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 : bwco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (95 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 54
  Gene deletion: b3553 b1478 b1241 b4069 b4384 b2744 b3708 b2297 b2458 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b2937 b3908 b1656 b1982 b0477 b4139 b2797 b3117 b1814 b4471 b1033 b4374 b2361 b2291 b0261 b1701 b1805 b2799 b3945 b1602 b0507 b2406 b3915 b1539 b2492 b0904 b2954 b1533 b1380 b2660 b1695 b4141 b1798 b3662 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.481384 (mmol/gDw/h)
  Minimum Production Rate : 0.029840 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.545441
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.649043
  EX_pi_e : 0.553834
  EX_so4_e : 0.240541
  EX_k_e : 0.093963
  EX_tungs_e : 0.029829
  EX_fe3_e : 0.007733
  EX_mg2_e : 0.004176
  EX_ca2_e : 0.002506
  EX_cl_e : 0.002506
  EX_cu2_e : 0.000341
  EX_mn2_e : 0.000333
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.569631
  EX_co2_e : 38.543592
  EX_h_e : 4.922639
  EX_ac_e : 0.399574
  Auxiliary production reaction : 0.029829
  EX_ade_e : 0.000539
  DM_5drib_c : 0.000323
  DM_4crsol_c : 0.000107

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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