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 : hxan_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b3708 b3008 b0910 b3926 b0871 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b2797 b3117 b1814 b4471 b1033 b1602 b2913 b4381 b0114 b1539 b2492 b0904 b1533 b3825 b1380 b0516 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.532033 (mmol/gDw/h)
  Minimum Production Rate : 0.108516 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.718921
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.237097
  EX_pi_e : 0.513203
  EX_so4_e : 0.133977
  EX_k_e : 0.103849
  EX_fe2_e : 0.008545
  EX_mg2_e : 0.004615
  EX_ca2_e : 0.002769
  EX_cl_e : 0.002769
  EX_cu2_e : 0.000377
  EX_mn2_e : 0.000368
  EX_zn2_e : 0.000181
  EX_ni2_e : 0.000172
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.701993
  EX_co2_e : 37.547303
  EX_h_e : 5.379717
  EX_hxan_e : 0.122795
  EX_mththf_e : 0.000238
  DM_5drib_c : 0.000120
  DM_4crsol_c : 0.000119

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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