EX_ca2_e : 0.002175
  EX_cl_e : 0.002175
  EX_cu2_e : 0.000296
  EX_mn2_e : 0.000289
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993289
  EX_h2o_e : 551.860959
  EX_co2_e : 36.683825
  EX_ade_e : 0.307220
  DM_5drib_c : 0.307032
  DM_4crsol_c : 0.306845
  EX_ac_e : 0.243275
  Auxiliary production reaction : 0.153376

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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