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 : g3pe_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 61: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3831 b2744 b3614 b0910 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b2440 b4374 b2361 b2291 b4138 b4123 b0621 b2239 b2406 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.718672 (mmol/gDw/h)
  Minimum Production Rate : 0.379563 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.246436
  EX_o2_e : 272.790795
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.160448
  EX_pi_e : 1.072798
  EX_so4_e : 0.180976
  EX_k_e : 0.140280
  EX_mg2_e : 0.006234
  EX_ca2_e : 0.003741
  EX_cl_e : 0.003741
  EX_cu2_e : 0.000510
  EX_mn2_e : 0.000497
  EX_zn2_e : 0.000245
  EX_ni2_e : 0.000232
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988457
  EX_h2o_e : 546.217303
  EX_co2_e : 23.567725
  EX_succ_e : 0.749425
  EX_ura_e : 0.509645
  EX_g3pe_e : 0.379563
  DM_5drib_c : 0.000162
  DM_4crsol_c : 0.000160

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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