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 : imp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4382 b4384 b2744 b3708 b3008 b0871 b2779 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b3665 b0114 b2366 b0529 b2492 b0904 b2947 b1533 b3927 b3821 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.694725 (mmol/gDw/h)
  Minimum Production Rate : 0.159877 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.963588
  EX_o2_e : 278.797598
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.144813
  EX_pi_e : 0.830013
  EX_so4_e : 0.174946
  EX_k_e : 0.135605
  EX_mg2_e : 0.006027
  EX_ca2_e : 0.003616
  EX_cl_e : 0.003616
  EX_cu2_e : 0.000493
  EX_mn2_e : 0.000480
  EX_zn2_e : 0.000237
  EX_ni2_e : 0.000224
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988842
  EX_h2o_e : 549.985583
  EX_co2_e : 29.882081
  Auxiliary production reaction : 0.159877
  EX_ade_e : 0.000468
  EX_mththf_e : 0.000311
  DM_5drib_c : 0.000156
  DM_4crsol_c : 0.000155

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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