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 : malcoame_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b1238 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b1033 b1623 b0261 b2799 b3945 b1602 b4381 b2406 b3915 b2366 b2492 b0904 b1533 b1380 b2660 b1695 b4141 b1798 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.467993 (mmol/gDw/h)
  Minimum Production Rate : 0.065039 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.924224
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.836066
  EX_pi_e : 0.646481
  EX_so4_e : 0.182868
  EX_k_e : 0.091349
  EX_fe3_e : 0.007518
  EX_mg2_e : 0.004060
  EX_ca2_e : 0.002436
  EX_cl_e : 0.002436
  EX_cu2_e : 0.000332
  EX_mn2_e : 0.000323
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.167316
  EX_co2_e : 37.793990
  EX_h_e : 5.351815
  EX_ac_e : 0.522478
  EX_ade_e : 0.065332
  Auxiliary production reaction : 0.065017
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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