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 (96 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b2836 b3553 b4069 b4384 b3708 b2297 b2458 b2779 b2925 b2097 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b2797 b3117 b1814 b4471 b3946 b0825 b1033 b3665 b1602 b2913 b4381 b2406 b3654 b3714 b3664 b1727 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b1380 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.358128 (mmol/gDw/h)
  Minimum Production Rate : 0.228235 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.830833
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.008929
  EX_pi_e : 0.573687
  EX_so4_e : 0.090184
  EX_k_e : 0.069904
  EX_fe2_e : 0.005752
  EX_mg2_e : 0.003107
  EX_ca2_e : 0.001864
  EX_cl_e : 0.001864
  EX_cu2_e : 0.000254
  EX_mn2_e : 0.000247
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 43.992260
  EX_co2_e : 32.325020
  EX_h_e : 9.441290
  EX_ac_e : 5.009491
  EX_12ppd__R_e : 0.300520
  Auxiliary production reaction : 0.228235
  DM_mththf_c : 0.000160
  DM_5drib_c : 0.000081
  DM_4crsol_c : 0.000080

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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