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 : 6hmhpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3553 b3399 b4069 b2744 b3115 b1849 b2296 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b4139 b1033 b0675 b2361 b0261 b3945 b1602 b4381 b2406 b3915 b1727 b0114 b0755 b3612 b0529 b2492 b0904 b2954 b3029 b1380 b2660 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.488173 (mmol/gDw/h)
  Minimum Production Rate : 0.049551 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.126399
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.519988
  EX_pi_e : 0.470895
  EX_so4_e : 0.122932
  EX_k_e : 0.095288
  EX_fe3_e : 0.007841
  EX_mg2_e : 0.004235
  EX_cl_e : 0.002541
  EX_ca2_e : 0.002541
  EX_cu2_e : 0.000346
  EX_mn2_e : 0.000337
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.429264
  EX_co2_e : 39.046361
  EX_h_e : 5.025337
  EX_ac_e : 0.284208
  Auxiliary production reaction : 0.049551
  DM_5drib_c : 0.000328
  DM_4crsol_c : 0.000109

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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