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 : uacgam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b3831 b3614 b0910 b3752 b2221 b4152 b0871 b2297 b2458 b2779 b2925 b2097 b2781 b1612 b1611 b4122 b1759 b3946 b0825 b1493 b3517 b4015 b0411 b0614 b4138 b4123 b0621 b2913 b4381 b0728 b0529 b2197 b3918 b1912 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.420425 (mmol/gDw/h)
  Minimum Production Rate : 0.222046 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.560309
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.358890
  EX_pi_e : 0.849636
  EX_so4_e : 0.105871
  EX_k_e : 0.082064
  EX_fe2_e : 0.006752
  EX_mg2_e : 0.003647
  EX_ca2_e : 0.002188
  EX_cl_e : 0.002188
  EX_cu2_e : 0.000298
  EX_mn2_e : 0.000291
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 45.706622
  EX_co2_e : 30.239218
  EX_h_e : 8.449351
  EX_succ_e : 1.542143
  EX_ac_e : 1.127787
  Auxiliary production reaction : 0.222046
  EX_ura_e : 0.076098
  DM_mththf_c : 0.000188
  DM_5drib_c : 0.000095
  DM_4crsol_c : 0.000094

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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