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 : ditp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1478 b2066 b1241 b0351 b4069 b4384 b2297 b2458 b2779 b2925 b2097 b3617 b2407 b1779 b2690 b2498 b0675 b0822 b0511 b0114 b0529 b2492 b0904 b0516 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.335076 (mmol/gDw/h)
  Minimum Production Rate : 0.428259 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 39.218013
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.332731
  EX_pi_e : 1.607994
  EX_so4_e : 0.084379
  EX_k_e : 0.065404
  EX_fe2_e : 0.005382
  EX_mg2_e : 0.002907
  EX_ca2_e : 0.001744
  EX_cl_e : 0.001744
  EX_cu2_e : 0.000238
  EX_mn2_e : 0.000232
  EX_zn2_e : 0.000114
  EX_ni2_e : 0.000108

Product: (mmol/gDw/h)
  EX_h2o_e : 53.493707
  EX_co2_e : 39.075878
  EX_h_e : 5.379393
  EX_ac_e : 1.443161
  Auxiliary production reaction : 0.428259
  EX_xan_e : 0.000226
  DM_mththf_c : 0.000150
  DM_5drib_c : 0.000075
  DM_4crsol_c : 0.000075

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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