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 : histd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b1241 b0351 b3831 b4069 b4384 b3708 b3614 b0910 b3752 b3926 b2297 b2458 b2781 b3617 b2407 b1759 b1982 b2797 b3117 b1814 b4471 b0261 b3945 b4381 b2406 b0112 b0452 b0114 b1539 b2492 b0904 b1533 b3918 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.577961 (mmol/gDw/h)
  Minimum Production Rate : 1.624680 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 22.213072
  EX_nh4_e : 11.325381
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.557505
  EX_so4_e : 0.145542
  EX_k_e : 0.112814
  EX_fe2_e : 0.009283
  EX_mg2_e : 0.005014
  EX_ca2_e : 0.003008
  EX_cl_e : 0.003008
  EX_cu2_e : 0.000410
  EX_mn2_e : 0.000399
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.251157
  EX_co2_e : 23.341876
  EX_h_e : 10.100599
  Auxiliary production reaction : 1.624680
  EX_ac_e : 1.331291
  EX_thym_e : 0.104706
  DM_5drib_c : 0.000388
  DM_4crsol_c : 0.000129

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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