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 (43 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b1241 b0351 b4069 b2744 b3614 b0910 b2297 b2458 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b1033 b4374 b0675 b2799 b3945 b1602 b2913 b4381 b3915 b1727 b0529 b2492 b0904 b1380 b1518 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.466748 (mmol/gDw/h)
  Minimum Production Rate : 0.019302 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.328320
  EX_o2_e : 285.233331
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.040836
  EX_pi_e : 0.488833
  EX_so4_e : 0.117536
  EX_k_e : 0.091106
  EX_mg2_e : 0.004049
  EX_ca2_e : 0.002429
  EX_cl_e : 0.002429
  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_fe3_e : 999.992504
  EX_h2o_e : 548.688140
  EX_co2_e : 37.450759
  EX_etoh_e : 1.142295
  EX_ac_e : 0.271734
  EX_3hpp_e : 0.123088
  Auxiliary production reaction : 0.019302
  DM_mththf_c : 0.000209
  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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