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 : acald_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (13 of 20: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b2779 b1004 b3713 b1109 b0046 b3236 b1033 b4015 b3945 b1602 b2913 b3915 b1380 b0606 b0221 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.588268 (mmol/gDw/h)
  Minimum Production Rate : 0.110338 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.585313
  EX_o2_e : 284.320727
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.353242
  EX_pi_e : 0.567447
  EX_so4_e : 0.148138
  EX_k_e : 0.114826
  EX_mg2_e : 0.005103
  EX_ca2_e : 0.003062
  EX_cl_e : 0.003062
  EX_cu2_e : 0.000417
  EX_mn2_e : 0.000406
  EX_zn2_e : 0.000201
  EX_ni2_e : 0.000190
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990552
  EX_h2o_e : 551.163435
  EX_co2_e : 35.633633
  EX_acald_e : 0.110338
  DM_5drib_c : 0.000132
  DM_4crsol_c : 0.000131

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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