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 : udpg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b2518 b3831 b3752 b4152 b2781 b1612 b1611 b4122 b0907 b1759 b3449 b4161 b4138 b4123 b0621 b4381 b2406 b0529 b2197 b3918 b1912 b1206 b2285 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.527333 (mmol/gDw/h)
  Minimum Production Rate : 0.136736 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.571941
  EX_o2_e : 282.864288
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.443071
  EX_pi_e : 0.782142
  EX_so4_e : 0.132793
  EX_k_e : 0.102932
  EX_mg2_e : 0.004575
  EX_ca2_e : 0.002745
  EX_cl_e : 0.002745
  EX_cu2_e : 0.000374
  EX_mn2_e : 0.000364
  EX_zn2_e : 0.000180
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991530
  EX_h2o_e : 550.043674
  EX_co2_e : 33.155859
  EX_succ_e : 0.549899
  EX_ura_e : 0.237221
  Auxiliary production reaction : 0.136736
  DM_5drib_c : 0.000119
  DM_4crsol_c : 0.000118

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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