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 : hpyr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4384 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b3449 b3945 b4381 b0114 b0755 b3612 b0529 b1539 b2492 b0904 b1533 b0515   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.737214 (mmol/gDw/h)
  Minimum Production Rate : 0.943210 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.760509
  EX_o2_e : 276.150474
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.472473
  EX_pi_e : 0.711121
  EX_so4_e : 0.185645
  EX_k_e : 0.143899
  EX_mg2_e : 0.006395
  EX_cl_e : 0.003837
  EX_ca2_e : 0.003837
  EX_cu2_e : 0.000523
  EX_mn2_e : 0.000509
  EX_zn2_e : 0.000251
  EX_ni2_e : 0.000238
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988160
  EX_h2o_e : 547.699156
  EX_co2_e : 26.400488
  Auxiliary production reaction : 0.943210
  EX_alltn_e : 0.127655
  DM_5drib_c : 0.000166
  DM_4crsol_c : 0.000164

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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