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 : ahcys_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b2836 b3553 b3399 b4382 b0238 b0125 b4069 b4384 b2744 b3708 b3008 b3752 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b2687 b1982 b0477 b2797 b3117 b1814 b4471 b1033 b1623 b0411 b1602 b2406 b1727 b0114 b2366 b2492 b0904 b2954 b1533 b3927 b1380 b2660 b4141 b1798 b3662 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.458976 (mmol/gDw/h)
  Minimum Production Rate : 0.145993 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.430626
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.832858
  EX_pi_e : 0.442731
  EX_so4_e : 0.261573
  EX_k_e : 0.089589
  EX_fe2_e : 0.007372
  EX_mg2_e : 0.003982
  EX_ca2_e : 0.002389
  EX_cl_e : 0.002389
  EX_cu2_e : 0.000325
  EX_mn2_e : 0.000317
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.501379
  EX_co2_e : 37.575352
  EX_h_e : 5.214427
  EX_ac_e : 0.413203
  EX_12ppd__R_e : 0.238157
  Auxiliary production reaction : 0.145993
  DM_5drib_c : 0.000308
  DM_4crsol_c : 0.000102

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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