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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b3553 b1478 b4382 b2066 b1241 b4069 b4384 b3708 b0910 b2297 b2458 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b0121 b1982 b0477 b4139 b2797 b3117 b1814 b4471 b1033 b2440 b4014 b0261 b2976 b2799 b3945 b1602 b2406 b3915 b0509 b3125 b2366 b2492 b0904 b2954 b1298 b1533 b3029 b1380 b2660 b4141 b1798 b3662 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483507 (mmol/gDw/h)
  Minimum Production Rate : 0.056819 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.981296
  EX_o2_e : 287.077744
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.622257
  EX_pi_e : 0.636844
  EX_so4_e : 0.178574
  EX_k_e : 0.094377
  EX_mg2_e : 0.004194
  EX_ca2_e : 0.002517
  EX_cl_e : 0.002517
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992232
  EX_h2o_e : 552.073017
  EX_co2_e : 38.110257
  EX_ac_e : 0.338309
  Auxiliary production reaction : 0.056817
  EX_ade_e : 0.000541
  DM_5drib_c : 0.000324
  DM_4crsol_c : 0.000108

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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