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 : ugmd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b2518 b3831 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b4161 b1701 b1805 b4138 b4123 b0621 b4381 b2406 b2197 b3918 b0789 b1249 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.624795 (mmol/gDw/h)
  Minimum Production Rate : 0.329982 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.409981
  EX_o2_e : 269.566702
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.283788
  EX_pi_e : 1.262646
  EX_so4_e : 0.157336
  EX_k_e : 0.121956
  EX_mg2_e : 0.005420
  EX_ca2_e : 0.003252
  EX_cl_e : 0.003252
  EX_cu2_e : 0.000443
  EX_mn2_e : 0.000432
  EX_zn2_e : 0.000213
  EX_ni2_e : 0.000202
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989965
  EX_h2o_e : 544.387870
  EX_co2_e : 19.747171
  EX_succ_e : 0.651531
  Auxiliary production reaction : 0.329982
  EX_ura_e : 0.113090
  DM_5drib_c : 0.000141
  DM_4crsol_c : 0.000139

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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