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 : seramp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b3831 b4069 b4384 b3708 b2297 b2458 b2779 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b2498 b0114 b1539 b2492 b0904 b1533 b3927 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.490943 (mmol/gDw/h)
  Minimum Production Rate : 0.124953 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.978913
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.052194
  EX_pi_e : 0.598520
  EX_so4_e : 0.123629
  EX_k_e : 0.095829
  EX_fe2_e : 0.007885
  EX_mg2_e : 0.004259
  EX_ca2_e : 0.002555
  EX_cl_e : 0.002555
  EX_cu2_e : 0.000348
  EX_mn2_e : 0.000339
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.365699
  EX_co2_e : 37.651242
  EX_h_e : 5.297276
  EX_ac_e : 0.285820
  Auxiliary production reaction : 0.124953
  DM_oxam_c : 0.000330
  DM_mththf_c : 0.000220
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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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