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 (73 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3399 b4069 b4384 b2744 b3708 b3008 b2297 b2458 b1850 b0160 b0030 b3124 b0583 b2883 b1779 b1982 b2797 b3117 b1814 b4471 b1623 b3665 b4374 b2361 b2291 b0261 b0411 b0112 b0114 b2366 b0529 b2492 b0904 b2947 b2578 b1533 b3927 b3821 b1380 b0514 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.609108 (mmol/gDw/h)
  Minimum Production Rate : 0.774049 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.342350
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.903869
  EX_pi_e : 0.587549
  EX_so4_e : 0.153386
  EX_k_e : 0.118894
  EX_fe2_e : 0.009783
  EX_mg2_e : 0.005284
  EX_ca2_e : 0.003170
  EX_cl_e : 0.003170
  EX_cu2_e : 0.000432
  EX_mn2_e : 0.000421
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 49.602547
  EX_co2_e : 29.640631
  EX_h_e : 7.502847
  Auxiliary production reaction : 0.774049
  EX_ac_e : 0.354614
  EX_ade_e : 0.000682
  DM_5drib_c : 0.000409
  DM_4crsol_c : 0.000136

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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