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 : 10fthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (23 of 46: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2744 b2297 b2458 b2926 b3617 b0160 b3124 b1982 b1033 b0675 b2361 b4014 b0261 b2976 b4388 b4381 b2406 b0112 b2789 b3127 b0114 b0755 b3612 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.279357 (mmol/gDw/h)
  Minimum Production Rate : 1.056142 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.574300
  EX_nh4_e : 10.417654
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.269470
  EX_so4_e : 0.070348
  EX_k_e : 0.054529
  EX_fe2_e : 0.004487
  EX_mg2_e : 0.002423
  EX_cl_e : 0.001454
  EX_ca2_e : 0.001454
  EX_cu2_e : 0.000198
  EX_mn2_e : 0.000193
  EX_zn2_e : 0.000095
  EX_ni2_e : 0.000090

Product: (mmol/gDw/h)
  EX_h2o_e : 48.921495
  EX_co2_e : 21.462492
  EX_h_e : 15.053602
  EX_ac_e : 1.909901
  EX_glyclt_e : 1.056329
  Auxiliary production reaction : 1.056142
  DM_oxam_c : 0.007622
  DM_5drib_c : 0.000187
  DM_4crsol_c : 0.000062

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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