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 : dimp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b4467 b1478 b3942 b1732 b1241 b4069 b3708 b2297 b2458 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b2797 b3117 b1814 b4471 b2210 b3551 b2799 b3945 b1602 b0153 b4219 b1832 b1778 b4381 b0590 b2406 b4064 b4464 b2366 b2492 b0904 b1533 b1380 b1710 b2480 b1517 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.462426 (mmol/gDw/h)
  Minimum Production Rate : 0.226061 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.653705
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.960466
  EX_pi_e : 0.672121
  EX_so4_e : 0.116448
  EX_k_e : 0.090262
  EX_fe2_e : 0.007427
  EX_mg2_e : 0.004012
  EX_ca2_e : 0.002407
  EX_cl_e : 0.002407
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.979569
  EX_co2_e : 38.157382
  EX_h_e : 5.484477
  EX_ac_e : 0.269218
  Auxiliary production reaction : 0.226061
  EX_ade_e : 0.012411
  EX_mththf_e : 0.000207
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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