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 : xdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4382 b0238 b0125 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b0030 b2883 b1982 b0477 b3616 b3589 b1623 b3665 b0411 b0114 b0529 b2492 b0904 b2954 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.577659 (mmol/gDw/h)
  Minimum Production Rate : 1.107455 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.398474
  EX_nh4_e : 10.670432
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.772124
  EX_so4_e : 0.145466
  EX_k_e : 0.112755
  EX_fe2_e : 0.009278
  EX_mg2_e : 0.005011
  EX_cl_e : 0.003007
  EX_ca2_e : 0.003007
  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 : 49.855598
  EX_co2_e : 21.307873
  EX_h_e : 10.584116
  EX_ac_e : 1.952046
  Auxiliary production reaction : 1.107455
  EX_ade_e : 0.000389
  DM_mththf_c : 0.000259
  DM_5drib_c : 0.000130
  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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