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 (93 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b2836 b3553 b1478 b1241 b3831 b4069 b4384 b1278 b3708 b3614 b0910 b2297 b2458 b2779 b2781 b0030 b1004 b3713 b1109 b0046 b3236 b0651 b2162 b1759 b1982 b2797 b3117 b1814 b4471 b1033 b2799 b3945 b1602 b2223 b4381 b2406 b3915 b4064 b4464 b0509 b3125 b1539 b2492 b0904 b1533 b1380 b3918 b2660 b1511 b4141 b1798 b3662 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.454785 (mmol/gDw/h)
  Minimum Production Rate : 0.074318 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.707618
  EX_o2_e : 286.730659
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.804142
  EX_pi_e : 0.661432
  EX_so4_e : 0.188773
  EX_k_e : 0.088771
  EX_mg2_e : 0.003945
  EX_cl_e : 0.002367
  EX_ca2_e : 0.002367
  EX_cu2_e : 0.000322
  EX_mn2_e : 0.000314
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992694
  EX_h2o_e : 551.864447
  EX_co2_e : 37.553747
  EX_ac_e : 0.354254
  EX_3hpp_e : 0.156565
  EX_ade_e : 0.074554
  DM_mththf_c : 0.074452
  Auxiliary production reaction : 0.074248
  DM_5drib_c : 0.000102
  DM_4crsol_c : 0.000101

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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