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 : h2mb4p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4382 b0238 b0125 b3831 b4384 b0910 b3752 b4152 b0871 b2779 b2925 b2097 b1612 b1611 b4122 b0477 b3946 b0825 b4388 b4138 b4123 b0621 b0114 b0529 b2492 b0904 b1813 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.596018 (mmol/gDw/h)
  Minimum Production Rate : 0.317111 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.792623
  EX_o2_e : 276.613244
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.289251
  EX_pi_e : 1.209143
  EX_so4_e : 0.150089
  EX_k_e : 0.116338
  EX_mg2_e : 0.005170
  EX_cl_e : 0.003102
  EX_ca2_e : 0.003102
  EX_cu2_e : 0.000423
  EX_mn2_e : 0.000412
  EX_zn2_e : 0.000203
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990427
  EX_h2o_e : 547.000256
  EX_co2_e : 26.942249
  EX_pyr_e : 0.935931
  EX_succ_e : 0.623849
  EX_ura_e : 0.424992
  Auxiliary production reaction : 0.317111
  DM_oxam_c : 0.002327
  EX_glyc__R_e : 0.000199
  DM_5drib_c : 0.000134
  DM_4crsol_c : 0.000133

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.

Last updated: 21-Sep-2023
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