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 : dhpmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b2744 b2297 b2458 b2779 b2883 b3616 b3589 b0411 b4381 b0112 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0529 b2492 b0904 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.479429 (mmol/gDw/h)
  Minimum Production Rate : 0.708531 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.395157
  EX_nh4_e : 10.981209
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.170991
  EX_so4_e : 0.120730
  EX_k_e : 0.093581
  EX_fe2_e : 0.007700
  EX_mg2_e : 0.004159
  EX_ca2_e : 0.002495
  EX_cl_e : 0.002495
  EX_cu2_e : 0.000340
  EX_mn2_e : 0.000331
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 49.318269
  EX_co2_e : 22.081749
  EX_h_e : 10.487719
  EX_thymd_e : 1.130382
  Auxiliary production reaction : 0.708531
  EX_ac_e : 0.279117
  DM_mththf_c : 0.000215
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107

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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