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 : 2tpr3dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (96 of 106: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3553 b1478 b4382 b1241 b4069 b4384 b3708 b2297 b2458 b0030 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b0411 b2799 b3945 b1602 b4381 b2406 b3915 b4064 b4464 b2366 b2492 b0904 b1533 b3821 b1380 b2660 b1695 b4141 b1798 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.419863 (mmol/gDw/h)
  Minimum Production Rate : 0.139971 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.322739
  EX_o2_e : 285.796740
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.216369
  EX_pi_e : 1.104807
  EX_so4_e : 0.245692
  EX_k_e : 0.081954
  EX_mg2_e : 0.003642
  EX_ca2_e : 0.002185
  EX_cl_e : 0.002185
  EX_cu2_e : 0.000298
  EX_mn2_e : 0.000290
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993255
  EX_h2o_e : 552.050910
  EX_co2_e : 36.483403
  EX_ac_e : 0.970529
  EX_ade_e : 0.140431
  Auxiliary production reaction : 0.139961
  DM_5drib_c : 0.000282
  DM_4crsol_c : 0.000094

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.

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Last updated: 21-Sep-2023
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