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 : dhgly_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b4382 b4069 b4384 b3752 b2297 b2458 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b3908 b1656 b1982 b4139 b1033 b1623 b0261 b2799 b3945 b1602 b0507 b2406 b3915 b1727 b0114 b0529 b2492 b0904 b2954 b3927 b1380 b2660 b3662 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.479352 (mmol/gDw/h)
  Minimum Production Rate : 0.044332 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.963468
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.445633
  EX_pi_e : 0.462386
  EX_so4_e : 0.120710
  EX_k_e : 0.093566
  EX_fe3_e : 0.007699
  EX_mg2_e : 0.004158
  EX_ca2_e : 0.002495
  EX_cl_e : 0.002495
  EX_cu2_e : 0.000340
  EX_mn2_e : 0.000331
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.245458
  EX_co2_e : 38.920607
  EX_h_e : 5.004253
  EX_ac_e : 0.279072
  EX_ade_e : 0.044868
  DM_5drib_c : 0.044654
  DM_4crsol_c : 0.044439
  Auxiliary production reaction : 0.044332

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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