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 : hdcea_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b2836 b3831 b1278 b3614 b0910 b3752 b4152 b2297 b2458 b2781 b0767 b3844 b1612 b1611 b4122 b1759 b4138 b4123 b0621 b2913 b4381 b2406 b2197 b3918 b1695 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.459766 (mmol/gDw/h)
  Minimum Production Rate : 0.484292 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 987.842909
  EX_o2_e : 266.478247
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.617515
  EX_pi_e : 0.443493
  EX_so4_e : 0.115778
  EX_k_e : 0.089743
  EX_mg2_e : 0.003988
  EX_cl_e : 0.002393
  EX_ca2_e : 0.002393
  EX_cu2_e : 0.000326
  EX_mn2_e : 0.000318
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992616
  EX_h2o_e : 536.004686
  EX_co2_e : 18.492835
  EX_succ_e : 3.259898
  Auxiliary production reaction : 0.484292
  EX_ura_e : 0.326042
  EX_ac_e : 0.267669
  EX_hxa_e : 0.001354
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000103

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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