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 : 2dr5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1478 b1241 b3831 b1278 b3752 b4152 b0871 b2925 b2097 b1612 b1611 b4122 b1779 b2690 b0675 b0822 b4138 b4123 b0621 b4381 b0114 b0529 b2492 b0904 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.349866 (mmol/gDw/h)
  Minimum Production Rate : 0.214110 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.776345
  EX_o2_e : 279.686204
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.274733
  EX_pi_e : 0.585589
  EX_so4_e : 0.088103
  EX_k_e : 0.068291
  EX_mg2_e : 0.003035
  EX_ca2_e : 0.001821
  EX_cl_e : 0.001821
  EX_cu2_e : 0.000248
  EX_mn2_e : 0.000242
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000113

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994381
  EX_h2o_e : 543.482079
  EX_co2_e : 27.614983
  EX_pyr_e : 4.777443
  EX_succ_e : 0.364837
  Auxiliary production reaction : 0.248107
  EX_ura_e : 0.248107
  DM_5drib_c : 0.000079
  DM_4crsol_c : 0.000078

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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