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 : gua_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (117 of 123: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b4269 b0493 b3588 b3003 b3011 b4384 b2744 b0910 b0871 b0030 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b3908 b1656 b1982 b0477 b4139 b0261 b1602 b4381 b2868 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b2660 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.505111 (mmol/gDw/h)
  Minimum Production Rate : 0.013217 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.162313
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.522939
  EX_pi_e : 0.487233
  EX_so4_e : 0.127197
  EX_k_e : 0.098594
  EX_fe2_e : 0.008113
  EX_mg2_e : 0.004382
  EX_ca2_e : 0.002629
  EX_cl_e : 0.002629
  EX_cu2_e : 0.000358
  EX_mn2_e : 0.000349
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.673882
  EX_co2_e : 39.199730
  EX_h_e : 4.708945
  Auxiliary production reaction : 0.013217
  EX_ade_e : 0.000340
  DM_5drib_c : 0.000114
  DM_4crsol_c : 0.000113

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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