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 : dcamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3553 b1478 b4382 b1241 b4069 b4384 b2297 b2458 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b0937 b1982 b1033 b0261 b2799 b3945 b1602 b2406 b0529 b2492 b0904 b1380 b2660 b3662 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.385208 (mmol/gDw/h)
  Minimum Production Rate : 0.605844 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.194192
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.191584
  EX_pi_e : 0.977417
  EX_so4_e : 0.097003
  EX_k_e : 0.075190
  EX_fe2_e : 0.006187
  EX_mg2_e : 0.003342
  EX_cl_e : 0.002005
  EX_ca2_e : 0.002005
  EX_cu2_e : 0.000273
  EX_mn2_e : 0.000266
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 52.553182
  EX_co2_e : 33.894789
  EX_h_e : 8.687192
  EX_ac_e : 0.904689
  Auxiliary production reaction : 0.605844
  EX_ade_e : 0.000431
  DM_5drib_c : 0.000258
  DM_4crsol_c : 0.000086

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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