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 : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3399 b4382 b0586 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b0160 b3844 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0675 b2361 b0261 b0507 b3709 b4381 b2406 b3161 b0112 b0452 b2975 b0114 b3603 b1539 b2492 b0904 b1533 b1473 b4141 b1798 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.350179 (mmol/gDw/h)
  Minimum Production Rate : 0.514743 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.799523
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.394660
  EX_pi_e : 1.882014
  EX_so4_e : 0.602925
  EX_k_e : 0.068352
  EX_fe2_e : 0.005624
  EX_mg2_e : 0.003038
  EX_ca2_e : 0.001823
  EX_cl_e : 0.001823
  EX_cu2_e : 0.000248
  EX_mn2_e : 0.000242
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000113

Product: (mmol/gDw/h)
  EX_h2o_e : 48.608533
  EX_co2_e : 29.047302
  EX_h_e : 7.141161
  EX_ac_e : 2.360238
  Auxiliary production reaction : 0.514743
  DM_oxam_c : 0.009555
  DM_5drib_c : 0.000235
  DM_4crsol_c : 0.000078

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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